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Method: Simultaneous assessment of human genome and methylome data in a single experiment using limited deamination of methylated cytosine
- Bo Yan,
- Duan Wang,
- and Laurence Ettwiller
Genome Res. June 2024 34: 904-913; Published in Advance June 10, 2024, doi:10.1101/gr.278294.123
...represent about or less than the average size of a single CpG island (CGI), a resolution that is compatible with most epigenetic applications. Indeed, functional genomic regions ranging between a few hundred and a few thousand bases tend to be regionally methylated or unmethylated in concert (Chen et al...
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Method: Methyl-SNP-seq reveals dual readouts of methylome and variome at molecule resolution while enabling target enrichment
- Bo Yan,
- Duan Wang,
- Romualdas Vaisvila,
- Zhiyi Sun,
- and Laurence Ettwiller
Genome Res. November/December 2022 32: 2079-2091; Published in Advance November 4, 2022, doi:10.1101/gr.277080.122
...million deconvoluted reads from two replicates. Although the Twist exome panel is designed to capture the gene body rather than the promoter regions, we still found 11,783 CpG islands captured with coverage above 50. Like the whole- sequencing, the methylation quantification of these CpG islands...
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Research: Transcriptional alterations in glioma result primarily from DNA methylation–independent mechanisms
- Franck Court,
- Elisa Le Boiteux,
- Anne Fogli,
- Mélanie Müller-Barthélémy,
- Catherine Vaurs-Barrière,
- Emmanuel Chautard,
- Bruno Pereira,
- Julian Biau,
- Jean-Louis Kemeny,
- Toufic Khalil,
- Lucie Karayan-Tapon,
- Pierre Verrelle,
- and Philippe Arnaud
Genome Res. October 2019 29: 1605-1621; Published in Advance September 18, 2019, doi:10.1101/gr.249219.119
...of DNA methylation–dependent and –independent mechanisms to transcriptional alterations at CpG island/promoter-associated genes in cancer, we studied 70 samples of adult glioma, a widespread type of brain tumor, classified according to their isocitrate dehydrogenase (IDH1) mutation status. We found...
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Research: Characterization of human transcription factor function and patterns of gene regulation in HepG2 cells
- Belle A. Moyers,
- E. Christopher Partridge,
- Mark Mackiewicz,
- Michael J. Betti,
- Roshan Darji,
- Sarah K. Meadows,
- Kimberly M. Newberry,
- Laurel A. Brandsmeier,
- Barbara J. Wold,
- Eric M. Mendenhall,
- and Richard M. Myers
Genome Res. November 2023 33: 1879-1892; Published in Advance October 18, 2023, doi:10.1101/gr.278205.123
...accurate correlation between predictions and observation (Fig. 2A), comparable with neural network models based on large amounts of sequence data (Agarwal and Shendure 2020). Prediction accuracy was robust to promoter subtypes (CpG island [CGI] promoters and non-CGI promoters) and was applicable across...
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Research: Age-related epigenetic drift in the pathogenesis of MDS and AML
- Shinji Maegawa,
- Sheryl M. Gough,
- Naoko Watanabe-Okochi,
- Yue Lu,
- Nianxiang Zhang,
- Ryan J. Castoro,
- Marcos R.H. Estecio,
- Jaroslav Jelinek,
- Shoudan Liang,
- Toshio Kitamura,
- Peter D. Aplan,
- and Jean-Pierre J. Issa
Genome Res. April 2014 24: 580-591; Published in Advance January 10, 2014, doi:10.1101/gr.157529.113
...23: 8429–8439. Antequera F, Bird A. 1993. Number of CpG islands and genes in human and mouse. Proc Natl Acad Sci 90: 11995–11999. Baylin SB, Herman JG. 2000. DNA hypermethylation in tumorigenesis: Epigenetics joins genetics. Trends in Genet 16: 168–174. Baylin SB, Ohm JE. 2006. Epigenetic gene...
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Perspective: Decrypting noncoding RNA interactions, structures, and functional networks
- Muller Fabbri,
- Leonard Girnita,
- Gabriele Varani,
- and George A. Calin
Genome Res. September 2019 29: 1377-1388; Published in Advance August 21, 2019, doi:10.1101/gr.247239.118
...is still underexplored in the field of ncRNA interaction, is to what extent the stoichiometry affects the relationship between ncRNAs and their binding/interacting molecular partners (Thomson and Dinger 2016). Epigenetic modifications (such as promoter CpG island hypermethylation) of host genes for nc...
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Research: A widespread role of the motif environment in transcription factor binding across diverse protein families
- Iris Dror,
- Tamar Golan,
- Carmit Levy,
- Remo Rohs,
- and Yael Mandel-Gutfreund
Genome Res. September 2015 25: 1268-1280; Published in Advance July 9, 2015, doi:10.1101/gr.184671.114
...differences [−log (q-value) ≥ 1.3] for each position 300 bp upstream of and downstream from the coremotif. (F ) Heatmap representing the differences in propeller twist 300 bp upstream of and downstream from the coremotifs: Red indicates positions at which the propeller twist was lower in the boundmotifs; blue...
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Research: High-throughput functional analysis of lncRNA core promoters elucidates rules governing tissue specificity
- Kaia Mattioli,
- Pieter-Jan Volders,
- Chiara Gerhardinger,
- James C. Lee,
- Philipp G. Maass,
- Marta Melé,
- and John L. Rinn
Genome Res. March 2019 29: 344-355; Published in Advance January 25, 2019, doi:10.1101/gr.242222.118
...that is present endogenously.We next sought to determine whether differences in expression patterns between biotypes are associated with known core promoter elements. Core promoters are often classified into two types: ubiquitously expressed promoters (associated with CpG islands and a depletion of TATA box...
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Research: Drosophila poised enhancers are generated during tissue patterning with the help of repression
- Nina Koenecke,
- Jeff Johnston,
- Qiye He,
- Samuel Meier,
- and Julia Zeitlinger
Genome Res. January 2017 27: 64-74; Published in Advance November 14, 2016, doi:10.1101/gr.209486.116
...of the embryo induces expression of Twist (Twi), which together with Dl activates mesodermal target genes (Jiang et al. 1991; Ip et al. 1992). We therefore analyzed Dl and Twi occupancy in Tl10b embryos and calculated their enrichments at active MEs and DEEs, which are actively repressed or remain uninduced...
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Research: Global DNA hypomethylation coupled to repressive chromatin domain formation and gene silencing in breast cancer
- Gary C. Hon,
- R. David Hawkins,
- Otavia L. Caballero,
- Christine Lo,
- Ryan Lister,
- Mattia Pelizzola,
- Armand Valsesia,
- Zhen Ye,
- Samantha Kuan,
- Lee E. Edsall,
- Anamaria Aranha Camargo,
- Brian J. Stevenson,
- Joseph R. Ecker,
- Vineet Bafna,
- Robert L. Strausberg,
- Andrew J. Simpson,
- and Bing Ren
Genome Res. February 2012 22: 246-258; Published in Advance December 7, 2011, doi:10.1101/gr.125872.111
...such as the breast cancer susceptibility gene BRCA1 (Tapia et al. 2008) supports the notion that tumor suppressors are frequently inactivated by DNA methylation at CpG islands and promoters. Genome-scale methods including MeDIP-seq (Ruike et al. 2010) and CHARM (Irizarry et al. 2009) have confirmed global...

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