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m(6)A-LAIC-seq reveals the census and complexity of the m(6)A epitranscriptome
Benoit Molinie1, Jinkai Wang2, Kok Seong Lim3
1Gastrointestinal Unit, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA.
Nature Methods
|July 5, 2016
Summary
N(6)-Methyladenosine (m(6)A) RNA modifications show cell-type-specific levels and link to alternative polyadenylation (APA) site usage. This new sequencing method reveals how m(6)A impacts transcriptome complexity by influencing APA site selection.
Area of Science:
- Molecular Biology
- Genomics
- RNA Biology
Background:
- N(6)-Methyladenosine (m(6)A) is a prevalent, reversible RNA modification impacting RNA metabolism.
- Quantitative data on m(6)A levels and its relationship with RNA isoforms are limited.
Purpose of the Study:
- To develop a method for quantifying m(6)A levels and characterizing RNA isoforms.
- To investigate the connection between m(6)A modification and alternative polyadenylation (APA) site usage.
Main Methods:
- Development of m(6)A-level and isoform-characterization sequencing (m(6)A-LAIC-seq).
- Application of m(6)A-LAIC-seq to analyze m(6)A modification patterns and APA site usage in cells.
Main Results:
- Cells display variable, nonstoichiometric m(6)A levels with cell-type specificity.
- Discovery of widespread differences in APA site usage between m(6)A-modified and non-modified transcripts.
- Identification of a bias for m(6)A-modified transcripts to utilize proximal APA sites, leading to shorter 3' UTRs.
Conclusions:
- m(6)A-LAIC-seq provides novel insights into transcriptome complexity.
- m(6)A modification is directly linked to the selection of alternative polyadenylation sites.
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