TY - JOUR
T1 - m 6 A-Atlas v2.0
T2 - updated resources for unraveling the N 6 -methyladenosine (m 6 A) epitr anscript ome among multiple species
AU - Liang, Zhanmin
AU - Ye, Haokai
AU - Ma, Jiongming
AU - Wei, Zhen
AU - Wang, Yue
AU - Zhang, Yuxin
AU - Huang, Daiyun
AU - Song, Bowen
AU - Meng, Jia
AU - Rigden, Daniel J.
AU - Chen, Kunqi
N1 - Publisher Copyright:
© The Author(s) 2023.
PY - 2024/1/5
Y1 - 2024/1/5
N2 - N 6 -Methyladenosine (m 6 A) is one of the most abundant internal chemical modifications on eukaryote mRNA and is in v olv ed in numerous essential molecular functions and biological processes. To facilitate the study of this important post-transcriptional modification, we present here m 6 A-Atlas v2.0, an updated version of m 6 A-Atlas. It was expanded to include a total of 797 091 reliable m 6 A sites from 13 high-resolution technologies and two single-cell m 6 A profiles. Additionally, three methods (exomeP eaks2, MA CS2 and TRESS) were used to identify > 16 million m 6 A enrichment peaks from 2712 MeRIP-seq experiments covering 651 conditions in 42 species. Quality control results of MeRIP-seq samples were also provided to help users to select reliable peaks. We also estimated the condition-specific quantitative m 6 A profiles (i.e. differential methylation) under 172 e xperimental conditions f or 19 species. Further, to pro vide insights into potential functional circuitry, the m 6 A epitranscriptomics were annotated with various genomic features, interactions with RNA-binding proteins and microRNA, potentially linked splicing events and single nucleotide polymorphisms. The collected m 6 A sites and their functional annotations can be freely queried and downloaded via a user-friendly graphical interface at: http:// rnamd.org/ m6a.
AB - N 6 -Methyladenosine (m 6 A) is one of the most abundant internal chemical modifications on eukaryote mRNA and is in v olv ed in numerous essential molecular functions and biological processes. To facilitate the study of this important post-transcriptional modification, we present here m 6 A-Atlas v2.0, an updated version of m 6 A-Atlas. It was expanded to include a total of 797 091 reliable m 6 A sites from 13 high-resolution technologies and two single-cell m 6 A profiles. Additionally, three methods (exomeP eaks2, MA CS2 and TRESS) were used to identify > 16 million m 6 A enrichment peaks from 2712 MeRIP-seq experiments covering 651 conditions in 42 species. Quality control results of MeRIP-seq samples were also provided to help users to select reliable peaks. We also estimated the condition-specific quantitative m 6 A profiles (i.e. differential methylation) under 172 e xperimental conditions f or 19 species. Further, to pro vide insights into potential functional circuitry, the m 6 A epitranscriptomics were annotated with various genomic features, interactions with RNA-binding proteins and microRNA, potentially linked splicing events and single nucleotide polymorphisms. The collected m 6 A sites and their functional annotations can be freely queried and downloaded via a user-friendly graphical interface at: http:// rnamd.org/ m6a.
UR - http://www.scopus.com/inward/record.url?scp=85175862970&partnerID=8YFLogxK
U2 - 10.1093/nar/gkad691
DO - 10.1093/nar/gkad691
M3 - Article
C2 - 37587690
AN - SCOPUS:85175862970
SN - 0305-1048
VL - 52
SP - D194-D202
JO - Nucleic Acids Research
JF - Nucleic Acids Research
IS - D1
ER -