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A systematic, label-free method for identifying RNA-associated proteins in vivo provides insights into vertebrate ciliary beating - RNA DIF-FRAC Xenopus laevis Animal Cap explants Replicate 1

ABSTRACT: The associated files are mass spec data from size exclusion chromatographic separations of Xenopus laevis animal cap explants with and without RNAse A treatment.

INSTRUMENT(S): Orbitrap Fusion

ORGANISM(S): Xenopus Laevis (african Clawed Frog)

TISSUE(S): Animal Cap, Early Embryonic Cell

SUBMITTER: Kevin Drew

LAB HEAD: Edward Marcotte

PROVIDER: PXD017659 | Pride | 2020-03-10

REPOSITORIES: Pride

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Dataset's files

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			Action	DRS
	xl_animalcaps_SEC_Control_01a_20181121..comet.pep.xml	Pepxml
	xl_animalcaps_SEC_Control_01a_20181121.MSGF+.pride.mztab.gz	Mztab
	xl_animalcaps_SEC_Control_01a_20181121.MSGF.mzid.gz	Mzid
	xl_animalcaps_SEC_Control_01a_20181121.mzXML	Mzxml
	xl_animalcaps_SEC_Control_01a_20181121.pride.mgf.gz	Mgf

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Publications

A systematic, label-free method for identifying RNA-associated proteins in vivo provides insights into vertebrate ciliary beating machinery.

Drew Kevin K Lee Chanjae C Cox Rachael M RM Dang Vy V Devitt Caitlin C CC McWhite Claire D CD Papoulas Ophelia O Huizar Ryan L RL Marcotte Edward M EM Wallingford John B JB

Developmental biology 20200906 1-2

Cell-type specific RNA-associated proteins are essential for development and homeostasis in animals. Despite a massive recent effort to systematically identify RNA-associated proteins, we currently have few comprehensive rosters of cell-type specific RNA-associated proteins in vertebrate tissues. Here, we demonstrate the feasibility of determining the RNA-associated proteome of a defined vertebrate embryonic tissue using DIF-FRAC, a systematic and universal (i.e., label-free) method. Application ...[more]

PMID: 32898505

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A systematic, label-free method for identifying RNA-associated proteins in vivo provides insights into vertebrate ciliary beating - RNA DIF-FRAC Xenopus laevis Animal Cap explants Replicate 2

Project description:The associated files are mass spec data from size exclusion chromatographic separations of Xenopus laevis animal cap explants with and without RNAse A treatment.

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Widespread RNA Binding by Chromatin Associated Proteins

Project description:Recent evidence suggests that RNA interaction can regulate the activity and localization of DNA binding proteins, particularly chromatin-associated proteins. However, it is unknown if these observations are specialized instances for a few key RNAs and chromatin factors in specific contexts, or a general mechanism underlying the establishment of chromatin state and regulation of gene expression. Here, we introduce formaldehyde RNA ImmunoPrecipitation (fRIP-Seq), a sensitive method for cataloging RNA-protein interactions, to survey the RNA associated with a panel of 24 chromatin-associated and traditional RNA binding proteins. For each protein that reproducibly bound measurable quantities of bulk RNA (90% of the panel), we detected enrichment for hundreds to thousands of both noncoding and mRNA transcripts. We found that the enriched sets of RNA share biochemical, functional, and epigenetic properties. Thus, these data provide strong evidence that non-random RNA association is a common feature across diverse classes of chromatin modifying complexes. RNA associated with 24 different proteins using fRIP was compared to total RNA-seq

2016-07-03 | E-GEOD-67963 | biostudies-arrayexpress

Tranposable elements modulate human mRNAs and lncRNAs via specific RNA-protein interactions.

Project description:Transposable elements (TEs) have significantly influenced the evolution of transcriptional regulatory networks in the human genome. Post-transcriptional regulation of human genes by TE-derived sequences has been observed in specific contexts, but has yet to be systematically and comprehensively investigated. Here, studied a collection of CLIP-Seq (CrossLinked ImmunoPrecipitation) experiments mapping the RNA binding sites for a diverse set of 46 human proteins across 68 experiments to explore the role of TEs in post-transcriptional regulation genome-wide via RNA-protein interactions. We detected widespread interactions between RNA binding proteins (RBPs) and various families of TE-derived sequence in the CLIP-Seq data. Alignment coverage clustered on specific positions of the TE consensus sequences, illuminating a diversity of TE-specific motifs for many RBPs. Evidence of binding and conservation of these motifs in the nonrepetitive transcriptome suggest that TEs have appropriated existing sequence preferences of the RBP. Upon depletion of the RBPs, transcripts possessing TE-derived binding sites were similarly regulated as those bound in nonrepetitive sequence. However, in a few cases the effect of RBP binding depended on the specific TE family boundM-bM-^@M-^Te.g., the ubiquitously expressed RBP HuR conferred opposite effects on stability to transcripts when bound to Alu elements versus other families. Our meta-analysis suggests a widespread role for TEs in shaping RNA-protein regulatory networks in the human genome. HuR formaldehyde RIP-Seq in K562 cells, with RIP and input sequenced in triplicate.

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Systematic Identification of Protein Phosphorylation-Mediated Interactions

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2020-09-22 | PXD021422 | Pride

Single-cell RNA sequencing of human embryonic stem cell-derived pancreatic cells enriched for early endocrine progenitors using a novel dual NEUROG3-reporter

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2022-12-31 | E-MTAB-11208 | biostudies-arrayexpress

In vivo targeting of de novo DNA methylation by histone modifications in yeast and mouse (ChIP-Seq yeast)

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