Effective Population Size Predicts Local Rates but Not Local Mitigation of Read-through Errors
Abstract In correctly predicting that selection efficiency is positively correlated with the effective population size (Ne), the nearly neutral theory provides a coherent understanding of between-species variation in numerous genomic parameters, including heritable error (germline mutation) rates. D...
Saved in:
Published in | Molecular biology and evolution Vol. 38; no. 1; pp. 244 - 262 |
---|---|
Main Authors | , |
Format | Journal Article |
Language | English |
Published |
United States
Oxford University Press
04.01.2021
|
Subjects | |
Online Access | Get full text |
Cover
Loading…
Abstract | Abstract
In correctly predicting that selection efficiency is positively correlated with the effective population size (Ne), the nearly neutral theory provides a coherent understanding of between-species variation in numerous genomic parameters, including heritable error (germline mutation) rates. Does the same theory also explain variation in phenotypic error rates and in abundance of error mitigation mechanisms? Translational read-through provides a model to investigate both issues as it is common, mostly nonadaptive, and has good proxy for rate (TAA being the least leaky stop codon) and potential error mitigation via “fail-safe” 3′ additional stop codons (ASCs). Prior theory of translational read-through has suggested that when population sizes are high, weak selection for local mitigation can be effective thus predicting a positive correlation between ASC enrichment and Ne. Contra to prediction, we find that ASC enrichment is not correlated with Ne. ASC enrichment, although highly phylogenetically patchy, is, however, more common both in unicellular species and in genes expressed in unicellular modes in multicellular species. By contrast, Ne does positively correlate with TAA enrichment. These results imply that local phenotypic error rates, not local mitigation rates, are consistent with a drift barrier/nearly neutral model. |
---|---|
AbstractList | Abstract
In correctly predicting that selection efficiency is positively correlated with the effective population size (Ne), the nearly neutral theory provides a coherent understanding of between-species variation in numerous genomic parameters, including heritable error (germline mutation) rates. Does the same theory also explain variation in phenotypic error rates and in abundance of error mitigation mechanisms? Translational read-through provides a model to investigate both issues as it is common, mostly nonadaptive, and has good proxy for rate (TAA being the least leaky stop codon) and potential error mitigation via “fail-safe” 3′ additional stop codons (ASCs). Prior theory of translational read-through has suggested that when population sizes are high, weak selection for local mitigation can be effective thus predicting a positive correlation between ASC enrichment and Ne. Contra to prediction, we find that ASC enrichment is not correlated with Ne. ASC enrichment, although highly phylogenetically patchy, is, however, more common both in unicellular species and in genes expressed in unicellular modes in multicellular species. By contrast, Ne does positively correlate with TAA enrichment. These results imply that local phenotypic error rates, not local mitigation rates, are consistent with a drift barrier/nearly neutral model. In correctly predicting that selection efficiency is positively correlated with the effective population size ([N.sub.e]), the nearly neutral theory provides a coherent understanding of between-species variation in numerous genomic parameters, including heritable error (germline mutation) rates. Does the same theory also explain variation in phenotypic error rates and in abundance of error mitigation mechanisms? Translational read- through provides a model to investigate both issues as it is common, mostly nonadaptive, and has good proxy for rate (TAA being the least leaky stop codon) and potential error mitigation via "fail-safe" 30 additional stop codons (ASCs). Prior theory of translational read-through has suggested that when population sizes are high, weak selection for local mitigation can be effective thus predicting a positive correlation between ASC enrichment and [N.sub.e]. Contra to prediction, we find that ASC enrichment is not correlated with [N.sub.e]. ASC enrichment, although highly phylogenetically patchy, is, however, more common both in unicellular species and in genes expressed in unicellular modes in multicellular species. By contrast, [N.sub.e] does positively correlate with TAA enrichment. These results imply that local phenotypic error rates, not local mitigation rates, are consistent with a drift barrier/nearly neutral model. Key words: nearly neutral theory, molecular evolution, translational read-through, additional stop codons, phenotypic error, error mitigation. In correctly predicting that selection efficiency is positively correlated with the effective population size (Ne), the nearly neutral theory provides a coherent understanding of between-species variation in numerous genomic parameters, including heritable error (germline mutation) rates. Does the same theory also explain variation in phenotypic error rates and in abundance of error mitigation mechanisms? Translational read-through provides a model to investigate both issues as it is common, mostly nonadaptive, and has good proxy for rate (TAA being the least leaky stop codon) and potential error mitigation via “fail-safe” 3′ additional stop codons (ASCs). Prior theory of translational read-through has suggested that when population sizes are high, weak selection for local mitigation can be effective thus predicting a positive correlation between ASC enrichment and Ne. Contra to prediction, we find that ASC enrichment is not correlated with Ne. ASC enrichment, although highly phylogenetically patchy, is, however, more common both in unicellular species and in genes expressed in unicellular modes in multicellular species. By contrast, Ne does positively correlate with TAA enrichment. These results imply that local phenotypic error rates, not local mitigation rates, are consistent with a drift barrier/nearly neutral model. In correctly predicting that selection efficiency is positively correlated with the effective population size ( N e ), the nearly neutral theory provides a coherent understanding of between-species variation in numerous genomic parameters, including heritable error (germline mutation) rates. Does the same theory also explain variation in phenotypic error rates and in abundance of error mitigation mechanisms? Translational read-through provides a model to investigate both issues as it is common, mostly nonadaptive, and has good proxy for rate (TAA being the least leaky stop codon) and potential error mitigation via “fail-safe” 3′ additional stop codons (ASCs). Prior theory of translational read-through has suggested that when population sizes are high, weak selection for local mitigation can be effective thus predicting a positive correlation between ASC enrichment and N e . Contra to prediction, we find that ASC enrichment is not correlated with N e . ASC enrichment, although highly phylogenetically patchy, is, however, more common both in unicellular species and in genes expressed in unicellular modes in multicellular species. By contrast, N e does positively correlate with TAA enrichment. These results imply that local phenotypic error rates, not local mitigation rates, are consistent with a drift barrier/nearly neutral model. |
