Show simple item record

dc.contributor.authorMedvedeva, Yulia A
dc.contributor.authorKhamis, Abdullah M.
dc.contributor.authorKulakovskiy, Ivan V
dc.contributor.authorBa Alawi, Wail
dc.contributor.authorBhuyan, Md Shariful I
dc.contributor.authorKawaji, Hideya
dc.contributor.authorLassmann, Timo
dc.contributor.authorHarbers, Matthias
dc.contributor.authorForrest, Alistair RR
dc.contributor.authorBajic, Vladimir B.
dc.date.accessioned2014-08-27T09:42:01Z
dc.date.available2014-08-27T09:42:01Z
dc.date.issued2014-03-26
dc.identifier.citationMedvedeva YA, Khamis AM, Kulakovskiy IV, Ba-Alawi W, Bhuyan MSI, et al. (2014) Effects of cytosine methylation on transcription factor binding sites. BMC Genomics 15: 119. doi:10.1186/1471-2164-15-119.
dc.identifier.issn14712164
dc.identifier.pmid24669864
dc.identifier.doi10.1186/1471-2164-15-119
dc.identifier.urihttp://hdl.handle.net/10754/325243
dc.description.abstractBackground: 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.
dc.language.isoen
dc.publisherSpringer Nature
dc.rightsThis is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited.
dc.rights.urihttp://creativecommons.org/licenses/by/2.0
dc.subjectBioinformatics
dc.subjectCAGE
dc.subjectComputational biology
dc.subjectCpG " traffic lights"
dc.subjectDNA methylation
dc.subjectRRBS
dc.subjectTranscription factor binding sites
dc.subjectTranscriptional regulation
dc.subjectcytosine
dc.subjecttranscription factor
dc.subjectbinding site
dc.subjectcap analysis of gene expression
dc.subjectcontrolled study
dc.subjectcorrelation analysis
dc.subjectCpG island
dc.subjectdinucleotide repeat
dc.subjectgene expression
dc.subjectgene expression profiling
dc.subjecthuman cell
dc.subjectpromoter region
dc.subjectregulatory mechanism
dc.subjecttranscription initiation site
dc.subjecttranscription regulation
dc.titleEffects of cytosine methylation on transcription factor binding sites
dc.typeArticle
dc.contributor.departmentComputational Bioscience Research Center (CBRC)
dc.contributor.departmentComputer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division
dc.identifier.journalBMC Genomics
dc.identifier.pmcidPMC3986887
dc.eprint.versionPublisher's Version/PDF
dc.contributor.institutionLaboratory of Bioinformatics and Systems Biology, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov str. 32, Moscow 119991GSP-1, Russian Federation
dc.contributor.institutionDepartment of Computational Systems Biology, Vavilov Institute of General Genetics, Russian Academy of Sciences, Gubkina str. 3, Moscow 119991, Russian Federation
dc.contributor.institutionRIKEN Omics Science Center, Yokohama, Kanagawa 230-0045, Japan
dc.contributor.institutionRIKEN Center for Life Science Technologies, Division of Genomic Technologies, Yokohama, Kanagawa 230-0045, Japan
dc.contributor.institutionRIKEN Preventive Medicine and Diagnosis Innovation Program, Wako, Saitama 351-0198, Japan
dc.contributor.affiliationKing Abdullah University of Science and Technology (KAUST)
kaust.personMedvedeva, Yulia
kaust.personBhuyan, Sharifulislam
kaust.personBajic, Vladimir B.
kaust.personKhamis, Abdullah M.
kaust.personBa Alawi, Wail
refterms.dateFOA2018-06-13T14:35:57Z


Files in this item

Thumbnail
Name:
Article-BMC_Genomi-Effects_of-2014.pdf
Size:
822.8Kb
Format:
PDF
Description:
Article - Full Text
Thumbnail
Name:
Supplement_1_-_BMC_Genomi-Effects_of-2014.1471-2164-15-119-S1.docx
Size:
11.40Kb
Format:
Microsoft Word 2007
Description:
Supplemental File 1
Thumbnail
Name:
Supplement_2_-_BMC_Genomi-Effects_of-2014.1471-2164-15-119-S2.xlsx
Size:
82.07Kb
Format:
Microsoft Excel 2007
Description:
Supplemental File 2
Thumbnail
Name:
Supplement_3_-_BMC_Genomi-Effects_of-2014.1471-2164-15-119-S3.xlsx
Size:
73.14Kb
Format:
Microsoft Excel 2007
Description:
Supplemental File 3
Thumbnail
Name:
Supplement_4_-_BMC_Genomi-Effects_of-2014.1471-2164-15-119-S4.xlsx
Size:
89.97Kb
Format:
Microsoft Excel 2007
Description:
Supplemental File 4
Thumbnail
Name:
Supplement_5_-_BMC_Genomi-Effects_of-2014.1471-2164-15-119-S5.xlsx
Size:
11.49Kb
Format:
Microsoft Excel 2007
Description:
Supplemental File 5
Thumbnail
Name:
Supplement_6_-_BMC_Genomi-Effects_of-2014.1471-2164-15-119-S6.pdf
Size:
33.84Kb
Format:
PDF
Description:
Supplemental File 6
Thumbnail
Name:
Supplement_7_-_BMC_Genomi-Effects_of-2014.1471-2164-15-119-S7.xlsx
Size:
38.34Kb
Format:
Microsoft Excel 2007
Description:
Supplemental File 7
Thumbnail
Name:
Supplement_8_-_BMC_Genomi-Effects_of-2014.1471-2164-15-119-S8.xlsx
Size:
40.36Kb
Format:
Microsoft Excel 2007
Description:
Supplemental File 8
Thumbnail
Name:
Supplement_9_-_BMC_Genomi-Effects_of-2014.1471-2164-15-119-S9.xlsx
Size:
35.25Kb
Format:
Microsoft Excel 2007
Description:
Supplemental File 9
Thumbnail
Name:
Supplement_10_-_BMC_Genomi-Effects_of-2014.1471-2164-15-119-S10.txt
Size:
4.034Kb
Format:
Text file
Description:
Supplemental File 10

This item appears in the following Collection(s)

Show simple item record

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited.
Except where otherwise noted, this item's license is described as This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited.