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Research: Cellular plasticity balances the metabolic and proliferation dynamics of a regenerating liver
- Ullas V. Chembazhi,
- Sushant Bangru,
- Mikel Hernaez,
- and Auinash Kalsotra
Genome Res. April 2021 31: 576-591; Published in Advance March 1, 2021, doi:10.1101/gr.267013.120
..., cellular proliferation, or both to restore normal liver function (Miyaoka et al. 2012). Consequently, in order to stimulate cell division and growth, the regenerating hepatocytes undergo global alterations in gene expression through dynamic changes in mRNA abundance, splicing, and translation (Bangru et al...
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Research: De novo transcriptome assembly of mouse male germ cells reveals novel genes, stage-specific bidirectional promoter activity, and noncoding RNA expression
- Mark E. Gill,
- Alexia Rohmer,
- Serap Erkek-Ozhan,
- Ching-Yeu Liang,
- Sunwoo Chun,
- Evgeniy A. Ozonov,
- and Antoine H.F.M. Peters
Genome Res. December 2023 33: 2060-2078; Published in Advance December 21, 2023, doi:10.1101/gr.278060.123
...).When we compared levels of sense and antisense RNA driven from the same promoters in spermatogenic cells and liver, we found patterns that differ between tissues (Fig. 6D). As expected (given the nature of anchor point selection), H3K4me3 levels are high in all promoters examined. As was seen looking only...
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Research: Human MAF1 targets and represses active RNA polymerase III genes by preventing recruitment rather than inducing long-term transcriptional arrest
- Andrea Orioli,
- Viviane Praz,
- Philippe Lhôte,
- and Nouria Hernandez
Genome Res. May 2016 26: 624-635; Published in Advance March 3, 2016, doi:10.1101/gr.201400.115
...III gene stability sheet in Supplemental Table S2), which we therefore refer to as “stable” in terms of Pol III occupancy after serum starvation (Fig. 1E,F, small blue dots). These genes included representatives of most tRNA isotypes and type III promoter genes Genomic regulation of RNA polymerase III...
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Research: Diurnal regulation of RNA polymerase III transcription is under the control of both the feeding–fasting response and the circadian clock
- François Mange,
- Viviane Praz,
- Eugenia Migliavacca,
- Ian M. Willis,
- Frédéric Schütz,
- Nouria Hernandez,
- and the CycliX Consortium
Genome Res. June 2017 27: 973-984; Published in Advance March 24, 2017, doi:10.1101/gr.217521.116
..., 1015 Lausanne, Switzerland; 3Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, USA; 4Bioinformatics Core Facility, Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland RNA polymerase III (Pol III) synthesizes short noncoding RNAs, many of which...
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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
...study detected occupancy by RNA Polymerase III (Pol III) for only 224 of 417 high-confidence tRNA genes in human liver, with other mammals showing similar patterns (Kutter et al. 2011).tRNA gene expression may coevolve with phenotypic differences between species. Data from previous studies suggest...
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Resource: A genome-wide interactome of DNA-associated proteins in the human liver
- Ryne C. Ramaker,
- Daniel Savic,
- Andrew A. Hardigan,
- Kimberly Newberry,
- Gregory M. Cooper,
- Richard M. Myers,
- and Sara J. Cooper
Genome Res. November 2017 27: 1950-1960; Published in Advance October 11, 2017, doi:10.1101/gr.222083.117
...IP-seq-grade antibodies and their expression levels in the liver, ultimately assaying 17 sequence-specific TFs, two DAPs involved in maintaining chromatin structure, CTCF and RAD21, and RNA polymerase II (POLR2A), which is directly involved in transcription. ChIP-seq experiments were conducted in accordance with ENCODE...
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Research: RNA components of the spliceosome regulate tissue- and cancer-specific alternative splicing
- Heidi Dvinge,
- Jamie Guenthoer,
- Peggy L. Porter,
- and Robert K. Bradley
Genome Res. October 2019 29: 1591-1604; Published in Advance August 21, 2019, doi:10.1101/gr.246678.118
...increase in intron retention (y-axis) following KD of U1 (left) or U4 (right) snRNA. Circle size is proportional to the number of genes for each (x,y) combination. (F) PCR of select splicing events: multiple adjacent cassette exons (beclin 1, BECN1), a combination of a cassette exon and alternative 5...
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Research: Dynamic shifts in occupancy by TAL1 are guided by GATA factors and drive large-scale reprogramming of gene expression during hematopoiesis
- Weisheng Wu,
- Christapher S. Morrissey,
- Cheryl A. Keller,
- Tejaswini Mishra,
- Maxim Pimkin,
- Gerd A. Blobel,
- Mitchell J. Weiss,
- and Ross C. Hardison
Genome Res. December 2014 24: 1945-1962; Published in Advance October 15, 2014, doi:10.1101/gr.164830.113
..., at multiple stages of hematopoietic differentiation. We combined ChIP-seq and RNA-seq data in six mouse cell types representing a progression from multilineage precursors to differentiated erythroblasts and megakaryocytes. We found that sites of occupancy shift dramatically during commitment to the erythroid...
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Research: Locus co-occupancy, nucleosome positioning, and H3K4me1 regulate the functionality of FOXA2-, HNF4A-, and PDX1-bound loci in islets and liver
- Brad G. Hoffman,
- Gordon Robertson,
- Bogard Zavaglia,
- Mike Beach,
- Rebecca Cullum,
- Sam Lee,
- Galina Soukhatcheva,
- Leping Li,
- Elizabeth D. Wederell,
- Nina Thiessen,
- Mikhail Bilenky,
- Timothee Cezard,
- Angela Tam,
- Baljit Kamoh,
- Inanc Birol,
- Derek Dai,
- YongJun Zhao,
- Martin Hirst,
- C. Bruce Verchere,
- Cheryl D. Helgason,
- Marco A. Marra,
- Steven J.M. Jones,
- and Pamela A. Hoodless
Genome Res. August 2010 20: 1037-1051; Published in Advance June 15, 2010, doi:10.1101/gr.104356.109
...available from adult-specific knockout models of Pdx1, we suppressed Pdx1 using siRNAs in islets and used Tag-seq to identify genes significantly altered by Pdx1 suppression as compared to islets treated with siRNAs targeting Ppib (negative control).We identified 409 RefSeq genes up-regulated (P < 0...
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Research: Polycomb misregulation in enterocytes drives tissue decline in the aging Drosophila intestine
- Sarah M. Leichter,
- Kami Ahmad,
- and Steven Henikoff
Genome Res. January 2026 36: 102-114; Published in Advance November 17, 2025, doi:10.1101/gr.281058.125
...the genes that lose H3K27me3 signal in both ISC/EBs and enteroendocrine cells, GO analysis revealed enrichment for transcriptional regulators and RNA polymerase II (RNAPII)–associated functions (Supplemental Fig. S3A,B; Supplemental Tables S15, S16). This included derepression of multiple transcription...
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