Audience | Academic |
Author | Hurst, Laurence D Ho, Alexander T |
AuthorAffiliation | Milner Centre for Evolution, University of Bath , Bath, United Kingdom |
AuthorAffiliation_xml | – name: Milner Centre for Evolution, University of Bath , Bath, United Kingdom |
Author_xml | – sequence: 1 givenname: Alexander T orcidid: 0000-0001-7824-8709 surname: Ho fullname: Ho, Alexander T email: a.t.ho@bath.ac.uk organization: Milner Centre for Evolution, University of Bath, Bath, United Kingdom – sequence: 2 givenname: Laurence D orcidid: 0000-0002-1002-1054 surname: Hurst fullname: Hurst, Laurence D organization: Milner Centre for Evolution, University of Bath, Bath, United Kingdom |
BackLink | https://www.ncbi.nlm.nih.gov/pubmed/32797190$$D View this record in MEDLINE/PubMed |
BookMark | eNqFkUuPFCEUhYkZ4zx069LUUhc1AwUFVRuTyaR9JO0jo24lt-HSjakqWqA60V8vptpxXBkWcA_nfIGcc3IyhQkJecroJaM9vxrDsMHD1ZgAGkYfkDPWclUzxfqTe-dTcp7SN0qZEFI-Iqe8UX2R6Rn5unIOTfYHrD6G_TxA9mGqPvmfZY5ovcmpWgcDQ3ULGVO1mXP1PuSj9s5nv10iwVW3CLbOuxjm7a5axRhiekweOhgSPjnuF-TLq9Xnmzf1-sPrtzfX69oIyXNtGhDWGJQ9c8Z2wDpBDUUmW7Rgbe865Fa2jLaydz1nUgG0fCOZpI1x0vIL8nLh7ufNiNbglCMMeh_9CPGHDuD1vzeT3-ltOGiluoKTBfD8CIjh-4wp69Eng8MAE4Y56UZwITpGJSvWy8W6hQG1n1woRFOWxdGbUo_zRb9WSnSyU738GzAxpBTR3b2LUf27Rb20qI8tlsCz-7-5s_-prRheLIYw7_8H-wXo2qys |
CitedBy_id | crossref_primary_10_1038_s41576_023_00686_7 crossref_primary_10_1093_gbe_evac115 crossref_primary_10_1093_molbev_msab326 |
Cites_doi | 10.1093/molbev/mst060 10.1016/j.compbiolchem.2011.03.001 10.1128/MCB.24.17.7769-7778.2004 10.1371/journal.pcbi.0030203 10.1038/nsmb.1550 10.1073/pnas.91.13.5798 10.1093/molbev/msw107 10.3748/wjg.v24.i45.5120 10.1073/pnas.1216223109 10.1261/rna.1736809 10.1016/S0014-5793(02)02301-3 10.1007/s00239-009-9220-y 10.7554/eLife.01179 10.1093/nar/gkg330 10.1093/gbe/evz275 10.1128/MCB.18.9.5272 10.1134/S0026893306040182 10.1371/journal.pgen.1001080 10.1007/978-0-387-89382-2_4 10.1093/nar/gkh1004 10.1016/j.gene.2011.04.002 10.1002/pmic.201400441 10.1534/genetics.116.192567 10.1038/286123a0 10.1073/pnas.1012918108 10.1016/j.cell.2006.04.035 10.1038/nrg3098 10.1371/journal.pgen.1008386 10.1371/journal.pone.0225804 10.1128/MR.53.3.273-298.1989 10.1038/nrg3092 10.1038/234337a0 10.1038/s41467-017-00370-5 10.1101/cshperspect.a013706 10.1038/s41467-019-11237-2 10.1261/rna.054452.115 10.1074/jbc.M808840200 10.1016/j.mib.2017.08.004 10.1042/EBC20160005 10.1186/gb-2005-6-4-r31 10.1038/nature06495 10.1101/cshperspect.a034728 10.1101/gr.119974.110 10.1093/molbev/msy011 10.1534/genetics.105.046599 10.1101/cshperspect.a004374 10.15252/msb.20199208 10.1016/j.cell.2010.03.031 10.1073/pnas.91.13.5848 10.1038/214452a0 10.1016/j.cell.2008.05.042 10.1002/wrna.1124 10.1074/jbc.M115.670901 10.1073/pnas.1424127112 10.1093/molbev/msv069 10.1104/pp.104.057935 10.1042/BST20180190 10.1002/1873-3468.13362 10.1093/molbev/msx320 10.1073/pnas.080076097 10.1016/S0168-1656(98)00073-X 10.1038/nature18308 10.1038/283041a0 10.1126/scisignal.3145re8 10.1074/jbc.M113.495184 10.1093/nar/gkz783 10.1093/molbev/msi126 10.1016/j.cell.2007.03.050 10.1146/annurev.es.23.110192.001403 10.1046/j.1365-2958.2002.02770.x 10.1006/jmbi.1993.1124 10.1002/yea.320111609 10.1093/molbev/msaa046 10.1038/nrg.2016.104 10.1038/225147a0 10.1089/dna.2019.4725 10.1038/21637 10.1016/j.cell.2014.04.033 10.1074/jbc.M114.606632 10.1534/genetics.116.193961 10.1038/sj.emboj.7600636 10.1186/s12864-016-2692-4 10.1093/nar/gks660 10.1073/pnas.1615832113 10.1016/S0092-8674(01)00508-6 10.1056/NEJMoa041974 10.1002/j.1460-2075.1995.tb00111.x 10.1038/s41467-019-09010-6 10.1093/molbev/msx171 10.1007/PL00006381 10.1093/nar/gkx1315 10.1371/journal.pgen.1008141 10.1126/science.1127422 10.1073/pnas.58.3.1144 10.1089/dna.2004.23.701 10.1016/0022-2836(73)90299-4 10.1016/j.molcel.2008.07.005 10.1017/S0016672300010284 10.1093/molbev/msx223 10.1038/nrg1125 10.1038/s41598-018-27570-3 10.1128/JB.01490-14 10.1007/BF00327411 10.1126/science.1089370 10.1371/journal.pone.0213030 10.1186/gb-2009-10-9-r101 10.1128/JB.102.2.467-475.1970 10.1371/journal.pgen.1002276 10.1093/molbev/msl172 10.1186/gb-2008-9-2-r29 10.1534/genetics.116.189894 10.1006/bbrc.1995.1775 10.1093/gbe/evs027 10.1093/molbev/msl166 10.1093/molbev/msx116 10.1126/science.290.5490.331 |
ContentType | Journal Article |
Copyright | The Author(s) 2020. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. 2020 The Author(s) 2020. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. COPYRIGHT 2021 Oxford University Press |
Copyright_xml | – notice: The Author(s) 2020. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. 2020 – notice: The Author(s) 2020. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. – notice: COPYRIGHT 2021 Oxford University Press |
DBID | TOX NPM AAYXX CITATION 7X8 5PM |
DOI | 10.1093/molbev/msaa210 |
DatabaseName | Oxford Journals Open Access Collection PubMed CrossRef MEDLINE - Academic PubMed Central (Full Participant titles) |
DatabaseTitle | PubMed CrossRef MEDLINE - Academic |
DatabaseTitleList | CrossRef PubMed |
Database_xml | – sequence: 1 dbid: NPM name: PubMed url: https://proxy.k.utb.cz/login?url=http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed sourceTypes: Index Database – sequence: 2 dbid: TOX name: Open Access: Oxford University Press Open Journals url: https://academic.oup.com/journals/ sourceTypes: Publisher |
DeliveryMethod | fulltext_linktorsrc |
Discipline | Biology |
EISSN | 1537-1719 |
Editor | Wilke, Claus |
Editor_xml | – sequence: 1 givenname: Claus surname: Wilke fullname: Wilke, Claus |
EndPage | 262 |
ExternalDocumentID | A774868796 10_1093_molbev_msaa210 32797190 10.1093/molbev/msaa210 |
Genre | Research Support, Non-U.S. Gov't Journal Article |
GrantInformation_xml | – fundername: ; grantid: ERC-2014-ADG 669207 |
GroupedDBID | --- -E4 -~X .2P .GJ .I3 .ZR 0R~ 18M 1TH 29M 2WC 4.4 48X 53G 5VS 5WA 70D AAFWJ AAIJN AAIMJ AAJKP AAJQQ AAMDB AAMVS AAOGV AAPNW AAPQZ AAPXW AAUQX AAVAP AAVLN ABEUO ABIXL ABKDP ABLJU ABNKS ABPTD ABQLI ABQTQ ABSAR ABSMQ ABTAH ABXVV ABZBJ ACGFO ACGFS ACIPB ACIWK ACMRT ACNCT ACPRK ACUFI ACUTO ACYTK ADBBV ADEYI ADEZT ADFTL ADGZP ADHKW ADHZD ADJQC ADOCK ADRIX ADRTK ADYVW ADZTZ ADZXQ AECKG AEGPL AEJOX AEKKA AEKSI AELWJ AEMDU AENEX AENZO AEPUE AETBJ AEWNT AFFNX AFIYH AFOFC AFPKN AFRAH AFULF AFXEN AGINJ AGKEF AGSYK AHMBA AHXPO AIAGR AIJHB AJEUX AKHUL AKWXX ALMA_UNASSIGNED_HOLDINGS ALTZX ALUQC APIBT APWMN ARIXL ASAOO ATDFG AXUDD AYOIW AZVOD BAWUL BAYMD BCRHZ BEYMZ BHONS BQDIO BQUQU BSWAC BTQHN BTRTY BVRKM C1A CAG CDBKE COF CS3 CXTWN CZ4 DAKXR DFGAJ DIK DILTD DU5 D~K E3Z EBS EE~ EJD EMOBN F5P F9B FHSFR FLIZI FOTVD GAUVT GJXCC GROUPED_DOAJ GX1 H13 H5~ HAR HH5 HW0 HZ~ IAO IGS IOX J21 KC5 KOP KQ8 KSI KSN M-Z M49 MBTAY ML0 MVM N9A NGC NLBLG NMDNZ NOYVH NTWIH NU- O0~ O9- OAWHX ODMLO OJQWA OK1 OVD O~Y P2P PAFKI PEELM PQQKQ Q1. Q5Y RD5 RHF RNI ROL ROX ROZ RPM RUSNO RW1 RXO RZO TEORI TJP TJX TLC TN5 TOX TR2 VQA W8F WOQ X7H XJT XSW YAYTL YHZ YKOAZ YXANX ZCA ZCG ZKX ZXP ZY4 ~02 ~91 ITC NPM 7X7 AAYXX ABEJV CITATION 7X8 5PM |
ID | FETCH-LOGICAL-c463t-c2a4dcce691fcd8a1840c0e165edadd9f8e3d6510569f93167aa53b61602cf6d3 |
IEDL.DBID | RPM |
ISSN | 1537-1719 0737-4038 |
IngestDate | Tue Sep 17 20:56:32 EDT 2024 Wed Dec 04 06:22:25 EST 2024 Tue Nov 12 23:49:15 EST 2024 Fri Dec 06 04:33:48 EST 2024 Wed Oct 16 00:44:22 EDT 2024 Wed Aug 28 03:17:04 EDT 2024 |
IsDoiOpenAccess | true |
IsOpenAccess | true |
IsPeerReviewed | true |
IsScholarly | true |
Issue | 1 |
Keywords | translational read-through error mitigation phenotypic error nearly neutral theory additional stop codons molecular evolution |
Language | English |
