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Research: Common cis-regulatory variation modifies the penetrance of pathogenic SHROOM3 variants in craniofacial microsomia
- Hao Zhu,
- Jiao Zhang,
- Soumya Rao,
- Matthew D. Durbin,
- Ying Li,
- Ruirui Lang,
- Jiqiang Liu,
- Baichuan Xiao,
- Hailin Shan,
- Ziqiu Meng,
- Jinmo Wang,
- Xiaokai Tang,
- Zhenni Shi,
- Liza L. Cox,
- Shouqin Zhao,
- Stephanie M. Ware,
- Tiong Y. Tan,
- Michelle de Silva,
- Lyndon Gallacher,
- Ting Liu,
- Jie Mi,
- Changqing Zeng,
- Hou-Feng Zheng,
- Qingguo Zhang,
- Stylianos E. Antonarakis,
- Timothy C. Cox,
- and Yong-Biao Zhang
Genome Res. May 2025 35: 1065-1079; Published in Advance April 15, 2025, doi:10.1101/gr.280047.124
...the common variants into five distinct haplotype blocks (H1–H5) situated within the SHROOM3 locus (Supplemental Fig. 4). To fine-map candidate pathogenic eQTLs influencing the penetrance of CFM through altered ASE, we utilized conditional association analyses on the lead variant in each LD block...
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Research: Xist upstream deletion leads to dysregulation of Xist and autosomal gene expression
- Sudeshna Majumdar,
- Lakshmi Sowjanya Bammidi,
- Hemant C. Naik,
- Avinchal Manhas,
- Runumi Baro,
- Akash Kalita,
- Amlan Jyoti Naskar,
- Sundarraj Nidharshan,
- Girija S. Bariha,
- Dimple Notani,
- and Srimonta Gayen
Genome Res. September 2025 35: 1992-2010; Published in Advance August 6, 2025, doi:10.1101/gr.279822.124
.... Notably, we find that many autosomal genes, including cohesin Rad21, are dysregulated in Xist-upstream-deleted cells. Additionally, we demonstrate that Xist-upstream deletion leads to alterations of topological contacts of the Xist locus with its upstream positive regulator Ftx and across the inactive X...
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Method: Chromosome engineering to correct a complex rearrangement on Chromosome 8 reveals the effects of 8p syndrome on gene expression and neural differentiation
- Sophia N. Lee,
- Erin C. Banda,
- Lu Qiao,
- Sarah L. Thompson,
- Karan Singh,
- Ryan A. Hagenson,
- Teresa Davoli,
- Stefan F. Pinter,
- and Jason M. Sheltzer
Genome Res. March 2026 36: 547-560; Published in Advance January 12, 2026, doi:10.1101/gr.280425.125
....Transcriptional similarities between invdupdel(8p) and Trisomy 21Previous reports have noted similarities between the clinical presentation of Down syndrome and other conditions caused by whole-chromosome aneuploidy (Krivega et al. 2022). On a cellular level, different autosomal trisomies result in similar changes in gene...
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Method: Simultaneous modeling of chromatin conformation changes from multiple single-cell interaction maps with ChromMovie
- Krzysztof H. Banecki,
- Haoxi Chai,
- Yijun Ruan,
- and Dariusz Plewczynski
Genome Res. April 8, 2026 ; Published in Advance April 8, 2026, doi:10.1101/gr.280985.125
...diploid cell maturation contact data from Chai et al. (2025), derived from vascular mouse brain tissue. The mouse cells were analyzed at 2, 11, 95, 365, and 720 days, resulting in five distinct frames for the ChromMovie simulation. Because the original data set did not exclusively represent a single cell...
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Research: Cell-type- and chromosome-specific chromatin landscapes and DNA replication programs of Drosophila testis tumor stem cell–like cells
- Jennifer A. Urban,
- Daniel Ringwalt,
- John M. Urban,
- Wingel Xue,
- Ryan Gleason,
- Keji Zhao,
- and Xin Chen
Genome Res. January 2026 36: 83-101; Published in Advance December 10, 2025, doi:10.1101/gr.280809.125
...unit variance, yielding RT Z-scores. We then categorized the into 12 chromosomal domains with their mean RT Z-scores: two major autosomal arms and their pericentromeric regions, the 4th, X, and Y Chromosomes, and a gene consensus for the ribosomal DNA (rDNA) locus (Fig. 5B). This allowed us...
