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Research: Plant polymerase IV sensitizes chromatin through histone modifications to preclude spread of silencing into protein-coding domains
- Vivek Hari Sundar G,
- Chenna Swetha,
- Debjani Basu,
- Kannan Pachamuthu,
- Steffi Raju,
- Tania Chakraborty,
- Rebecca A. Mosher,
- and P.V. Shivaprasad
Genome Res. May 2023 33: 715-728; Published in Advance June 5, 2023, doi:10.1101/gr.277353.122
...is mediated using several factors including chromatin modifiers. However, factors that avoid the intrusion of silencing signals into protein-coding genes are poorly understood. Here we show that a plant specific paralog of RNA polymerase (Pol) II, named Pol IV, is involved in avoidance of facultative...
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Research: Synergistic regulation by H3K36 and H3K27 methylation defines the chromatin landscape to control virulence and secondary metabolism in a fungal pathogen
- Xingmin Han,
- Chenghui Xu,
- Yiyi Ren,
- Meiling Guo,
- Jiayue Yan,
- Xuan Wang,
- Chao Liu,
- Qin Gu,
- Xing-Xing Shen,
- Zhonghua Ma,
- and Yun Chen
Genome Res. November 2025 35: 2472-2487; Published in Advance October 14, 2025, doi:10.1101/gr.280560.125
...strategies likely compensate for the absence of classical methylation marks. For instance, short double-stranded RNAs induce RNA silencing through distinct mechanisms (Meister and Tuschl 2004). Telomere-associated factors such as DNA helicase Dna2p, telomerase Dot1, and ubiquitinase Dot4p may also contribute...
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Research: Characterization of the distribution and dynamics of chromatin states in the C. elegans germline reveals substantial H3K4me3 remodeling during oogenesis
- Mariateresa Mazzetto,
- Lauren E. Gonzalez,
- Nancy Sanchez,
- and Valerie Reinke
Genome Res. January 2024 34: 57-69; Published in Advance December 26, 2023, doi:10.1101/gr.278247.123
...and suggest the possibility of transcription from heterochromatic regions, as well as a role for post-transcriptional regulation.Chromatin state of gene targets of small RNA pathwaysThe disconnect between chromatin state and transcript abundance for many of the pregametic, spermatogenesis, and oogenesis...
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Research: Polycomb-dependent differential chromatin compartmentalization determines gene coregulation in Arabidopsis
- Ying Huang,
- Sanchari Sicar,
- Juan S. Ramirez-Prado,
- Deborah Manza-Mianza,
- Javier Antunez-Sanchez,
- Rim Brik-Chaouche,
- Natalia Y. Rodriguez-Granados,
- Jing An,
- Catherine Bergounioux,
- Magdy M. Mahfouz,
- Heribert Hirt,
- Martin Crespi,
- Lorenzo Concia,
- Fredy Barneche,
- Simon Amiard,
- Aline V. Probst,
- Jose Gutierrez-Marcos,
- Federico Ariel,
- Cécile Raynaud,
- David Latrasse,
- and Moussa Benhamed
Genome Res. July 2021 31: 1230-1244; Published in Advance June 3, 2021, doi:10.1101/gr.273771.120
...RNA bait library specifically targeting 4650 regions that accumulate H3K27me3 and included a subset of loci differentially methylated between shoots and roots (Supplemental Fig. S9). The comparison of both Hi-C and C-Hi-C matrixes allowed us to identify a significant enrichment of chromatin contacts...
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Research: The role of insulators and transcription in 3D chromatin organization of flies
- Keerthi T. Chathoth,
- Liudmila A. Mikheeva,
- Gilles Crevel,
- Jareth C. Wolfe,
- Ioni Hunter,
- Saskia Beckett-Doyle,
- Sue Cotterill,
- Hongsheng Dai,
- Andrew Harrison,
- and Nicolae Radu Zabet
Genome Res. April 2022 32: 682-698; Published in Advance March 30, 2022, doi:10.1101/gr.275809.121
...in both the mRNA levels and protein levels and do not affect the cell cycle (the efficiency of knockdown achieved here is similar to the ones reported by other studies in Drosophila cells [Supplemental Fig. S1; Schwartz et al. 2012; Ramírez et al. 2018; Zenk et al. 2021]). High-resolution contact maps...