License | This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. The Author(s) 2020. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. http://creativecommons.org/licenses/by/4.0 |
LinkModel | DirectLink |
MergedId | FETCHMERGED-LOGICAL-c463t-c2a4dcce691fcd8a1840c0e165edadd9f8e3d6510569f93167aa53b61602cf6d3 |
Notes | ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 |
ORCID | 0000-0002-1002-1054 0000-0001-7824-8709 |
OpenAccessLink | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7783166/ |
PMID | 32797190 |
PQID | 2434481061 |
PQPubID | 23479 |
PageCount | 19 |
ParticipantIDs | pubmedcentral_primary_oai_pubmedcentral_nih_gov_7783166 proquest_miscellaneous_2434481061 gale_infotracacademiconefile_A774868796 crossref_primary_10_1093_molbev_msaa210 pubmed_primary_32797190 oup_primary_10_1093_molbev_msaa210 |
PublicationCentury | 2000 |
PublicationDate | 2021-01-04 |
PublicationDateYYYYMMDD | 2021-01-04 |
PublicationDate_xml | – month: 01 year: 2021 text: 2021-01-04 day: 04 |
PublicationDecade | 2020 |
PublicationPlace | United States |
PublicationPlace_xml | – name: United States |
PublicationTitle | Molecular biology and evolution |
PublicationTitleAlternate | Mol Biol Evol |
PublicationYear | 2021 |
Publisher | Oxford University Press |
Publisher_xml | – name: Oxford University Press |
References | Clegg (2021010500404501900_msaa210-B16) 1971; 234 Salas-Marco (2021010500404501900_msaa210-B86) 2004; 24 Inada (2021010500404501900_msaa210-B42) 2005; 24 Tuller (2021010500404501900_msaa210-B102) 2010; 141 Rajon (2021010500404501900_msaa210-B79) 2011; 108 Katoh (2021010500404501900_msaa210-B47) 2005; 16 Liang (2021010500404501900_msaa210-B60) 2005; 6 Fleming (2021010500404501900_msaa210-B28) 2019; 14 Wei (2021010500404501900_msaa210-B110) 2016; 33 Tate (2021010500404501900_msaa210-B100) 1999; 64 Falini (2021010500404501900_msaa210-B26) 2005; 352 Pina (2021010500404501900_msaa210-B78) 2005; 138 Dimitrova (2021010500404501900_msaa210-B21) 2009; 284 Vidal (2021010500404501900_msaa210-B103) 1999; 399 Drummond (2021010500404501900_msaa210-B23) 2008; 134 Zenkin (2021010500404501900_msaa210-B120) 2006; 313 Keightley (2021010500404501900_msaa210-B49) 2000; 290 Sanchez (2021010500404501900_msaa210-B88) 1998; 63 Gao (2021010500404501900_msaa210-B32) 2007; 129 Rodnina (2021010500404501900_msaa210-B81) 2020; 48 Bossi (2021010500404501900_msaa210-B9) 1980; 286 Burger (2021010500404501900_msaa210-B12) 2006; 172 Dever (2021010500404501900_msaa210-B20) 2012; 4 Nichols (2021010500404501900_msaa210-B74) 1970; 225 Roth (2021010500404501900_msaa210-B83) 1970; 102 Xiong (2021010500404501900_msaa210-B117) 2017; 205 Kochetov (2021010500404501900_msaa210-B54) 2011; 481 Hodgkinson (2021010500404501900_msaa210-B40) 2011; 12 Wei (2021010500404501900_msaa210-B111) 2017; 205 Major (2021010500404501900_msaa210-B66) 2002; 514 Brogna (2021010500404501900_msaa210-B11) 2009; 16 Chen (2021010500404501900_msaa210-B15) 2013; 30 Hollingsworth (2021010500404501900_msaa210-B41) 2013; 288 Warnecke (2021010500404501900_msaa210-B108) 2008; 9 Kobayashi (2021010500404501900_msaa210-B53) 2012; 40 Kumar (2021010500404501900_msaa210-B58) 2017; 34 Pang (2021010500404501900_msaa210-B76) 2002; 87 Faure (2021010500404501900_msaa210-B27) 2019; 4 Mikuni (2021010500404501900_msaa210-B70) 1994; 91 Jorgensen (2021010500404501900_msaa210-B45) 1993; 230 Lynch (2021010500404501900_msaa210-B63) 2007 Cridge (2021010500404501900_msaa210-B17) 2018; 46 Klauer (2021010500404501900_msaa210-B52) 2012; 3 Ohta (2021010500404501900_msaa210-B75) 1992; 23 Li (2021010500404501900_msaa210-B59) 2019; 15 Wickner (2021010500404501900_msaa210-B113) 1995; 11 Capecchi (2021010500404501900_msaa210-B13) 1967; 58 Willensdorfer (2021010500404501900_msaa210-B114) 2007; 3 Geller (2021010500404501900_msaa210-B33) 1980; 283 Jaillon (2021010500404501900_msaa210-B44) 2008; 451 Meer (2021010500404501900_msaa210-B68) 2020; 12 Wu (2021010500404501900_msaa210-B116) 2015; 32 Cusack (2021010500404501900_msaa210-B18) 2011; 7 Kuersten (2021010500404501900_msaa210-B57) 2003; 4 Keiler (2021010500404501900_msaa210-B50) 2014; 196 Wagner (2021010500404501900_msaa210-B105) 2005; 22 Doronina (2021010500404501900_msaa210-B22) 2006; 40 Arribere (2021010500404501900_msaa210-B4) 2016; 534 Zhang (2021010500404501900_msaa210-B121) 1998; 18 Namy (2021010500404501900_msaa210-B73) 2010 Bergmann (2021010500404501900_msaa210-B7) 2010; 3 Belinky (2021010500404501900_msaa210-B6) 2018; 8 Vidal (2021010500404501900_msaa210-B104) 2000; 97 Meng (2021010500404501900_msaa210-B69) 1995; 211 Harrison (2021010500404501900_msaa210-B37) 2019; 14 Ryden (2021010500404501900_msaa210-B85) 1984; 193 Rogozin (2021010500404501900_msaa210-B82) 2016; 113 Hashimoto (2021010500404501900_msaa210-B38) 2019; 593 Alkalaeva (2021010500404501900_msaa210-B3) 2006; 125 Liu (2021010500404501900_msaa210-B62) 2018; 35 Beznoskova (2021010500404501900_msaa210-B8) 2016; 22 Chen (2021010500404501900_msaa210-B14) 2011; 3 Adachi (2021010500404501900_msaa210-B2) 2009; 68 Warnecke (2021010500404501900_msaa210-B107) 2011; 12 Sung (2021010500404501900_msaa210-B97) 2012; 109 Trotta (2021010500404501900_msaa210-B101) 2016; 17 Zavialov (2021010500404501900_msaa210-B119) 2001; 107 Grentzmann (2021010500404501900_msaa210-B36) 1994; 91 Williams (2021010500404501900_msaa210-B115) 2004; 32 Seligmann (2021010500404501900_msaa210-B90) 2011; 35 Seligmann (2021010500404501900_msaa210-B92) 2004; 23 Strigini (2021010500404501900_msaa210-B96) 1973; 75 Namy (2021010500404501900_msaa210-B71) 2003; 31 Liu (2021010500404501900_msaa210-B61) 2018; 35 Tate (2021010500404501900_msaa210-B99) 2018; 46 Ho (2021010500404501900_msaa210-B39) 2019; 15 Freeland (2021010500404501900_msaa210-B29) 1998; 47 Jungreis (2021010500404501900_msaa210-B46) 2011; 21 Giacomelli (2021010500404501900_msaa210-B34) 2007; 24 Mayr (2021010500404501900_msaa210-B67) 2019; 11 Gamba (2021010500404501900_msaa210-B31) 2018; 42 Gossmann (2021010500404501900_msaa210-B35) 2012; 4 Korkmaz (2021010500404501900_msaa210-B55) 2014; 289 Eswarappa (2021010500404501900_msaa210-B25) 2014; 157 Sayani (2021010500404501900_msaa210-B89) 2008; 31 Shibata (2021010500404501900_msaa210-B93) 2015; 290 Abrahams (2021010500404501900_msaa210-B1) 2017; 34 Behringer (2021010500404501900_msaa210-B5) 2016; 204 Parker (2021010500404501900_msaa210-B77) 1989; 53 Dunn (2021010500404501900_msaa210-B24) 2013; 2 Wang (2021010500404501900_msaa210-B106) 2015; 15 Jackson (2021010500404501900_msaa210-B43) 2016; 60 Weber (2021010500404501900_msaa210-B109) 2020; 16 Tabrez (2021010500404501900_msaa210-B98) 2017; 8 Whitney (2021010500404501900_msaa210-B112) 2010; 6 Namy (2021010500404501900_msaa210-B72) 2002; 43 Brock (2021010500404501900_msaa210-B10) 2019; 10 de Oliveira (2021010500404501900_msaa210-B19) 2019; 10 Stoletzki (2021010500404501900_msaa210-B95) 2006; 24 Yang (2021010500404501900_msaa210-B118) 2017; 34 Kimura (2021010500404501900_msaa210-B51) 1967; 9 Roy (2021010500404501900_msaa210-B84) 2015; 112 Seligmann (2021010500404501900_msaa210-B91) 2019; 38 Sambrook (2021010500404501900_msaa210-B87) 1967; 214 Lynch (2021010500404501900_msaa210-B65) 2003; 302 Fu (2021010500404501900_msaa210-B30) 2018; 24 Kawashima (2021010500404501900_msaa210-B48) 2009; 15 Ramani (2021010500404501900_msaa210-B80) 2009; 10 Lynch (2021010500404501900_msaa210-B64) 2016; 17 Kosinski (2021010500404501900_msaa210-B56) 2020; 37 Stansfield (2021010500404501900_msaa210-B94) 1995; 14 |
