Quantitative profiling of N6-methyladenosine at single-base resolution in stem-differentiating xylem of Populus trichocarpa using Nanopore direct RNA sequencing
There are no comprehensive methods to identify N 6 -methyladenosine (m 6 A) at single-base resolution for every single transcript, which is necessary for the estimation of m 6 A abundance. We develop a new pipeline called Nanom6A for the identification and quantification of m 6 A modification at sin...
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| Published in | Genome Biology Vol. 22; no. 1; p. 22 |
|---|---|
| Main Authors | , , , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
London
BioMed Central
07.01.2021
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| Subjects | |
| Online Access | Get full text |
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| Abstract | There are no comprehensive methods to identify
N
6
-methyladenosine (m
6
A) at single-base resolution for every single transcript, which is necessary for the estimation of m
6
A abundance. We develop a new pipeline called Nanom6A for the identification and quantification of m
6
A modification at single-base resolution using Nanopore direct RNA sequencing based on an XGBoost model. We validate our method using methylated RNA immunoprecipitation sequencing (MeRIP-Seq) and m
6
A-sensitive RNA-endoribonuclease–facilitated sequencing (m6A-REF-seq), confirming high accuracy. Using this method, we provide a transcriptome-wide quantification of m
6
A modification in stem-differentiating xylem and reveal that different alternative polyadenylation (APA) usage shows a different ratio of m
6
A. |
|---|---|
| AbstractList | There are no comprehensive methods to identify
N
6
-methyladenosine (m
6
A) at single-base resolution for every single transcript, which is necessary for the estimation of m
6
A abundance. We develop a new pipeline called Nanom6A for the identification and quantification of m
6
A modification at single-base resolution using Nanopore direct RNA sequencing based on an XGBoost model. We validate our method using methylated RNA immunoprecipitation sequencing (MeRIP-Seq) and m
6
A-sensitive RNA-endoribonuclease–facilitated sequencing (m6A-REF-seq), confirming high accuracy. Using this method, we provide a transcriptome-wide quantification of m
6
A modification in stem-differentiating xylem and reveal that different alternative polyadenylation (APA) usage shows a different ratio of m
6
A. There are no comprehensive methods to identify N6-methyladenosine (m6A) at single-base resolution for every single transcript, which is necessary for the estimation of m6A abundance. We develop a new pipeline called Nanom6A for the identification and quantification of m6A modification at single-base resolution using Nanopore direct RNA sequencing based on an XGBoost model. We validate our method using methylated RNA immunoprecipitation sequencing (MeRIP-Seq) and m6A-sensitive RNA-endoribonuclease–facilitated sequencing (m6A-REF-seq), confirming high accuracy. Using this method, we provide a transcriptome-wide quantification of m6A modification in stem-differentiating xylem and reveal that different alternative polyadenylation (APA) usage shows a different ratio of m6A. There are no comprehensive methods to identify N⁶-methyladenosine (m⁶A) at single-base resolution for every single transcript, which is necessary for the estimation of m⁶A abundance. We develop a new pipeline called Nanom6A for the identification and quantification of m⁶A modification at single-base resolution using Nanopore direct RNA sequencing based on an XGBoost model. We validate our method using methylated RNA immunoprecipitation sequencing (MeRIP-Seq) and m⁶A-sensitive RNA-endoribonuclease–facilitated sequencing (m6A-REF-seq), confirming high accuracy. Using this method, we provide a transcriptome-wide quantification of m⁶A modification in stem-differentiating xylem and reveal that different alternative polyadenylation (APA) usage shows a different ratio of m⁶A. There are no comprehensive methods to identify N6-methyladenosine (m6A) at single-base resolution for every single transcript, which is necessary for the estimation of m6A abundance. We develop a new pipeline called Nanom6A for the identification and quantification of m6A modification at single-base resolution using Nanopore direct RNA sequencing based on an XGBoost model. We validate our method using methylated RNA immunoprecipitation sequencing (MeRIP-Seq) and m6A-sensitive RNA-endoribonuclease-facilitated sequencing (m6A-REF-seq), confirming high accuracy. Using this method, we provide a transcriptome-wide quantification of m6A modification in stem-differentiating xylem and reveal that different alternative polyadenylation (APA) usage shows a different ratio of m6A.There are no comprehensive methods to identify N6-methyladenosine (m6A) at single-base resolution for every single transcript, which is necessary for the estimation of m6A abundance. We develop a new pipeline called Nanom6A for the identification and quantification of m6A modification at single-base resolution using Nanopore direct RNA sequencing based on an XGBoost model. We validate our method using methylated RNA immunoprecipitation sequencing (MeRIP-Seq) and m6A-sensitive RNA-endoribonuclease-facilitated sequencing (m6A-REF-seq), confirming high accuracy. Using this method, we provide a transcriptome-wide quantification of m6A modification in stem-differentiating xylem and reveal that different alternative polyadenylation (APA) usage shows a different ratio of m6A. |
| ArticleNumber | 22 |
| Author | Reddy, Anireddy S. N. Kohnen, Markus V. Gu, Lianfeng Xi, Feihu Gao, Yubang Liu, Xuqing Wu, Bizhi Wang, Huihui |
| Author_xml | – sequence: 1 givenname: Yubang surname: Gao fullname: Gao, Yubang – sequence: 2 givenname: Xuqing surname: Liu fullname: Liu, Xuqing – sequence: 3 givenname: Bizhi surname: Wu fullname: Wu, Bizhi – sequence: 4 givenname: Huihui surname: Wang fullname: Wang, Huihui – sequence: 5 givenname: Feihu surname: Xi fullname: Xi, Feihu – sequence: 6 givenname: Markus V. surname: Kohnen fullname: Kohnen, Markus V. – sequence: 7 givenname: Anireddy S. N. surname: Reddy fullname: Reddy, Anireddy S. N. – sequence: 8 givenname: Lianfeng orcidid: 0000-0002-3810-2411 surname: Gu fullname: Gu, Lianfeng |
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| Snippet | There are no comprehensive methods to identify
N
6
-methyladenosine (m
6
A) at single-base resolution for every single transcript, which is necessary for the... There are no comprehensive methods to identify N6-methyladenosine (m6A) at single-base resolution for every single transcript, which is necessary for the... There are no comprehensive methods to identify N⁶-methyladenosine (m⁶A) at single-base resolution for every single transcript, which is necessary for the... |
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| SubjectTerms | Algorithms Datasets Enzymes Gene expression genome Immunoprecipitation Method methylation N6-methyladenosine nanopores Polyadenylation Populus trichocarpa precipitin tests Ribonucleic acid RNA Standard deviation Transcription Transcriptomes Xylem |
| Title | Quantitative profiling of N6-methyladenosine at single-base resolution in stem-differentiating xylem of Populus trichocarpa using Nanopore direct RNA sequencing |
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