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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
..., University of Cambridge, Cambridge CB3 0DH, United Kingdom Abstract Most vertebrate promoters lie in unmethylated CpG-dense islands, whereas methylation of the more sparsely distributed CpGs in the remainder of the genome is thought to contribute to transcriptional repression. Nonmethylated CG...
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Research: Comparative methylomics reveals gene-body H3K36me3 in Drosophila predicts DNA methylation and CpG landscapes in other invertebrates
- Lisa Nanty,
- Guillermo Carbajosa,
- Graham A. Heap,
- Francis Ratnieks,
- David A. van Heel,
- Thomas A. Down,
- and Vardhman K. Rakyan
Genome Res. November 2011 21: 1841-1850; Published in Advance September 22, 2011, doi:10.1101/gr.121640.111
...analysis of CpG dinucleotides in the human distinguishes two distinct classes of promoters. Proc Natl Acad Sci 103: 1412–1417. Suzuki MM, Kerr AR, De Sousa D, Bird A. 2007. CpGmethylation is targeted to transcription units in an invertebrate . Genome Res 17: 625– 631. Weber M, Hellmann I, Stadler MB, Ramos...
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Research: DNA methylation changes induced by long and short photoperiods in Nasonia
- Mirko Pegoraro,
- Akanksha Bafna,
- Nathaniel J. Davies,
- David M. Shuker,
- and Eran Tauber
Genome Res. February 2016 26: 203-210; Published in Advance December 15, 2015, doi:10.1101/gr.196204.115
...at an average depth of 95.72× for the SD sample and 88.97× for the LD sample. The LD reads covered 1,304,087 CpG sites (4.65% of all genomic CpGs), whereas the SD reads covered 1,385,067 CpG (4.94%). We detected 1618 and 2018 methyl CpGs in the LD and SD samples, respectively, using a 1% false discovery rate...
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Research: LSH and G9a/GLP complex are required for developmentally programmed DNA methylation
- Kevin Myant,
- Ausma Termanis,
- Arvind Y.M. Sundaram,
- Tristin Boe,
- Chao Li,
- Cara Merusi,
- Joe Burrage,
- Jose I. de Las Heras,
- and Irina Stancheva
Genome Res. January 2011 21: 83-94; Published in Advance December 13, 2010, doi:10.1101/gr.108498.110
...-rich sequences (CpG islands), and this modification contributes to stability, transcriptional silencing of genes and retrotransposons, regulation of genomic imprinting, and X chromosome inactivation in females (Bird 2002; Jaenisch and Bird 2003). Although DNA methylation is relatively stable and heritable...
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Research: Homotypic clusters of transcription factor binding sites are a key component of human promoters and enhancers
- Valer Gotea,
- Axel Visel,
- John M. Westlund,
- Marcelo A. Nobrega,
- Len A. Pennacchio,
- and Ivan Ovcharenko
Genome Res. May 2010 20: 565-577; Published in Advance April 2, 2010, doi:10.1101/gr.104471.109
...that promoter regions of many genes are GC-rich and enriched in CpG islands (CGIs) (Larsen et al. 1992). Indeed, we found that many HCTs are located in GC-rich regions, especially those of PWMs with abundant (>1000) HCTs (Fig. 3; Supplemental Table S2). These all have GC content higher than 60...
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RESOURCE: An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs)
- Vardhman K. Rakyan,
- Thomas A. Down,
- Natalie P. Thorne,
- Paul Flicek,
- Eugene Kulesha,
- Stefan Gräf,
- Eleni M. Tomazou,
- Liselotte Bäckdahl,
- Nathan Johnson,
- Marlis Herberth,
- Kevin L. Howe,
- David K. Jackson,
- Marcos M. Miretti,
- Heike Fiegler,
- John C. Marioni,
- Ewan Birney,
- Tim J.P. Hubbard,
- Nigel P. Carter,
- Simon Tavaré,
- and Stephan Beck
Genome Res. September 2008 18: 1518-1529; Published in Advance June 24, 2008, doi:10.1101/gr.077479.108
...CpG density, gene expression, transcription factor motifs, gene ontology, and correlation with other epigenetic marks such as histone modifications. DNA methylation is indispensable for function in mammals. It is the only known epigenetic modification of mammalian DNA and plays critical roles...
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Research: Ultra-long-range interactions between active regulatory elements
- Elias T. Friman,
- Ilya M. Flyamer,
- Davide Marenduzzo,
- Shelagh Boyle,
- and Wendy A. Bickmore
Genome Res. August 2023 33: 1269-1283; Published in Advance July 14, 2023, doi:10.1101/gr.277567.122
...) prompted us to test the relationship between CGIs and ULIs. This showed a correlation between interactions and the density of CpG dinucleotides at CGIs devoid of polycomb (Fig. 2A). Interaction strength at TSSs also scaled strongly with the level of transcription (Fig. 2B). Notably, TSSs in quartile 4...
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Method: Identification of the shortest species-specific oligonucleotide sequences
- Ioannis Mouratidis,
- Maxwell A. Konnaris,
- Nikol Chantzi,
- Candace S.Y. Chan,
- Michail Patsakis,
- Kimonas Provatas,
- Austin Montgomery,
- Fotis A. Baltoumas,
- Congzhou M. Sha,
- Manvita Mareboina,
- Georgios A. Pavlopoulos,
- Dionysios V. Chartoumpekis,
- and Ilias Georgakopoulos-Soares
Genome Res. February 2025 35: 279-295; Published in Advance January 2, 2025, doi:10.1101/gr.280070.124
...) Average number of GpC and CpG occurrences per prime. Error bars in D represent SD. (E) Number of quasi-primes detected in each reference .There are more omers than expected across s in each taxonomyIn a previous study, we demonstrated that the human exhibits a higher prevalence of omers than...
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Resource: Remodeling of epigenome and transcriptome landscapes with aging in mice reveals widespread induction of inflammatory responses
- Bérénice A. Benayoun,
- Elizabeth A. Pollina,
- Param Priya Singh,
- Salah Mahmoudi,
- Itamar Harel,
- Kerriann M. Casey,
- Ben W. Dulken,
- Anshul Kundaje,
- and Anne Brunet
Genome Res. April 2019 29: 697-709; Published in Advance March 11, 2019, doi:10.1101/gr.240093.118
...27me3, etc.) (Supplemental Table S2A; Shen et al. 2012; Yue et al. 2014), and features from the underlying DNA sequence (e.g., %CpG in promoter, etc.). The models were trained with sets of features that were either (1) “dynamic”—reflecting the age-related changes in the chromatin environment of genes...
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LETTER: Antisense Transcripts With FANTOM2 Clone Set and Their Implications for Gene Regulation
- Hidenori Kiyosawa,
- Itaru Yamanaka,
- Naoki Osato,
- Shinji Kondo,
- RIKEN GER Group,
- GSLMembers,
- and Yoshihide Hayashizaki
Genome Res. June 2003 13: 1324-1334; doi:10.1101/gr.982903
...is indicated by a green line only in a region of DNA that satisfies the criterion (2). Therefore, the green line represents the existence of a CpG island in the DNA region, because the region satisfies all three criteria explained above. Search for EST Sequences Homologous to Bidirectional Transcription Pairs...

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