References_xml | – volume: 30 start-page: 1559 issue: 7 year: 2013 ident: 2021010500404501900_msaa210-B15 article-title: No gene-specific optimization of mutation rate in Escherichia coli publication-title: Mol Biol Evol doi: 10.1093/molbev/mst060 contributor: fullname: Chen – volume: 35 start-page: 81 issue: 2 year: 2011 ident: 2021010500404501900_msaa210-B90 article-title: Error compensation of tRNA misacylation by codon-anticodon mismatch prevents translational amino acid misinsertion publication-title: Comput Biol Chem doi: 10.1016/j.compbiolchem.2011.03.001 contributor: fullname: Seligmann – volume: 24 start-page: 7769 issue: 17 year: 2004 ident: 2021010500404501900_msaa210-B86 article-title: GTP hydrolysis by eRF3 facilitates stop codon decoding during eukaryotic translation termination publication-title: Mol Cell Biol doi: 10.1128/MCB.24.17.7769-7778.2004 contributor: fullname: Salas-Marco – volume: 3 start-page: 2058 year: 2007 ident: 2021010500404501900_msaa210-B114 article-title: Phenotypic mutation rates and the abundance of abnormal proteins in yeast publication-title: PLoS Comp Biol doi: 10.1371/journal.pcbi.0030203 contributor: fullname: Willensdorfer – volume: 16 start-page: 107 issue: 2 year: 2009 ident: 2021010500404501900_msaa210-B11 article-title: Nonsense-mediated mRNA decay (NMD) mechanisms publication-title: Nat Struct Mol Biol doi: 10.1038/nsmb.1550 contributor: fullname: Brogna – volume: 91 start-page: 5798 issue: 13 year: 1994 ident: 2021010500404501900_msaa210-B70 article-title: Identification of the PRFC gene, which encodes peptide-chain-release factor-3 of Escherichia coli publication-title: Proc Natl Acad Sci U S A doi: 10.1073/pnas.91.13.5798 contributor: fullname: Mikuni – volume: 33 start-page: 2357 issue: 9 year: 2016 ident: 2021010500404501900_msaa210-B110 article-title: Coevolution between stop codon usage and release factors in bacterial species publication-title: Mol Biol Evol doi: 10.1093/molbev/msw107 contributor: fullname: Wei – volume: 24 start-page: 5120 issue: 45 year: 2018 ident: 2021010500404501900_msaa210-B30 article-title: Glucocorticoid receptor regulates expression of microRNA-22 and downstream signaling pathway in apoptosis of pancreatic acinar cells publication-title: World J Gastroenterol doi: 10.3748/wjg.v24.i45.5120 contributor: fullname: Fu – volume: 109 start-page: 18488 issue: 45 year: 2012 ident: 2021010500404501900_msaa210-B97 article-title: Drift-barrier hypothesis and mutation-rate evolution publication-title: Proc Natl Acad Sci U S A doi: 10.1073/pnas.1216223109 contributor: fullname: Sung – volume: 15 start-page: 2236 issue: 12 year: 2009 ident: 2021010500404501900_msaa210-B48 article-title: Nonsense-mediated mRNA decay mutes the splicing defects of spliceosome component mutations publication-title: RNA doi: 10.1261/rna.1736809 contributor: fullname: Kawashima – volume: 514 start-page: 84 issue: 1 year: 2002 ident: 2021010500404501900_msaa210-B66 article-title: Tandem termination signals: myth or reality? publication-title: FEBS Lett doi: 10.1016/S0014-5793(02)02301-3 contributor: fullname: Major – volume: 68 start-page: 424 issue: 4 year: 2009 ident: 2021010500404501900_msaa210-B2 article-title: Tandem stop codons in ciliates that reassign stop codons publication-title: J Mol Evol doi: 10.1007/s00239-009-9220-y contributor: fullname: Adachi – volume: 2 start-page: e01179 year: 2013 ident: 2021010500404501900_msaa210-B24 article-title: Ribosome profiling reveals pervasive and regulated stop codon readthrough in Drosophila melanogaster publication-title: Elife doi: 10.7554/eLife.01179 contributor: fullname: Dunn – volume: 87 start-page: 2556 issue: 6 year: 2002 ident: 2021010500404501900_msaa210-B76 article-title: A novel nonstop mutation in the stop codon and a novel missense mutation in the type II 3 beta-hydroxysteroid dehydrogenase (3 beta-HSD) gene causing, respectively, nonclassic and classic 3 beta-HSD deficiency congenital adrenal hyperplasia publication-title: J Clin Endocrinol Metab contributor: fullname: Pang – volume: 31 start-page: 2289 issue: 9 year: 2003 ident: 2021010500404501900_msaa210-B71 article-title: Identification of stop codon readthrough genes in Saccharomyces cerevisiae publication-title: Nucleic Acids Res doi: 10.1093/nar/gkg330 contributor: fullname: Namy – volume: 12 start-page: 3754 issue: 1 year: 2020 ident: 2021010500404501900_msaa210-B68 article-title: High transcriptional error rates vary as a function of gene expression level publication-title: Genome Biol Evol doi: 10.1093/gbe/evz275 contributor: fullname: Meer – volume: 18 start-page: 5272 issue: 9 year: 1998 ident: 2021010500404501900_msaa210-B121 article-title: At least one intron is required for the nonsense-mediated decay of triosephosphate isomerase mRNA: a possible link between nuclear splicing and cytoplasmic translation publication-title: Mol Cell Biol doi: 10.1128/MCB.18.9.5272 contributor: fullname: Zhang – volume: 40 start-page: 731 year: 2006 ident: 2021010500404501900_msaa210-B22 article-title: When nonsense makes sense and vice versa: non-canonical decoding events at stop codons in eukaryotes publication-title: Mol Biol doi: 10.1134/S0026893306040182 contributor: fullname: Doronina – volume: 6 start-page: e1001080 issue: 8 year: 2010 ident: 2021010500404501900_msaa210-B112 article-title: Did genetic drift drive increases in genome complexity? publication-title: PLoS Genet doi: 10.1371/journal.pgen.1001080 contributor: fullname: Whitney – start-page: 79 volume-title: Recoding: expansion of decoding rules enriches gene expression year: 2010 ident: 2021010500404501900_msaa210-B73 doi: 10.1007/978-0-387-89382-2_4 contributor: fullname: Namy – volume: 32 start-page: 6605 issue: 22 year: 2004 ident: 2021010500404501900_msaa210-B115 article-title: Genome-wide prediction of stop codon readthrough during translation in the yeast Saccharomyces cerevisiae publication-title: Nucleic Acids Res doi: 10.1093/nar/gkh1004 contributor: fullname: Williams – volume: 481 start-page: 1 issue: 1 year: 2011 ident: 2021010500404501900_msaa210-B54 article-title: Tandem termination signal in plant mRNAs publication-title: Gene doi: 10.1016/j.gene.2011.04.002 contributor: fullname: Kochetov – volume: 15 start-page: 3163 issue: 18 year: 2015 ident: 2021010500404501900_msaa210-B106 article-title: Version 4.0 of PaxDb: protein abundance data, integrated across model organisms, tissues, and cell-lines publication-title: Proteomics doi: 10.1002/pmic.201400441 contributor: fullname: Wang – volume: 205 start-page: 397 issue: 1 year: 2017 ident: 2021010500404501900_msaa210-B117 article-title: Drift barriers to quality control when genes are expressed at different levels publication-title: Genetics doi: 10.1534/genetics.116.192567 contributor: fullname: Xiong – volume: 286 start-page: 123 issue: 5769 year: 1980 ident: 2021010500404501900_msaa210-B9 article-title: The influence of codon context on genetic-code translation publication-title: Nature doi: 10.1038/286123a0 contributor: fullname: Bossi – volume: 108 start-page: 1082 issue: 3 year: 2011 ident: 2021010500404501900_msaa210-B79 article-title: Evolution of molecular error rates and the consequences for evolvability publication-title: Proc Natl Acad Sci U S A doi: 10.1073/pnas.1012918108 contributor: fullname: Rajon – volume: 125 start-page: 1125 issue: 6 year: 2006 ident: 2021010500404501900_msaa210-B3 article-title: In vitro reconstitution of eukaryotic translation reveals cooperativity between release factors eRF1 and eRF3 publication-title: Cell doi: 10.1016/j.cell.2006.04.035 contributor: fullname: Alkalaeva – volume: 12 start-page: 756 issue: 11 year: 2011 ident: 2021010500404501900_msaa210-B40 article-title: Variation in the mutation