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Chromatin and transcription in ES cells: from single cells to genome wide views

Objective

How embryonic stem cells (ESCs) maintain their dual capacity to self-renew and to differentiate into all cell types is one of the fundamental questions in biology. Although this question remains largely open, there is growing evidence suggesting that chromatin plasticity is a fundamental hallmark of ESCs, providing their necessary flexibility.
Previously we found that ESCs possess a relatively open chromatin conformation, giving rise to permissive transcriptional program. Here I propose to investigate the mechanisms that support chromatin plasticity and pluripotency in ESCs.
Using a simple biochemical assay which I developed (DCAP: Differential Chromatin Associated Proteins), based on micrococcal nuclease (MNase) digestion combined with multi-dimensional protein identification technology (MudPIT), I seek to identify ESC-specific chromatin proteins. Selected proteins will be knocked-down (or out) and their ESC function will be evaluated.
In addition, I will conduct a hypothesis-driven research using mutant ESCs and epigenetic-related drugs to search for potential mechanisms, (i.e. histone modifications, DNA methylation), that may support chromatin plasticity in ESCs. Based on our intriguing preliminary data, I will also focus on the link between the nuclear lamina and ESC plasticity.
Thirdly, we will analyze non-polyadenylated transcription using genome-wide tiling arrays and RNA-seq. We will design custom microarrays containing the identified sequences, which will allow us to reveal, using ChIP-chip experiments, the mechanistic regulation of the non-polyadenylated transcripts. Finally, we will knockout, using zinc-finger nuclease technology, selected highly conserved candidates in search of their function.
Understanding chromatin regulation, plasticity and function will enable one to intelligently manipulate ESCs to transition between the pluripotent, multipotent and unipotent states and to expedite their use in the clinic.

Field of science

  • /natural sciences/biological sciences/biochemistry/biomolecules/proteins
  • /medical and health sciences/medical biotechnology/cells technologies/stem cells

Call for proposal

ERC-2011-StG_20101109
See other projects for this call

Funding Scheme

ERC-SG - ERC Starting Grant

Host institution

THE HEBREW UNIVERSITY OF JERUSALEM
Address
Edmond J Safra Campus Givat Ram
91904 Jerusalem
Israel
Activity type
Higher or Secondary Education Establishments
EU contribution
€ 1 500 000
Principal investigator
Eran Meshorer (Dr.)
Administrative Contact
Hani Ben-Yehuda (Ms.)

Beneficiaries (1)

THE HEBREW UNIVERSITY OF JERUSALEM
Israel
EU contribution
€ 1 500 000
Address
Edmond J Safra Campus Givat Ram
91904 Jerusalem
Activity type
Higher or Secondary Education Establishments
Principal investigator
Eran Meshorer (Dr.)
Administrative Contact
Hani Ben-Yehuda (Ms.)