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Series GSE115232 Query DataSets for GSE115232
Status Public on Feb 12, 2019
Title The 3' end processing factor PCF11 regulates gene expression based on gene size and intronic polyadenylation
Organism Mus musculus
Experiment type Other
Expression profiling by high throughput sequencing
Summary Genes with different sizes have distinct expression patterns and functions. Here we show that the 3' end processing PCF11 modulates gene expression according to gene size. Gene density and polyA site strength, but not orientation between neighboring genes, impact short gene regulation by PCF11. In contrast, long gene modulation involves intronic polyadenylation (IPA), which is widespread in large introns. Downregulation of PCF11, which takes place in cell differentiation, contributes to short and long gene expressions with functions related to cell proliferation, cell morphology, adhesion, and migration. Mild, exogenous upregulation of PCF11 perturbs the gene expression program in cell differentiation. Further, PCF11 is auto-regulated through a highly conserved IPA site, the removal of which leads to PCF11 overexpression and global activation of proximal PASs sites. Together, our data indicate that PCF11 level impacts gene expression based on size and its autoregulation maintains homeostasis of PAS usage in the cell.
 
Overall design In total 2 RNA-seq libraries from 3T3-L1 cells for gene expression analysis;
In total 4 3'READS libraries for the analysis of APA during C2C12 cell differentiation;
In total 4 3'READS libraries for analysis of APA isoform stability under siPcf11 using 4sU metabolic labeling in C2C12 cells;
In total 4 3'READS libraries for analysis of APA under siPcf11 using total RNA from C2C12 cells;
In total 4 3'READS libraries for analysis of APA under Pcf11-IPAKO using total RNA from 4T1 cells;
In total 4 3'READS libraries for analysis of APA under siPcf11 using total RNA from NIH3T3 cells;

 
Contributor(s) Wang R, Zheng D, Wei L, Ding Q, Tian B
Citation(s) 30840896, 34289366
NIH grant(s)
Grant ID Grant title Affiliation Name
R01 GM084089 Regulation of Alternatiive Cleavage and Polyadenylation RUTGERS, THE STATE UNIVERSITY OF NEW JERSEY--RBHS-NEW JERSEY MEDICAL SCHOOL BIN TIAN
Submission date Jun 01, 2018
Last update date Oct 19, 2021
Contact name Bin Tian
E-mail(s) btian@rutgers.edu
Organization name Rutgers New Jersey Medical School
Department Department of Microbiology, Biochemistry and Molecular Genetics
Street address 205 South Orange Ave.
City Newark
State/province NJ
ZIP/Postal code 07103
Country USA
 
Platforms (2)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
GPL19057 Illumina NextSeq 500 (Mus musculus)
Samples (22)
GSM3171721 Ctrl_C2C12_4sU_1_3READS
GSM3171722 Ctrl_C2C12_4sU_2_3READS
GSM3171723 Ctrl_C2C12_input_1_3READS
Relations
BioProject PRJNA474216
SRA SRP149561

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE115232_RAW.tar 7.6 Mb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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