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Research: Identification of the male-specific region on the guppy Y Chromosome from a haplotype-resolved assembly
- Kang Du,
- Oliver Deusch,
- Ilja Bezrukov,
- Christa Lanz,
- Yann Guiguen,
- Margarete Hoffmann,
- Anette Habring,
- Detlef Weigel,
- Manfred Schartl,
- and Christine Dreyer
Genome Res. March 2025 35: 489-498; Published in Advance March 5, 2025, doi:10.1101/gr.279582.124
...Poecilia wingei and Poecilia obscura (Nanda et al. 2014). This analysis revealed polymorphisms in heterochromatin content of the Y as well as differences in distance of the genetic marker M_229 to the physical chromosome end between populations. The sex determination locus (SDL) was mapped to the most...
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Research: The grasshopper genome reveals long-term gene content conservation of the X Chromosome and temporal variation in X Chromosome evolution
- Xinghua Li,
- Judith E. Mank,
- and Liping Ban
Genome Res. July 2024 34: 997-1007; Published in Advance August 5, 2024, doi:10.1101/gr.278794.123
...chromosomes. These are difficult alternatives to differentiate without knowledge of the specific sex-determining locus throughout this group.Fast-X and Slow-X evolutionThe X Chromosome has several properties that distinguish it from the autosomes (Vicoso and Charlesworth 2006; Meisel and Connallon 2013...
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Method: Ultra-long sequencing for contiguous haplotype resolution of the human immunoglobulin heavy-chain locus
- Mari B. Gornitzka,
- Egil Røsjø,
- Uddalok Jana,
- Easton E. Ford,
- Alan Tourancheau,
- William D. Lees,
- Zachary Vanwinkle,
- Melissa L. Smith,
- Corey T. Watson,
- and Andreas Lossius
Genome Res. October 2025 35: 2240-2251; Published in Advance August 21, 2025, doi:10.1101/gr.280400.125
....7 per 100 kb). When we mapped the Q100 Chromosome 14 and our ONT IGH assemblies to the custom IGH reference, we observed, as expected, that large portions of the HG002 IGH locus and corresponding genes were deleted relative to the custom IGH reference (Fig. 3A,B). Notably, our assembly of haplotype 2...
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Research: AGAP duplicons associate with structural diversity at Chromosome 10q11.22
- Stefania Fornezza,
- Vincenza Simona Delvecchio,
- William T. Harvey,
- Philip C. Dishuck,
- Evan E. Eichler,
- and Giuliana Giannuzzi
Genome Res. October 2024 34: 1487-1499; Published in Advance September 25, 2024, doi:10.1101/gr.279454.124
...of the region is available from the T2T (Telomere-to-Telomere) CHM13 human sequence (Nurk et al. 2022). The architecture of this locus is the result of several structural changes that occurred in the human lineage after divergence with the chimpanzee (Dennis et al. 2017).Previous works showed that genes mapped...
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Method: OMKar automates genome karyotyping using optical maps to identify constitutional abnormalities
- Siavash Raeisi Dehkordi,
- Zhaoyang Jia,
- Joey Estabrook,
- Jen Hauenstein,
- Neil Miller,
- Naz Güleray-Lafci,
- Jürgen Neesen,
- Alex Hastie,
- Alka Chaubey,
- Andy Wing Chun Pang,
- Paul Dremsek,
- and Vineet Bafna
Genome Res. December 2025 35: 2671-2681; Published in Advance November 14, 2025, doi:10.1101/gr.280536.125
...on microscopic chromosome examination, a complex and expertise-dependent process with megabase-scale resolution. Optical mapping (OGM) technology offers an efficient approach to detect large-scale genomic lesions. Here, we introduce OMKar, a computational method that generates virtual karyotypes from OGM data...
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