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Maternal mRNA degradation by TUT4 and TUT7 in the zebrafish maternal-to-zygotic transition

ABSTRACT: Maternal mRNA degradation by TUT4 and TUT7 in the zebrafish maternal-to-zygotic transition

PROVIDER: PRJNA436017 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR6784680_1.fastq.gz	Fastqsanger.gz
	SRR6784680_2.fastq.gz	Fastqsanger.gz
	SRR6784690_1.fastq.gz	Fastqsanger.gz
	SRR6784690_2.fastq.gz	Fastqsanger.gz
	SRR6784681_1.fastq.gz	Fastqsanger.gz

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Maternal mRNA degradation by TUT4 and TUT7 in the zebrafish maternal-to-zygotic transition

Project description:During the maternal-to-zygotic transition (MZT), maternal RNAs are actively degraded and replaced by newly-synthesized zygotic transcripts in a highly coordinated manner. However, it remains largely unknown how maternal mRNA decay is triggered in early vertebrate embryos. Here, through genome-wide profiling of RNA abundance and 3′ modification, we show that uridylation is induced at the onset of maternal mRNA clearance. The temporal control of uridylation is conserved in vertebrates. When the homologs of terminal uridylyltransferases TUT4 and TUT7 (TUT4/7) are depleted in zebrafish and Xenopus, maternal mRNA clearance is significantly delayed, leading to developmental defects during gastrulation. Short-tailed mRNAs are selectively uridylated by TUT4/7, with the highly uridylated transcripts degraded faster during the MZT than those with unmodified poly(A) tails. Our study demonstrates that uridylation plays a crucial role in timely mRNA degradation, thereby allowing the progression of early development.

2018-04-13 | GSE111152 | GEO

Uridylation by TUT4 and TUT7 marks mRNA for degradation [TAIL-Seq]

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Uridylation by TUT4 and TUT7 marks mRNA for degradation [RNA-Seq]

Project description: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. HeLa cells were knocked down of control or TUT4/7, then total RNAs were prepared for RNA-seq on 0, 1, 2, 4h after actinomycin D treatment. The whole processes of experiments were repeated two times.

2014-12-04 | E-GEOD-59626 | biostudies-arrayexpress

Uridylation by TUT4 and TUT7 marks mRNA for degradation [TAIL-Seq]

Project description: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. 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.

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Small RNA profiling of TUT4 and TUT7-deficient mouse pachytene-diplotene cells.

Project description:To study the impact of TUT4 and TUT7 on miRNA and piRNA biology, Tut4 and Tut7 were conditionally deleted in differentiating spermatogonia. Total RNA samples from TUT4 and TUT7-deficient pachytene-diplotene cells were used to generate small RNAs libraries.

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Array profiling of different TUT4 and TUT7 deficient mouse tissues/cells against controls

Project description:To study the impact of the proteins TUT4 and TUT7 on the transcriptome their genes were conditionally deleted in GV oocytes, MEFs, ECSs, liver and Bone marrow. Total RNA samples from the TUT4 and TUT7 deficient tissues/cells (together with their control tissues/cells) were subjected to array profiling.

2017-08-17 | E-MTAB-5056 | biostudies-arrayexpress

MicroRNA profiling of different TUT4 and TUT7 deficient mouse tissues/cells against controls

Project description:To study the impact of the proteins TUT4 and TUT7 on the miRNome, their genes were conditionally deleted in MEFs, ESCs, liver and bone marrow. Total RNA samples from the TUT4 and TUT7 deficient tissues/cells (together with their control tissues/cells) were used to generate microRNA libraries.

2017-08-17 | E-MTAB-5677 | biostudies-arrayexpress

Uridylation by TUT4 and TUT7 marks mRNA for degradation

Project description:Uridylation by TUT4 and TUT7 marks mRNA for degradation

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