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Research: Cohesin and CTCF do not assemble TADs in Xenopus sperm and male pronuclei
- Gregor Jessberger,
- Csilla Várnai,
- Roman R. Stocsits,
- Wen Tang,
- Georg Stary,
- and Jan-Michael Peters
Genome Res. December 2023 33: 2094-2107; Published in Advance December 21, 2023, doi:10.1101/gr.277865.123
...that are separated by >5 Mb are not correlated in XL-177 cells (the autocorrelation is ∼0), even genomic regions that are as far apart from each other as 10 Mb are still correlated in sperm (Fig. 1I). These results suggest that a crude compartmentalization is preserved when chromatin is packaged into Xenopus sperm...
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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
...Medicine, Oslo University Hospital, 0424 Oslo, Norway Corresponding authors: david.tremethick@anu.edu.au, jonas.paulsen@ibv.uio.noAbstractBreast cancer entails intricate alterations in organization and expression. However, how three-dimensional (3D) chromatin structure changes in the progression from...
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Research: Unexpectedly low recombination rates and presence of hotspots in termite genomes
- Turid Everitt,
- Tilman Rönneburg,
- Daniel Elsner,
- Anna Olsson,
- Yuanzhen Liu,
- Tuuli Larva,
- Judith Korb,
- and Matthew T. Webster
Genome Res. May 2025 35: 1124-1137; Published in Advance March 20, 2025, doi:10.1101/gr.279180.124
...with an active PRDM9 protein include nearly all mammals and many vertebrate taxa (Baker et al. 2017). In species without PRDM9, recombination can be directed to hotspots defined by other features, such as CpG islands and promoters that have open chromatin. Such hotspots have been characterized in the s...
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Letter: Drosophila ORC localizes to open chromatin and marks sites of cohesin complex loading
- Heather K. MacAlpine,
- Raluca Gordân,
- Sara K. Powell,
- Alexander J. Hartemink,
- and David M. MacAlpine
Genome Res. February 2010 20: 201-211; Published in Advance December 7, 2009, doi:10.1101/gr.097873.109
...of DNA in the nucleus is packaged into nucleosomes and higher-order chromatin structure. The accessibility of chromatin is an inherited feature established, in part, by primary DNA sequence, transcription factors, insulator elements, transcription machinery, and histone variants. Indeed, we found...
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Research: Extreme heterochiasmy and high rates of sex-reversed recombination result in large yet homomorphic sex chromosomes in the Emei moustache toad
- Siyu Xie,
- Jun Li,
- Wanyan Chen,
- Lydia J.M. Fong,
- Chunhua Huang,
- Yan Feng,
- Qingbo Ai,
- Mian Zhao,
- Judith E. Mank,
- and Hua Wu
Genome Res. June 2025 35: 1325-1336; Published in Advance April 24, 2025, doi:10.1101/gr.280161.124
...that occasional XY recombination may hinder sexualization of gene regulation in L. boringii.Finally, we identified five potential candidate genes on Chr 1 that are involved in gonad development and differentiation. zp3 is critical in the process of sperm—egg interaction in African clawed frogs (Omata and Katagiri...
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Resource: Epigenomic analysis reveals prevalent contribution of transposable elements to cis-regulatory elements, tissue-specific expression, and alternative promoters in zebrafish
- Hyung Joo Lee,
- Yiran Hou,
- Ju Heon Maeng,
- Nakul M. Shah,
- Yujie Chen,
- Heather A. Lawson,
- Hongbo Yang,
- Feng Yue,
- and Ting Wang
Genome Res. July 2022 32: 1424-1436; Published in Advance June 1, 2022, doi:10.1101/gr.276052.121
...involved in many biological processes such as innate immune response (Chuong et al. 2016) and pregnancy (Lynch et al. 2011; Chuong et al. 2013). TEs can also act as tissue-specific enhancers (Xie et al. 2013; Todd et al. 2019) and chromatin boundaries (Schmidt et al. 2012; Choudhary et al. 2020). Further...
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Research: miRNA-like secondary structures in maize (Zea mays) genes and transposable elements correlate with small RNAs, methylation, and expression
- Galen T. Martin,
- Edwin Solares,
- Jeanelle Guadardo-Mendez,
- Aline Muyle,
- Alexandros Bousios,
- and Brandon S. Gaut
Genome Res. November 2023 33: 1932-1946; Published in Advance November 2, 2023, doi:10.1101/gr.277459.122
...for Dicer-like mechanisms.After performing computational annotation to predict miRNA-like regions in the genes and TEs of maize, we investigate the relationship between these regions to smRNAs, methylation levels, chromatin accessibility, and, where applicable, gene expression (Supplemental Fig. S1...
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Research: Evolutionary origins and diversification of testis-specific short histone H2A variants in mammals
- Antoine Molaro,
- Janet M. Young,
- and Harmit S. Malik
Genome Res. April 2018 28: 460-473; Published in Advance March 16, 2018, doi:10.1101/gr.229799.117
...@fhcrc.orgAbstractEukaryotic s must accomplish both compact packaging for stability and inheritance, as well as accessibility for gene expression. They do so using post-translational modifications of four ancient canonical histone proteins (H2A, H2B, H3, and H4) and by deploying histone variants with specialized chromatin...
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Research: Variation in mutation, recombination, and transposition rates in Drosophila melanogaster and Drosophila simulans
- Yiguan Wang,
- Paul McNeil,
- Rashidatu Abdulazeez,
- Marta Pascual,
- Susan E. Johnston,
- Peter D. Keightley,
- and Darren J. Obbard
Genome Res. April 2023 33: 587-598; Published in Advance April 10, 2023, doi:10.1101/gr.277383.122
..., populations, and species, and the variation can be attributed to both genetic factors (e.g., rate and landscape modifier loci, architecture, and chromatin structure) and environmental factors (e.g., age, temperature, and pathogen infection) (Stapley et al. 2017). Genome-wide estimates of recombination rate...
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Research: Transposable element accumulation drives size differences among polymorphic Y Chromosomes in Drosophila
- Alison H. Nguyen,
- Weixiang Wang,
- Emily Chong,
- Kamalakar Chatla,
- and Doris Bachtrog
Genome Res. June 2022 32: 1074-1088; Published in Advance May 2, 2022, doi:10.1101/gr.275996.121
...of sections from the largest Y (Dobzhansky 1935, 1937). He also concluded that morphological and physiological characteristics of a male are not affected by the type of its Y Chromosome.Here, we take advantage of recent advances in sequencing technology to revisit the large difference in Y size among D...

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