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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Feb 19, 2016 |
| Title |
PAPERCLIP Identifies MicroRNA Targets and a Role of CstF64/64tau in Promoting Non-canonical poly(A) Site Usage. |
| Organisms |
Homo sapiens; Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
Other
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| Summary |
Accurate and precise annotation of 3' UTRs is critical for understanding how mRNAs are regulated by microRNAs (miRNAs) and RNA-binding proteins (RBPs). Here, we describe a method, poly(A) binding protein-mediated mRNA 3' end retrieval by crosslinking immunoprecipitation (PAPERCLIP), that shows high specificity for mRNA 3' ends and compares favorably with existing 3' end mapping methods. PAPERCLIP uncovers a previously unrecognized role of CstF64/64tau in promoting the usage of a selected group of non-canonical poly(A) sites, the majority of which contain a downstream GUKKU motif. Furthermore, in the mouse brain, PAPERCLIP discovers extended 3' UTR sequences harboring functional miRNA binding sites and reveals developmentally regulated APA shifts, including one in Atp2b2 that is evolutionarily conserved in humans and results in the gain of a functional binding site of miR-137. PAPERCLIP provides a powerful tool to decipher post-transcriptional regulation of mRNAs through APA in vivo.
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| Overall design |
PAPERCLIP protocol and RNA-Seq on human cell lines and mouse whole brain cortex.
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| Contributor(s) |
Hwang H, Darnell RB |
| Citation(s) |
27050522 |
| Submission date |
Feb 19, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Hun-Way Hwang |
| E-mail(s) |
Hunway.Hwang@pitt.edu
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| Organization name |
University of Pittsburgh
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| Department |
Department of Pathology
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| Lab |
S754 Scaife Hall
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| Street address |
3550 Terrace Street
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| City |
Pittsburgh |
| State/province |
PA |
| ZIP/Postal code |
15261 |
| Country |
USA |
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| Platforms (4)
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| GPL11154 |
Illumina HiSeq 2000 (Homo sapiens) |
| GPL13112 |
Illumina HiSeq 2000 (Mus musculus) |
| GPL15520 |
Illumina MiSeq (Homo sapiens) |
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| Samples (32)
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| GSM1614166 |
PAPERCLIP for HEK293 cells, replicate 2 |
| GSM1614167 |
PAPERCLIP for adult mouse cortex, replicate 1 |
| GSM1614168 |
PAPERCLIP for adult mouse cortex, replicate 2 |
| GSM1614169 |
PAPERCLIP for embryonic mouse cortex, replicate 1 |
| GSM1614170 |
PAPERCLIP for embryonic mouse cortex, replicate 2 |
| GSM1614171 |
PAPERCLIP for si-Ctrl, replicate 1 |
| GSM1614172 |
PAPERCLIP for si-Ctrl, replicate 2 |
| GSM1614173 |
PAPERCLIP for si-CFIm68, replicate 1 |
| GSM1614174 |
PAPERCLIP for si-CFIm68, replicate 2 |
| GSM1614175 |
PAPERCLIP for si-CstF64/64tau, replicate 1 |
| GSM1614176 |
PAPERCLIP for si-CstF64/64tau, replicate 2 |
| GSM1614177 |
3' end sequencing for HeLa cells |
| GSM1614178 |
RNA-seq for HeLa cells |
| GSM1614179 |
RNA-seq for adult mouse cortex |
| GSM1857615 |
PAPERCLIP for si-Ctrl in LN229, replicate 1 |
| GSM1857616 |
PAPERCLIP for si-Ctrl in LN229, replicate 2 |
| GSM1857617 |
PAPERCLIP for si-CFIm68 in LN229, replicate 1 |
| GSM1857618 |
PAPERCLIP for si-CFIm68 in LN229, replicate 2 |
| GSM1857619 |
PAPERCLIP for si-CstF64/64tau in LN229, replicate 1 |
| GSM1857620 |
PAPERCLIP for si-CstF64/64tau in LN229, replicate 2 |
| GSM1857621 |
PAPERCLIP for pEN2, replicate 1 |
| GSM1857622 |
PAPERCLIP for pEN2, replicate 2 |
| GSM1857623 |
PAPERCLIP for pEN2-GU mutant, replicate 1 |
| GSM1857624 |
PAPERCLIP for pEN2-GU mutant, replicate 2 |
| GSM1857625 |
PAPERCLIP for pEN2-AR mutant, replicate 1 |
| GSM1857626 |
PAPERCLIP for pEN2-AR mutant, replicate 2 |
| GSM2012263 |
RNA-seq for embryo mouse cortex, replicate 1 |
| GSM2012264 |
RNA-seq for adult mouse cortex, replicate 2 |
| GSM2012265 |
RNA-seq for embryo mouse cortex, replicate 2 |
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| Relations |
| BioProject |
PRJNA275863 |
| SRA |
SRP055175 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE66092_00081814.remake.bedgraph.gz |
54.0 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE66092_00091013.uniq.bedgraph.gz |
22.7 Mb |
(ftp)(http) |
BEDGRAPH |
| GSE66092_B3p121_3Seq_81117_hg19_EndAssigned_Filtered.bed.gz |
811.3 Kb |
(ftp)(http) |
BED |
| GSE66092_B6_AdultCortex_BC2_10117_GeneAssigned4.bed.gz |
131.3 Kb |
(ftp)(http) |
BED |
| GSE66092_B6_EmbryoCortex_BC2_13413_GeneAssigned4.bed.gz |
173.4 Kb |
(ftp)(http) |
BED |
| GSE66092_CPSF6.distal.prox.edgeR.pA.2sites.FDR.0.05.txt.gz |
276.5 Kb |
(ftp)(http) |
TXT |
| GSE66092_CSTF2_2T.distal.prox.edgeR.pA.2sites.FDR.0.05.txt.gz |
41.8 Kb |
(ftp)(http) |
TXT |
| GSE66092_HEK293_BC2_16414_GeneAssigned.bed.gz |
193.3 Kb |
(ftp)(http) |
BED |
| GSE66092_HeLa_No1No6_BC2_17652_GeneAssigned.bed.gz |
205.5 Kb |
(ftp)(http) |
BED |
| GSE66092_RAW.tar |
2.0 Mb |
(http)(custom) |
TAR (of TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
| Processed data provided as supplementary file |
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