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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
...), only contain the histone fold domain (Henneman et al. 2018; Stevens et al. 2020), whereas those of eukaryotes have long tails (that are the primary sites of post-translational modifications). Another major difference is that unlike the eukaryotic octamer nucleosome, archaeal histone dimers can...
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Research: H3K36 dimethylation shapes the epigenetic interaction landscape by directing repressive chromatin modifications in embryonic stem cells
- Haifen Chen,
- Bo Hu,
- Cynthia Horth,
- Eric Bareke,
- Phillip Rosenbaum,
- Sin Young Kwon,
- Jacinthe Sirois,
- Daniel N. Weinberg,
- Faith M. Robison,
- Benjamin A. Garcia,
- Chao Lu,
- William A. Pastor,
- and Jacek Majewski
Genome Res. May 2022 32: 825-837; Published in Advance April 8, 2022, doi:10.1101/gr.276383.121
...eventually opted for mass spectrometry normalization. In our experience, we found this method to perform most reliably, but more research on optimizing quantitative normalization is necessary, particularly to distinguish small changes in the levels of epigenetic modifications.In this work, we focused...
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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
...directs genomic localization of Mbd2 and Mbd3 in embryonic stem cells. eLife 5: e21964. ↵Hake SB, Garcia BA, Duncan EM, Kauer M, Dellaire G, Shabanowitz J, Bazett-Jones DP, Allis CD, Hunt DF. 2006. Expression patterns and post-translational modifications associated with mammalian histone H3 variants. J...
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Research: Plasticity in patterns of histone modifications and chromosomal proteins in Drosophila heterochromatin
- Nicole C. Riddle,
- Aki Minoda,
- Peter V. Kharchenko,
- Artyom A. Alekseyenko,
- Yuri B. Schwartz,
- Michael Y. Tolstorukov,
- Andrey A. Gorchakov,
- Jacob D. Jaffe,
- Cameron Kennedy,
- Daniela Linder-Basso,
- Sally E. Peach,
- Gregory Shanower,
- Haiyan Zheng,
- Mitzi I. Kuroda,
- Vincenzo Pirrotta,
- Peter J. Park,
- Sarah C.R. Elgin,
- and Gary H. Karpen
Genome Res. February 2011 21: 147-163; Published in Advance December 22, 2010, doi:10.1101/gr.110098.110
...remain poorly characterized. At the core of chromatin are the histone proteins, which assemble DNA into nucleosomes, providing the basis for higher order chromatin packaging. A variety of post-translational histone modifications are used in combination to define alternative chromatin states (Jenuwein...
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Methods: Improving gene annotation using peptide mass spectrometry
- Stephen Tanner,
- Zhouxin Shen,
- Julio Ng,
- Liliana Florea,
- Roderic Guigó,
- Steven P. Briggs,
- and Vineet Bafna
Genome Res. February 2007 17: 231-239; Published in Advance December 22, 2006, doi:10.1101/gr.5646507
...al. 2006 ), and relative protein expression levels between tissues ( Lill 2003 ). These topics are a subject of ongoing research. Our search did not consider post-translational modifications explicitly. Some modified peptides were annotated with a sequence with the same mass as the true (modified...
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Review: A systematic guide for identifying transcription factors that directly regulate the expression of a gene of interest
- Andrew D. Bates,
- Dawid Grzela,
- Maciej Studzian,
- Louise Brennan,
- Moli Williams,
- Conor Fawcett,
- Beth Hammond,
- Manreen Grewal,
- Marcin Ratajewski,
- Lukasz Pulaski,
- and Urszula L. McClurg
Genome Res. March 2026 36: 433-459; Published in Advance February 17, 2026, doi:10.1101/gr.281154.125
...) regulate the expression of my gene of interest (GOI) directly on its promoter. However, answering this is not straightforward. Genes exist within multilayered microenvironments of proximal and distal promoter–enhancer interactions, DNA accessibility, histone post-translational modifications (PTMs), and DNA...
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Method: Application of histone modification-specific interaction domains as an alternative to antibodies
- Goran Kungulovski,
- Ina Kycia,
- Raluca Tamas,
- Renata Z. Jurkowska,
- Srikanth Kudithipudi,
- Chisato Henry,
- Richard Reinhardt,
- Paul Labhart,
- and Albert Jeltsch
Genome Res. November 2014 24: 1842-1853; Published in Advance October 9, 2014, doi:10.1101/gr.170985.113
...on the same histone tail or on the same nucleosome. Since mass spectrometry cannot pinpoint the direct interaction of an antibody and a target modification, it is impossible to decide if coenrichment of a secondary modification is due to a cross-reactivity of the reagent or if the secondarymark is associated...
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Method: Integration of high-throughput proteomic data and complementary omics layers with PriOmics
- Robin Kosch,
- Katharina Limm,
- Annette M. Staiger,
- Nadine S. Kurz,
- Nicole Seifert,
- Bence Oláh,
- Stefan Solbrig,
- Viola Poeschel,
- Gerhard Held,
- Marita Ziepert,
- Norbert Schmitz,
- Emil Chteinberg,
- Reiner Siebert,
- Rainer Spang,
- Helena U. Zacharias,
- German Ott,
- Peter J. Oefner,
- and Michael Altenbuchinger
Genome Res. January 2026 36: 197-213; Published in Advance November 18, 2025, doi:10.1101/gr.279487.124
...modifications (CTMs/PTMs). Yet, it remains an open question how to holistically explore such data and their relationship to complementary omics/phenotypic information. Graphical models are particularly suited to study molecular networks and underlying regulatory mechanisms, as they can distinguish direct from...
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Methods: Spatial mapping of protein abundances in the mouse brain by voxelation integrated with high-throughput liquid chromatography–mass spectrometry
- Vladislav A. Petyuk,
- Wei-Jun Qian,
- Mark H. Chin,
- Haixing Wang,
- Eric A. Livesay,
- Matthew E. Monroe,
- Joshua N. Adkins,
- Navdeep Jaitly,
- David J. Anderson,
- David G. Camp II,
- Desmond J. Smith,
- and Richard D. Smith
Genome Res. March 2007 17: 328-336; Published in Advance January 25, 2007, doi:10.1101/gr.5799207
...known common post-translational modification. Indeed the number of matches does not vary significantly as long as the mass shift value stays an integer (Supplemental Fig. 7). Features detected in all LC-FTICR datasets were matched against a merged normal and shifted database. We assumed that all matches...
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LETTER: H3K27me3 forms BLOCs over silent genes and intergenic regions and specifies a histone banding pattern on a mouse autosomal chromosome
- Florian M. Pauler,
- Mathew A. Sloane,
- Ru Huang,
- Kakkad Regha,
- Martha V. Koerner,
- Ido Tamir,
- Andreas Sommer,
- Andras Aszodi,
- Thomas Jenuwein,
- and Denise P. Barlow
Genome Res. February 2009 19: 221-233; Published in Advance December 1, 2008, doi:10.1101/gr.080861.108
...class, which could offer unique domains for the specific regulation of genes or the silencing of autonomous retrotransposons. Post-translational modifications on histone tails either reflect or directly influence the transcriptional status of genes and are classified as active, when they correlate...

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