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Resource: Zebrafish transposable elements show extensive diversification in age, genomic distribution, and developmental expression
- Ni-Chen Chang,
- Quirze Rovira,
- Jonathan Wells,
- Cédric Feschotte,
- and Juan M. Vaquerizas
Genome Res. July 2022 32: 1408-1423; Published in Advance January 5, 2022, doi:10.1101/gr.275655.121
...TE classes. (A) DNA transposons, including rolling-circle elements (Helitrons), take up approximately four times more genomic space than retroelements and contain a greater number of distinct superfamilies. (B) Overall, there is a moderate correlation between the copy number of TE families...
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Research: Independent expansion, selection, and hypervariability of the TBC1D3 gene family in humans
- Xavi Guitart,
- David Porubsky,
- DongAhn Yoo,
- Max L. Dougherty,
- Philip C. Dishuck,
- Katherine M. Munson,
- Alexandra P. Lewis,
- Kendra Hoekzema,
- Jordan Knuth,
- Stephen Chang,
- Tomi Pastinen,
- and Evan E. Eichler
Genome Res. November 2024 34: 1798-1810; Published in Advance August 6, 2024, doi:10.1101/gr.279299.124
.... This sequence was enriched for both TBC1D3 and NPIPA1, using the hybridization capture protocol described by Dougherty et al. (2018), with probes provided in Supplemental Table S11. FLNC libraries were mapped to respective species libraries with minimap2 using the parameters -ax splice ‐‐sam...
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Research: Microbiota regulate intestinal epithelial gene expression by suppressing the transcription factor Hepatocyte nuclear factor 4 alpha
- James M. Davison,
- Colin R. Lickwar,
- Lingyun Song,
- Ghislain Breton,
- Gregory E. Crawford,
- and John F. Rawls
Genome Res. July 2017 27: 1195-1206; Published in Advance April 6, 2017, doi:10.1101/gr.220111.116
...(Fig. 2G). Interestingly, the top two diseases associated with this gene set were obesity-related traits and IBD (Fig. 2G; Supplemental Table S11). Based on these results, we hypothesized that Hnf4a DNA binding is lost upon microbial colonization within CRRs associated with microbiota-suppressed genes...
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Research: The role of transposon activity in shaping cis-regulatory element evolution after whole-genome duplication
- Øystein Monsen,
- Lars Grønvold,
- Alex Datsomor,
- Thomas Harvey,
- James Kijas,
- Alexander Suh,
- Torgeir R. Hvidsten,
- and Simen Rød Sandve
Genome Res. March 2025 35: 475-488; Published in Advance February 12, 2025, doi:10.1101/gr.278931.124
...default settings with the ssal_repeats_v5.1 library. RepeatMasker takes a library of TE consensus sequences and detects whole and fragmented parts of these consensuses across the using a BLAST-like algorithm. The output file contains the genomic coordinates of the annotation, as well as various quality...
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Method: Tissular chromatin-state cartography based on double-barcoded DNA arrays that capture unloaded PA-Tn5 transposase
- Maria Grazia Mendoza-Ferri,
- Gwendoline Lozachmeur,
- Maximilien Duvina,
- Laetitia Perret,
- Didier Merciris,
- Anne Gigout,
- and Marco Antonio Mendoza-Parra
Genome Res. July 2025 35: 1633-1645; Published in Advance May 13, 2025, doi:10.1101/gr.280305.124
...-barcoded spatial epigenomic technology. (A) DNA arrays are printed by depositing first probes in rows, followed by deposition of a second type of probes in columns. The first type of probe is composed of a T7 promoter (T7p) sequence, a unique molecular barcode associated to the row (BCr1, …BCri), and bridge...
