ArticleGenome research2006
Genomic localization of RNA binding proteins reveals links between pre-mRNA processing and transcription.
Article in Genome research, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed, 64 citations in OpenAlex.
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- Towards understanding cancer dormancy over strategic hitching up mechanisms to technologies.Molecular cancer · 2025Review
- TRANSAID: a hybrid deep learning framework for translation site prediction with integrated biological feature scoring.Frontiers in bioinformatics · 2025Article
- Phase separation of RNA-binding protein promotes polymerase binding and transcription.Nature chemical biology · 2022Article
- Long non-coding RNA NR2F1-AS1 induces breast cancer lung metastatic dormancy by regulating NR2F1 and ΔNp63.Nature communications · 2021Article
- RADAR: annotation and prioritization of variants in the post-transcriptional regulome of RNA-binding proteins.Genome biology · 2020Article
- Does co-transcriptional regulation of alternative splicing mediate plant stress responses?Nucleic acids research · 2019Review
- The structural basis of CstF-77 modulation of cleavage and polyadenylation through stimulation of CstF-64 activity.Nucleic acids research · 2018Article
- Pervasive Targeting of Nascent Transcripts by Hfq.Cell reports · 2018Article
- The hnRNP RALY regulates transcription and cell proliferation by modulating the expression of specific factors including the proliferation marker E2F1.The Journal of biological chemistry · 2017Article
- Localization of RNAPII and 3' end formation factor CstF subunits on C. elegans genes and operons.Transcription · 2016Article
- A short conserved motif in ALYREF directs cap- and EJC-dependent assembly of export complexes on spliced mRNAs.Nucleic acids research · 2016Article
- TDP-1, the Caenorhabditis elegans ortholog of TDP-43, limits the accumulation of double-stranded RNA.The EMBO journal · 2014Article
- The spt5 C-terminal region recruits yeast 3' RNA cleavage factor I.Molecular and cellular biology · 2012Article
- The Role of Polypyrimidine Tract-Binding Proteins and Other hnRNP Proteins in Plant Splicing Regulation.Frontiers in plant science · 2012Article
- Polyadenylation-dependent control of long noncoding RNA expression by the poly(A)-binding protein nuclear 1.PLoS genetics · 2012Article
- Differential patterns of intronic and exonic DNA regions with respect to RNA polymerase II occupancy, nucleosome density and H3K36me3 marking in fission yeast.Genome biology · 2011Article
- The in vivo kinetics of RNA polymerase II elongation during co-transcriptional splicing.PLoS biology · 2011Article
- Two polypyrimidine tracts in the nitric oxide synthase 2 gene: similar regulatory sequences with different properties.Molecular biology reports · 2010Article
- PPS, a large multidomain protein, functions with sex-lethal to regulate alternative splicing in Drosophila.PLoS genetics · 2010Article
Corrections and comments
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
Abstract
Pre-mRNA processing often occurs in coordination with transcription thereby coupling these two key regulatory events. As such, many proteins involved in mRNA processing associate with the transcriptional machinery and are in proximity to DNA. This proximity allows for the mapping of the genomic associations of RNA binding proteins by chromatin immunoprecipitation (ChIP) as a way of determining their sites of action on the encoded mRNA. Here, we used ChIP combined with high-density microarrays to localize on the human genome three functionally distinct RNA binding proteins: the splicing factor polypyrimidine tract binding protein (PTBP1/hnRNP I), the mRNA export factor THO complex subunit 4 (ALY/THOC4), and the 3' end cleavage stimulation factor 64 kDa (CSTF2). We observed interactions at promoters, internal exons, and 3' ends of active genes. PTBP1 had biases toward promoters and often coincided with RNA polymerase II (RNA Pol II). The 3' processing factor, CSTF2, had biases toward 3' ends but was also observed at promoters. The mRNA processing and export factor, ALY, mapped to some exons but predominantly localized to introns and did not coincide with RNA Pol II. Because the RNA binding proteins did not consistently coincide with RNA Pol II, the data support a processing mechanism driven by reorganization of transcription complexes as opposed to a scanning mechanism. In sum, we present the mapping in mammalian cells of RNA binding proteins across a portion of the genome that provides insight into the transcriptional assembly of RNA-protein complexes.
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