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Series GSE59627 Query DataSets for GSE59627
Status Public on Dec 04, 2014
Title Uridylation by TUT4 and TUT7 marks mRNA for degradation [TAIL-Seq]
Organism Homo sapiens
Experiment type Other
Summary Uridylation occurs pervasively on mRNAs in mammals, yet its mechanism and significance remain unknown. Here we identify TUT4 and TUT7 (also known as ZCCHC11 and ZCCHC6, respectively) as the enzymes that uridylate mRNAs. Uridylation readily occurs on deadenylated mRNAs that are not associated with poly(A) binding protein (PABPC1) in cells. Consistently, purified TUT4 and TUT7 (TUT4/7) selectively uridylate RNAs with short A tails (< ~25 nt) while PABPC1 antagonizes uridylation of polyadenylated mRNAs in vitro. In cells depleted of TUT4/7, the vast majority of mRNAs lose the U tails, and their half-lives are extended. Suppression of mRNA decay factors leads to the accumulation of uridylated mRNAs. In line with this, microRNA induces uridylation of its targets, and TUT4/7 is required for enhanced decay of microRNA targets. Our study explains the mechanism underlying selective uridylation of deadenylated mRNAs, and demonstrates a fundamental role of the U tail as a molecular mark for global mRNA decay.
Overall design Thirteen separate sets of TAIL-seq experiments were performed. Each set includes a negative control for transfection, immunoprecipitation, or knockout cell generation. Experimental samples were treated with various conditions including siRNA transfection, transdominant negative protein expression, TALEN-based gene knockout, or immunoprecipitation.

The 'README-TAIL-seq.txt' include detailed information about structure of seq entries in FASTQ files and of processed data for 3' end modifications.
Contributor(s) Lim J, Ha M, Chang H, Kim VN
Citation(s) 25480299
Submission date Jul 21, 2014
Last update date May 15, 2019
Contact name Hyeshik Chang
Organization name Seoul National University
Department School of Biological Sciences
Lab Hyeshik Chang Lab
Street address Building 203 Room 525, School of Biological Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu
City Seoul
State/province South Korea
ZIP/Postal code 08826
Country South Korea
Platforms (2)
GPL15520 Illumina MiSeq (Homo sapiens)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (39)
GSM1440663 TAIL-seq exp #1 siLuc
GSM1440664 TAIL-seq exp #1 siTUT1356
GSM1440665 TAIL-seq exp #1 siTUT247
This SubSeries is part of SuperSeries:
GSE59628 Uridylation by TUT4 and TUT7 marks mRNA for degradation
BioProject PRJNA255775
SRA SRP044680

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
GSE59627_RAW.tar 605.9 Mb (http)(custom) TAR (of TXT)
GSE59627_README-TAIL-seq.txt 4.1 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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