rate across mammalian genomes publication-title: Nat Rev Genet doi: 10.1038/nrg3098 contributor: fullname: Hodgkinson – volume: 15 start-page: e1008386 issue: 9 year: 2019 ident: 2021010500404501900_msaa210-B39 article-title: In eubacteria, unlike eukaryotes, there is no evidence for selection favouring fail-safe 3′ additional stop codons publication-title: PLoS Genet doi: 10.1371/journal.pgen.1008386 contributor: fullname: Ho – volume: 14 start-page: e0225804 issue: 11 year: 2019 ident: 2021010500404501900_msaa210-B28 article-title: Selection for tandem stop codons in ciliate species with reassigned stop codons publication-title: PLoS One doi: 10.1371/journal.pone.0225804 contributor: fullname: Fleming – volume: 53 start-page: 273 issue: 3 year: 1989 ident: 2021010500404501900_msaa210-B77 article-title: Errors and alternatives in reading the universal genetic code publication-title: Microbiol Rev doi: 10.1128/MR.53.3.273-298.1989 contributor: fullname: Parker – volume: 12 start-page: 875 issue: 12 year: 2011 ident: 2021010500404501900_msaa210-B107 article-title: Error prevention and mitigation as forces in the evolution of genes and genomes publication-title: Nat Rev Genet doi: 10.1038/nrg3092 contributor: fullname: Warnecke – volume: 234 start-page: 337 issue: 5328 year: 1971 ident: 2021010500404501900_msaa210-B16 article-title: Haemoglobin constant spring - a chain termination mutant? publication-title: Nature doi: 10.1038/234337a0 contributor: fullname: Clegg – volume: 4 start-page: 23 year: 2019 ident: 2021010500404501900_msaa210-B27 article-title: Possible functionality of start and stop codons present at specific and conserved positions in animal mitochondrial genes specifying tRNA publication-title: Int J Zool Stud contributor: fullname: Faure – volume: 8 start-page: 306 issue: 1 year: 2017 ident: 2021010500404501900_msaa210-B98 article-title: Differential alternative splicing coupled to nonsense-mediated decay of mRNA ensures dietary restriction-induced longevity publication-title: Nat Commun doi: 10.1038/s41467-017-00370-5 contributor: fullname: Tabrez – volume: 4 start-page: a013706 issue: 7 year: 2012 ident: 2021010500404501900_msaa210-B20 article-title: The elongation, termination, and recycling phases of translation in eukaryotes publication-title: Cold Spring Harb Perspect Biol doi: 10.1101/cshperspect.a013706 contributor: fullname: Dever – volume: 10 year: 2019 ident: 2021010500404501900_msaa210-B19 article-title: Conditional expression explains molecular evolution of social genes in a microbe publication-title: Nat Commun doi: 10.1038/s41467-019-11237-2 contributor: fullname: de Oliveira – volume: 22 start-page: 456 year: 2016 ident: 2021010500404501900_msaa210-B8 article-title: Rules of UGA-N decoding by near-cognate tRNAs and analysis of readthrough on short uORFs in yeast publication-title: RNA doi: 10.1261/rna.054452.115 contributor: fullname: Beznoskova – volume: 284 start-page: 10343 issue: 16 year: 2009 ident: 2021010500404501900_msaa210-B21 article-title: Nascent peptide-dependent translation arrest leads to Not4p-mediated protein degradation by the proteasome publication-title: J Biol Chem doi: 10.1074/jbc.M808840200 contributor: fullname: Dimitrova – volume: 42 start-page: 13 year: 2018 ident: 2021010500404501900_msaa210-B31 article-title: Transcription fidelity and its roles in the cell publication-title: Curr Opin Microbiol doi: 10.1016/j.mib.2017.08.004 contributor: fullname: Gamba – volume: 60 start-page: 173 issue: 2 year: 2016 ident: 2021010500404501900_msaa210-B43 article-title: Cellular proteostasis: degradation of misfolded proteins by lysosomes publication-title: Essays Biochem doi: 10.1042/EBC20160005 contributor: fullname: Jackson – volume: 6 start-page: R31 issue: 4 year: 2005 ident: 2021010500404501900_msaa210-B60 article-title: Conservation of tandem stop codons in yeasts publication-title: Genome Biol doi: 10.1186/gb-2005-6-4-r31 contributor: fullname: Liang – volume: 451 start-page: 359 issue: 7176 year: 2008 ident: 2021010500404501900_msaa210-B44 article-title: Translational control of intron splicing in eukaryotes publication-title: Nature doi: 10.1038/nature06495 contributor: fullname: Jaillon – volume: 11 start-page: a034728 issue: 10 year: 2019 ident: 2021010500404501900_msaa210-B67 article-title: What are 3′ UTRs doing? publication-title: Cold Spring Harb Perspect Biol doi: 10.1101/cshperspect.a034728 contributor: fullname: Mayr – volume: 21 start-page: 2096 issue: 12 year: 2011 ident: 2021010500404501900_msaa210-B46 article-title: Evidence of abundant stop codon readthrough in Drosophila and other metazoa publication-title: Genome Res doi: 10.1101/gr.119974.110 contributor: fullname: Jungreis – volume: 35 start-page: 963 issue: 4 year: 2018 ident: 2021010500404501900_msaa210-B61 article-title: Human C-to-U coding RNA editing is largely nonadaptive publication-title: Mol Biol Evol doi: 10.1093/molbev/msy011 contributor: fullname: Liu – volume: 172 start-page: 197 issue: 1 year: 2006 ident: 2021010500404501900_msaa210-B12 article-title: Why are phenotypic mutation rates much higher than genotypic mutation rates? publication-title: Genetics doi: 10.1534/genetics.105.046599 contributor: fullname: Burger – volume: 3 start-page: a004374 issue: 8 year: 2011 ident: 2021010500404501900_msaa210-B14 article-title: Cellular strategies of protein quality control publication-title: Cold Spring Harb Perspect Biol doi: 10.1101/cshperspect.a004374 contributor: fullname: Chen – volume: 16 start-page: e9208 issue: 5 year: 2020 ident: 2021010500404501900_msaa210-B109 article-title: Impact of C-terminal amino acid composition on protein expression in bacteria publication-title: Mol Syst Biol doi: 10.15252/msb.20199208 contributor: fullname: Weber – volume: 16 start-page: 22 issue: 1 year: 2005 ident: 2021010500404501900_msaa210-B47 article-title: Improvement in the accuracy of multiple sequence alignment program MAFFT publication-title: Genome Inform contributor: fullname: Katoh – volume: 141 start-page: 344 issue: 2 year: 2010 ident: 2021010500404501900_msaa210-B102 article-title: An evolutionarily conserved mechanism for controlling the efficiency of protein translation publication-title: Cell doi: 10.1016/j.cell.2010.03.031 contributor: fullname: Tuller – volume: 91 start-page: 5848 issue: 13 year: 1994 ident: 2021010500404501900_msaa210-B36 article-title: Localization and characterization of the gene encoding release factor RF3 in Escherichia coli publication-title: Proc Natl Acad Sci U S A doi: 10.1073/pnas.91.13.5848 contributor: fullname: Grentzmann – volume: 214 start-page: 452 issue: 5087 year: 1967 ident: 2021010500404501900_msaa210-B87 article-title: A strong suppressor specific for UGA publication-title: Nature doi: 10.1038/214452a0 contributor: fullname: Sambrook – volume: 134 start-page: 341 issue: 2 year: 2008 ident: 2021010500404501900_msaa210-B23 article-title: Mistranslation-induced protein misfolding as a dominant constraint on coding-sequence evolution publication-title: Cell doi: 10.1016/j.cell.2008.05.042 contributor: fullname: Drummond – volume: 3 start-page: 649 issue: 5 year: 2012 ident: 2021010500404501900_msaa210-B52 article-title: Degradation of mRNAs that lack a stop codon: a decade of nonstop progress publication-title: Wiley Interdiscip Rev RNA doi: 10.1002/wrna.1124 contributor: fullname: Klauer – volume: 290 start-page: 28428 issue: 47 year: 2015 ident: 2021010500404501900_msaa210-B93 article-title: Degradation of stop codon read-through mutant proteins via the ubiquitin-proteasorne system causes hereditary