Open AccessMapping 3′ mRNA Isoforms on a Genomic Scale
Author(s) -
Jin Yi,
Geisberg Joseph V.,
Moqtaderi Zarmik,
Ji Zhe,
Hoque Mainul,
Tian Bin,
Struhl Kevin
Publication year - 2015
Publication title -
current protocols in molecular biology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.533
H-Index - 42
eISSN - 1934-3647
pISSN - 1934-3639
DOI - 10.1002/0471142727.mb0423s110
Subject(s) - computational biology , biology , identification (biology) , gene isoform , dna sequencing , genome , sequence (biology) , messenger rna , genetics , deep sequencing , gene , botany
Most eukaryotic genes are transcribed into mRNAs with alternative poly(A) sites. Emerging evidence suggests that mRNA isoforms with alternative poly(A) sites can perform critical regulatory functions in numerous biological processes. In recent years, a number of strategies utilizing high‐throughput sequencing technologies have been developed to aid in the identification of genome‐wide poly(A) sites. This unit describes a modified protocol for a recently published 3′READS (3′ region extraction and deep sequencing) method that accurately identifies genome‐wide poly(A) sites and that can be used to quantify the relative abundance of the resulting 3′ mRNA isoforms. This approach minimizes nonspecific sequence reads due to internal priming and typically yields a high percentage of sequence reads that are ideally suited for accurate poly(A) identification. © 2015 by John Wiley & Sons, Inc.