A genome-wide analysis of CpG dinucleotides in the human genome distinguishes two distinct classes of promoters

By Serge Saxonov, P. Berg, Douglas L. Brutlag. Proceedings of the National Academy of Sciences of the United States of America, 2006

1,459 citations recorded by the source corpus.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/26a441f4c98f4ebb0cd28b1dc86532d24b178c6f

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In Molecular Biology

Citations in the corpus

Direct detection of DNA methylation during single-molecule, real-time sequencing (2010, background): “In vertebrates, mC usually occurs in C-G dinucleotides, which often cluster in regions called CpG islands that are at or near transcription start site”
DNA methylation and cancer. (2010, background): “According to the calculation of CpG prevalence, nearly 60% of human promoters are characterized by high-CpG content (Saxonov et al., 2006).”
Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiation. (2008, background): “Mammalian RNA polymerase II (RNAPII)-dependent promoters associated with CpG islands are typically non-tissue-specific and regulate housekeeping genes or genes with complex expression patterns, such as the developmental genes expressed during embryonic differentiation (Saxonov et al. 2006).”
The genomic landscape of the somatic linker histone subtypes H1.1 to H1.5 in human cells. (2013, background): “CpG Islands Are Depleted of Histone H1 Subtypes In human cells, 70% of promoters are associated with CpG islands and therefore can be classified according to their CG content (Saxonov et al., 2006).”
Histone modification levels are predictive for gene expression (2010, background): “as defined previously (31), with the promoters having a normalized CpG con-”
Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome (2007, background): “However, current estimates are mostly derived indirectly from sequence rather than actual measurement of DNA methylatio”
DNA methylation and healthy human aging (2015, background): “While this term was originally coined to describe a multivariate age predictor, it is clear that the phenomenon of the epigenetic clock is also reflected in studies that reported highly age-associated CpGs.”
Modeling gene expression using chromatin features in various cellular contexts (2012, positive): “Previous studies have shown that CpG-rich promoters are associated with ubiquitously expressed genes while CpG-poor (and often TATA-containing) promoters are associated with cell type-specific genes [27-29] and have different patterns of histone modifications [29].”
Dynamic changes in the human methylome during differentiation. (2010, background): “1985), which are found within the promoters of ;70% of human genes (Saxonov et al. 2006).”
A Novel CpG Island Set Identifies Tissue-Specific Methylation at Developmental Gene Loci (2008, neutral): “uncertainty concerning CGI identification [15].”
CpG islands – ‘A rough guide’ (2009, background): “These conspicuous unique sequences are approximately 1 kb in length and overlap the promoter regions of 60–70% of all human genes [4,6,8–10].”