disorders publication-title: J Biol Chem doi: 10.1074/jbc.M115.670901 contributor: fullname: Shibata – volume: 64 start-page: 1342 issue: 12 year: 1999 ident: 2021010500404501900_msaa210-B100 article-title: UGA: a dual signal for ‘stop’ and for recoding in protein synthesis publication-title: Biochemistry (Mosc) contributor: fullname: Tate – volume: 112 start-page: 3038 issue: 10 year: 2015 ident: 2021010500404501900_msaa210-B84 article-title: Nonsense suppression by near-cognate tRNAs employs alternative base pairing at codon positions 1 and 3 publication-title: Proc Natl Acad Sci U S A doi: 10.1073/pnas.1424127112 contributor: fullname: Roy – volume: 32 start-page: 1847 issue: 7 year: 2015 ident: 2021010500404501900_msaa210-B116 article-title: Why selection might be stronger when populations are small: intron size and density predict within and between-species usage of exonic splice associated cis-motifs publication-title: Mol Biol Evol doi: 10.1093/molbev/msv069 contributor: fullname: Wu – volume: 138 start-page: 744 issue: 2 year: 2005 ident: 2021010500404501900_msaa210-B78 article-title: Gene family analysis of the Arabidopsis pollen transcriptome reveals biological implications for cell growth, division control, and gene expression regulation publication-title: Plant Physiol doi: 10.1104/pp.104.057935 contributor: fullname: Pina – volume: 46 start-page: 1615 issue: 6 year: 2018 ident: 2021010500404501900_msaa210-B99 article-title: ‘Stop' in protein synthesis is modulated with exquisite subtlety by an extended RNA translation signal publication-title: Biochem Soc Trans doi: 10.1042/BST20180190 contributor: fullname: Tate – volume: 593 start-page: 777 issue: 8 year: 2019 ident: 2021010500404501900_msaa210-B38 article-title: Translation arrest as a protein quality control system for aberrant translation of the 3′-UTR in mammalian cells publication-title: FEBS Lett doi: 10.1002/1873-3468.13362 contributor: fullname: Hashimoto – volume: 35 start-page: 666 issue: 3 year: 2018 ident: 2021010500404501900_msaa210-B62 article-title: Most m(6)A RNA modifications in protein-coding regions are evolutionarily unconserved and likely nonfunctional publication-title: Mol Biol Evol doi: 10.1093/molbev/msx320 contributor: fullname: Liu – volume: 97 start-page: 4920 issue: 9 year: 2000 ident: 2021010500404501900_msaa210-B104 article-title: A decamer duplication in the 3′ region of the BRI gene originates an amyloid peptide that is associated with dementia in a Danish kindred publication-title: Proc Natl Acad Sci U S A doi: 10.1073/pnas.080076097 contributor: fullname: Vidal – volume: 63 start-page: 179 issue: 3 year: 1998 ident: 2021010500404501900_msaa210-B88 article-title: Elimination of an HuIFN alpha 2b readthrough species, produced in Escherichia coli, by replacing its natural translational stop signal publication-title: J Biotechnol doi: 10.1016/S0168-1656(98)00073-X contributor: fullname: Sanchez – volume-title: The origins of genome architecture year: 2007 ident: 2021010500404501900_msaa210-B63 contributor: fullname: Lynch – volume: 534 start-page: 719 issue: 7609 year: 2016 ident: 2021010500404501900_msaa210-B4 article-title: Translation readthrough mitigation publication-title: Nature doi: 10.1038/nature18308 contributor: fullname: Arribere – volume: 283 start-page: 41 issue: 5742 year: 1980 ident: 2021010500404501900_msaa210-B33 article-title: A UGA termination suppression tRNATrp active in rabbit reticulocytes publication-title: Nature doi: 10.1038/283041a0 contributor: fullname: Geller – volume: 3 start-page: re8 issue: 145 year: 2010 ident: 2021010500404501900_msaa210-B7 article-title: Apoptosis, stem cells, and tissue regeneration publication-title: Sci Signal doi: 10.1126/scisignal.3145re8 contributor: fullname: Bergmann – volume: 288 start-page: 29047 issue: 40 year: 2013 ident: 2021010500404501900_msaa210-B41 article-title: The severe autosomal dominant retinitis pigmentosa rhodopsin mutant Ter349Glu mislocalizes and induces rapid rod cell death publication-title: J Biol Chem doi: 10.1074/jbc.M113.495184 contributor: fullname: Hollingsworth – volume: 48 start-page: 1056 issue: 3 year: 2020 ident: 2021010500404501900_msaa210-B81 article-title: Translational recoding: canonical translation mechanisms reinterpreted publication-title: Nucleic Acids Res doi: 10.1093/nar/gkz783 contributor: fullname: Rodnina – volume: 22 start-page: 1365 issue: 6 year: 2005 ident: 2021010500404501900_msaa210-B105 article-title: Energy constraints on the evolution of gene expression publication-title: Mol Biol Evol doi: 10.1093/molbev/msi126 contributor: fullname: Wagner – volume: 129 start-page: 929 issue: 5 year: 2007 ident: 2021010500404501900_msaa210-B32 article-title: RF3 induces ribosomal conformational changes responsible for dissociation of class I release factors publication-title: Cell doi: 10.1016/j.cell.2007.03.050 contributor: fullname: Gao – volume: 23 start-page: 263 issue: 1 year: 1992 ident: 2021010500404501900_msaa210-B75 article-title: The nearly neutral theory of molecular evolution publication-title: Annu Rev Ecol Syst doi: 10.1146/annurev.es.23.110192.001403 contributor: fullname: Ohta – volume: 43 start-page: 641 issue: 3 year: 2002 ident: 2021010500404501900_msaa210-B72 article-title: Translational readthrough of the PDE2 stop codon modulates cAMP levels in Saccharomyces cerevisiae publication-title: Mol Microbiol doi: 10.1046/j.1365-2958.2002.02770.x contributor: fullname: Namy – volume: 230 start-page: 41 issue: 1 year: 1993 ident: 2021010500404501900_msaa210-B45 article-title: Release factor-dependent false stops are infrequent in Escherichia coli publication-title: J Mol Biol doi: 10.1006/jmbi.1993.1124 contributor: fullname: Jorgensen – volume: 11 start-page: 1671 issue: 16 year: 1995 ident: 2021010500404501900_msaa210-B113 article-title: PSI and URE3 as yeast prions publication-title: Yeast doi: 10.1002/yea.320111609 contributor: fullname: Wickner – volume: 37 start-page: 1761 issue: 6 year: 2020 ident: 2021010500404501900_msaa210-B56 article-title: Readthrough errors purge deleterious cryptic sequences, facilitating the birth of coding sequences publication-title: Mol Biol Evol doi: 10.1093/molbev/msaa046 contributor: fullname: Kosinski – volume: 17 start-page: 704 issue: 11 year: 2016 ident: 2021010500404501900_msaa210-B64 article-title: Genetic drift, selection and the evolution of the mutation rate publication-title: Nat Rev Genet doi: 10.1038/nrg.2016.104 contributor: fullname: Lynch – volume: 225 start-page: 147 issue: 5228 year: 1970 ident: 2021010500404501900_msaa210-B74 article-title: Nucleotide sequence from polypeptide chain termination region of coat protein cistron in bacteriophage-R17 RNA publication-title: Nature doi: 10.1038/225147a0 contributor: fullname: Nichols – volume: 38 start-page: 786 issue: 8 year: 2019 ident: 2021010500404501900_msaa210-B91 article-title: Localized context-dependent effects of the “ambush” hypothesis: more off-frame stop codons downstream of shifty codons publication-title: DNA Cell Biol doi: 10.1089/dna.2019.4725 contributor: fullname: Seligmann – volume: 399 start-page: 776 issue: 6738 year: 1999 ident: 2021010500404501900_msaa210-B103 article-title: A stop-codon mutation in the BRI gene associated with familial British dementia publication-title: Nature doi: 10.1038/21637 contributor: fullname: Vidal – volume: 157 start-page: 1605 issue: 7 year: 2014 ident: 2021010500404501900_msaa210-B25 article-title: Programmed translational readthrough generates antiangiogenic VEGF-Ax publication-title: Cell doi: 