Epigenomics Profiling Core
Services
- Epigenomics Profiling
- DNA Methylation Analysis
- High-Throughput ChIP
The Epigenomics Profiling Core (EpiCore) facilitates researchers’ efforts to define the epigenetic mechanisms that alter the state of chromatin to regulate transcription in normal versus disease conditions. It is funded, in part, through the Department of Epigenetics and Molecular Carcinogenesis.
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, CUT&RUN 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
Chromatin Analysis by Chromatin Immunoprecipitation (ChIP), CUT&RUN and ATAC-seq
One of the major questions for researchers interested in understanding chromatin dynamics is how protein-DNA interactions alter the epigenetic landscape. Many features that control chromatin structure play a critical role in regulating gene expression. Thus, genome-wide mapping of transcription factors, chromatin-associated proteins, and chromatin states such as those defined by specific histone post-translational modifications, have become a major research focus. The EpiCore offers the following services to examine chromatin changes.
Chromatin Immunoprecipitation (ChIP) Services
Chromatin Immunoprecipitation followed by high-throughput sequencing (ChIP-seq) is used to identify regions enriched for chromatin-bound proteins across the genome. We provide full-service protocols starting from preparation of chromatin from cells or tissues, pull-down of protein-bound DNA, and preparation of ChIP DNA libraries ready for Next-Generation Sequencing (NGS). We also offer detection of enriched proteins of interest at a specific genomic locus using ChIP-qPCR. Please see our services page for the full range of ChIP services available at the EpiCore as well as project-and assay-specific sample requirements.
CUT&RUN Services
The EpiCore now offers CUT&RUN (Cleavage Under Targets and Release Using Nuclease). CUT&RUN requires lower amounts of starting sample and significantly fewer sequencing reads than traditional ChIP-seq methods. CUT&RUN services at the EpiCore include performing the start-to-end CUT&RUN reaction, protein-bound DNA pull down and library preparation for NGS. Please see our services page for the full range of CUT&RUN services available at the EpiCore as well as sample requirements.
ATAC-Seq Services
ATAC-seq (Assay for Transposase Accessible Chromatin with high-throughput sequencing) is widely used to map chromatin accessibility, transcription factor binding, and nucleosome positioning across the genome. The EpiCore offers a full-service ATAC-seq protocol starting with isolation of nuclei from cells and/or tissues, transposition, and sequencing library preparation of open chromatin to profile chromatin accessibility. The resulting libraries are submitted to the NGS core for sequencing. Please see our services page for more information about the ATAC-seq services available at the EpiCore as well as sample requirements.
Please contact Abhinav Jain, Ph.D., (ajain@mdanderson.org) to schedule an appointment, primary consultation, and project-specific sample requirements for ChIP-seq, CUT&RUN 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
ChIP-Seq, ATAC-seq and CUT&RUN Services
Abhinav Jain, Ph.D.
Co-director, Epigenomics Profiling Core
Director, ATAC-seq, CUT&RUN and ChIP-Seq Services
Office phone: 713-745-2640
Email: ajain@mdanderson.org