ArticleGenome research2008
A genomic analysis of RNA polymerase II modification and chromatin architecture related to 3' end RNA polyadenylation.
Article in Genome research, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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Who cites it
35 citing papers in PubMed, 54 citations in OpenAlex.
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- Intergenic RNA mainly derives from nascent transcripts of known genes.Genome biology · 2021Article
- So close, no matter how far: multiple paths connecting transcription to mRNA translation in eukaryotes.EMBO reports · 2020Review
- Emerging Roles of RNA 3'-end Cleavage and Polyadenylation in Pathogenesis, Diagnosis and Therapy of Human Disorders.Biomolecules · 2020Review
- Regulation of alternative polyadenylation in the yeast Saccharomyces cerevisiae by histone H3K4 and H3K36 methyltransferases.Nucleic acids research · 2020Article
- Control of RNA Pol II Speed by PNUTS-PP1 and Spt5 Dephosphorylation Facilitates Termination by a "Sitting Duck Torpedo" Mechanism.Molecular cell · 2019Article
- Interactions between the transcription and replication machineries regulate the RNA and DNA synthesis in the herpesviruses.Virus genes · 2019Review
- Posttranscriptional Regulation of HLA-A Protein Expression by Alternative Polyadenylation Signals Involving the RNA-Binding Protein Syncrip.Journal of immunology (Baltimore, Md. : 1950) · 2017Article
- Nuclear speckles: molecular organization, biological function and role in disease.Nucleic acids research · 2017Review
- Processing and transcriptome expansion at the mRNA 3' end in health and disease: finding the right end.Pflugers Archiv : European journal of physiology · 2016Review
- Coordination of RNA Polymerase II Pausing and 3' End Processing Factor Recruitment with Alternative Polyadenylation.Molecular and cellular biology · 2016Article
- Intergenic Alu exonisation facilitates the evolution of tissue-specific transcript ends.Nucleic acids research · 2015Article
- Effects of Transcription Elongation Rate and Xrn2 Exonuclease Activity on RNA Polymerase II Termination Suggest Widespread Kinetic Competition.Molecular cell · 2015Article
- In vitro application of ribonucleases: comparison of the effects on mRNA and miRNA stability.BMC research notes · 2015Article
- Article
- Chromatin loop organization of the junb locus in mouse dendritic cells.Nucleic acids research · 2013Article
- Distinct polyadenylation landscapes of diverse human tissues revealed by a modified PA-seq strategy.BMC genomics · 2013Article
- An alternative polyadenylation mechanism coopted to the Arabidopsis RPP7 gene through intronic retrotransposon domestication.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
- Inhibition of cdk9 during herpes simplex virus 1 infection impedes viral transcription.PloS one · 2013Article
- Alterations in polyadenylation and its implications for endocrine disease.Frontiers in endocrinology · 2013Article
Corrections and comments
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Authors and funding
8 authors at 1 institution in 1 country.
Funding
Abstract
Genomic analyses have been applied extensively to analyze the process of transcription initiation in mammalian cells, but less to transcript 3' end formation and transcription termination. We used a novel approach to prepare 3' end fragments from polyadenylated RNA, and mapped the position of the poly(A) addition site using oligonucleotide arrays tiling 1% of the human genome. This approach revealed more 3' ends than had been annotated. The distribution of these ends relative to RNA polymerase II (PolII) and di- and trimethylated lysine 4 and lysine 36 of histone H3 was compared. A substantial fraction of unannotated 3' ends of RNA are intronic and antisense to the embedding gene. Poly(A) ends of annotated messages lie on average 2 kb upstream of the end of PolII binding (termination). Near the termination sites, and in some internal sites, unphosphorylated and C-terminal domain (CTD) serine 2 phosphorylated PolII (POLR2A) accumulate, suggesting pausing of the polymerase and perhaps dephosphorylation prior to release. Lysine 36 trimethylation occurs across transcribed genes, sometimes alternating with stretches of DNA in which lysine 36 dimethylation is more prominent. Lysine 36 methylation decreases at or near the site of polyadenylation, sometimes disappearing before disappearance of phosphorylated RNA PolII or release of PolII from DNA. Our results suggest that transcription termination loss of histone 3 lysine 36 methylation and later release of RNA polymerase. The latter is often associated with polymerase pausing. Overall, our study reveals extensive sites of poly(A) addition and provides insights into the events that occur during 3' end formation.
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