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Research: HDA6-dependent histone deacetylation regulates mRNA polyadenylation in Arabidopsis
- Juncheng Lin,
- Fu-Yu Hung,
- Congting Ye,
- Liwei Hong,
- Yuan-Hsin Shih,
- Keqiang Wu,
- and Qingshun Q. Li
Genome Res. October 2020 30: 1407-1417; Published in Advance August 5, 2020, doi:10.1101/gr.255232.119
...361102, China Corresponding authors: liqq@xmu.edu.cn, kewu@ntu.edu.twAbstractEukaryotic histone deacetylation, critical for maintaining nucleosome structure and regulating gene expression, is mediated by histone deacetylases (HDACs). Although nucleosomes have been reported to regulate m...
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Research: Distinct classes of lamina-associated domains are defined by differential patterns of repressive histone methylation
- Caden J. Martin,
- Elizabeth A. Oser,
- Prabakaran Nagarajan,
- Liudmila V. Popova,
- Benjamin D. Sunkel,
- Benjamin Z. Stanton,
- and Mark R. Parthun
Genome Res. September 2025 35: 1959-1974; Published in Advance August 5, 2025, doi:10.1101/gr.280380.124
...Caden J. Martin1, Elizabeth A. Oser1, Prabakaran Nagarajan1, Liudmila V. Popova1, Benjamin D. Sunkel2, Benjamin Z. Stanton2 and Mark R. Parthun1 1Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, Ohio 43210, USA; 2Abigail Wexner Research Institute...
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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
...(HDACs). Deacetylation of histone tails results in chromatin tightening, and therefore, HDACs are generally regarded as transcriptional repressors. Counterintuitively, simultaneous deletion of Hdac1 and Hdac2 in embryonic stem cells (ESCs) reduces expression of the pluripotency-associated transcription...
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Research: The chromatin landscape of the histone-possessing Bacteriovorax bacteria
- Georgi K. Marinov,
- Benjamin Doughty,
- Anshul Kundaje,
- and William J. Greenleaf
Genome Res. January 2025 35: 109-123; Published in Advance November 21, 2024, doi:10.1101/gr.279418.124
..., Stanford University, Stanford, California 94305, USA; 4Department of Applied Physics, Stanford University, Stanford, California 94305, USA; 5Arc Institute, Palo Alto, California 94304, USA Corresponding author: marinovg@stanford.eduAbstractHistone proteins have traditionally been thought to be restricted...
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Research: Variation in histone configurations correlates with gene expression across nine inbred strains of mice
- Anna L Tyler,
- Catrina Spruce,
- Romy Kursawe,
- Annat Haber,
- Robyn L Ball,
- Wendy A Pitman,
- Alexander D Fine,
- Narayanan Raghupathy,
- Michael Walker,
- Vivek M Philip,
- Christopher L Baker,
- J. Matthew Mahoney,
- Gary A. Churchill,
- Jennifer J Trowbridge,
- Michael L Stitzel,
- Kenneth Paigen,
- Petko M Petkov,
- and Gregory W Carter
Genome Res. May 22, 2023 gr.277467.122; Published in Advance May 22, 2023, doi:10.1101/gr.277467.122
...of State 5 with reduced expression within hepatocytes is consistent with the377 annotation of bivalent promoter. Genes marked with this state were enriched for vascular development378 and Wnt signaling, further supporting the annotation. When positions marked with State 5 varied379 across strains, the most...
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Research: Distinct contributions of DNA methylation and histone acetylation to the genomic occupancy of transcription factors
- Martin Cusack,
- Hamish W. King,
- Paolo Spingardi,
- Benedikt M. Kessler,
- Robert J. Klose,
- and Skirmantas Kriaucionis
Genome Res. October 2020 30: 1393-1406; Published in Advance September 22, 2020, doi:10.1101/gr.257576.119
...of these elements has elevated binding of the YY1 and GABPA transcription factors and increased expression. The pronounced additive effect of HDAC inhibition in DNA methylation–deficient cells demonstrates that DNA methylation and histone deacetylation act largely independently to suppress transcription factor...
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Research: Functional noncoding SNPs in human endothelial cells fine-map vascular trait associations
- Anu Toropainen,
- Lindsey K. Stolze,
- Tiit Örd,
- Michael B. Whalen,
- Paula Martí Torrell,
- Verena M. Link,
- Minna U. Kaikkonen,
- and Casey E. Romanoski
Genome Res. March 2022 32: 409-424; Published in Advance February 22, 2022, doi:10.1101/gr.276064.121
...accessibility, and H3K27 acetylation to nominate a set of likely functional noncoding SNPs. Together with information from -wide association studies (GWASs) for vascular disease traits, we tested the ability of 34,344 variants to perturb enhancer function in ECs using the highly multiplexed STARR-seq assay...
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Research: A nucleosome turnover map reveals that the stability of histone H4 Lys20 methylation depends on histone recycling in transcribed chromatin
- J. Peter Svensson,
- Manu Shukla,
- Victoria Menendez-Benito,
- Ulrika Norman-Axelsson,
- Pauline Audergon,
- Indranil Sinha,
- Jason C. Tanny,
- Robin C. Allshire,
- and Karl Ekwall
Genome Res. June 2015 25: 872-883; Published in Advance March 16, 2015, doi:10.1101/gr.188870.114
...into nucleosomes, histones aremodified as theymature, first by deacetylation and later by successive methylation (Scharf et al. 2009a). Some modifications require a full cell cycle to reestablish the conserved epigenetic pattern of the chromatin (Scharf et al. 2009a). High histone turnover rates are primarily...
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Research: The gene repressor complex NuRD interacts with the histone variant H3.3 at promoters of active genes
- Daniel C. Kraushaar,
- Zuozhou Chen,
- Qingsong Tang,
- Kairong Cui,
- Junfang Zhang,
- and Keji Zhao
Genome Res. November 2018 28: 1646-1655; Published in Advance September 25, 2018, doi:10.1101/gr.236224.118
...remodeling and histone deacetylation (Xue et al. 1998; Zhang et al. 1998). The NuRD complex plays a major role in transcriptional regulation and DNA damage repair (Torchy et al. 2015; Spruijt et al. 2016; Gong et al. 2017). The NuRD complex is composed of six subunits each with multiple isoforms: HDAC1...
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Research: Epigenetic analyses of planarian stem cells demonstrate conservation of bivalent histone modifications in animal stem cells
- Anish Dattani,
- Damian Kao,
- Yuliana Mihaylova,
- Prasad Abnave,
- Samantha Hughes,
- Alvina Lai,
- Sounak Sahu,
- and A. Aziz Aboobaker
Genome Res. October 2018 28: 1543-1554; Published in Advance August 24, 2018, doi:10.1101/gr.239848.118
...and as such this modification is enriched toward the 3′ end of genes (Li et al. 2002; Wagner and Carpenter 2012). H3K36me3 is hypothesized to prevent spurious transcriptional initiation at cryptic promoter-like sequences within exons and, in yeast, this is achieved by the recruitment of histone deacetylase complexes (HDAC...

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