Epigenomics Profiling Core
Services
- Epigenomics Profiling
- DNA Methylation Analysis
- High-Throughput ChIP
The Epigenomics Profiling Core (EpiCore) is funded by the Center for Cancer Epigenetics and the Department of Epigenetics and Molecular Carcinogenesis. The overall goal of this core is to facilitate researchers’ efforts to define the epigenetic mechanisms that alter the state of chromatin to regulate transcription in normal versus disease conditions.
Our Purpose
The Epigenomics Profiling Core actively participates in and contributes to the growing epigenetics community at MD Anderson and across the Texas Medical Center by providing services to analyze epigenetic alterations and chromatin accessibility. Our current services are focused on DNA methylation analysis, ATAC-seq, and high-throughput chromatin immunoprecipitation (ChIP).
EpiCore Overview
DNA Methylation Analysis Services
Methylation events occurring at specific sites in DNA were one of the earliest identified epigenetic modifications to chromatin. DNA methylation is essential for normal development and is associated with key regulatory processes, such as gene insulation and imprinting. DNA methylation, which can be reversed, commonly affects gene transcription. This is particularly true when methylation occurs within gene promoters and genomic regulatory elements. Thus, alterations in DNA methylation patterns reflect important epigenetic changes. The DNA Methylation Analysis Service provides investigators access to both global and gene-specific DNA methylation analysis through a wide array of methods.
Our DNA Methylation Analysis services include:
• Consultation with investigators to select the best DNA methylation analysis method for their research
• Single-locus assay design and optimization for Pyrosequencing-Methylation Analysis (PMA)
• Assessment of global DNA methylation by pyrosequencing for analysis of repetitive elements (e.g. LINE-1 and Alu repeats)
• Genome-wide methods to study DNA methylation
• Whole-genome DNA methylation studies using Methyl-Seq
Please contact Marcos Estecio, Ph.D., (mestecio@mdanderson.org) to schedule an appointment and primary consultation for DNA Methylation Analysis Services.
For additional scheduling, please use iLab
High-Throughput ChIP-Seq and ATAC-Seq Services
One of the major questions for researchers interested in understanding chromatin dynamics is how protein-DNA interactions alter the epigenetic landscape to alter gene expression. Chromatin immunoprecipitation (ChIP) is used to interrogate protein-DNA interactions at specific genomic sites. ChIP-Seq (ChIP followed by deep sequencing of DNA) enables identification of regions enriched for chromatin-bound proteins across the genome. The High-Throughput ChIP-Seq Service provides an innovative, cost-effective, 96-well platform to deliver high-quality, sequencing-ready libraries to map histone modifications, transcriptional co-regulators and transcription factors genome-wide.
Our ChIP services include:
• Consultation with investigators to choose the best method of analysis
• Extraction of high-quality chromatin from cell and tissue samples
• ChIP-qPCR (gene-specific)
• ChIP-Seq (genome-wide)
• Sequencing library preparation from the immunoprecipitated material
For our ChIP-seq services, we routinely use a set of validated antibodies for specific histone marks*, but we can also use investigator preferred-antibodies.
*H3K4me3, H3K27me3 (promoters)
*H3K4me1, H3K27ac (enhancers)
*H3K36me3, H3K79me2 (gene bodies)
*H3K9me3 (heterochromatin)
ATAC-Seq Services
The Epigenomics Profiling Core (EpiCore) is now offering an ATAC-seq (Assay for Transposase Accessible Chromatin with high-throughput sequencing) service. This service helps customers address scientific questions regarding chromatin accessibility, transcription factor binding and nucleosome positioning across the genome with with reduced mitochondrial DNA contamination compared to more traditional methods. The core offers a full protocol starting from cells, and performing DNA tagmentation and library preparation for next-generation sequencing.
Please contact Abhinav Jain, Ph.D., (ajain@mdanderson.org) to schedule an appointment and primary consultation for High-Throughput ChIP-Seq and ATAC-seq Services.
For additional scheduling, please use iLab
EpiCore Workflow
Following a discussion with the core directors regarding investigator needs and sample requirements, the investigator submits his or her samples to the
Bioinformatics Support
Researchers with projects that involve next-generation sequencing services should always consult a bioinformatician before planning the detailed project. For assistance with bioinformatics analyses, MD Anderson users may consult with their institutionally assigned, departmental bioinformatician, seek advice on potential bioinformatics collaborators from the EpiCore directors.
Contact Information
DNA Methylation Analysis Services
Marcos R. Estecio, Ph.D.
Co-director, Epigenomics Profiling Core
Director, DNA Methylation Analysis Services
Office phone: 713-792-9108
Email: mestecio@mdanderson.org
High-Throughput ChIP-Seq Services
Abhinav Jain, Ph.D.
Co-director, Epigenomics Profiling Core
Director, High-Throughput ChIP-Seq Services
Office phone: 713-745-2640
Email: ajain@mdanderson.org