MeDReaders: A database for transcription factors that bind to methylated DNA

Guohua Wang, Ximei Luo, Jianan Wang, Jun Wan, Shuli Xia, Heng Zhu, Jiang Qian, Yadong Wang

Research output: Contribution to journalArticle

Abstract

Understanding the molecular principles governing interactions between transcription factors (TFs) and DNA targets is one of the main subjects for transcriptional regulation. Recently, emerging evidence demonstrated that some TFs could bind to DNA motifs containing highly methylated CpGs both in vitro and in vivo. Identification of such TFs and elucidation of their physiological roles now become an important stepping-stone toward understanding the mechanisms underlying the methylation-mediated biological processes, which have crucial implications for human disease and disease development. Hence, we constructed a database, named as MeDReaders, to collect information about methylated DNA binding activities. A total of 731 TFs, which could bind to methylated DNA sequences, were manually curated in human and mouse studies reported in the literature. In silico approaches were applied to predict methylated and unmethylated motifs of 292 TFs by integrating whole genome bisulfite sequencing (WGBS) and ChIP-Seq datasets in six human cell lines and one mouse cell line extracted from ENCODE and GEO database. MeDReaders database will provide a comprehensive resource for further studies and aid related experiment designs. The database implemented unified access for users to most TFs involved in such methylation-associated binding actives. The website is available at http://medreader.org/.

Original languageEnglish (US)
Pages (from-to)D146-D151
JournalNucleic Acids Research
Volume46
Issue numberD1
DOIs
StatePublished - Jan 1 2018

Fingerprint

Transcription Factors
Databases
DNA
Methylation
Biological Phenomena
Cell Line
Nucleotide Motifs
Computer Simulation
Genome

ASJC Scopus subject areas

  • Genetics

Cite this

MeDReaders : A database for transcription factors that bind to methylated DNA. / Wang, Guohua; Luo, Ximei; Wang, Jianan; Wan, Jun; Xia, Shuli; Zhu, Heng; Qian, Jiang; Wang, Yadong.

In: Nucleic Acids Research, Vol. 46, No. D1, 01.01.2018, p. D146-D151.

Research output: Contribution to journalArticle

Wang, Guohua ; Luo, Ximei ; Wang, Jianan ; Wan, Jun ; Xia, Shuli ; Zhu, Heng ; Qian, Jiang ; Wang, Yadong. / MeDReaders : A database for transcription factors that bind to methylated DNA. In: Nucleic Acids Research. 2018 ; Vol. 46, No. D1. pp. D146-D151.
@article{2add88953c094f49b0eebcd28dfdf7d8,
title = "MeDReaders: A database for transcription factors that bind to methylated DNA",
abstract = "Understanding the molecular principles governing interactions between transcription factors (TFs) and DNA targets is one of the main subjects for transcriptional regulation. Recently, emerging evidence demonstrated that some TFs could bind to DNA motifs containing highly methylated CpGs both in vitro and in vivo. Identification of such TFs and elucidation of their physiological roles now become an important stepping-stone toward understanding the mechanisms underlying the methylation-mediated biological processes, which have crucial implications for human disease and disease development. Hence, we constructed a database, named as MeDReaders, to collect information about methylated DNA binding activities. A total of 731 TFs, which could bind to methylated DNA sequences, were manually curated in human and mouse studies reported in the literature. In silico approaches were applied to predict methylated and unmethylated motifs of 292 TFs by integrating whole genome bisulfite sequencing (WGBS) and ChIP-Seq datasets in six human cell lines and one mouse cell line extracted from ENCODE and GEO database. MeDReaders database will provide a comprehensive resource for further studies and aid related experiment designs. The database implemented unified access for users to most TFs involved in such methylation-associated binding actives. The website is available at http://medreader.org/.",
author = "Guohua Wang and Ximei Luo and Jianan Wang and Jun Wan and Shuli Xia and Heng Zhu and Jiang Qian and Yadong Wang",
year = "2018",
month = "1",
day = "1",
doi = "10.1093/nar/gkx1096",
language = "English (US)",
volume = "46",
pages = "D146--D151",
journal = "Nucleic Acids Research",
issn = "1362-4962",
publisher = "Oxford University Press",
number = "D1",

}

TY - JOUR

T1 - MeDReaders

T2 - A database for transcription factors that bind to methylated DNA

AU - Wang, Guohua

AU - Luo, Ximei

AU - Wang, Jianan

AU - Wan, Jun

AU - Xia, Shuli

AU - Zhu, Heng

AU - Qian, Jiang

AU - Wang, Yadong

PY - 2018/1/1

Y1 - 2018/1/1

N2 - Understanding the molecular principles governing interactions between transcription factors (TFs) and DNA targets is one of the main subjects for transcriptional regulation. Recently, emerging evidence demonstrated that some TFs could bind to DNA motifs containing highly methylated CpGs both in vitro and in vivo. Identification of such TFs and elucidation of their physiological roles now become an important stepping-stone toward understanding the mechanisms underlying the methylation-mediated biological processes, which have crucial implications for human disease and disease development. Hence, we constructed a database, named as MeDReaders, to collect information about methylated DNA binding activities. A total of 731 TFs, which could bind to methylated DNA sequences, were manually curated in human and mouse studies reported in the literature. In silico approaches were applied to predict methylated and unmethylated motifs of 292 TFs by integrating whole genome bisulfite sequencing (WGBS) and ChIP-Seq datasets in six human cell lines and one mouse cell line extracted from ENCODE and GEO database. MeDReaders database will provide a comprehensive resource for further studies and aid related experiment designs. The database implemented unified access for users to most TFs involved in such methylation-associated binding actives. The website is available at http://medreader.org/.

AB - Understanding the molecular principles governing interactions between transcription factors (TFs) and DNA targets is one of the main subjects for transcriptional regulation. Recently, emerging evidence demonstrated that some TFs could bind to DNA motifs containing highly methylated CpGs both in vitro and in vivo. Identification of such TFs and elucidation of their physiological roles now become an important stepping-stone toward understanding the mechanisms underlying the methylation-mediated biological processes, which have crucial implications for human disease and disease development. Hence, we constructed a database, named as MeDReaders, to collect information about methylated DNA binding activities. A total of 731 TFs, which could bind to methylated DNA sequences, were manually curated in human and mouse studies reported in the literature. In silico approaches were applied to predict methylated and unmethylated motifs of 292 TFs by integrating whole genome bisulfite sequencing (WGBS) and ChIP-Seq datasets in six human cell lines and one mouse cell line extracted from ENCODE and GEO database. MeDReaders database will provide a comprehensive resource for further studies and aid related experiment designs. The database implemented unified access for users to most TFs involved in such methylation-associated binding actives. The website is available at http://medreader.org/.

UR - http://www.scopus.com/inward/record.url?scp=85040926690&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85040926690&partnerID=8YFLogxK

U2 - 10.1093/nar/gkx1096

DO - 10.1093/nar/gkx1096

M3 - Article

C2 - 29145608

AN - SCOPUS:85040926690

VL - 46

SP - D146-D151

JO - Nucleic Acids Research

JF - Nucleic Acids Research

SN - 1362-4962

IS - D1

ER -