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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: Long-read genome assembly of the insect model organism Tribolium castaneum reveals spread of satellite DNA in gene-rich regions by recurrent burst events
- Marin Volarić,
- Evelin Despot-Slade,
- Damira Veseljak,
- Brankica Mravinac,
- and Nevenka Meštrović
Genome Res. November 2024 34: 1878-1894; Published in Advance October 22, 2024, doi:10.1101/gr.279225.124
...that the (peri)centromeric TCAST satDNAs account for only 3.6 Mb, it is evident that the TcasONT assembly has an increase of 22.6 Mb in TRs outside of (peri)centromeric regions, which mainly include an increase in “classical” satDNAs with >50-bp-long monomer units.Characterization of Cast1–Cast9 satDNAs...
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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: Active retrotransposons help maintain pericentromeric heterochromatin required for faithful cell division
- Yajing Hao,
- Dongpeng Wang,
- Shuheng Wu,
- Xiao Li,
- Changwei Shao,
- Peng Zhang,
- Jia-Yu Chen,
- Do-Hwan Lim,
- Xiang-Dong Fu,
- Runsheng Chen,
- and Shunmin He
Genome Res. November 2020 30: 1570-1582; Published in Advance October 15, 2020, doi:10.1101/gr.256131.119
...showing a high percentage (65%–75%) of RNA reads mapped to repeat-derived transcripts, but a much smaller fraction (10%–20%) of DNA reads assigned to repeat-rich genomic loci (Supplemental Fig. S1B). To fully utilize these multimapped reads, we took a previously established ShortStack strategy to make...
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Research: Extreme genome scrambling in marine planktonic Oikopleura dioica cryptic species
- Charles Plessy,
- Michael J. Mansfield,
- Aleksandra Bliznina,
- Aki Masunaga,
- Charlotte West,
- Yongkai Tan,
- Andrew W. Liu,
- Jan Grašič,
- María Sara del Río Pisula,
- Gaspar Sánchez-Serna,
- Marc Fabrega-Torrus,
- Alfonso Ferrández-Roldán,
- Vittoria Roncalli,
- Pavla Navratilova,
- Eric M. Thompson,
- Takeshi Onuma,
- Hiroki Nishida,
- Cristian Cañestro,
- and Nicholas M. Luscombe
Genome Res. March 2024 34: 426-440; Published in Advance April 15, 2024, doi:10.1101/gr.278295.123
...pseudoautosomal region (PAR) connected to sex-specific regions by a ribosomal DNA locus (Denoeud et al. 2010; Bliznina et al. 2021). The Y-specific region is repeat-rich and gene-poor and differs from all other genomic regions. Chromosome contact analysis of O. dioica suggests that there is relatively little...
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Research: Whole-genome long-read sequencing downsampling and its effect on variant-calling precision and recall
- William T. Harvey,
- Peter Ebert,
- Jana Ebler,
- Peter A. Audano,
- Katherine M. Munson,
- Kendra Hoekzema,
- David Porubsky,
- Christine R. Beck,
- Tobias Marschall,
- Kiran Garimella,
- and Evan E. Eichler
Genome Res. December 2023 33: 2029-2040; Published in Advance December 7, 2023, doi:10.1101/gr.278070.123
...). These nonrandom error profiles impact precision and recall, especially for indel variant calls. When comparing the difference between all indel calls annotated with and without homopolymers, ONT call sets display a large difference between homopolymer and non-homopolymer DNA sequence precision and recall...
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Research: Evolutionary expansion of DNA hypomethylation in the mammalian germline genome
- Jianghan Qu,
- Emily Hodges,
- Antoine Molaro,
- Pascal Gagneux,
- Matthew D. Dean,
- Gregory J. Hannon,
- and Andrew D. Smith
Genome Res. February 2018 28: 145-158; Published in Advance December 19, 2017, doi:10.1101/gr.225896.117
...Chase, Maryland 20815, USA; 7Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, United Kingdom; 8The New York Genome Center, New York, New York 10013, USA Corresponding author: andrewds@usc.eduAbstractDNA methylation in the germline is among the most...
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Research: The aberrant epigenome of DNMT3B-mutated ICF1 patient iPSCs is amenable to correction, with the exception of a subset of regions with H3K4me3- and/or CTCF-based epigenetic memory
- Varsha Poondi Krishnan,
- Barbara Morone,
- Shir Toubiana,
- Monika Krzak,
- Salvatore Fioriniello,
- Floriana Della Ragione,
- Maria Strazzullo,
- Claudia Angelini,
- Sara Selig,
- and Maria R. Matarazzo
Genome Res. February 2023 33: 169-183; Published in Advance February 24, 2023, doi:10.1101/gr.276986.122
...syndrome, highlighting the complex genetic heterogeneity of the disease (de Greef et al. 2011; Thijssen et al. 2015). In ICF1 patients, DNA hypomethylation is apparent at specific heterochromatic regions, including the pericentromeric and subtelomeric repeats (Jeanpierre et al. 1993; Yehezkel et al. 2008...
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Research: A genome-wide transcriptome and translatome analysis of Arabidopsis transposons identifies a unique and conserved genome expression strategy for Ty1/Copia retroelements
- Stefan Oberlin,
- Alexis Sarazin,
- Clément Chevalier,
- Olivier Voinnet,
- and Arturo Marí-Ordóñez
Genome Res. September 2017 27: 1549-1562; Published in Advance August 7, 2017, doi:10.1101/gr.220723.117
...domain. ACTIN 2 (ACT2) PCR uses primers flanking an intron to amplify a longer PCR product corresponding to the genomic DNA (gDNA) and a shorter cDNA form. It serves as a loading control and validates the absence of genomic DNA contamination. (C) Schematic representation of the region surrounding the EVD...
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Method: Characterizing polymorphic inversions in human genomes by single-cell sequencing
- Ashley D. Sanders,
- Mark Hills,
- David Porubský,
- Victor Guryev,
- Ester Falconer,
- and Peter M. Lansdorp
Genome Res. November 2016 26: 1575-1587; Published in Advance July 29, 2016, doi:10.1101/gr.201160.115
...in the Watson-Crick state along the DNA strand of a chromosome (Fig. 1B). By sequencing only template strands, inversions are visualized as genomic regions where sequence reads of the inverted DNA segment map to the complementary DNA strandwith respect to the surrounding sequence. To survey inversions...

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