10.1016/j.cell.2014.04.033 contributor: fullname: Eswarappa – volume: 289 start-page: 30334 issue: 44 year: 2014 ident: 2021010500404501900_msaa210-B55 article-title: Comprehensive analysis of stop codon usage in bacteria and its correlation with release factor abundance publication-title: J Biol Chem doi: 10.1074/jbc.M114.606632 contributor: fullname: Korkmaz – volume: 205 start-page: 539 issue: 2 year: 2017 ident: 2021010500404501900_msaa210-B111 article-title: The role of +4U as an extended translation termination signal in bacteria publication-title: Genetics doi: 10.1534/genetics.116.193961 contributor: fullname: Wei – volume: 24 start-page: 1584 issue: 8 year: 2005 ident: 2021010500404501900_msaa210-B42 article-title: Translation of aberrant mRNAs lacking a termination codon or with a shortened 3′-UTR is repressed after initiation in yeast publication-title: EMBO J doi: 10.1038/sj.emboj.7600636 contributor: fullname: Inada – volume: 17 start-page: 366 issue: 1 year: 2016 ident: 2021010500404501900_msaa210-B101 article-title: Selective forces and mutational biases drive stop codon usage in the human genome: a comparison with sense codon usage publication-title: BMC Genomics doi: 10.1186/s12864-016-2692-4 contributor: fullname: Trotta – volume: 40 start-page: 9319 issue: 18 year: 2012 ident: 2021010500404501900_msaa210-B53 article-title: Structural basis for translation termination by archaeal RF1 and GTP-bound EF1 alpha complex publication-title: Nucleic Acids Res doi: 10.1093/nar/gks660 contributor: fullname: Kobayashi – volume: 113 start-page: 13109 issue: 46 year: 2016 ident: 2021010500404501900_msaa210-B82 article-title: Evolutionary switches between two serine codon sets are driven by selection publication-title: Proc Natl Acad Sci U S A doi: 10.1073/pnas.1615832113 contributor: fullname: Rogozin – volume: 107 start-page: 115 issue: 1 year: 2001 ident: 2021010500404501900_msaa210-B119 article-title: A posttermination ribosomal complex is the guanine nucleotide exchange factor for peptide release factor RF3 publication-title: Cell doi: 10.1016/S0092-8674(01)00508-6 contributor: fullname: Zavialov – volume: 352 start-page: 254 issue: 3 year: 2005 ident: 2021010500404501900_msaa210-B26 article-title: Cytoplasmic nucleophosmin in acute myelogenous leukemia with a normal karyotype publication-title: N Engl J Med doi: 10.1056/NEJMoa041974 contributor: fullname: Falini – volume: 14 start-page: 4365 issue: 17 year: 1995 ident: 2021010500404501900_msaa210-B94 article-title: The products of the SUP45 (ERF1) and SUP35 genes interact to mediate translation termination in Saccharomyces cerevisiae publication-title: EMBO J doi: 10.1002/j.1460-2075.1995.tb00111.x contributor: fullname: Stansfield – volume: 10 start-page: 1044 issue: 1 year: 2019 ident: 2021010500404501900_msaa210-B10 article-title: Stem cell proliferation is induced by apoptotic bodies from dying cells during epithelial tissue maintenance publication-title: Nat Commun doi: 10.1038/s41467-019-09010-6 contributor: fullname: Brock – volume: 34 start-page: 2125 issue: 9 year: 2017 ident: 2021010500404501900_msaa210-B118 article-title: Intra and interspecific variations of gene expression levels in yeast are largely neutral: (Nei Lecture, SMBE 2016, Gold Coast) publication-title: Mol Biol Evol doi: 10.1093/molbev/msx171 contributor: fullname: Yang – volume: 47 start-page: 238 issue: 3 year: 1998 ident: 2021010500404501900_msaa210-B29 article-title: The genetic code is one in a million publication-title: J Mol Evol doi: 10.1007/PL00006381 contributor: fullname: Freeland – volume: 46 start-page: 1927 issue: 4 year: 2018 ident: 2021010500404501900_msaa210-B17 article-title: Eukaryotic translational termination efficiency is influenced by the 3′ nucleotides within the ribosomal mRNA channel publication-title: Nucleic Acids Res doi: 10.1093/nar/gkx1315 contributor: fullname: Cridge – volume: 15 start-page: e1008141 issue: 5 year: 2019 ident: 2021010500404501900_msaa210-B59 article-title: Stop-codon read-through arises largely from molecular errors and is generally nonadaptive publication-title: PLoS Genet doi: 10.1371/journal.pgen.1008141 contributor: fullname: Li – volume: 313 start-page: 518 issue: 5786 year: 2006 ident: 2021010500404501900_msaa210-B120 article-title: Transcript-assisted transcriptional proofreading publication-title: Science doi: 10.1126/science.1127422 contributor: fullname: Zenkin – volume: 58 start-page: 1144 issue: 3 year: 1967 ident: 2021010500404501900_msaa210-B13 article-title: Polypeptide chain termination in vitro - isolation of a release factor publication-title: Proc Natl Acad Sci U S A doi: 10.1073/pnas.58.3.1144 contributor: fullname: Capecchi – volume: 23 start-page: 701 issue: 10 year: 2004 ident: 2021010500404501900_msaa210-B92 article-title: The ambush hypothesis: hidden stop codons prevent off-frame gene reading publication-title: DNA Cell Biol doi: 10.1089/dna.2004.23.701 contributor: fullname: Seligmann – volume: 75 start-page: 659 issue: 4 year: 1973 ident: 2021010500404501900_msaa210-B96 article-title: Analysis of specific misreading in Escherichia coli publication-title: J Mol Biol doi: 10.1016/0022-2836(73)90299-4 contributor: fullname: Strigini – volume: 31 start-page: 360 issue: 3 year: 2008 ident: 2021010500404501900_msaa210-B89 article-title: Widespread impact of nonsense-mediated mRNA decay on the yeast intronome publication-title: Mol Cell doi: 10.1016/j.molcel.2008.07.005 contributor: fullname: Sayani – volume: 9 start-page: 23 issue: 1 year: 1967 ident: 2021010500404501900_msaa210-B51 article-title: On the evolutionary adjustment of mutation rates publication-title: Genet Res doi: 10.1017/S0016672300010284 contributor: fullname: Kimura – volume: 34 start-page: 3064 issue: 12 year: 2017 ident: 2021010500404501900_msaa210-B1 article-title: Adenine enrichment at the fourth CDS residue in bacterial genes is consistent with error proofing for +1 frameshifts publication-title: Mol Biol Evol doi: 10.1093/molbev/msx223 contributor: fullname: Abrahams – volume: 4 start-page: 626 issue: 8 year: 2003 ident: 2021010500404501900_msaa210-B57 article-title: The power of the 3′ UTR: translational control and development publication-title: Nat Rev Genet doi: 10.1038/nrg1125 contributor: fullname: Kuersten – volume: 8 start-page: 9260 issue: 1 year: 2018 ident: 2021010500404501900_msaa210-B6 article-title: Purifying and positive selection in the evolution of stop codons publication-title: Sci Rep doi: 10.1038/s41598-018-27570-3 contributor: fullname: Belinky – volume: 196 start-page: 2123 issue: 12 year: 2014 ident: 2021010500404501900_msaa210-B50 article-title: Resolving nonstop translation complexes is a matter of life or death publication-title: J Bacteriol doi: 10.1128/JB.01490-14 contributor: fullname: Keiler – volume: 193 start-page: 38 issue: 1 year: 1984 ident: 2021010500404501900_msaa210-B85 article-title: A temperature-sensitive mutant of Escherichia coli that shows enhanced misreading of UAG/A and increased efficiency for some transfer-RNA nonsense suppressors publication-title: Mol Gen Genet doi: 10.1007/BF00327411 contributor: fullname: Ryden – volume: 302 start-page: 1401 issue: 5649 year: 2003 ident: 2021010500404501900_msaa210-B65 article-title: The origins of genome complexity publication-title: Science doi: 10.1126/science.1089370 contributor: fullname: Lynch – volume: 14 start-page: e0213030 issue: 3 year: 2019 ident: 2021010500404501900_msaa210-B37 article-title: Evolutionary behaviour of bacterial prion-like proteins publication-title: PLoS One doi: 10.1371/journal.pone.0213030 