Genetic regulation of disease risk and endometrial gene expression highlights potential target genes for endometriosis and polycystic ovarian syndrome
Gene expression varies markedly across the menstrual cycle and expression levels for many genes are under genetic control. We analyzed gene expression and mapped expression quantitative trait loci (eQTLs) in endometrial tissue samples from 229 women and then analyzed the overlap of endometrial eQTL...
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Published in | Scientific reports Vol. 8; no. 1; pp. 11424 - 19 |
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Main Authors | , , , , , , , , , , , , , |
Format | Journal Article |
Language | English |
Published |
London
Nature Publishing Group UK
30.07.2018
Nature Publishing Group |
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Abstract | Gene expression varies markedly across the menstrual cycle and expression levels for many genes are under genetic control. We analyzed gene expression and mapped expression quantitative trait loci (eQTLs) in endometrial tissue samples from 229 women and then analyzed the overlap of endometrial eQTL signals with genomic regions associated with endometriosis and other reproductive traits. We observed a total of 45,923
cis
-eQTLs for 417 unique genes and 2,968
trans
-eQTLs affecting 82 unique genes. Two eQTLs were located in known risk regions for endometriosis including
LINC00339
on chromosome 1 and
VEZT
on chromosome 12 and there was evidence for eQTLs that may be target genes in genomic regions associated with other reproductive diseases. Dynamic changes in expression of individual genes across cycle include alterations in both mean expression and transcriptional silencing. Significant effects of cycle stage on mean expression levels were observed for (2,427/15,262) probes with detectable expression in at least 90% of samples and for (2,877/9,626) probes expressed in some, but not all samples. Pathway analysis supports similar biological control of both altered expression levels and transcriptional silencing. Taken together, these data identify strong genetic effects on genes with diverse functions in human endometrium and provide a platform for better understanding genetic effects on endometrial-related pathologies. |
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AbstractList | Gene expression varies markedly across the menstrual cycle and expression levels for many genes are under genetic control. We analyzed gene expression and mapped expression quantitative trait loci (eQTLs) in endometrial tissue samples from 229 women and then analyzed the overlap of endometrial eQTL signals with genomic regions associated with endometriosis and other reproductive traits. We observed a total of 45,923 cis-eQTLs for 417 unique genes and 2,968 trans-eQTLs affecting 82 unique genes. Two eQTLs were located in known risk regions for endometriosis including LINC00339 on chromosome 1 and VEZT on chromosome 12 and there was evidence for eQTLs that may be target genes in genomic regions associated with other reproductive diseases. Dynamic changes in expression of individual genes across cycle include alterations in both mean expression and transcriptional silencing. Significant effects of cycle stage on mean expression levels were observed for (2,427/15,262) probes with detectable expression in at least 90% of samples and for (2,877/9,626) probes expressed in some, but not all samples. Pathway analysis supports similar biological control of both altered expression levels and transcriptional silencing. Taken together, these data identify strong genetic effects on genes with diverse functions in human endometrium and provide a platform for better understanding genetic effects on endometrial-related pathologies. Gene expression varies markedly across the menstrual cycle and expression levels for many genes are under genetic control. We analyzed gene expression and mapped expression quantitative trait loci (eQTLs) in endometrial tissue samples from 229 women and then analyzed the overlap of endometrial eQTL signals with genomic regions associated with endometriosis and other reproductive traits. We observed a total of 45,923 cis -eQTLs for 417 unique genes and 2,968 trans -eQTLs affecting 82 unique genes. Two eQTLs were located in known risk regions for endometriosis including LINC00339 on chromosome 1 and VEZT on chromosome 12 and there was evidence for eQTLs that may be target genes in genomic regions associated with other reproductive diseases. Dynamic changes in expression of individual genes across cycle include alterations in both mean expression and transcriptional silencing. Significant effects of cycle stage on mean expression levels were observed for (2,427/15,262) probes with detectable expression in at least 90% of samples and for (2,877/9,626) probes expressed in some, but not all samples. Pathway analysis supports similar biological control of both altered expression levels and transcriptional silencing. Taken together, these data identify strong genetic effects on genes with diverse functions in human endometrium and provide a platform for better understanding genetic effects on endometrial-related pathologies. Abstract Gene expression varies markedly across the menstrual cycle and expression levels for many genes are under genetic control. We analyzed gene expression and mapped expression quantitative trait loci (eQTLs) in endometrial