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| Status |
Public on Dec 17, 2012 |
| Title |
Analysis of alternative cleavage and polyadenylation by 3' region extraction and deep sequencing |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Alternative cleavage and polyadenylation (APA) generates diverse mRNA isoforms. We developed 3' region extraction and deep sequencing (3'READS) to address mispriming issues that commonly plague poly(A) site (pA) identification, and we used the method to comprehensively map pAs in the mouse genome. Thorough annotation of gene 3' ends revealed over 5,000 previously overlooked pAs (~8% of total) flanked by A-rich sequences, underscoring the necessity of using an accurate tool for pA mapping. About 79% of mRNA genes and 66% of long noncoding RNA genes undergo APA, but these two gene types have distinct usage patterns for pAs in introns and upstream exons. Quantitative analysis of APA isoforms by 3'READS indicated that promoter-distal pAs, regardless of intron or exon locations, become more abundant during embryonic development and cell differentiation and that upregulated isoforms have stronger pAs, suggesting global modulation of the 3' end–processing activity in development and differentiation.
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| Overall design |
3'READS to map pAs in mouse genome
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| Contributor(s) |
Hoque M, JI Z, Zheng D, Luo W, Li W, You B, Park JY, Yehia G, Tian B |
| Citation(s) |
23241633 |
| Submission date |
Nov 19, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Zhe Ji |
| E-mail(s) |
zhe.ji@northwestern.edu
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| Organization name |
Northwestern University
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| Street address |
303 E Superior St, Lurie 6-107
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| City |
Chicago |
| State/province |
ILLINOIS |
| ZIP/Postal code |
60611 |
| Country |
USA |
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| Platforms (1) |
| GPL11002 |
Illumina Genome Analyzer IIx (Mus musculus) |
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| Samples (4)
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| Relations |
| BioProject |
PRJNA181289 |
| SRA |
SRP017249 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE42398_RAW.tar |
17.1 Mb |
(http)(custom) |
TAR (of BED) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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