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Research: Extreme HOT regions are CpG-dense promoters in C. elegans and humans
- Ron A.-J. Chen,
- Przemyslaw Stempor,
- Thomas A. Down,
- Eva Zeiser,
- Sky K. Feuer,
- and Julie Ahringer
Genome Res. July 2014 24: 1138-1146; Published in Advance March 20, 2014, doi:10.1101/gr.161992.113
...with nucleosome depletion Mammalian CpG-rich promoters show strong nucleosome depletion that appears at least partially independent of transcriptional Genome Research 1139 www..org HOT regions are CpG-dense promoters in C. elegans activity, suggesting that CpG density plays a role in promoter accessibility...
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Research: Polycomb repressive complex 1 shapes the nucleosome landscape but not accessibility at target genes
- Hamish W. King,
- Nadezda A. Fursova,
- Neil P. Blackledge,
- and Robert J. Klose
Genome Res. October 2018 28: 1494-1507; Published in Advance August 28, 2018, doi:10.1101/gr.237180.118
...at lysine 119 (H2AK119ub1), whereas PRC2 methylates histone H3 on lysine 27 (H3K27me3). In vertebrates, PRC1 and PRC2 are targeted by various mechanisms to gene promoters, particularly those associated with nonmethylated CpG islands (CGIs) (Bracken and Helin 2009; Simon and Kingston 2013; Blackledge et al...
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Method: Massively parallel cis-regulatory analysis in the mammalian central nervous system
- Susan Q. Shen,
- Connie A. Myers,
- Andrew E.O. Hughes,
- Leah C. Byrne,
- John G. Flannery,
- and Joseph C. Corbo
Genome Res. February 2016 26: 238-255; Published in Advance November 17, 2015, doi:10.1101/gr.193789.115
..., California 94720, USA Cis-regulatory elements (CREs, e.g., promoters and enhancers) regulate gene expression, and variants within CREs can modulate disease risk. Next-generation sequencing has enabled the rapid generation of genomic data that predict the locations of CREs, but a bottleneck lies...
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Research: DNase-seq predicts regions of rotational nucleosome stability across diverse human cell types
- Deborah R. Winter,
- Lingyun Song,
- Sayan Mukherjee,
- Terrence S. Furey,
- and Gregory E. Crawford
Genome Res. July 2013 23: 1118-1129; Published in Advance May 8, 2013, doi:10.1101/gr.150482.112
...levels of DARNS despite the fact that in aggregate the 10.4-bp period was still present (see Methods) (Supplemental Fig. S8A,C). Thus, our data were in agreement with the established profile of nucleosomes around genes. CpG islands, often found at gene promoters, occur in various sizes and have been...
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Research: CG dinucleotides enhance promoter activity independent of DNA methylation
- Dominik Hartl,
- Arnaud R. Krebs,
- Ralph S. Grand,
- Tuncay Baubec,
- Luke Isbel,
- Christiane Wirbelauer,
- Lukas Burger,
- and Dirk Schübeler
Genome Res. April 2019 29: 554-563; Published in Advance February 1, 2019, doi:10.1101/gr.241653.118
...: dirk@fmi.chAbstractMost mammalian RNA polymerase II initiation events occur at CpG islands, which are rich in CpGs and devoid of DNA methylation. Despite their relevance for gene regulation, it is unknown to what extent the CpG dinucleotide itself actually contributes to promoter activity. To address...
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Method: Simple and efficient profiling of transcription initiation and transcript levels with STRIPE-seq
- Robert A. Policastro,
- R. Taylor Raborn,
- Volker P. Brendel,
- and Gabriel E. Zentner
Genome Res. June 2020 30: 910-923; Published in Advance July 6, 2020, doi:10.1101/gr.261545.120
..., current protocols for -wide TSS profiling are laborious and/or expensive. We present Survey of TRanscription Initiation at Promoter Elements with high-throughput sequencing (STRIPE-seq), a simple, rapid, and cost-effective protocol for sequencing capped RNA 5′ ends from as little as 50 ng total RNA...
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Research: The chromatin environment shapes DNA replication origin organization and defines origin classes
- Christelle Cayrou,
- Benoit Ballester,
- Isabelle Peiffer,
- Romain Fenouil,
- Philippe Coulombe,
- Jean-Christophe Andrau,
- Jacques van Helden,
- and Marcel Méchali
Genome Res. December 2015 25: 1873-1885; Published in Advance November 11, 2015, doi:10.1101/gr.192799.115
...1992). Conversely, recent analyses revealed the presence of GC-rich elements in eukaryotic origins, such as CpG islands (CGI) (Delgado et al. 1998; Prioleau 2009; Cayrou et al. 2011; Costas et al. 2011) and an Origin G-rich Repeated Element (OGRE) that can form G4 (Cayrou et al. 2011, 2012a). G4were...
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Research: High-throughput functional comparison of promoter and enhancer activities
- Thomas A. Nguyen,
- Richard D. Jones,
- Andrew R. Snavely,
- Andreas R. Pfenning,
- Rory Kirchner,
- Martin Hemberg,
- and Jesse M. Gray
Genome Res. August 2016 26: 1023-1033; Published in Advance June 16, 2016, doi:10.1101/gr.204834.116
...atlas. Nature 507: 462–470. Fenouil R, Cauchy P, Koch F, Descostes N, Cabeza JZ, Innocenti C, Ferrier P, Spicuglia S, Gut M, Gut I, et al. 2012. CpG islands and GC content dictate nucleosome depletion in a transcription-independent manner at mammalian promoters. Genome Res 22: 2399–2408. Fisch TM...
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Research: Tandem repeat variation in human and great ape populations and its impact on gene expression divergence
- Tugce Bilgin Sonay,
- Tiago Carvalho,
- Mark D. Robinson,
- Maja P. Greminger,
- Michael Krützen,
- David Comas,
- Gareth Highnam,
- David Mittelman,
- Andrew Sharp,
- Tomàs Marques-Bonet,
- and Andreas Wagner
Genome Res. November 2015 25: 1591-1599; Published in Advance August 19, 2015, doi:10.1101/gr.190868.115
...organs) and lowly expressed genes (P < 10−129 in all organs). Second, as CpG islands and promoter GC content have gene regulatory roles through epigenetic mechanisms (Fenouil et al. 2012), we asked whether promoters with and without TRs differ in their CpG content. Although we found a small increase...
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Research: Enhancer RNA profiling predicts transcription factor activity
- Joseph G. Azofeifa,
- Mary A. Allen,
- Josephina R. Hendrix,
- Timothy Read,
- Jonathan D. Rubin,
- and Robin D. Dowell
Genome Res. March 2018 28: 334-344; Published in Advance February 15, 2018, doi:10.1101/gr.225755.117
...polymerase II (RNAP) to identify individual transcripts within nascent transcription data (Azofeifa and Dowell 2017). Although Tfit does not implicitly assume polymerase initiation will be bidirectional, we observed bidirectional transcription at both promoters and enhancers (Azofeifa and Dowell 2017...
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