CpG islands and the regulation of transcription.

By A. Deaton, A. Bird. Genes & Development, 2011

3,085 citations recorded by the source corpus.

Vertebrate CpG islands (CGIs) are short interspersed DNA sequences that deviate significantly from the average genomic pattern by being GC-rich, CpG-rich, and predominantly nonmethylated. Most, perhaps all, CGIs are sites of transcription initiation, including thousands that are remote from currently annotated promoters. Shared DNA sequence features adapt CGIs for promoter function by destabilizing nucleosomes and attracting proteins that create a transcriptionally permissive chromatin state. Silencing of CGI promoters is achieved through dense CpG methylation or polycomb recruitment, again using their distinctive DNA sequence composition. CGIs are therefore generically equipped to influence local chromatin structure and simplify regulation of gene activity.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/9bd17c83ab4488aa4e70fc86a6135d1cfe162662

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Citations in the corpus

• Reversing DNA Methylation: Mechanisms, Genomics, and Biological Functions (2014, neutral): “Oxidized Methylcytosines at Gene Promoters Approximately 70% of mammalian promoters are associated with short CpG-dense sequences (termed CpG islands [CGIs], on average 1 kilobase [kb] long) (Deaton and Bird, 2011).”
• Genome-wide prediction of cis-regulatory regions using supervised deep learning methods (2016, background): “This builds on the longrecognized capacity for the inclusion of CpG islands as features to improve promoter prediction [38].”
• Analysing and interpreting DNA methylation data (2012, background): “This range coincides with typical sizes of gene‑ regulatory regions, and it is widely believed that DMRs can control cell‑type‑specific transcriptional repression of an associated gene 1,3,88 .”
• methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles (2012, background): “DNA methylation is a critical epigenetic modification that guides development, cellular differentiation and the manifestation of some cancers [1,2].”
• Gene regulation by the act of long non-coding RNA transcription (2013, background): “Transcriptional interference acting by promoter DNA methylation In mammalian genomes DNA methylation is generally associated with silent CpG island promoters, but the majority of CpG island promoters remain methylation free independent of their expression status [67-69].”
• Differential DNA Methylation in Purified Human Blood Cells: Implications for Cell Lineage and Studies on Disease Susceptibility (2012, background): “Furthermore, recent findings in murine immune cells show that differential DNA methylation occurs primarily in CpG islands located inside gene bodies which are infrequently annotated with promoter CpG islands or CpG island shores [1].”
• DNA methylation dynamics during epigenetic reprogramming in the germline and preimplantation embryos (2014, background): “While ‘‘single’’ CpGs are generally hypermethylated (60%–90%, depending on cell type), CpG islands (CGIs; 500- to 2000-base-pair-long regions with increased CpG density) remain predominantly hypomethylated (Deaton and Bird 2011).”
• A double take on bivalent promoters. (2013, background): “CpG islands are a prominent feature of promoters in vertebrate genomes and are present at ;70% of all promoters (Saxonov et al. 2006; Deaton and Bird 2011).”
• Mapping and elucidating the function of modified bases in DNA (2017, background): “4 inactivation, genomic imprinting [G] and transposon silencing [G].(11,12,13,14)”
• DNA Demethylation Dynamics (2011, background): “…gene silencing that leads to genomic imprinting, X chromosome inactivation, suppression of transposable elements, and the establishment and maintenance of stable cellular identities (Bird, 2002; De Carvalho et al., 2010; Deaton and Bird, 2011; Goll and Bestor, 2005; Jaenisch and Bird, 2003).”
• Nutrition and epigenetics: An interplay of dietary methyl donors, one-carbon metabolism, and DNA methylation (2012, neutral): “The majority of unmethylated CpG sites occur within CpG islands, defined as discreet regions containing a preponderance of CpG content [11].”
• The interplay of histone modifications – writers that read (2015, neutral): “Notably, the distribution of H3K4me3 is highly coupled to the presence of CpG islands, regions of CpG-and GC-dense DNA that are predominately unmethylated and found at 50 – 70% of vertebrate promoters [24].”