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RESEARCH: Homologs of the Yeast Longevity Gene LAG1 in Caenorhabditis elegans and Human
- James C. Jiang,
- Paul A. Kirchman,
- Marek Zagulski,
- Jay Hunt,
- and S. Michal Jazwinski
Genome Res. December 1, 1998 8: 1259-1272; doi:10.1101/gr.8.12.1259
...this worm’s adult life span ( Kenyon et al. 1993 ; Larsen et al. 1995 ). The daf-2 gene, at the head of this pathway, encodes an insulin receptor homolog ( Kimura et al. 1997 ), and its downstream effector daf-16 codes for a transcription factor of the forkhead family that includes HNF-3 ( Lin et al. 1997...
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Research: Damage-responsive elements in Drosophila regeneration
- Elena Vizcaya-Molina,
- Cecilia C. Klein,
- Florenci Serras,
- Rakesh K. Mishra,
- Roderic Guigó,
- and Montserrat Corominas
Genome Res. December 2018 28: 1852-1866; Published in Advance November 20, 2018, doi:10.1101/gr.233098.117
...into the to induce changes in transcription and chromatin dynamics throughout the entire process. Recent studies in zebrafish have characterized cell-type–specific regulatory elements for heart regeneration (Kang et al. 2016; Goldman et al. 2017). Nevertheless, an integrated view of other regenerative systems...
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Resource: A ChIP-exo screen of 887 Protein Capture Reagents Program transcription factor antibodies in human cells
- William K.M. Lai,
- Luca Mariani,
- Gerson Rothschild,
- Edwin R. Smith,
- Bryan J. Venters,
- Thomas R. Blanda,
- Prashant K. Kuntala,
- Kylie Bocklund,
- Joshua Mairose,
- Sarah N. Dweikat,
- Katelyn Mistretta,
- Matthew J. Rossi,
- Daniela James,
- James T. Anderson,
- Sabrina K. Phanor,
- Wanwei Zhang,
- Zibo Zhao,
- Avani P. Shah,
- Katherine Novitzky,
- Eileen McAnarney,
- Michael-C. Keogh,
- Ali Shilatifard,
- Uttiya Basu,
- Martha L. Bulyk,
- and B. Franklin Pugh
Genome Res. September 2021 31: 1663-1679; Published in Advance August 23, 2021, doi:10.1101/gr.275472.121
...and proteins, protein binding microarray (PBM) experiments, and targeted in vivo delivery of effector molecules (Chames et al. 2009; Park 2009; Siggers et al. 2011a; Mahmood and Yang 2012; Engelen et al. 2015; Lin et al. 2015). One advantage of target-specific antibodies is their ability to recognize proteins...
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Research: Identification of a core TP53 transcriptional program with highly distributed tumor suppressive activity
- Zdenek Andrysik,
- Matthew D. Galbraith,
- Anna L. Guarnieri,
- Sara Zaccara,
- Kelly D. Sullivan,
- Ahwan Pandey,
- Morgan MacBeth,
- Alberto Inga,
- and Joaquín M. Espinosa
Genome Res. October 2017 27: 1645-1657; Published in Advance September 13, 2017, doi:10.1101/gr.220533.117
...–specific regulatory events acting subsequent to TP53 binding to chromatin. To confirm that these differenceswere not due to our choice of statistical and fold change cut-offs, we generated heat maps ranking each set of cell-type–specific ChIP peaks or genes according to the FDR-adjusted P-value, which showed...
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Method: High-throughput single-cell functional elucidation of neurodevelopmental disease–associated genes reveals convergent mechanisms altering neuronal differentiation
- Matthew A. Lalli,
- Denis Avey,
- Joseph D. Dougherty,
- Jeffrey Milbrandt,
- and Robi D. Mitra
Genome Res. September 2020 30: 1317-1331; Published in Advance September 4, 2020, doi:10.1101/gr.262295.120
...-cell transcriptional profiling in differentiating human neurons to rapidly assay the functions of multiple genes in a disease-relevant context, assess potentially convergent mechanisms, and prioritize genes for specific functional assays. For a set of 13 autism spectrum disorder (ASD)–associated genes, we show...
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Research: DNA methylation profiling in human B cells reveals immune regulatory elements and epigenetic plasticity at Alu elements during B-cell activation
- Anne Y. Lai,
- Deepak Mav,
- Ruchir Shah,
- Sara A. Grimm,
- Dhiral Phadke,
- Katerina Hatzi,
- Ari Melnick,
- Cissy Geigerman,
- Steve E. Sobol,
- David L. Jaye,
- and Paul A. Wade
Genome Res. December 2013 23: 2030-2041; Published in Advance September 6, 2013, doi:10.1101/gr.155473.113
...at several loss-of-methylation DMRs (Supplemental Fig. S3B). The relationship between DNA methylation dynamics and gene expression was further examined. Gene set enrichment analysis (GSEA) (Subramanian et al. 2005) revealed that genes with down-regulated transcription during the naive to GC or the naive...
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Research: A chromatin link to caste identity in the carpenter ant Camponotus floridanus
- Daniel F. Simola,
- Chaoyang Ye,
- Navdeep S. Mutti,
- Kelly Dolezal,
- Roberto Bonasio,
- Jürgen Liebig,
- Danny Reinberg,
- and Shelley L. Berger
Genome Res. March 2013 23: 486-496; Published in Advance December 3, 2012, doi:10.1101/gr.148361.112
...SE over genes. (TSS) Transcription start site; (Exon) first (1), internal (i ), and last (n) exons; (TTS) transcription termination site; (kb) kilobase. (C ) Visualization of the 351-dimensional ChIPseq data set summarized for 9861 protein-coding genes, grouped by k-means clustering into k = 4...
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Research: GC content, but not nucleosome positioning, directly contributes to intron splicing efficiency in Paramecium
- Stefano Gnan,
- Mélody Matelot,
- Marion Weiman,
- Olivier Arnaiz,
- Frédéric Guérin,
- Linda Sperling,
- Mireille Bétermier,
- Claude Thermes,
- Chun-Long Chen,
- and Sandra Duharcourt
Genome Res. April 2022 32: 699-709; Published in Advance March 9, 2022, doi:10.1101/gr.276125.121
..., and it is species and cell type specific (Allan et al. 2013; Beshnova et al. 2014). Genome-wide studies have shown that nucleosomes are preferentially positioned in exons compared with introns in diverse organisms, including Schizosaccharomyces pombe, Drosophila, worms, and humans (Andersson et al. 2009; Nahkuri et...
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Perspective: Epigenomics and the structure of the living genome
- Nir Friedman and
- Oliver J. Rando
Genome Res. October 2015 25: 1482-1490; doi:10.1101/gr.190165.115
...of combinatorial histone modifications on antibody and effector protein recognition. Curr Biol 21: 53–58. Gilbert N, Boyle S, Fiegler H, Woodfine K, Carter NP, Bickmore WA. 2004. Chromatin architecture of the human : Gene-rich domains are enriched in open chromatin fibers. Cell 118: 555–566. Gilchrist DA...
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