contributor: fullname: Harrison – volume: 10 start-page: R101 issue: 9 year: 2009 ident: 2021010500404501900_msaa210-B80 article-title: High resolution transcriptome maps for wild-type and nonsense-mediated decay-defective Caenorhabditis elegans publication-title: Genome Biol doi: 10.1186/gb-2009-10-9-r101 contributor: fullname: Ramani – volume: 102 start-page: 467 issue: 2 year: 1970 ident: 2021010500404501900_msaa210-B83 article-title: UGA nonsense mutations in Salmonella typhimurium publication-title: J Bacteriol doi: 10.1128/JB.102.2.467-475.1970 contributor: fullname: Roth – volume: 7 start-page: e1002276 issue: 10 year: 2011 ident: 2021010500404501900_msaa210-B18 article-title: Preventing dangerous nonsense: selection for robustness to transcriptional error in human genes publication-title: PLoS Genet doi: 10.1371/journal.pgen.1002276 contributor: fullname: Cusack – volume: 24 start-page: 457 issue: 2 year: 2007 ident: 2021010500404501900_msaa210-B34 article-title: The conversion of 3′ UTRs into coding regions publication-title: Mol Biol Evol doi: 10.1093/molbev/msl172 contributor: fullname: Giacomelli – volume: 9 start-page: r29 issue: 2 year: 2008 ident: 2021010500404501900_msaa210-B108 article-title: Finding exonic islands in a sea of non-coding sequence: splicing related constraints on protein composition and evolution are common in intron-rich genomes publication-title: Genome Biol doi: 10.1186/gb-2008-9-2-r29 contributor: fullname: Warnecke – volume: 204 start-page: 1239 issue: 3 year: 2016 ident: 2021010500404501900_msaa210-B5 article-title: Selection on position of nonsense codons in introns publication-title: Genetics doi: 10.1534/genetics.116.189894 contributor: fullname: Behringer – volume: 211 start-page: 40 issue: 1 year: 1995 ident: 2021010500404501900_msaa210-B69 article-title: Analysis of translational termination of recombinant human methionyl-neurotrophin 3 in Escherichia coli publication-title: Biochem Biophys Res Commun doi: 10.1006/bbrc.1995.1775 contributor: fullname: Meng – volume: 4 start-page: 658 issue: 5 year: 2012 ident: 2021010500404501900_msaa210-B35 article-title: The effect of variation in the effective population size on the rate of adaptive molecular evolution in eukaryotes publication-title: Genome Biol Evol doi: 10.1093/gbe/evs027 contributor: fullname: Gossmann – volume: 24 start-page: 374 issue: 2 year: 2006 ident: 2021010500404501900_msaa210-B95 article-title: Synonymous codon usage in Escherichia coli: selection for translational accuracy publication-title: Mol Biol Evol doi: 10.1093/molbev/msl166 contributor: fullname: Stoletzki – volume: 34 start-page: 1812 issue: 7 year: 2017 ident: 2021010500404501900_msaa210-B58 article-title: TimeTree: a resource for timelines, timetrees, and divergence times publication-title: Mol Biol Evol doi: 10.1093/molbev/msx116 contributor: fullname: Kumar – volume: 290 start-page: 331 issue: 5490 year: 2000 ident: 2021010500404501900_msaa210-B49 article-title: Deleterious mutations and the evolution of sex publication-title: Science doi: 10.1126/science.290.5490.331 contributor: fullname: Keightley |
SSID | ssj0014466 |
Score | 2.4205508 |
Snippet | Abstract
In correctly predicting that selection efficiency is positively correlated with the effective population size (Ne), the nearly neutral theory provides... In correctly predicting that selection efficiency is positively correlated with the effective population size (Ne), the nearly neutral theory provides a... In correctly predicting that selection efficiency is positively correlated with the effective population size ([N.sub.e]), the nearly neutral theory provides a... In correctly predicting that selection efficiency is positively correlated with the effective population size ( N e ), the nearly neutral theory provides a... |
SourceID | pubmedcentral proquest gale crossref pubmed oup |
SourceType | Open Access Repository Aggregation Database Index Database Publisher |
StartPage | 244 |
SubjectTerms | Analysis Codon Discoveries Evolution Gene mutations Genes |
Title | Effective Population Size Predicts Local Rates but Not Local Mitigation of Read-through Errors |
URI | https://www.ncbi.nlm.nih.gov/pubmed/32797190 https://search.proquest.com/docview/2434481061 https://pubmed.ncbi.nlm.nih.gov/PMC7783166 |
Volume | 38 |
hasFullText | 1 |
inHoldings | 1 |
isFullTextHit | |
isPrint | |
link | http://utb.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwnR3Jatww9JEEWnIp3TtdgloKPTmOLVmSjyEkhNJJQ5vAnGq0koGMHTyeQvL1fbLlYaaXQi8G25Js9J7evgB8tsIzLbhNNIIgYTKjifbUJVwyL7XX1vVZrtMLfn7Nvs6K2Q4UYy5MH7Rv9Pywvl0c1vObPrbybmHSMU4svZyeCCFpxnm6C7vIfkcVPboORgeloAKVIyrXlRppumhutfudLpZKoaazD49pLkqRBXq8wZQiad7Kd9sQO_-OntxgR2dP4UmUI8nx8L_PYMfVz-HR0Fny_gX8GqoSIykjl-sWXeTn_AHv2-Cb6ZbkW2Bj5EcQNoledeSi6eKz6XyovIFTGk9CnH0S-_mQ07Zt2uVLuD47vTo5T2IrhcQwTrvE5IpZYxwvM2-sVEGvM0cu44WzSOFKLx21PAhbvPRlyI5XqqCaZ_woN55b-gr26qZ2b4BwVECYzp3IUJZSZaGdDZZlVZS5cblVE_gy7mV1N1TMqAZPN60GAFQRADgybHUVjhLupFExIwC_E4pSVccomkouRckn8Amh8c_lPo7AqvCMBMeHql2zWlY5o6iFBuV3Aq8H4K3XGlFgAmILrOsBof729htEy74Od0TDt_898x3s5yFEJlh02HvY69qV-4AyTqcPetvAQY_ZeL36PvsD5IAAag |
link.rule.ids | 230,314,727,780,784,864,885,1604,27924,27925,53791,53793 |
linkProvider | National Library of Medicine |
linkToHtml | http://utb.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwnV1Lb9QwEB6VIqAXxJuFAgYhcUrTxI4fx6pqtcDuqoJW6gnLT7FSN6myWST49dh5rHZ7qdRjEtuxPOPxjGfmG4DPlnmiGbWJDiRICM9woj12CeXEc-21dW2W63RGxxfk22VxuQPFkAvTBu0bPT8orxYH5fx3G1t5vTDpECeWnk2PGeM4ozS9B_cLzEQ2GOm982BwUTLMgnmE-RqrEaeL6kq7P-liqVSwdfbgIc6ZYFmUyBvHUi-ctzLeNhTPm_GTGwfS6RN43GuS6Kib8VPYceUzeNDVlvz7HH51uMRBmKGzdZEu9HP-LzzX0TvTLNEkHmToR1Q3kV41aFY1_bvpvMPeCF0qj2KkfdJX9EEndV3VyxdwcXpyfjxO-mIKiSEUN4nJFbHGOCoybyxX0bIzhy6jhbNBxgnPHbY0qltUeBHz45UqsKYZPcyNpxa_hN2yKt1rQDSYIETnjmVBm1Ki0M7Gu2VViNy43KoRfBnWUl53mBmy83Vj2RFA9gQILeNSy7iZwkoa1ecEhP9EWCp5FJRTTjkTdASfAjVuHe7jQCwZdkl0fajSVaulzAkOdmg0f0fwqiPeeqyBBUbAtsi6bhARuLe_BMZskbh7Rnxz554f4NH4fDqRk6-z729hL48BM_F-h-zDblOv3Lug8TT6fcvf_wFw2AGu |
linkToPdf | http://utb.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwnV3db9MwELdgiGkvE5-j48sgJJ6yLLFjO4_TWDVgrSpg0p6w_CkqrUmVpkjw13NOnKrlBYnHJLZj-c7nO9_d7xB6Z7mnmjObaCBBQkVGEu2JS5igXmivreuyXCdTdnlNP90UN1ulvrqgfaPnJ9Xt4qSa_-hiK5cLkw5xYulscs65IBlj6dL69C66VxBgssFQjw6EwU3JCQcTiYgNXiNJF_Wtdj_TxUopsHcO0D7JecmzIJW3jqYooHey3raUz79jKLcOpfEDdBi1SXzWz_ohuuOqR-h-X1_y12P0vccmBoGGZ5tCXfjr_Dc8N8FD067wVTjM8JegcmK9bvG0buO7ybzH34Autcch2j6JVX3wRdPUzeoJuh5ffDu_TGJBhcRQRtrE5IpaYxwrM2-sUMG6M6cuY4WzIOdKLxyxLKhcrPRlyJFXqiCaZew0N55Z8hTtVXXlniHMwAyhOnc8A41KlYV2Ntwvq6LMjcutGqH3w1rKZY-bIXt_N5E9AWQkALQMSy3DhoKVNCrmBcB_AjSVPAMFVTDBSzZCb4Ea_xzuzUAsCTsluD9U5er1SuaUgC0aTOAROuqJtxlrYIER4jtk3TQIKNy7X4A5OzTuyIzH_93zNdqffRjLq4_Tz8_RQR5iZsIVD32B9tpm7V6C0tPqVx17_wEc1wLB |
openUrl | ctx_ver=Z39.88-2004&ctx_enc=info%3Aofi%2Fenc%3AUTF-8&rfr_id=info%3Asid%2Fsummon.serialssolutions.com&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=Effective+Population+Size+Predicts+Local+Rates+but+Not+Local+Mitigation+of+Read-through+Errors&rft.jtitle=Molecular+biology+and+evolution&rft.au=Ho%2C+Alexander+T&rft.au=Hurst%2C+Laurence+D&rft.date=2021-01-04&rft.pub=Oxford+University+Press&rft.issn=0737-4038&rft.volume=38&rft.issue=1&rft.spage=244&rft_id=info:doi/10.1093%2Fmolbev%2Fmsaa210&rft.externalDocID=A774868796 |
thumbnail_l | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/lc.gif&issn=1537-1719&client=summon |
thumbnail_m | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/mc.gif&issn=1537-1719&client=summon |
thumbnail_s | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/sc.gif&issn=1537-1719&client=summon |