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Review: The superpowers of imprinting control regions
- Bertille Montibus,
- Franck Court,
- and Philippe Arnaud
Genome Res. January 2026 36: 1-19; Published in Advance December 10, 2025, doi:10.1101/gr.281215.125
...disomy (UPD) of specific chromosomes or chromosomal regions (i.e., mice that inherit two maternal copies and no paternal copies, or vice versa, of a chromosome or part of a chromosome) have helped further define the genomic regions involved in this phenomenon. These studies identified several genomic...
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Research: MHC in newts illuminates the evolutionary dynamics of complex regions in giant genomes
- Wiesław Babik,
- Katarzyna Dudek,
- Gemma Palomar,
- Marzena Marszałek,
- Grzegorz Dubin,
- Maximina H. Yun,
- and Magdalena Migalska
Genome Res. February 2026 36: 303-317; Published in Advance January 12, 2026, doi:10.1101/gr.281127.125
...allograft rejection in vertebrates—hence, its name (Klein 1986). Subsequent research revealed that these incompatibilities are primarily caused by a subset of genes now known as the classical MHC genes, which encode molecules essential to the molecular-level self/nonself recognition and the initiation...
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Method: Taurine pangenome uncovers a segmental duplication upstream of KIT associated with depigmentation in white-headed cattle
- Sotiria Milia,
- Alexander S. Leonard,
- Xena Marie Mapel,
- Sandra Milena Bernal Ulloa,
- Cord Drögemüller,
- and Hubert Pausch
Genome Res. April 2025 35: 1041-1052; Published in Advance December 18, 2024, doi:10.1101/gr.279064.124
...similarity ratio within 1 kb bins (with respect to the ARS-UCD1.2 reference ) of the pan graph between white-headed and color-headed groups. There were two separate regions of interest, both on Chromosome 6 upstream of KIT (indicated with 1 and 2 in the inset). (D) An ∼150 kb region containing the two...
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Research: Genetic variation in recalcitrant repetitive regions of the Drosophila melanogaster genome
- Harsh G. Shukla,
- Mahul Chakraborty,
- and J.J. Emerson
Genome Res. September 2025 35: 2023-2040; Published in Advance July 16, 2025, doi:10.1101/gr.280728.125
...on both sides of Stellate that correspond to a subset of the ∼200-kb unit of the four-unit tandem array in our assembly (Fig. 6C). We also inspected the tandem euchromatic cluster in iso-1 HetEnr and found a total of 12 copies. Ours represents a third assembly of the euchromatic cluster from the iso-1...
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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
...RAmbler, hifiasm, LJA, HiCANU, and Verkko on the subset of HiFi reads mapped to these regions. SDA was excluded because it “is no longer maintained and should not be used … assembly tools like Flye, HiCanu, and hifiasm outperform any results previously possible with SDA” (quote from https...
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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
...) in Grapholita molesta. The white color denotes the fusion position. (D) Multiple features along F(20 + 17,Z) in G. molesta, including chromosome composition, subchromosomal domains, A/B compartments, the frequency of DNA methylation (CpG), the density of chromatin accessibility regions (ATAC-seq), gene...
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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
...type–dependent differences in CTCF retention and that mitotic chromosome conformation is adaptable through modulation of loop sizes to generate chromosomes of appropriate dimensions.ResultsA subset of CTCF sites remains bound in mitotic mESCsIn recent years, several genomics studies have reported...
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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
...to POD5 and then grouped by channel with: pod5 convert fast5 ‐‐force-overwrite ‐‐threads 90 ${FAST5}/*.fast5 ${POD5}/output.pod5 pod5 subset ‐‐force_overwrite ‐‐output ${POD5_GROUPED} ‐‐summary $SEQSUMMARY ‐‐columns $POD5_GROUPING -M ${POD5}/output.pod5 ## Call Simplex data with Dorado: MODEL...
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Research: Estrogen-induced chromatin looping changes identify a subset of functional regulatory elements
- Hosiana Abewe,
- Alexandra Richey,
- Jeffery M. Vahrenkamp,
- Matthew Ginley-Hidinger,
- Craig M. Rush,
- Noel Kitchen,
- Xiaoyang Zhang,
- and Jason Gertz
Genome Res. March 2025 35: 393-403; Published in Advance March 3, 2025, doi:10.1101/gr.279699.124
...) interactions, and these interactions are commonly altered in cancer. Yet, the functional relationship between changes in 3D interactions associated with regulatory regions and differential gene expression appears context-dependent. In this study, we used HiChIP to capture changes in 3D interactions between...
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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
...chromosomes of the Emei moustache toad and examined potential mechanisms of maintaining homomorphy. Although the sex chromosomes are homomorphic, we observed an extensive region of X–Y genetic differentiation, spanning ∼349 Mb, among the largest known to date in vertebrates. Despite this large size...

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