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Research: Chromatin activation as a unifying principle underlying pathogenic mechanisms in multiple myeloma
- Raquel Ordoñez,
- Marta Kulis,
- Nuria Russiñol,
- Vicente Chapaprieta,
- Arantxa Carrasco-Leon,
- Beatriz García-Torre,
- Stella Charalampopoulou,
- Guillem Clot,
- Renée Beekman,
- Cem Meydan,
- Martí Duran-Ferrer,
- Núria Verdaguer-Dot,
- Roser Vilarrasa-Blasi,
- Paula Soler-Vila,
- Leire Garate,
- Estíbaliz Miranda,
- Edurne San José-Enériz,
- Juan R. Rodriguez-Madoz,
- Teresa Ezponda,
- Rebeca Martínez-Turrilas,
- Amaia Vilas-Zornoza,
- David Lara-Astiaso,
- Daphné Dupéré-Richer,
- Joost H.A. Martens,
- Halima El-Omri,
- Ruba Y. Taha,
- Maria J. Calasanz,
- Bruno Paiva,
- Jesus San Miguel,
- Paul Flicek,
- Ivo Gut,
- Ari Melnick,
- Constantine S. Mitsiades,
- Jonathan D. Licht,
- Elias Campo,
- Hendrik G. Stunnenberg,
- Xabier Agirre,
- Felipe Prosper,
- and Jose I. Martin-Subero
Genome Res. September 2020 30: 1217-1227; Published in Advance August 20, 2020, doi:10.1101/gr.265520.120
...sequencing (WGBS), and gene expression by RNA-seq. The major limiting factor for such multi-omics characterization was the high amount of starting material needed from each individual patient. To overcome this limitation, we also analyzed the chromatin regulatory landscape of an extended series of MM...
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Research: Genome-wide analysis of chromatin packing in Arabidopsis thaliana at single-gene resolution
- Chang Liu,
- Congmao Wang,
- George Wang,
- Claude Becker,
- Maricris Zaidem,
- and Detlef Weigel
Genome Res. August 2016 26: 1057-1068; Published in Advance May 25, 2016, doi:10.1101/gr.204032.116
...over long distances. In line with the globally dispersed distribution of RNA polymerase II in A. thaliana nuclear space, actively transcribed genes do not show a strong tendency to associate with each other. In general, there are often contacts between 5′ and 3′ ends of genes, forming local chromatin...
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Research: Prepatterning of differentiation-driven nuclear lamin A/C-associated chromatin domains by GlcNAcylated histone H2B
- Torunn Rønningen,
- Akshay Shah,
- Anja R. Oldenburg,
- Kristin Vekterud,
- Erwan Delbarre,
- Jan Øivind Moskaug,
- and Philippe Collas
Genome Res. December 2015 25: 1825-1835; Published in Advance September 10, 2015, doi:10.1101/gr.193748.115
...IP-seq enrichment profiles showing ChIP/input ratios (scale −0.4 to +0.4 centered on 0), LADs mapped with EDD, and RNA-seq gene expression profiles (scale 0–1000 FPKM). (B) Number of LADs identified at each differentiation stage. (C) Median LAD lengths at all differentiation time points confounded (All) and at each...
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Research: CHH islands: de novo DNA methylation in near-gene chromatin regulation in maize
- Jonathan I. Gent,
- Nathanael A. Ellis,
- Lin Guo,
- Alex E. Harkess,
- Yingyin Yao,
- Xiaoyu Zhang,
- and R. Kelly Dawe
Genome Res. April 2013 23: 628-637; Published in Advance December 26, 2012, doi:10.1101/gr.146985.112
...to direct these heterochromatic structural states, often overlapping with defense mechanisms against foreign nucleic acids. A prominent example is RNA interference (RNAi) (Fire et al. 1998), which can not only degrade RNA, but can also induce transcriptional gene silencing. In fact, short interfering RNA...
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Research: Cotranscriptional histone H2B monoubiquitylation is tightly coupled with RNA polymerase II elongation rate
- Gilad Fuchs,
- Dror Hollander,
- Yoav Voichek,
- Gil Ast,
- and Moshe Oren
Genome Res. October 2014 24: 1572-1583; Published in Advance July 21, 2014, doi:10.1101/gr.176487.114
...with accumulation of RNA polymerase II (Pol II), suggesting that H2Bub1 levels within gene bodies reflect changes in Pol II elongation rates that are probably associated with cotranscriptional splicing. In support of this notion, we find a significant correlation between H2Bub1 levels and experimentally measured...

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