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Research: GC skew defines distinct RNA polymerase pause sites in CpG island promoters
- Wendy A. Kellner,
- Joshua S.K. Bell,
- and Paula M. Vertino
Genome Res. November 2015 25: 1600-1609; Published in Advance August 14, 2015, doi:10.1101/gr.189068.114
...and RNAprocessing functions, while the distal class tended toward cell division and metabolic processes (Supplemental Data). Themost striking observation was in the silent class, which is strongly enriched in developmental regulators and genes subject to Polycomb-mediated repression in stem cells and other tissues...
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Research: High-resolution mapping defines the cooperative architecture of Polycomb response elements
- Guillermo A. Orsi,
- Sivakanthan Kasinathan,
- Kelly T. Hughes,
- Sarah Saminadin-Peter,
- Steven Henikoff,
- and Kami Ahmad
Genome Res. May 2014 24: 809-820; Published in Advance March 25, 2014, doi:10.1101/gr.163642.113
...is accomplished by enhanced Polycomb recruitment both to PREs and to target promoters of repressed genes. These results suggest that the stability of multifactor complexes at promoters and regulatory elements is a crucial aspect of developmentally regulated gene expression. Footnotes ↵ 7...
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Research: Modeling of epigenome dynamics identifies transcription factors that mediate Polycomb targeting
- Phil Arnold,
- Anne Schöler,
- Mikhail Pachkov,
- Piotr J. Balwierz,
- Helle Jørgensen,
- Michael B. Stadler,
- Erik van Nimwegen,
- and Dirk Schübeler
Genome Res. January 2013 23: 60-73; Published in Advance September 10, 2012, doi:10.1101/gr.142661.112
...K27me3 at the NP stage are not significantly transcriptionally up-regulated (Supplemental Fig. 10). We thus conclude that the crosstalk between REST and the Polycomb pathway is independent of transcriptional changes at a substantial number of REST targets. Promoter fragments containing REST or SNAIL...
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Research: Tyrosine 1–phosphorylated RNA polymerase II transcribes PROMPTs to facilitate proximal promoter pausing and induce global transcriptional repression in response to DNA damage
- Kamal Ajit,
- Adele Alagia,
- Kaspar Burger,
- and Monika Gullerova
Genome Res. February 2024 34: 201-216; Published in Advance March 11, 2024, doi:10.1101/gr.278644.123
...by trimethylation of lysine 27 on histone 3 (H3K27me3), is associated with RNA Pol II proximal promoter pausing. Recently, the Polycomb repressive complex II (PRC2) has been shown to act as a master regulator of transcriptional repression through RNA Pol II proximal promoter pausing in mouse embryonic stem cells...
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Resource: The landscape of RNA polymerase II transcription initiation in C. elegans reveals promoter and enhancer architectures
- Ron A.-J. Chen,
- Thomas A. Down,
- Przemyslaw Stempor,
- Q. Brent Chen,
- Thea A. Egelhofer,
- LaDeana W. Hillier,
- Tess E. Jeffers,
- and Julie Ahringer
Genome Res. August 2013 23: 1339-1347; Published in Advance April 2, 2013, doi:10.1101/gr.153668.112
...aligned TSSs of sharp and broad promoters using the WebLogo sequence analysis tool (Fig. 2A; Crooks et al. 2004). As in other organisms (Zhang and Dietrich 2005; Carninci et al. 2006), we found that transcription preferentially initiated at the adenine of a TCA sequence, with a stronger preference...
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Resource: Diverse patterns of genomic targeting by transcriptional regulators in Drosophila melanogaster
- Matthew Slattery,
- Lijia Ma,
- Rebecca F. Spokony,
- Robert K. Arthur,
- Pouya Kheradpour,
- Anshul Kundaje,
- Nicolas Nègre,
- Alex Crofts,
- Ryan Ptashkin,
- Jennifer Zieba,
- Alexander Ostapenko,
- Sarah Suchy,
- Alec Victorsen,
- Nader Jameel,
- A. Jason Grundstad,
- Wenxuan Gao,
- Jennifer R. Moran,
- E. Jay Rehm,
- Robert L. Grossman,
- Manolis Kellis,
- and Kevin P. White
Genome Res. July 2014 24: 1224-1235; Published in Advance July 1, 2014, doi:10.1101/gr.168807.113
...with distinct chromatin state preferences. The data also highlight the stringency of the Polycomb regulatory network, and show association of the Trithorax-like (Trl) protein with hotspots of DNA binding throughout development. Furthermore, the data identify more than 5800 instances in which TRFs target DNA...
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Research: Genome-wide DNA methylation patterns in LSH mutant reveals de-repression of repeat elements and redundant epigenetic silencing pathways
- Weishi Yu,
- Carl McIntosh,
- Ryan Lister,
- Iris Zhu,
- Yixing Han,
- Jianke Ren,
- David Landsman,
- Eunice Lee,
- Victorino Briones,
- Minoru Terashima,
- Robert Leighty,
- Joseph R. Ecker,
- and Kathrin Muegge
Genome Res. October 2014 24: 1613-1623; Published in Advance August 28, 2014, doi:10.1101/gr.172015.114
...of H3K4me3 modification is unremarkable (Fig. 5A). Regions with moderate CG methylation reduction exhibit concomitant decreases in H3K27me3. These regions include immune response genes, genes involved in cell adhesion, and Hox genes; the latter had been previously reported to display reduced Polycomb...
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Research: Different chromatin interfaces of the Drosophila dosage compensation complex revealed by high-shear ChIP-seq
- Tobias Straub,
- Angelika Zabel,
- Gregor D. Gilfillan,
- Christian Feller,
- and Peter B. Becker
Genome Res. March 2013 23: 473-485; Published in Advance December 11, 2012, doi:10.1101/gr.146407.112
..., the profiles of Drosophila polycomb proteins look strikingly different if ChIP-chip (modEncode) and ChiP-seq (Enderle et al. 2011) profiles are compared, with loss of broad distributions in ChIP-seq data. It is possible that cases like the one we describe are confined to ribonucleoprotein assemblies...
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Resource: High-resolution mapping of open chromatin in the rice genome
- Wenli Zhang,
- Yufeng Wu,
- James C. Schnable,
- Zixian Zeng,
- Michael Freeling,
- Gregory E. Crawford,
- and Jiming Jiang
Genome Res. January 2012 22: 151-162; Published in Advance November 22, 2011, doi:10.1101/gr.131342.111
...of genes in A. thaliana (Zhang et al. 2007). Importantly, most H3K27me3-targeted genes are expressed in a tissue-specific manner (Zhang et al. 2007; Lafos et al. 2011). Since Polycomb-mediated repression can be easily reversed, H3K27me3 may facilitate the repression of these genes in appropriate tissues...
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Mini-Review: The paradox of R-loops: guardians of the genome or drivers of disease?
- Shachinthaka D. Dissanayaka Mudiyanselage,
- Phillip Wulfridge,
- and Kavitha Sarma
Genome Res. September 2025 35: 1919-1928; Published in Advance August 6, 2025, doi:10.1101/gr.278992.124
...the process of transcription as the nascent RNA strand exits RNA polymerase II (Pol II) and hybridizes to the template DNA strand (Ginno et al. 2012; Sanz et al. 2016). In addition, recent studies showed that some long noncoding RNAs (lncRNAs) can associate to distant genomic regions through the formation...

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