ArticleGenome research2012
Dynamic transitions in RNA polymerase II density profiles during transcription termination.
Article in Genome research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
32 citing papers in PubMed, 49 citations in OpenAlex.
- Natural degradation of RNA polymerase II is essential for oocyte chromatin reorganization and maternal-to-zygotic transition.Nature communications · 2025Article
- Fateful Decisions of Where to Cut the Line: Pathology Associated with Aberrant 3' End Processing and Transcription Termination.Journal of molecular biology · 2025Review
- Article
- CHEX-seq detects single-cell genomic single-stranded DNA with catalytical potential.Nature communications · 2023Article
- Article
- The Paf1 complex positively regulates enhancer activity in mouse embryonic stem cells.Life science alliance · 2021Article
- Systematic refinement of gene annotations by parsing mRNA 3' end sequencing datasets.Methods in enzymology · 2021Article
- The yeast exoribonuclease Xrn1 and associated factors modulate RNA polymerase II processivity in 5' and 3' gene regions.The Journal of biological chemistry · 2020Article
- A combinatorial view of old and new RNA polymerase II modifications.Transcription · 2020Review
- R-Loops Promote Antisense Transcription across the Mammalian Genome.Molecular cell · 2019Article
- Article
- Rev-erbα dynamically modulates chromatin looping to control circadian gene transcription.Science (New York, N.Y.) · 2018Article
- Alternative polyadenylation of mRNA precursors.Nature reviews. Molecular cell biology · 2017Review
- The Nrd1-like protein Seb1 coordinates cotranscriptional 3' end processing and polyadenylation site selection.Genes & development · 2016Article
- Chromatin structure and pre-mRNA processing work together.Transcription · 2016Article
- Localization of RNAPII and 3' end formation factor CstF subunits on C. elegans genes and operons.Transcription · 2016Article
- EWS and FUS bind a subset of transcribed genes encoding proteins enriched in RNA regulatory functions.BMC genomics · 2015Article
- Genome-wide modeling of transcription kinetics reveals patterns of RNA production delays.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
- Effects of Transcription Elongation Rate and Xrn2 Exonuclease Activity on RNA Polymerase II Termination Suggest Widespread Kinetic Competition.Molecular cell · 2015Article
- Position-specific binding of FUS to nascent RNA regulates mRNA length.Genes & development · 2015Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Eukaryotic protein-coding genes are transcribed by RNA polymerase II (RNAPII) through a cycle composed of three main phases: initiation, elongation, and termination. Recent studies using chromatin immunoprecipitation coupled to high-throughput sequencing suggest that the density of RNAPII molecules is higher at the 3'-end relative to the gene body. Here we show that this view is biased due to averaging density profiles for "metagene" analysis. Indeed, the majority of genes exhibit little, if any, detectable accumulation of polymerases during transcription termination. Compared with genes with no enrichment, genes that accumulate RNAPII at the 3'-end are shorter, more frequently contain the canonical polyadenylation [poly(A)] signal AATAAA and G-rich motifs in the downstream sequence element, and have higher levels of expression. In 1% to 4% of actively transcribing genes, the RNAPII enriched at the 3'-end is phosphorylated on Ser5, and we provide evidence suggesting that these genes have their promoter and terminator regions juxtaposed. We also found a striking correlation between RNAPII accumulation and nucleosome organization, suggesting that the presence of nucleosomes after the poly(A) site induces pausing of polymerases, leading to their accumulation. Yet we further observe that nucleosome occupancy at the 3'-end of genes is dynamic and correlates with RNAPII density. Taken together, our results provide novel insight to transcription termination, a fundamental process that remains one of the least understood stages of the transcription cycle.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.