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Research: Incomplete erasure of histone marks during epigenetic reprogramming in medaka early development
- Hiroto S. Fukushima,
- Hiroyuki Takeda,
- and Ryohei Nakamura
Genome Res. April 2023 33: 572-586; Published in Advance April 28, 2023, doi:10.1101/gr.277577.122
...analyzed histone modification dynamics during epigenetic reprogramming in Japanese killifish, medaka (Oryzias latipes) embryos. Our data revealed that H3K27ac, H3K27me3, and H3K9me3 escape complete reprogramming, whereas H3K4 methylation is completely erased during cleavage stage. Furthermore, we...
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Research: Linking the dynamics of chromatin occupancy and transcription with predictive models
- Trung Q. Tran,
- Heather K. MacAlpine,
- Vinay Tripuraneni,
- Sneha Mitra,
- David M. MacAlpine,
- and Alexander J. Hartemink
Genome Res. June 2021 31: 1035-1046; Published in Advance April 23, 2021, doi:10.1101/gr.267237.120
...and changing chromatin state. This state is determined, in part, by the dynamic binding of proteins to the DNA. These proteins—including histones, transcription factors (TFs), and polymerases—interact with one another, the , and other molecules to allow the chromatin to adopt one of exceedingly many possible...
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Resource: A systematic analysis of Trypanosoma brucei chromatin factors identifies novel protein interaction networks associated with sites of transcription initiation and termination
- Desislava P. Staneva,
- Roberta Carloni,
- Tatsiana Auchynnikava,
- Pin Tong,
- Juri Rappsilber,
- A. Arockia Jeyaprakash,
- Keith R. Matthews,
- and Robin C. Allshire
Genome Res. November 2021 31: 2138-2154; Published in Advance August 18, 2021, doi:10.1101/gr.275368.121
...(two each of H2A, H2B, H3, and H4) around which ∼147 bp of DNA is wrapped. Nucleosomes are organized into chromatin fibers that provide the dynamic organizational platform underpinning eukaryotic gene expression regulation. Formation of transcriptionally active and silent chromatin states depends...
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Research: Adaptation of centromeres to breakage through local genomic and epigenomic remodeling in wheat
- Jingwei Zhou,
- Yuhong Huang,
- Huan Ma,
- Yiqian Chen,
- Chuanye Chen,
- Fangpu Han,
- and Handong Su
Genome Res. November 2025 35: 2461-2471; Published in Advance September 30, 2025, doi:10.1101/gr.280913.125
...retain essential functions, their chromatin organization may differ from canonical centromeres.Concerted local open chromatin and transcriptional dynamics contribute to genomic stabilization following centromere misdivisionTo investigate how gene expression and chromatin structure respond to centromere...
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Research: H2A.B facilitates transcription elongation at methylated CpG loci
- Yibin Chen,
- Qiang Chen,
- Richard C. McEachin,
- James D. Cavalcoli,
- and Xiaochun Yu
Genome Res. April 2014 24: 570-579; Published in Advance January 8, 2014, doi:10.1101/gr.156877.113
..., Szenker E, Garrett N, Almouzni G, Gurdon JB. 2012. HIRA dependent H3.3 deposition is required for transcriptional reprogramming following nuclear transfer to Xenopus oocytes. Epigenetics Chromatin 5: 17. KimM, Park YK, Kang TW, Lee SH, Rhee YH, Park JL, Kim HJ, Lee D, Kim SY, Kim YS. 2013. Dynamic changes...
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Research: The aberrant epigenome of DNMT3B-mutated ICF1 patient iPSCs is amenable to correction, with the exception of a subset of regions with H3K4me3- and/or CTCF-based epigenetic memory
- Varsha Poondi Krishnan,
- Barbara Morone,
- Shir Toubiana,
- Monika Krzak,
- Salvatore Fioriniello,
- Floriana Della Ragione,
- Maria Strazzullo,
- Claudia Angelini,
- Sara Selig,
- and Maria R. Matarazzo
Genome Res. February 2023 33: 169-183; Published in Advance February 24, 2023, doi:10.1101/gr.276986.122
...syndrome, highlighting the complex genetic heterogeneity of the disease (de Greef et al. 2011; Thijssen et al. 2015). In ICF1 patients, DNA hypomethylation is apparent at specific heterochromatic regions, including the pericentromeric and subtelomeric repeats (Jeanpierre et al. 1993; Yehezkel et al. 2008...
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Research: Chromosome-scale assemblies of Acanthamoeba castellanii genomes provide insights into Legionella pneumophila infection–related chromatin reorganization
- Cyril Matthey-Doret,
- Morgan J. Colp,
- Pedro Escoll,
- Agnès Thierry,
- Pierrick Moreau,
- Bruce Curtis,
- Tobias Sahr,
- Matt Sarrasin,
- Michael W. Gray,
- B. Franz Lang,
- John M. Archibald,
- Carmen Buchrieser,
- and Romain Koszul
Genome Res. September 2022 32: 1698-1710; Published in Advance September 15, 2022, doi:10.1101/gr.276375.121
...transcriptional shift observed in RNA-seq under infection conditions.At first glance, the contact maps show a clustering of subtelomeric regions, but do not display a Rabl conformation, in which centromeres cluster to the spindle-pole body (Rabl 1885). However, the precise positions of centromeres are needed...
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Method: Quantitative BrdU immunoprecipitation method demonstrates that Fkh1 and Fkh2 are rate-limiting activators of replication origins that reprogram replication timing in G1 phase
- Jared M. Peace,
- Sandra K. Villwock,
- John L. Zeytounian,
- Yan Gan,
- and Oscar M. Aparicio
Genome Res. March 2016 26: 365-375; Published in Advance January 4, 2016, doi:10.1101/gr.196857.115
...that Fkh1 can reprogram origin firing in late G1. This result also demonstrates that Fkh1OE can stimulate additional origin firing independently of Fkh2. To scrutinize this activity of Fkh1 within heterochromatin, we more closely examined the activity of originswithin subtelomeric heterochromatin...
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Research: Novel H3K4me3 marks are enriched at human- and chimpanzee-specific cytogenetic structures
- Giuliana Giannuzzi,
- Eugenia Migliavacca,
- and Alexandre Reymond
Genome Res. September 2014 24: 1455-1468; Published in Advance June 10, 2014, doi:10.1101/gr.167742.113
...involvement in speciation remains unclear. We show that subtelomeric regions—regions that have a species-specific organization, are more divergent in sequence, and are enriched in genes and recombination hotspots—are significantly enriched for species-specific histone modifications that decorate transcription...
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Method: Capturing in vivo RNA transcriptional dynamics from the malaria parasite Plasmodium falciparum
- Heather J. Painter,
- Manuela Carrasquilla,
- and Manuel Llinás
Genome Res. June 2017 27: 1074-1086; Published in Advance April 17, 2017, doi:10.1101/gr.217356.116
...-GFP in 3D7 parasites, we found that sexual stage commitment is governed by transcriptional reprogramming and stabilization of a subset of essential gametocyte transcripts. We also measured mRNA dynamics in F12 gametocyte-deficient parasites and demonstrate that the transcriptional program required...

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