Epigenetics Core

Subhashinee Samudra K. Wijeratne, Ph.D.

Dept. of Nutrition and Health Sciences, UNL

Processes in EpigeneticsThe study of heritable changes in gene expression or cellular phenotype caused by mechanisms other than changes in the underlying DNA sequence.

Chromatin remodeling• DNA methylation• Histone modifications

RNA interference

Requirements for epigenetic studies• Personnel

Formal training in epigenetics study design Laboratory techniques Data analysis

• Equipment

The Epigenetics Core will be the only facility in the State of Nebraska with in-depth capabilities and expertise with regard to the analysis of epigenetic marks.

Epigenetics Core

Specific Aim 1Renovate institutionally committed space on the University of Nebraska-Lincoln (UNL) campus to create a epigenetics core research facility dedicated to serving the needs of Center and non-Center researchers.

Epigenetics Core

Ruth Leverton Hall, East Campus, UNL.

Approximately 800 sq.ft.

Leverton Hall• Nutrition and Health Sciences. • NPOD administrative office. • Easy access.• Parking availability.

Funds • Alteration and renovation of the space.• Purchase and installation of fixed equipment. • Moveable/portable equipment.

Core Location

Epigenetics Core- Floor Plan

Specific Aim 2Provide means by which NPOD project leaders and other Center members can discover new signaling mechanisms at a reasonable cost, while receiving valuable guidance regarding experimental design, data analysis, and data interpretation.

Epigenetics Core

SMVT LTR22 LTR15 GAPDH0123456789

K16A

cH4

Enric

hmen

t

Specific Aim 3Provide training for NPOD investigators and members of their laboratories on experimental procedure and techniques.

Epigenetics Core

Consulting: Study designsServices

DNA methylation. Histone modification marks. Sample preparation for subsequent second-generation

sequencing. Mapping of epigenetic marks and transcription factor

binding sites in mammalian chromatin.

ServicesSample Analysis

Consulting services on data analysis and interpretation.

Antibody testing.

Services

Comprehensive service package: Including cell culture, antibody testing, consulting on experimental designs, sample analysis, biostatistical analysis (large data sets), and staff training for user laboratories.

Data Analysis

Training sessions

Free training sessions to members affiliated with the NPOD

• Enhance the research expertise in members’ laboratories.

• To develop an epigenetics workforce in Nebraska.

Investigators from other institutions:

• Develop more formalized training sessions (and charge a nominal fee).

Services

Priority

Junior Investigators > Other center members > External users

Fee Structure

• Each JI : $2,000 credit /year of project funding.

• Remaining credit:• Carry forward to the next year.• Transfer to another center member.

Once the credits are exhausted JIs will be required to pay a fee that covers the cost of supplies, etc.

The same fee will be paid by other center members and external users.

Services

Regis Moreau (Anti-lipemic Mechanism of (R)-alpha-lipoic Acid)

Dmitri Fomenko (Selenoproteins and Selenium-dependent Redox Signaling Alter Diabetes Risk)

Jennifer Wood (Abnormalities in Epigenetic Regulation of Skeletal and Cardiac Muscle Differentiation by Maternal Obesity)

Saraswathi Viswanathan (The Lipid-lowering Effects of ω-3 Fatty Acids are Mediated by Pregnane X Receptor and Constitutive Androstane Receptor Signaling)

Immediate UsersNPOD Project Leaders

ChIP, Realtime PCR and SequencingMicroChIP with Realtime PCRDNA methylation with Realtime PCR and cloning Antibody validation

Other Users Other NPOD Users

Dr. Donald Becker, Dr. Cyrus Desouza, Dr. Robert Lewis, Dr. Etsuko Moriyama, Dr. Janos Zempleni, Dr. John Davis, Dr. Angela Pannier, Dr. Andrea Cupp, Dr. Samodha Fernando,Dr. Vicki Schlegel, Dr. Xin Bi

Other Center members with research programs in epigenetics

Dr. Patrick Dussault and Dr. Mark Wilson

Non-Center members at UNL and UNMCDr. Zoya Avramova, Dr. Gloria Borgstahl, Dr. Heriberto Cerutti,

Dr. Judy Christman, Dr. Michael Fromm, Dr. Steve Ladunga, Dr. Yuri Lyubchenko

Users from other Institutes/collaboratorsDr. Emily Ho, Dr. Ji-Young Lee, Dr. Don Mock, Dr. Donato Romagnolo, Dr. John West

Increase the competiveness of University of Nebraska researchers in securing external funding.

Create an environment conducive to the development of highly talented junior investigator transitioning to independent status.

Support the development of important new collaborations among Center members and beyond, and help in the development of a national workforce.

Expected Outcomes of the Epigenetics Core

Initial

The Center.

In the long-term

Self-sustained through service fees paid by Center members and non-members alike.

The Epigenetics Core will be the only facility in NE that offers a comprehensive service, including cell culture, antibody testing, experimental design assistance, sample analysis, biostatistical analysis, and laboratory staff training.

Support for the Epigenetics Core

Core PersonnelCore Director : Subhashinee Samudra K. Wijeratne, Ph.D.

• Five years of experience in epigenetics and cell biology. • Formal training in food science and nutrition.

• Serves as main consultant for projects.• Responsible for budget, and staff supervision.

Co-Director: Sridhar Malkaram, Ph.D.

• Four years experience in epigenetics and computational biology.

• Formal training in molecular and computational biology. • Study design and data analysis (bioinformatics) consultant.

Laboratory Technician: Mengna Xia, M.S

• Formal training in animal genetics, breeding, and reproduction.

• Two years of experience in epigenetics research.

• Analyzing epigenetic marks in mammalian chromatin and testing antibody specificities.

Core Personnel

Centrifuges and microcentrifuges

Digital Sonicator

Thermocycler

Cell Incubator

Refrigerated Shaking Incubator

Nanodrop Spectrophotometer

Freezers (-80C and -20C)

Real Time PCR

Equipment

Western Blot units

Agarose Gel Electrophoresis Units

Cold Storage Unit

LiCOR Imaging System

Balances

Thermal Mixer and Tube Rotator

Inverted Microscope

Sterile Cabinet (48'')

Equipment