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Publication Details
AFRICAN RESEARCH NEXUS
SHINING A SPOTLIGHT ON AFRICAN RESEARCH
biochemistry, genetics and molecular biology
Effects of cytosine methylation on transcription factor binding sites
BMC Genomics, Volume 15, No. 1, Article 119, Year 2014
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Description
Background: DNA methylation in promoters is closely linked to downstream gene repression. However, whether DNA methylation is a cause or a consequence of gene repression remains an open question. If it is a cause, then DNA methylation may affect the affinity of transcription factors (TFs) for their binding sites (TFBSs). If it is a consequence, then gene repression caused by chromatin modification may be stabilized by DNA methylation. Until now, these two possibilities have been supported only by non-systematic evidence and they have not been tested on a wide range of TFs. An average promoter methylation is usually used in studies, whereas recent results suggested that methylation of individual cytosines can also be important.Results: We found that the methylation profiles of 16.6% of cytosines and the expression profiles of neighboring transcriptional start sites (TSSs) were significantly negatively correlated. We called the CpGs corresponding to such cytosines " traffic lights" We observed a strong selection against CpG " traffic lights" within TFBSs. The negative selection was stronger for transcriptional repressors as compared with transcriptional activators or multifunctional TFs as well as for core TFBS positions as compared with flanking TFBS positions.Conclusions: Our results indicate that direct and selective methylation of certain TFBS that prevents TF binding is restricted to special cases and cannot be considered as a general regulatory mechanism of transcription. © 2013 Medvedeva et al.; licensee BioMed Central Ltd.
Authors & Co-Authors
Medvedeva, Yulia A.
Saudi Arabia, Thuwal
King Abdullah University of Science and Technology
Khamis, Abdullah M.
Saudi Arabia, Thuwal
King Abdullah University of Science and Technology
Kulakovskiy, Ivan V.
Russian Federation, Moscow
Engelhardt Institute of Molecular Biology, Russian Academy of Sciences
Russian Federation, Moscow
Vavilov Institute of General Genetics, Russian Academy of Sciences
Ba-Alawi, Wail
Saudi Arabia, Thuwal
King Abdullah University of Science and Technology
Bhuyan, Md Shariful I.
Saudi Arabia, Thuwal
King Abdullah University of Science and Technology
Kawaji, Hideya
Japan, Wako
Riken
Lassmann, Timo
Japan, Wako
Riken
Harbers, Matthias
Japan, Wako
Riken
Forrest, Alistair R.R.
Japan, Wako
Riken
Bajic, Vladimir B.
Saudi Arabia, Thuwal
King Abdullah University of Science and Technology
Statistics
Citations: 225
Authors: 10
Affiliations: 4
Identifiers
Doi:
10.1186/1471-2164-15-119
e-ISSN:
14712164
Research Areas
Genetics And Genomics