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CD3254-RXRα Axis Promotes Chemical Reprogramming via RNA Exosome-Mediated MMVL30 Degradation and Inflammation Suppression

ABSTRACT: CD3254-RXRα Axis Promotes Chemical Reprogramming via RNA Exosome-Mediated MMVL30 Degradation and Inflammation Suppression

PROVIDER: PRJNA860971 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR20353900_1.fastq.gz	Fastqsanger.gz
	SRR20353900_2.fastq.gz	Fastqsanger.gz
	SRR20353901_1.fastq.gz	Fastqsanger.gz
	SRR20353901_2.fastq.gz	Fastqsanger.gz
	SRR20351906_1.fastq.gz	Fastqsanger.gz

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CD3254-RXRα Axis Promotes Chemical Reprogramming via RNA Exosome-Mediated MMVL30 Degradation and Inflammation Suppression [CUT&Tag]

Project description:CD3254-RXRα Axis Promotes Chemical Reprogramming via RNA Exosome-Mediated MMVL30 Degradation and Inflammation Suppression [CUT&Tag]

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CD3254-RXRα Axis Promotes Chemical Reprogramming via RNA Exosome-Mediated MMVL30 Degradation and Inflammation Suppression [RNA-seq]

Project description:CD3254-RXRα Axis Promotes Chemical Reprogramming via RNA Exosome-Mediated MMVL30 Degradation and Inflammation Suppression [RNA-seq]

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CD3254-RXRα Axis Promotes Chemical Reprogramming via RNA Exosome-Mediated MMVL30 Degradation and Inflammation Suppression [RNA-seq]

Project description:We show that CD-RXRα axis significantly promotes mouse chemical reprogramming of fibroblasts. To identify the molecular mechanisms of CD-RXRα axis in chemical reprogramming, we compared reprogramming efficiency for CD-treated, Rxra-OE and shE3 cells. We then performed RNA-seq for 3 different treatments of 6 samples.

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CD3254-RXRα Axis Promotes Chemical Reprogramming via RNA Exosome-Mediated MMVL30 Degradation and Inflammation Suppression [CUT&Tag]

Project description:We show that CD-RXRα axis significantly promotes mouse chemical reprogramming of fibroblasts. To identify the molecular mechanisms of CD-RXRα axis in chemical reprogramming, we construct Flag-Rxra-OE cells. We performed Flag-Rxra CUT&Tag with reprogramming intermediate, also we performed CUT&Tag with or without CD treatment for reprogramming intermediates.

2023-05-03 | GSE208767 | GEO

CD3254-RXRα Axis Promotes Chemical Reprogramming via RNA Exosome-Mediated MMVL30 Degradation and Inflammation Suppression

Project description:This SuperSeries is composed of the SubSeries listed below.

2023-05-03 | GSE208771 | GEO

The roles of 3’-exoribonucleases and the exosome in trypanosome mRNA degradation

Project description:The roles of 3’-exoribonucleases and the exosome in trypanosome mRNA degradation; 30 min after actinomycin D +sinefungin, RNAi against CAf1, CNOT10, PAN2. These are really old data that hadn't been deposited.The datasets called RNA1, RNA2, RNA3 and RNA4 are almost certainly, from their location in the folder and from new alignment results, from the RRP45 RNAi.

2021-03-11 | E-MTAB-10260 | biostudies-arrayexpress

Transcription profiling by tiling array of combinations of Rrp6p and Dis3p catalytic mutants to investigate extensive degradation of RNA precursors by the exosome in yeast

Project description:The exosome is a complex involved in the maturation of rRNA and sn-snoRNA, the degradation of short lived non-coding RNAs and in the quality control of RNAs produced in mutants. It contains two catalytic subunits, Rrp6p and Dis3p, whose specific functions are not fully understood. We analyzed the transcriptome of combinations of Rrp6p and Dis3p catalytic mutants by high-resolution tiling arrays. We show that Dis3p and Rrp6p have both overlapping and specific roles in degradation of distinct classes of substrates. We found that transcripts derived from more than half of intron-containing genes are degraded before processing. Surprisingly, we also show that the exosome degrades large amounts of tRNA precursors despite the absence of processing defects. These results underscore the notion that large amounts of RNAs produced in wild type cells are discarded before entering functional pathways, suggesting that kinetic competition with degradation proofreads the efficiency and accuracy of processing.

2012-09-19 | E-MTAB-1246 | biostudies-arrayexpress

ChIP-seq Profiling of RXRα in Proliferating C2C12 Myoblasts

Project description:In this dataset, we present ChIP-seq profiling of RXRα in proliferating C2C12 myoblasts, which serves as an extension of Series GSE94558. The overall data provides genome-wide occupancy of RXRα in normal myoblast proliferation.

2024-10-31 | GSE279060 | GEO

The RNA Exosome Promotes Transcription Termination of backtracked RNA Polymerase II

Project description:Large fractions of genomes are expressed in most eukaryotic cells, generating a diverse repertoire of protein-coding and non-coding transcripts. With such complexity, and as the number of mRNA molecules per cell are often low, it is clear that errors anywhere in the gene expression process could have profound consequences on cellular functions. The exosome is a conserved RNA degradation machine that plays a fundamental role in monitoring the quality of gene expression in the nucleus. The current view is that the nuclear exosome constantly scrutinizes transcription and contributes to post-transcriptional turnover of faulty mRNAs. Yet, how nuclear RNA surveillance by the exosome is coordinated with transcription is still unknown. Here we show that the exosome can directly target the transcription machinery by terminating transcription events associated with paused and backtracked RNA polymerase II (RNAPII), contrary to the notion that the exosome acts exclusively on RNAs that have been released by RNAPII. Our data support a mechanism by which RNAPII backtracking provides a free RNA 3' end for the core exosome, resulting in transcription termination with the concomitant degradation of the associated transcript. These findings uncover a mechanism of co-transcriptional RNA surveillance whereby termination of transcription by the exosome prevents aberrant read-through RNAs and transcriptional interference at neighboring genes.

2014-09-20 | E-MTAB-2237 | biostudies-arrayexpress

The fission yeast MTREC complex targets CUTs and unspliced mRNAs to the nuclear exosome [expression array]

Project description:Cryptic unstable transcripts (CUTs) are rapidly degraded by the nuclear exosome, however, the way they are recognized and targeted to the exosome is not fully understood. The recently identified Schizosaccharomyces pombe MTREC complex has been shown to promote degradation of meiotic mRNAs and regulatory ncRNAs. Here, we report that the MTREC complex is also the major nuclear exosome targeting complex for CUTs and unspliced mRNAs. MTREC complex specifically binds to CUTs, meiotic mRNAs and unspliced mRNA transcripts and targets these RNAs for degradation by the nuclear exosome, while the TRAMP complex has only a minor role in this process. The MTREC complex physically interacts with the nuclear exosome and with various RNA-binding and -processing complexes, coupling RNA processing to the RNA degradation machinery. Our study reveals the central role of the evolutionarily conserved MTREC complex in RNA quality control, and in the recognition and elimination of aberrant, cryptic transcripts. Genome-wide expression analysis of MTREC, Nuclear Exosome, TRAMP, Nrd complex members All experiments were performed twice in biological replicates, except that rmn1Δ and mmi1Δ mei4-P572 were perfomed once.

2015-05-22 | E-GEOD-64979 | biostudies-arrayexpress

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