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Genomic signatures that define DNA methylation changes at cis-regulatory elements in cancer

Grant number: 14/27145-1
Support type:Scholarships in Brazil - Scientific Initiation
Effective date (Start): May 01, 2015
Effective date (End): April 30, 2016
Field of knowledge:Biological Sciences - Genetics - Human and Medical Genetics
Principal researcher:Houtan Noushmehr
Grantee:Victor Hugo Calegari de Toledo
Home Institution: Faculdade de Medicina de Ribeirão Preto (FMRP). Universidade de São Paulo (USP). Ribeirão Preto , SP, Brazil

Abstract

Analyzing tumor cell gene expression is essential when it comes to understanding cancer physiopathology. Identifying transcription factor binding sites (TFBSs) that exhibit differential methylation patterns establishes a correlation between RNA polymerization and epigenetic changes at cis-regulatory elements in the genome. In this context, this project aims to combine data generated through ChIP-seq and DNA binding motif analyses available from ENCODE and TRANSFAC databases to evaluate TCGA DNA methylation changes between normal and cancer cells at the level of the individual protein/DNA interaction site. All analytical methods will be implemented by using the open-source R programming language, Bioconductor packages, and HOMER software in order to identify molecular signatures capable of defining the establishment of abnormal DNA methylation profiles at genomic regulatory elements and eases further studies by our group in order to characterize specific transcriptional networks implicated with cancer progression.

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