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Research: Loss of multilevel 3D genome organization during breast cancer progression
- Roberto Rossini,
- Saleh Oshaghi,
- Maxim Nekrasov,
- Aurélie Bellanger,
- Renae Domaschenz,
- Yasmin Dijkwel,
- Mohamed Abdelhalim,
- Rahul Agrawal,
- Marit Ledsaak,
- Philippe Collas,
- Ragnhild Eskeland,
- David Tremethick,
- and Jonas Paulsen
Genome Res. January 2026 36: 20-37; Published in Advance October 9, 2025, doi:10.1101/gr.280791.125
...that typically suggest chromatin looping and extrusion of intrachromosomal DNA (Fig. 4D). This again indicates an insertion event. Investigating the region using a different balancing scheme that explicitly models and accounts for copy-number alterations (Servant et al. 2018) reveals similar trends...
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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
...that the different patterns of PTM enrichment between the three LAD clusters could affect their three-dimensional organization within the nucleus. We performed 3D DNA FISH to test whether the association with the nuclear lamina varies between clusters, using Lamin A/C staining to visualize the nuclear periphery (Fig...
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Research: Meta-analysis of activated neurons reveals dynamic regulation of diverse classes of alternative splicing
- Keegan S. Krick,
- Marissa Maroni,
- Erica Korb,
- Kristen W. Lynch,
- and Elizabeth A. Heller
Genome Res. June 2025 35: 1301-1312; Published in Advance April 24, 2025, doi:10.1101/gr.280082.124
...affinities following from differences in RNA Polymerase II kinetics owing to local GC content.Alternative splicing occurs predominantly cotranscriptionally and thus takes place in close proximity to the DNA from which the transcript originated (Reimer et al. 2021). Beyond being impacted by transcription...
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Research: Loss of histone H3.3 results in DNA replication defects and altered origin dynamics in C. elegans
- Maude Strobino,
- Joanna M. Wenda,
- Laura Padayachy,
- and Florian A. Steiner
Genome Res. December 2020 30: 1740-1751; Published in Advance November 10, 2020, doi:10.1101/gr.260794.120
...developed to map replication origins in different organisms (Prioleau and MacAlpine 2016), mostly by mapping different replication elements such as nascent DNA strands (Besnard et al. 2012), replication bubbles (Mesner et al. 2013), Okazaki fragments (Petryk et al. 2016), replication initiation sites...
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Research: Characterization of DNA methylation reader proteins in Arabidopsis thaliana
- Jonathan Cahn,
- James P.B. Lloyd,
- Ino D. Karemaker,
- Pascal W.T.C. Jansen,
- Jahnvi Pflueger,
- Owen Duncan,
- Jakob Petereit,
- Ozren Bogdanovic,
- A. Harvey Millar,
- Michiel Vermeulen,
- and Ryan Lister
Genome Res. December 2024 34: 2229-2243; Published in Advance December 4, 2024, doi:10.1101/gr.279379.124
...identified, which are bound by different subsets of mC readers, and show different chromatin environments as highlighted by DNA methylation levels in each context, the transcript abundance, and the presence of annotated gene and TE features. (F) Browser displays a representative locus for each cluster...
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Research: Nascent chromatin occupancy profiling reveals locus- and factor-specific chromatin maturation dynamics behind the DNA replication fork
- Mónica P. Gutiérrez,
- Heather K. MacAlpine,
- and David M. MacAlpine
Genome Res. July 2019 29: 1123-1133; Published in Advance June 19, 2019, doi:10.1101/gr.243386.118
...-2004-5-4-r22 ↵Cayrou C, Ballester B, Peiffer I, Fenouil R, Coulombe P, Andrau J-C, van Helden J, Méchali M. 2015. The chromatin environment shapes DNA replication origin organization and defines origin classes. Genome Res 25: 1873–1885. doi:10.1101/gr.192799.115 ↵Chang...
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Research: Neuron-specific chromatin disruption at CpG islands and aging-related regions in Kabuki syndrome mice
- Leandros Boukas,
- Teresa Romeo Luperchio,
- Afrooz Razi,
- Kasper D. Hansen,
- and Hans T. Bjornsson
Genome Res. May 2024 34: 696-710; Published in Advance May 3, 2024, doi:10.1101/gr.278416.123
...in neurons but not B or T cellsIt is known that the chromatin accessibility of CpG islands is related to the absence of DNA methylation and the presence of specific histone modifications (Thomson et al. 2010; Bian et al. 2011; Wachter et al. 2014; Li et al. 2016b; Kurup et al. 2019; Hughes et al. 2020). We...
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Research: Aberrant homeodomain–DNA cooperative dimerization underlies distinct developmental defects in two dominant CRX retinopathy models
- Yiqiao Zheng,
- Gary D. Stormo,
- and Shiming Chen
Genome Res. February 2025 35: 242-256; Published in Advance December 23, 2024, doi:10.1101/gr.279340.124
...dimerization in ensuring proper temporal chromatin and gene expression changes in photoreceptor development.HD residue 50 (corresponding to CRX K88) determines paired-class HDs’ DNA-binding specificity at monomeric and dimeric HD motifs as well as HD's cooperative binding at palindrome dimeric motifs (Hanes...
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Research: Differences in firing efficiency, chromatin, and transcription underlie the developmental plasticity of the Arabidopsis DNA replication origins
- Joana Sequeira-Mendes,
- Zaida Vergara,
- Ramon Peiró,
- Jordi Morata,
- Irene Aragüez,
- Celina Costas,
- Raul Mendez-Giraldez,
- Josep M. Casacuberta,
- Ugo Bastolla,
- and Crisanto Gutierrez
Genome Res. May 2019 29: 784-797; Published in Advance March 7, 2019, doi:10.1101/gr.240986.118
...eukaryotic systems.Replication of the large and complex s of multicellular organisms occurs during S-phase, once per cell cycle. Full replication depends on the coordinated function of thousands of DNA replication origins (ORIs) scattered across the (Méchali 2010; Sanchez et al. 2012; Méchali et al. 2013...
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Research: Chromatin structure influences rate and spectrum of spontaneous mutations in Neurospora crassa
- Mariana Villalba de la Peña,
- Pauliina A.M. Summanen,
- Martta Liukkonen,
- and Ilkka Kronholm
Genome Res. April 2023 33: 599-611; Published in Advance March 15, 2023, doi:10.1101/gr.276992.122
...of active transcription. However, our data set does not contain enough mutations to address if gene expression levels quantitatively influence the mutation rate in N. crassa.What is the mechanism causing mutation rate variation across the ? Chromatin structure is involved in DNA repair, and this may explain...
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