Seminar: Sarantis Chlamydas

Advances in chromatin immuno-precipitation for epigenetics and genomics studies

Date:
13 February 2017 16:00 hrs. - 17:00 hrs.
Location:
Figdor Lecture Theatre, 8th floor RIMLS Building, Geert Grooteplein 26-28, route 289
Title:
Advances in chromatin immuno-precipitation for epigenetics and genomics studies
Speaker(s):

Sarantis Chlamydas, Product Manager, Active Motif-Enabling Epigenetics

Host(s):

Jo Zhou, Dept. of Molecular Developmental Biology, RIMLS

13-02-2017 16:00:0013-02-2017 17:00:00Europe/AmsterdamAdvances in chromatin immuno-precipitation for epigenetics and genomics studies Figdor Lecture Theatre, 8th floor RIMLS Building, Geert Grooteplein 26-28, route 289Rimlsrimls@radboudumc.nl

Remarks / more information:

undefinedActive Motif has developed a variety of tools and services to overcome many of current  challenges in the field of Epigenetics and Transcriptomics, including normalizing across samples, performing ChIP on targets for which ChIP grade antibodies are not available, increasing resolution and identifying binding partners, recombinant enzymes for in vitro screening assays and  transcription platforms for validation of effects in different biological pathways including non coding RNAs regulation.

Many global differences in histone modification levels cannot be seen when performing ChIP-Seq.  To address this we have developed a Spike-In strategy specifically for ChIP, which not only normalizes for biological variation across samples but also for technical variation that can occur during the ChIP procedure. This Spike-In can be applied to all ChIP experiments and used specifically to compare treated and untreated samples or when knocking down a protein of interest.

The localization resolution of a given factor in ChIP is determined by the average size of chromatin fragments and is typically a few hundred base pairs. Dr. Frank Pugh, here at Penn State, developed ChIP-exo (U.S. Patent No. 8367334 b2), which combines ChIP with exonuclease digestion to significantly increase ChIP-seq resolution for a variety of factors. Active Motif has exclusively licensed and commercialized this technology for use with a variety of factors enabling high resolution ChIP-Seq.

DNA binding proteins typically form complexes when binding to chromatin and the subunits of a given complex can impact which genomic regions are bound.  To determine whether proteins co-localize on chromatin people typically perform multiple ChIP-Seq reactions and compare localization patterns bioinformatically. This approach requires multiple reactions and only works when looking at known proteins, which have ChIP grade antibodies. To overcome this Active Motif has commercialized RIME (Rapid Immunoprecipitation Mass spectrometry of Endogenous proteins) developed by Dr. Jason Carroll, which enables the unbiased Mass Spec based detection of chromatin based protein-protein interactions.

For the studies related to Histone Modifications,Active Motif’s Epigenetic Services now offers a Histone PTM Quantitation Assay using our Histone PTM Luminex bead sets.  This new service meets the growing need of scientists to detect changes in specific, global histone modifications levels.  Changes in global histone modifications have been detected in disease models, cells with mutations in epigenetic modifier proteins and epigenetic inhibitor treated cells.  The service can be used to screen multiple samples for a desired change in an epigenetic mark.   The added advantage of screening multiple marks is the potential to identify unanticipated changes in other PTMs.

 



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