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TranscriptomicsA comprehensive Xist interactome reveals cohesin repulsion and an RNA-directed chromosome conformation
The inactive X chromosome (Xi) serves as a model to understand gene silencing on a global scale. Here, we perform identification of direct RNA interacting proteins? (iDRiP) to isolate a comprehensive protein interactome for Xist, an RNA required for Xi silencing. We discover multiple classes of inte...
ORGANISM(S): Mus musculus 
2015-06-19 | E-GEOD-67516 | biostudies-arrayexpress
GenomicsX-chromosome dynamics revealed by the RNA interactome and chromosomal binding of CTCF
CTCF is a master regulator that plays a role in genome architecture and gene expression. A key aspect of CTCF’s mechanism involves bringing together distant genetic elements for intra- and inter-chromosomal interactions. Evidence from epigenetic processes, such as X-chromosome inactivation (XCI), su...
ORGANISM(S): Mus musculus 
2015-01-09 | E-GEOD-58242 | biostudies-arrayexpress
ProteomicsSerial interactome capture of the human cell nucleus
Novel RNA-guided cellular functions are paralleled by an increasing number of RNA binding proteins (RBPs). We present “serial interactome capture” (serIC), a multiple purification procedure of UV-crosslinked poly(A)-RNA-protein complexes that enables global RBP detection with maximal specificity. We...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2016-10-21 | MSV000080265 | MassIVE
ProteomicsSerial interactome capture of the human cell nucleus
Novel RNA-guided cellular functions are paralleled by an increasing number of RNA binding proteins (RBPs). We present “serial interactome capture” (serIC), a multiple purification procedure of UV-crosslinked poly(A)-RNA-protein complexes that enables global RBP detection with maximal specificity. We...
ORGANISM(S): Homo sapiens (Human) 
2016-03-31 | PXD003664 | Pride
Rna binding proteins  interactome capture  nuclear rna binding proteome 
UnknownRNA-binding proteins and heat-shock protein 90 are constituents of the cytoplasmic capping enzyme interactome.
Not available
S-EPMC6204893 | biostudies-literature
ProteomicsThe concept of "RNA dependence" - Proteome-wide and quantitative identification of protein interactions dependent on RNA
The general role of RNA in the cell beyond protein biosynthesis is only beginning to emerge with little knowledge about the structural or organizational functions of RNA. In turn, functional non-coding RNAs (ncRNAs) are often identified by their regulation or impact on cellular phenotypes. However, ...
ORGANISM(S): Homo Sapiens (ncbitaxon:9606) 
2018-06-13 | MSV000082468 | MassIVE
ProteomicsThe nuclear RNA-interactome of human embryonic stem cells (hESCs)
Here, we performed RNA-interactome capture (RIC) on nuclear fractions from human embryonic stem cells (hESCs). The poly(A)+ RNA-bound proteome was determined by UV light-mediated cross-linking (CL) of RNAs to proteins in living cells, followed by nuclei isolation, oligo(dT) purification of poly(A)-R...
ORGANISM(S): Homo sapiens (Human) 
2023-05-05 | PXD025262 | Pride
Nuclear rna interactome Ric Hescs Rna-binding proteome Mass spectrometry Rbps Rna-binding proteins Rbpome Human embryonic stem cells Rna-interactome capture 
ProteomicsIdentifying cellular RNA-binding proteins during infection uncovers a role for MKRN2 in influenza mRNA trafficking.
Utilisation of RNA-binding proteins (RBPs) is an important aspect of post-transcriptional regulation of viral RNA. Viruses such as influenza A viruses (IAV) interact with RBPs to regulate processes including splicing, nuclear export and trafficking, while also encoding RBPs within their genomes, suc...
ORGANISM(S): Homo sapiens (Human) 
2024-04-16 | PXD048870 | Pride
Influenza mkrn2 rna-binding 
GenomicsGenome-wide ChIP-Seq reveals a dramatic shift in the binding of the transcription factor erythroid Kruppel-like factor during erythrocyte differentiation
Erythropoiesis is dependent on the activity of transcription factors, including the erythroid-specific erythroid Kruppel-like factor (EKLF). ChIP followed by massively parallel sequencing (ChIP-Seq) is a powerful, unbiased method to map transfactor occupancy. We used ChIP-Seq to study the interactom...
ORGANISM(S): Mus musculus 
2013-06-17 | E-GEOD-48020 | biostudies-arrayexpress
ProteomicsRNA interactome capture identifies key proteins for herpesviral gene expression
The primary mRNA sequence determines its secondary structure and the repertoire of interacting RNA binding proteins (RBPs). The resulting mRNA ribonucleoprotein complex (mRNP) then influences all stages of the life of an mRNA. Here, we determined the mRNP composition of individual Kaposi Sarcoma Her...
ORGANISM(S): Homo sapiens (Human) Human gammaherpesvirus 8 
2026-01-23 | PXD056253 | Pride
Kshv Au-rich sequences Srsf3 Rna-binding-proteins Rna interactome capture Rna stability Codon optimization Herpesviral gene expression Rbps Lytic transcripts Orf57 
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