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Research: Epigenetic and evolutionary features of ape subterminal heterochromatin
- DongAhn Yoo,
- Katherine M. Munson,
- and Evan E. Eichler
Genome Res. January 2026 36: 38-49; Published in Advance October 22, 2025, doi:10.1101/gr.280987.125
...-order blocks (k1) of subterminal satellites identified in this study (Fig. 2B), as well as multicopy orthologs of Pan lineage SDs in gorilla and human are the remnants of the ancient African great ape subterminal heterochromatin in these s.Although the general organization of the subterminal heterochromatic...
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Research: Mitotic chromosomes harbor cell type– and species-specific structural features within a universal loop array conformation
- Marlies E. Oomen,
- A. Nicole Fox,
- Inma Gonzalez,
- Amandine Molliex,
- Thaleia Papadopoulou,
- Pablo Navarro,
- and Job Dekker
Genome Res. August 2025 35: 1733-1744; Published in Advance June 6, 2025, doi:10.1101/gr.280648.125
...these findings. We then investigate roles of mitotically bookmarked CTCF in prometaphase chromosome organization by Hi-C. We do not find any remaining interphase structures, such as TADs or loops, at bookmarked CTCF sites in mESCs. This suggests that mitotic loop extruders condensin I and II are not blocked...
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Research: Suv39h-catalyzed H3K9me3 is critical for euchromatic genome organization and the maintenance of gene transcription
- Christine R. Keenan,
- Hannah D. Coughlan,
- Nadia Iannarella,
- Andres Tapia del Fierro,
- Andrew Keniry,
- Timothy M. Johanson,
- Wing Fuk Chan,
- Alexandra L. Garnham,
- Lachlan W. Whitehead,
- Marnie E. Blewitt,
- Gordon K. Smyth,
- and Rhys S. Allan
Genome Res. April 2024 34: 556-571; Published in Advance May 6, 2024, doi:10.1101/gr.279119.124
...that the nuclear lamina-tethering of Suv39-dependent H3K9me3 domains provides an essential scaffold to support euchromatic organization and the maintenance of gene transcription for healthy cellular function.Gene silencing in regions of heterochromatin is critical to cell identity and appropriate cell...
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Research: Genome-wide profiles of H3K9me3, H3K27me3 modifications, and DNA methylation during diapause of Asian corn borer (Ostrinia furnacalis)
- Pengfei Lv,
- Xingzhuo Yang,
- Xianguo Zhao,
- Zhangwu Zhao,
- and Juan Du
Genome Res. May 2024 34: 725-739; Published in Advance June 12, 2024, doi:10.1101/gr.278661.123
...diapause (H3K27me3/H3K9me3/DNA methylation–changed genes). To compile a list of previously reported diapause genes, we first conducted a comprehensive search in the NCBI protein library using the keyword “diapause” to identify proteins associated with diapause across a wide range of organisms. This initial...
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Research: Hierarchical architecture of neo-sex chromosomes and accelerated adaptive evolution in tortricid moths
- Fangyuan Yang,
- Li-Jun Cao,
- Petr Nguyen,
- Zhong-Zheng Ma,
- Jin-Cui Chen,
- Wei Song,
- and Shu-Jun Wei
Genome Res. January 2025 35: 66-77; Published in Advance January 6, 2025, doi:10.1101/gr.279569.124
...synteny blocks as well as the recent adaptation and divergence in the Tortricidae.On the neo-Z, three distinct subchromatin domains corresponding to the three ancestral chromosomal elements suggest a limited effect of fusion on the 3D architecture. This contrasts sharply with the chromatin remodeling...
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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
...rates, we performed a mutation accumulation (MA) experiment in the filamentous fungus Neurospora crassa and sequenced the s of the 40 MA lines that had been propagated asexually for approximately 1015 mitoses. We detected 1322 mutations in total and observed that the mutation rate was higher in regions...
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Method: RAmbler resolves complex repeats in human Chromosomes 8, 19, and X
- Sakshar Chakravarty,
- Glennis Logsdon,
- and Stefano Lonardi
Genome Res. April 2025 35: 863-876; Published in Advance March 4, 2025, doi:10.1101/gr.279308.124
...(RA.HG38.HG01346 and RA.T2T.CHM13) against (A,B) the GRCh38.p13 assembly (HG38) and (C,D) the T2T-CHM13.v2.0 assembly (T2T) of human Chromosomes 8, 19, and X. In all plots, blocks (i), (ii), and (iii) are noncentromeric repeats in Chromosome 19; blocks (iv) and (v) are the centromeric regions...
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Method: Gapless assembly of complete human and plant chromosomes using only nanopore sequencing
- Sergey Koren,
- Zhigui Bao,
- Andrea Guarracino,
- Shujun Ou,
- Sara Goodwin,
- Katharine M. Jenike,
- Julian Lucas,
- Brandy McNulty,
- Jimin Park,
- Mikko Rautiainen,
- Arang Rhie,
- Dick Roelofs,
- Harrie Schneiders,
- Ilse Vrijenhoek,
- Koen Nijbroek,
- Olle Nordesjo,
- Sergey Nurk,
- Mike Vella,
- Katherine R. Lawrence,
- Doreen Ware,
- Michael C. Schatz,
- Erik Garrison,
- Sanwen Huang,
- William Richard McCombie,
- Karen H. Miga,
- Alexander H.J. Wittenberg,
- and Adam M. Phillippy
Genome Res. November 2024 34: 1919-1930; Published in Advance November 6, 2024, doi:10.1101/gr.279334.124
...in the HSat3 array located on this chromosome, which has a unique inverted arrangement of repeat blocks (Altemose et al. 2022; Hoyt et al. 2022; Nurk et al. 2022) and matched a pattern of coverage dropouts at the inversion breakpoints (interestingly, only at half of the breakpoints, e.g., from rev...
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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
...of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada Corresponding author: wuhua@ccnu.edu.cnAbstractUnlike the highly degenerated sex chromosomes in birds and mammals, many amphibians possess homomorphic sex chromosomes, which may result...
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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
...and YL males. We collected H3K9me3 profiles from brains of young YS and YL males in order to compare the global heterochromatin landscape in males with different Y Chromosomes. The heterochromatin sink effect of the Y would predict that global H3K9me3 levels may be lower for repeats in males...

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