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Research: The impact of SWI/SNF and NuRD inactivation on gene expression is tightly coupled with levels of RNA polymerase II occupancy at promoters
- Sachin Pundhir,
- Jinyu Su,
- Marta Tapia,
- Anne Meldgaard Hansen,
- James Seymour Haile,
- Klaus Hansen,
- and Bo Torben Porse
Genome Res. March 2023 33: 332-345; Published in Advance March 16, 2023, doi:10.1101/gr.277089.122
....Z and H3.3 histone variants in NuRD- and SWI/SNF-mediated changes in Pol II release kinetics at target promotersSWI/SNF and NuRD predominantly target nucleosomes flanking the TSS at gene promoters (de Dieuleveult et al. 2016), and canonical H3 and H2A components of these nucleosomes are frequently...
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Research: Histone deacetylases maintain expression of the pluripotent gene network via recruitment of RNA polymerase II to coding and noncoding loci
- Richard D.W. Kelly,
- Kristy R. Stengel,
- Aditya Chandru,
- Lyndsey C. Johnson,
- Scott W. Hiebert,
- and Shaun M. Cowley
Genome Res. January 2024 34: 34-46; Published in Advance January 30, 2024, doi:10.1101/gr.278050.123
.... Among the 18 HDAC enzymes present within mammalian cells, HDAC1, HDAC2, and HDAC3 (class I HDACs) have well-described roles in regulating gene expression as the catalytic core of seven multiprotein complexes: SIN3, NuRD, CoREST, MiDAC, MIER and RERE (HDAC1 and HDAC2), and NCoR (HDAC3) (Millard et al...
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Research: ZNF91 deletion in human embryonic stem cells leads to ectopic activation of SVA retrotransposons and up-regulation of KRAB zinc finger gene clusters
- Nina L. Haring,
- Elisabeth J. van Bree,
- Whitney S. Jordaan,
- Judith R.E. Roels,
- Gonzalo Congrains Sotomayor,
- Tiziana M. Hey,
- Fred T.G. White,
- Marc D. Galland,
- Marten P. Smidt,
- and Frank M.J. Jacobs
Genome Res. April 2021 31: 551-563; Published in Advance March 15, 2021, doi:10.1101/gr.265348.120
.... 2010; Pontis et al. 2019). Profiling of enhancer-associated histone marks (H3K27ac and H3K4me1) in liver cells derived from six primate species revealed that young TEs account for most of the newly evolved cis-regulatory elements that drive species-specific gene expression (Trizzino et al. 2017...
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Research: MYT1L is required for suppressing earlier neuronal development programs in the adult mouse brain
- Jiayang Chen,
- Nicole A. Fuhler,
- Kevin K. Noguchi,
- and Joseph D. Dougherty
Genome Res. April 2023 33: 541-556; Published in Advance April 26, 2023, doi:10.1101/gr.277413.122
...of active histone marks. Further, we showed that MYT1L interacts with HDAC2 and transcriptional repressor SIN3B in vivo, providing potential mechanisms underlying repressive effects on histone acetylation and gene expression. Overall, our findings provide a comprehensive map of MYT1L binding in vivo...
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Mini-Review: The chromatin tapestry as a framework for neurodevelopment
- Ben Nolan,
- Timothy E. Reznicek,
- Christopher T. Cummings,
- and M. Jordan Rowley
Genome Res. October 2024 34: 1477-1486; doi:10.1101/gr.278408.123
...; Goodman and Bonni 2019; Goodman et al. 2020; Sood et al. 2020). The nucleosome remodeling and deacetylation complex (NuRD) include CHD3/4/5 in a mutually exclusive fashion, where each protein guides the complex to a unique role in neural differentiation, including gene repression and activation of layer...
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Review: The superpowers of imprinting control regions
- Bertille Montibus,
- Franck Court,
- and Philippe Arnaud
Genome Res. January 2026 36: 1-19; Published in Advance December 10, 2025, doi:10.1101/gr.281215.125
...the coordinated interaction of multiple factors that ensure the fine-tuned regulation of gene expression.Among the regulatory mechanisms, cis-regulatory regions play a key role in the precise and timely recruitment of transcription factors and other regulatory molecules to activate and maintain appropriate...
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Research: Transposable elements and their KZFP controllers are drivers of transcriptional innovation in the developing human brain
- Christopher J. Playfoot,
- Julien Duc,
- Shaoline Sheppard,
- Sagane Dind,
- Alexandre Coudray,
- Evarist Planet,
- and Didier Trono
Genome Res. September 2021 31: 1531-1545; Published in Advance August 16, 2021, doi:10.1101/gr.275133.120
...-transferase SETDB1, the histone deacetylating NuRD complex, CBX5 (also known as HP1) and DNA methyltransferases (Ecco et al. 2017). Many KZFPs bind to and repress TEs, a finding that led to the “arms race” hypothesis, which states that waves of genomic invasion by TEs throughout evolution drove the selection...
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Research: KDM1A maintains genome-wide homeostasis of transcriptional enhancers
- Saurabh Agarwal,
- Katherine M. Bonefas,
- Patricia M. Garay,
- Emily Brookes,
- Yumie Murata-Nakamura,
- Robert S. Porter,
- Todd S. Macfarlan,
- Bing Ren,
- and Shigeki Iwase
Genome Res. February 2021 31: 186-197; Published in Advance January 7, 2021, doi:10.1101/gr.234559.118
...HDAC-containing corepressor complexes, including CoREST (Hakimi et al. 2002; Shi et al. 2005) and NuRD (Wang et al. 2009), we included H3K27ac and HDAC1 in the ChIP-seq analysis. The spatial distributions of these histone modifications and HDAC1 appeared highly similar between the two genotypes at most...
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Research: Polycomb repressive complex 1 shapes the nucleosome landscape but not accessibility at target genes
- Hamish W. King,
- Nadezda A. Fursova,
- Neil P. Blackledge,
- and Robert J. Klose
Genome Res. October 2018 28: 1494-1507; Published in Advance August 28, 2018, doi:10.1101/gr.237180.118
...by the nucleosome remodeling and deacetylase (NuRD) complex that co-occupies many PcG target sites (Yildirim et al. 2011; Reynolds et al. 2012) and has been demonstrated to limit chromatin accessibility at regulatory elements (Ramírez et al. 2012; de Dieuleveult et al. 2016). Ultimately, it remains unclear what...
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Research: Temporal uncoupling of the DNA methylome and transcriptional repression during embryogenesis
- Ozren Bogdanović,
- Steven W. Long,
- Simon J. van Heeringen,
- Arie B. Brinkman,
- Jose Luis Gómez-Skarmeta,
- Hendrik G. Stunnenberg,
- Peter L. Jones,
- and Gert Jan C. Veenstra
Genome Res. August 2011 21: 1313-1327; Published in Advance June 2, 2011, doi:10.1101/gr.114843.110
...from transcriptional start sites marked with histone H3 lysine 4 trimethylation (H3K4me3), we find both promoters and gene bodies of active genes robustly methylated. In contrast, DNA methylation is absent in large H3K27me3 domains, indicating that these two repression pathways have different roles...

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