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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
...@tamu.edu, jje@uci.eduAbstractMany essential functions of organisms are encoded in highly repetitive genomic regions, including histones involved in DNA packaging, centromeres that are core components of chromosome segregation, ribosomal RNA comprising the protein translation machinery, telomeres that ensure...
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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
...and structurally variable regions in the , shaped by a complex dynamics of host-pathogen coevolution (for review, see Radwan et al. 2020). Beyond immunological significance, the MHC has thus become a prime model in evolutionary and comparative genomics, offering insights into birth-and-death processes, concerted...
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Method: Accurate assembly of circular RNAs with TERRACE
- Tasfia Zahin,
- Qian Shi,
- Xiaofei Carl Zang,
- and Mingfu Shao
Genome Res. September 2024 34: 1365-1370; Published in Advance July 26, 2024, doi:10.1101/gr.279106.124
...-end total RNA-seq data. TERRACE uses the splice graph as the underlying data structure that organizes the splicing and coverage information. We transform the problem of assembling circRNAs into finding paths that “bridge” the three fragments in the splice graph induced by back-spliced reads. We adopt...
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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
...editing efficiency, we amplified genomic DNA from puromycin-selected, doubly transfected C1 cells using primers targeting regions surrounding sites recognized by sgRNAs in RE1, -2, or -3 (Supplemental Fig. S49A). PCR products were analyzed by gel electrophoresis, purified, and sequenced (Supplemental Fig...
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Resource: CGC1, a new reference genome for Caenorhabditis elegans
- Kazuki Ichikawa,
- Massa J. Shoura,
- Karen L. Artiles,
- Dae-Eun Jeong,
- Chie Owa,
- Haruka Kobayashi,
- Yoshihiko Suzuki,
- Manami Kanamori,
- Yu Toyoshima,
- Yuichi Iino,
- Ann E. Rougvie,
- Lamia Wahba,
- Andrew Z. Fire,
- Erich M. Schwarz,
- and Shinichi Morishita
Genome Res. August 2025 35: 1902-1918; Published in Advance July 15, 2025, doi:10.1101/gr.280274.124
...derivative of the N2 strain. We use improved long-read sequencing and manual assembly of 43 recalcitrant genomic regions to overcome deficiencies of prior N2 and VC2010 assemblies and to assemble tandem repeat loci, including a 772 kb sequence for the 45S rRNA genes. Although many differences from earlier...
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Mini-Review: Evolution of genome-wide methylation profiling technologies
- Carolina Montano and
- Winston Timp
Genome Res. April 2025 35: 572-582; doi:10.1101/gr.278407.123
...opportunities to uncover novel genomic and epigenomic mechanisms implicated in disease. Sequencing reads generated by LRS not only detect single nucleotide variations (SNVs) and structural variations (SVs) but also probe previously uncharacterized repetitive regions and regions with atypical GC content...
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Research: Genome-wide nucleosome and transcription factor responses to genetic perturbations reveal chromatin-mediated mechanisms of transcriptional regulation
- Kevin Moyung,
- Yulong Li,
- Heather K. MacAlpine,
- Alexander J. Hartemink,
- and David M. MacAlpine
Genome Res. January 2026 36: 115-128; Published in Advance December 9, 2025, doi:10.1101/gr.279637.124
...typically exhibit promoter regions in which nucleosomes have been evicted or shifted out to allow TFs to bind, as well as gene bodies in which nucleosomes have been disrupted by the passage of RNA polymerase (Jiang and Pugh 2009).We analyzed the features of chromatin structure that differed among...
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Mini-Review: The paradox of R-loops: guardians of the genome or drivers of disease?
- Shachinthaka D. Dissanayaka Mudiyanselage,
- Phillip Wulfridge,
- and Kavitha Sarma
Genome Res. September 2025 35: 1919-1928; Published in Advance August 6, 2025, doi:10.1101/gr.278992.124
.... Schematic overviews of key methodologies used for mapping R-loops. (A) In DRIP, fragmented genomic DNA is incubated with the S9.6 antibody to immunoprecipitate DNA–RNA hybrids for sequencing. (B) bisDRIP combines DRIP with nondenaturing bisulfite treatment to selectively deaminate ssDNA regions and convert...
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Resource: Building better genome annotations across the tree of life
- Adam H. Freedman and
- Timothy B. Sackton
Genome Res. May 2025 35: 1261-1276; Published in Advance April 15, 2025, doi:10.1101/gr.280377.124
...that could be made and prevented the framing of research findings in a genomic context. Although the advent of RNA-seq inched nonmodel organism research closer to understanding patterns at functional loci, de novo assembled transcriptomes presented novel analytical challenges and potential distortions...
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Method: KAS-ATAC reveals the genome-wide single-stranded accessible chromatin landscape of the human genome
- Samuel H. Kim,
- Georgi K. Marinov,
- and William J. Greenleaf
Genome Res. January 2025 35: 124-134; Published in Advance November 21, 2024, doi:10.1101/gr.279621.124
...of nascent RNA identifies a unified architecture of initiation regions at mammalian promoters and enhancers. Nat Genet 46: 1311–1320. doi:10.1038/ng.3142 ↵Crawford GE, Holt IE, Whittle J, Webb BD, Tai D, Davis S, Margulies EH, Chen Y, Bernat JA, Ginsburg D, et al. 2006. Genome-wide mapping of DNase...

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