tissue samples from 229 women and then analyzed the overlap of endometrial eQTL signals with genomic regions associated with endometriosis and other reproductive traits. We observed a total of 45,923 cis -eQTLs for 417 unique genes and 2,968 trans -eQTLs affecting 82 unique genes. Two eQTLs were located in known risk regions for endometriosis including LINC00339 on chromosome 1 and VEZT on chromosome 12 and there was evidence for eQTLs that may be target genes in genomic regions associated with other reproductive diseases. Dynamic changes in expression of individual genes across cycle include alterations in both mean expression and transcriptional silencing. Significant effects of cycle stage on mean expression levels were observed for (2,427/15,262) probes with detectable expression in at least 90% of samples and for (2,877/9,626) probes expressed in some, but not all samples. Pathway analysis supports similar biological control of both altered expression levels and transcriptional silencing. Taken together, these data identify strong genetic effects on genes with diverse functions in human endometrium and provide a platform for better understanding genetic effects on endometrial-related pathologies. |
ArticleNumber | 11424 |
Author | McRae, Allan Girling, Jane E. Fung, Jenny N. Powell, Joseph E. Teh, Wan Tinn Montgomery, Grant W. Lukowski, Samuel W. Yang, Jian Zhu, Zhihong Healey, Martin McKinnon, Brett D. Rogers, Peter A. W. Mortlock, Sally Holdsworth-Carson, Sarah J. |
Author_xml | – sequence: 1 givenname: Jenny N. surname: Fung fullname: Fung, Jenny N. email: j.fung1@uq.edu.au organization: The Institute for Molecular Bioscience, The University of Queensland – sequence: 2 givenname: Sally surname: Mortlock fullname: Mortlock, Sally organization: The Institute for Molecular Bioscience, The University of Queensland – sequence: 3 givenname: Jane E. surname: Girling fullname: Girling, Jane E. organization: Gynaecology Research Centre, The University of Melbourne, Department of Obstetrics and Gynaecology, Royal Women’s Hospital, Department of Anatomy, University of Otago – sequence: 4 givenname: Sarah J. surname: Holdsworth-Carson fullname: Holdsworth-Carson, Sarah J. organization: Gynaecology Research Centre, The University of Melbourne, Department of Obstetrics and Gynaecology, Royal Women’s Hospital – sequence: 5 givenname: Wan Tinn surname: Teh fullname: Teh, Wan Tinn organization: Gynaecology Research Centre, The University of Melbourne, Department of Obstetrics and Gynaecology, Royal Women’s Hospital – sequence: 6 givenname: Zhihong surname: Zhu fullname: Zhu, Zhihong organization: The Institute for Molecular Bioscience, The University of Queensland – sequence: 7 givenname: Samuel W. orcidid: 0000-0002-8598-7902 surname: Lukowski fullname: Lukowski, Samuel W. organization: The Institute for Molecular Bioscience, The University of Queensland – sequence: 8 givenname: Brett D. surname: McKinnon fullname: McKinnon, Brett D. organization: The Institute for Molecular Bioscience, The University of Queensland, Department of Obstetrics and Gynaecology, University hospital of Berne – sequence: 9 givenname: Allan surname: McRae fullname: McRae, Allan organization: The Institute for Molecular Bioscience, The University of Queensland – sequence: 10 givenname: Jian orcidid: 0000-0003-2001-2474 surname: Yang fullname: Yang, Jian organization: The Institute for Molecular Bioscience, The University of Queensland – sequence: 11 givenname: Martin surname: Healey fullname: Healey, Martin organization: Gynaecology Research Centre, The University of Melbourne, Department of Obstetrics and Gynaecology, Royal Women’s Hospital – sequence: 12 givenname: Joseph E. surname: Powell fullname: Powell, Joseph E. organization: The Institute for Molecular Bioscience, The University of Queensland – sequence: 13 givenname: Peter A. W. surname: Rogers fullname: Rogers, Peter A. W. organization: Gynaecology Research Centre, The University of Melbourne, Department of Obstetrics and Gynaecology, Royal Women’s Hospital – sequence: 14 givenname: Grant W. orcidid: 0000-0002-4140-8139 surname: Montgomery fullname: Montgomery, Grant W. organization: The Institute for Molecular Bioscience, The University of Queensland |
BackLink | https://www.ncbi.nlm.nih.gov/pubmed/30061686$$D View this record in MEDLINE/PubMed |
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Snippet | Gene expression varies markedly across the menstrual cycle and expression levels for many genes are under genetic control. We analyzed gene expression and... Abstract Gene expression varies markedly across the menstrual cycle and expression levels for many genes are under genetic control. We analyzed gene expression... |
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SubjectTerms | 38 38/39 45 45/61 631/114/2407 631/208/200 Biological control Chromosome 1 Chromosome 12 DNA probes Endometriosis Endometrium Gene expression Gene mapping Gene silencing Genetic control Genetic effects Genotype & phenotype Health risks Humanities and Social Sciences Menstrual cycle multidisciplinary Polycystic ovary syndrome Probes Quantitative trait loci Science Science (multidisciplinary) |
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Title | Genetic regulation of disease risk and endometrial gene expression highlights potential target genes for endometriosis and polycystic ovarian syndrome |
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