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Research: Transposon wave remodeled the epigenomic landscape in the rapid evolution of X-Chromosome dosage compensation
- David C.H. Metzger,
- Imogen Porter,
- Brendan Mobley,
- Benjamin A. Sandkam,
- Lydia J.M. Fong,
- Andrew P. Anderson,
- and Judith E. Mank
Genome Res. November 2023 33: 1917-1931; Published in Advance November 21, 2023, doi:10.1101/gr.278127.123
...the . CpG loci tend to be found in dense clusters in gene promoters called CpG islands (CGIs), and differential methylation of these CGIs plays an important role in gene regulation (Schmitz et al. 2019). Although this relationship between CGI methylation and gene expression regulation is thought...
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Research: Revisiting chromatin packaging in mouse sperm
- Qiangzong Yin,
- Chih-Hsiang Yang,
- Olga S. Strelkova,
- Jingyi Wu,
- Yu Sun,
- Sneha Gopalan,
- Liyan Yang,
- Job Dekker,
- Thomas G. Fazzio,
- Xin Zhiguo Li,
- Johan Gibcus,
- and Oliver J. Rando
Genome Res. December 2023 33: 2079-2093; Published in Advance December 21, 2023, doi:10.1101/gr.277845.123
...-Toneu and Peters 2023). A number of studies have mapped the locations of retained nucleosomes, with the majority of reports in humans and mice finding nucleosomes enriched at CpG island regulatory elements associated with key developmental genes (Arpanahi et al. 2009; Hammoud et al. 2009; Brykczynska et al. 2010...
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Resource: Comparing genomic and epigenomic features across species using the WashU Comparative Epigenome Browser
- Xiaoyu Zhuo,
- Silas Hsu,
- Deepak Purushotham,
- Prashant Kumar Kuntala,
- Jessica K. Harrison,
- Alan Y. Du,
- Samuel Chen,
- Daofeng Li,
- and Ting Wang
Genome Res. May 2023 33: 824-835; Published in Advance May 8, 2023, doi:10.1101/gr.277550.122
...of million years of independent evolution, recapitulating the discovery made by Zhang et al. (2016). Even conserved CpG islands between these two species are sparse. However, except for a few species-specific transposable elements, the displayed regions are hypomethylated, with an average methylation of 0...
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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
...such as horses (Haase et al. 2007), cattle (Durkin et al. 2012; Küttel et al. 2019; Artesi et al. 2020) and pigs (Rubin et al. 2012; Fontanesi 2022).We also observe that the colored-head associated “deletion” allele (with respect to the Hereford-based ARS-UCD1.2 reference) is extremely common and therefore most...
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Research: Somatic retrotransposition in the developing rhesus macaque brain
- Victor Billon,
- Francisco J. Sanchez-Luque,
- Jay Rasmussen,
- Gabriela O. Bodea,
- Daniel J. Gerhardt,
- Patricia Gerdes,
- Seth W. Cheetham,
- Stephanie N. Schauer,
- Prabha Ajjikuttira,
- Thomas J. Meyer,
- Cora E. Layman,
- Kimberly A. Nevonen,
- Natasha Jansz,
- Jose L. Garcia-Perez,
- Sandra R. Richardson,
- Adam D. Ewing,
- Lucia Carbone,
- and Geoffrey J. Faulkner
Genome Res. July 2022 32: 1298-1314; Published in Advance June 21, 2022, doi:10.1101/gr.276451.121
...displaying CpG dinucleotides (orange lines) forming a CpG island (pink bar). The positions of primers used to assess L1RSPRDM4 methylation via locus-specific bisulfite sequencing in panel C are shown. The second panel displays animal ON22213 ONT read alignments, with unmethylated CpGs colored in blue...
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Method: Predicting transfer RNA gene activity from sequence and genome context
- Bryan P. Thornlow,
- Joel Armstrong,
- Andrew D. Holmes,
- Jonathan M. Howard,
- Russell B. Corbett-Detig,
- and Todd M. Lowe
Genome Res. January 2020 30: 85-94; Published in Advance December 19, 2019, doi:10.1101/gr.256164.119
...islands scores as the observed frequency of CpG dinucleotides compared to their expected frequency given the G + C content of a region. We found that these scores, when calculated for the 350 bases upstream of each gene, are significantly correlated with active tRNA genes (Spearman's rank correlation, P...
