MDACC Epigenomics Profiling Core Facility

About the core

The Epigenomics Profiling Core is funded jointly by the Center for Cancer Epigenetics and Department of Epigenetics and Molecular Carcinogenesis. The mission of Epigenomics Profiling core is to actively participate and contribute to the growing Epigenetics community at the University of Texas M.D. Anderson Cancer Center (UTMDACC) by providing services to analyze alterations to chromatin such as, DNA methylation and DNA-bound protein modifications (ChIP). The overall goal of this core is to facilitate researchers’ efforts to understand Epigenetic mechanisms that alter the chromatin state that regulate the transcription output in normal vs. disease conditions. This new core facility is an expansion of previously established DNA Methylation Core combined with now available High-throughput ChIP-Seq (HT ChIP-Seq) services. The core is located at the Basic Science Research Building of the MD Anderson Cancer Center and is fully equipped for molecular biology research.

Overview of Services

DNA Methylation Analysis: Methylation that occur at specific sites of DNA is one of the earliest identified modifications to chromatin. DNA methylation is essential for normal development and is associated with a number of key processes, such as imprinting. DNA methylation, which is reversible if occurs at regulatory elements of the genome affects the transcription of neighboring genes. Thus, alterations in DNA methylation is one of the key components of Epigenetic modifications to chromatin. The core will provide investigators with access to global and gene-specific DNA methylation analysis. Services include: consultation with investigators to chose the best method of analysis; sample preparation, assay design and processing of the most used methods to study DNA methylation, both gene-specific and genome-wide (PyroMeth, RRBS and Methyl-Seq); and assessment of global DNA methylation by pyrosequencing methylation analysis of repetitive elements (LINE-1 and Alu repeats). Please contact Dr. Marcos Estecio to set up an appointment and primary consult for DNA methylation services.

High-throughput ChIP-Seq: One of the major questions for researchers interested in understanding chromatin dynamics is to investigate how protein-DNA interactions alter Epigenetic profiles and subsequent gene expression.  Chromatin immunoprecipitation (ChIP) is a technique to investigate protein-DNA interactions at a specific genomic-site. ChIP-Seq (ChIP followed by deep sequencing of DNA) is an extension of ChIP technology to determine the chromatin enrichment of a transcription factor on a genome-wide scale.  In the past few years, ChIP-Seq has become a very useful technique to understand the chromatin states that regulate the transcription output. The overall goal of the core is to provide support to investigators interested in characterizing the interactions of post-translational modifications of histones (epigenetic marks that define a chromatin state or Epigenome) or transcription factors at specific genomic loci or genome-wide (Cistrome). This innovative platform provides ChIP services followed by library preparation in a cost effective high-throughput (HT) format from cell lines and tissues to assess the chromatin-enrichment of well-established histone marks or your protein of interest. The core has adapted a high-throughput method to perform multiple ChIPs (HT ChIP-seq) in a 96-well format, which not only saves time and costs but is doable with limited starting material and high reproducibility. The resource provides services including: processing of the samples (cells or tissues) to make high quality chromatin for ChIP, ChIP with a set of validated antibodies for histone marks (Promoter marks: H3K4me3 and H3K27me3, Enhancer marks: H3K4me1 and H3K27ac, Gene body marks for transcription activity: H3K36me3 and H3K79me2, and Heterochromatin mark: H3K9me3), ChIP with investigator preferred custom antibodies, and library preparation from ChIP DNA and multi-plexing for high-throughput DNA sequencing. These services are aimed to deliver high quality sequencing-ready libraries to map chromatin states (histone modifications), or profile binding of epigenetic modifiers (transcription co-regulators) or DNA binding proteins (transcription factors) on a genomic scale. Please contact Dr. Abhinav Jain to set up an appointment and primary consult for ChIP services.

Leadership

DNA Methylation

Marcos Estecio, Ph.D., Co-Director

Associate Professor

mestecio@mdanderson.org

713-792-9108

Guillermo Garcia-Manero, MD, Co-Director

Professor

ggarciam@mdanderson.org

713-745-3428

High-throughput ChIP-Seq

Abhinav Jain, Ph.D., Co-Director

Assistant Professor

ajain@mdanderson.org

713-794-6366

Location and Hours of Operation

Links and Resources

DNA Methylation Core - MDAnderson

High-throughput ChIP-Seq - MD Anderson

Contacts