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Research: Atypical epigenetic and small RNA control of degenerated transposons and their fragments in clonally reproducing Spirodela polyrhiza
- Rodolphe Dombey,
- Daniel Buendía-Ávila,
- Verónica Barragán-Borrero,
- Laura Diezma-Navas,
- Arturo Ponce-Mañe,
- José Mario Vargas-Guerrero,
- Rana Elias,
- and Arturo Marí-Ordóñez
Genome Res. March 2025 35: 522-544; Published in Advance March 4, 2025, doi:10.1101/gr.279532.124
...genetic composition of silencing pathways, sRNAs, and epigenetic modifications commonly associated with TE control in angiosperms.ResultsGenome sequencing of S. polyrhiza 9509 from the Landolt collectionThe s of several S. polyrhiza accessions (clones) have been sequenced (Wang et al. 2014; Michael et al...
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Research: Mutational scanning of CRX classifies clinical variants and reveals biochemical properties of the transcriptional effector domain
- James L. Shepherdson,
- David M. Granas,
- Jie Li,
- Zara Shariff,
- Stephen P. Plassmeyer,
- Alex S. Holehouse,
- Michael A. White,
- and Barak A. Cohen
Genome Res. October 2024 34: 1540-1552; Published in Advance September 25, 2024, doi:10.1101/gr.279415.124
.... A clonal cell line carrying a CRX-responsive fluorescent reporter and genomic landing pad (LP) was generated, and a library of CRX variants was integrated into the LP so that each cell expresses a single variant. Following fluorescence-activated cell sorting (FACS), sequencing was used to determine...
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Research: Spatiotemporal kinetics of CAF-1-dependent chromatin maturation ensures transcription fidelity during S-phase
- Boning Chen,
- Heather K. MacAlpine,
- Alexander J. Hartemink,
- and David M. MacAlpine
Genome Res. December 2023 33: 2108-2118; Published in Advance December 11, 2023, doi:10.1101/gr.278273.123
...U-labeled DNA fragments were biotinylated with click chemistry and enriched using streptavidin–biotin isolation before being subjected to paired-end sequencing. DNA fragments protected by the histone octamer should be ∼150 bp in length, whereas small DNA binding factors such as transcription factors...
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Research: Variation in histone configurations correlates with gene expression across nine inbred strains of mice
- Anna L Tyler,
- Catrina Spruce,
- Romy Kursawe,
- Annat Haber,
- Robyn L Ball,
- Wendy A Pitman,
- Alexander D Fine,
- Narayanan Raghupathy,
- Michael Walker,
- Vivek M Philip,
- Christopher L Baker,
- J. Matthew Mahoney,
- Gary A. Churchill,
- Jennifer J Trowbridge,
- Michael L Stitzel,
- Kenneth Paigen,
- Petko M Petkov,
- and Gregory W Carter
Genome Res. May 22, 2023 gr.277467.122; Published in Advance May 22, 2023, doi:10.1101/gr.277467.122
...genetic regulation of both modalities. This is seen as a87 clustering of individuals from the same strain in principal component plots of transcriptomic and88 epigenetic features (Fig. 1). Patterns of gene expression (Fig. 1A), DNA methylation (Fig. 1B)89 and individual histone modifications (Fig. 1C...
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Research: Single-cell multi-omics of human preimplantation embryos shows susceptibility to glucocorticoids
- Cheng Zhao,
- Savana Biondic,
- Katherine Vandal,
- Åsa K. Björklund,
- Michael Hagemann-Jensen,
- Theresa Maria Sommer,
- Jesica Canizo,
- Stephen Clark,
- Pascal Raymond,
- Daniel R. Zenklusen,
- Nicolas Rivron,
- Wolf Reik,
- and Sophie Petropoulos
Genome Res. September 2022 32: 1627-1641; Published in Advance August 10, 2022, doi:10.1101/gr.276665.122
...and glucocorticoid-exposed embryos. (A) Process flow diagram of single-cell sequencing data analysis on preimplantation embryos. Single cells were collected from in vitro cultured embryos on E7 (glucocorticoid-treated and control). Libraries were generated using scM&T-seq for the simultaneous measure...
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