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Resource: Comprehensive analyses of 723 transcriptomes enhance genetic and biological interpretations for complex traits in cattle
- Lingzhao Fang,
- Wentao Cai,
- Shuli Liu,
- Oriol Canela-Xandri,
- Yahui Gao,
- Jicai Jiang,
- Konrad Rawlik,
- Bingjie Li,
- Steven G. Schroeder,
- Benjamin D. Rosen,
- Cong-jun Li,
- Tad S. Sonstegard,
- Leeson J. Alexander,
- Curtis P. Van Tassell,
- Paul M. VanRaden,
- John B. Cole,
- Ying Yu,
- Shengli Zhang,
- Albert Tenesa,
- Li Ma,
- and George E. Liu
Genome Res. May 2020 30: 790-801; Published in Advance May 18, 2020, doi:10.1101/gr.250704.119
...Bismark v0.19.0 (Krueger and Andrews 2011). We only kept CpG sites with at least fivefold coverage for subsequent analyses. We employed an entropy-based framework to determine tissue-specific DNA methylation regions, as implemented in the SMART2 software (Liu et al. 2015). We only considered tissue...
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Research: Derepression of Polycomb targets during pancreatic organogenesis allows insulin-producing beta-cells to adopt a neural gene activity program
- Joris van Arensbergen,
- Javier García-Hurtado,
- Ignasi Moran,
- Miguel Angel Maestro,
- Xiaobo Xu,
- Mark Van de Casteele,
- Anouchka L. Skoudy,
- Matteo Palassini,
- Harry Heimberg,
- and Jorge Ferrer
Genome Res. June 2010 20: 722-732; Published in Advance April 15, 2010, doi:10.1101/gr.101709.109
...Lohuizen 2008; Schwartz and Pirrotta 2008). Large-scale studies revealed that PcG-dependent H3K27 methylation is not a universal mechanism for the repression of all inactive genes, but instead represses a restricted subset of genes, typically CpG island genes encoding for developmental regulators (Boyer et...
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Research: Evolutionary conservation of the eumetazoan gene regulatory landscape
- Michaela Schwaiger,
- Anna Schönauer,
- André F. Rendeiro,
- Carina Pribitzer,
- Alexandra Schauer,
- Anna F. Gilles,
- Johannes B. Schinko,
- Eduard Renfer,
- David Fredman,
- and Ulrich Technau
Genome Res. April 2014 24: 639-650; Published in Advance March 18, 2014, doi:10.1101/gr.162529.113
...the function of these histone modifications at regulatory elements is still unclear (Calo and Wysocka 2013), it suggests conserved targeting mechanisms of the histone modifying enzymes to chromatin. Studies in mammalian cells have shown that H3K4me3 at CpG islands inhibits the methylation of CpGs (Ooi et al...
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Research: Long terminal repeats power evolution of genes and gene expression programs in mammalian oocytes and zygotes
- Vedran Franke,
- Sravya Ganesh,
- Rosa Karlic,
- Radek Malik,
- Josef Pasulka,
- Filip Horvat,
- Maja Kuzman,
- Helena Fulka,
- Marketa Cernohorska,
- Jana Urbanova,
- Eliska Svobodova,
- Jun Ma,
- Yutaka Suzuki,
- Fugaku Aoki,
- Richard M. Schultz,
- Kristian Vlahovicek,
- and Petr Svoboda
Genome Res. August 2017 27: 1384-1394; Published in Advance May 18, 2017, doi:10.1101/gr.216150.116
...MLT1 and MLT2 represent the ancestral mammalian LTR subgroups, and theMT, ORR1, andMT2 subgroups radiated during rodent evolution (Fig. 1A–C; Supplemental Fig. S1B). Sequence analysis also showed that, except for MT2, ERVL LTRs are depleted of CpG dinucleotides, suggesting that MT2 LTRs evolved...
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