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Series GSE62001 Query DataSets for GSE62001
Status Public on Apr 01, 2015
Title Regulation of alternative cleavage and polyadenylation by 3’ end processing and splicing factors
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Alternative cleavage and polyadenylation (APA) results in mRNA isoforms containing different 3’ untranslated regions (3’UTRs) and/or coding sequences. How core cleavage and polyadenylation (C/P) factors regulate APA is not well understood. Using siRNA knockdown coupled with deep sequencing, we found that several C/P factors can play significant roles in 3’UTR-APA. Whereas Pcf11 and Fip1 enhance usage of proximal poly(A) sites (pAs), CFI-25/68, PABPN1, and PABPC1 promote usage of distal pAs. Strong cis element biases were found for pAs regulated by CFI or Fip1, and the distance between pAs plays an important role in APA regulation. In addition, intronic pAs are substantially regulated by splicing factors, with U1 mostly influencing C/P events in 5’ introns and U2 impacting those in efficiently spliced introns. Furthermore, PABPN1 regulates expression of transcripts with pAs near the transcription start site, a property possibly related to its role in RNA degradation. Finally, we found that groups of APA events regulated by C/P factors are also modulated in cell differentiation and development with distinct trends. Together, our results indicate that the abundance of different C/P factors and splicing factors plays diverse roles in APA, and is relevant to APA regulation in biological conditions.
Overall design knockdown experiments of 23 C/P factors, 3 splicing factors and U1D in mouse C2C12 myoblast cells
Contributor(s) Li W, You B, Zheng D, Hoque M, Luo W, Ji Z, Park J, Tian B
Citation(s) 25906188
Submission date Oct 02, 2014
Last update date May 15, 2019
Contact name Wencheng Li
Organization name PTC Therapeutics
Street address 100 Corporate Count
City South Plainfield
State/province NJ - New Jersey
ZIP/Postal code 07080
Country USA
Platforms (3)
GPL9250 Illumina Genome Analyzer II (Mus musculus)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
Samples (54)
GSM1518071 siCPSF-160.1
GSM1518072 siCPSF-100.3
GSM1518073 siCPSF-73.1
BioProject PRJNA262911
SRA SRP048599

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Supplementary file Size Download File type/resource
GSE62001_mm9.pA.read_counts.add8T.txt.gz 3.2 Mb (ftp)(http) TXT
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Raw data are available in SRA
Processed data are available on Series record

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