PhD Heterochromatin maintenance in response to DNA damage

Summary

This PhD position is on of the 15 positions available for highly motivated Early Stage Researcher (ESR) as part of the new H2020, EU-funded, Marie Skłodowska-Curie Joint Training and Research Programme on Chromatin Dynamics & the DNA Damage Response aDDRess. The aDDRess consortium is a joint European Program of excellence in training and research with a core intellectual focus on, chromatin dynamics, DNA damage signaling and repair mechanisms and their impact on development and disease. aDDRess-ITN ( www.itn-aDDRess.gr ) brings together leading academic and industry research groups located throughout EU to train a new generation of researchers. We are now looking for 15 highly motivated Early Stage Researchers (ESRs) to work towards their PhD on Chromatin Dynamics and the DNA damage Response.

The PhD position is located in the lab of epigenetic and cell fate at the University of Paris Diderot, in the epigenome and integrity team : http://parisepigenetics.com/ei-en/

i. Objective of research:

Explore the mechanisms for heterochromatin maintenance following UV damage in human cells

ii. Current state of the art:

Genotoxic stress drives human diseases by compromising not only genome stability but also the integrity of its organisation into chromatin, where DNA wraps around histone proteins to form nucleosomes and higher-order structures. Among higher-order chromatin structures, heterochromatin domains pose a barrier to signaling and repair of DNA damage and display high mutation rates in human cancers. While several recent studies have begun to characterize how DNA damage repair proceeds in heterochromatin, whether heterochromatin features are preserved or altered during this process and by which mechanisms is still elusive. To fill this gap, we propose to investigate how DNA damage repair operates in heterochromatin domains, focusing on the inactive X chromosome in female mammals, a typical example of facultative heterochromatin. Easily detectable as a dense dot upon DNA staining also known as the Barr body, the inactive X chromosome is characterized by Xist RNA coating, chromatin compaction, enrichment in macroH2A histone variant and H3K27me3 modification, and silencing of most of the X-linked genes. Building on our previous expertise on the chromatin response to UV damage, we will examine these heterochromatin features following cell exposure to UVC irradiation, which generates pyrimidine dimers that are repaired by the Nucleotide Excision Repair pathway.

iii. Research methodology and approach:

To dissect the mechanisms for heterochromatin maintenance in response to UV damage, as a cellular model, we will use human primary fibroblasts, such as IMR90, a female cell line fully proficient in UV damage repair. By inflicting global UVC irradiation or UVC laser damage targeted to the Barr body, we will first test whether Nucleotide Excision Repair factor recruitment proceeds efficiently within facultative heterochromatin, which is still uncharacterized. We will also examine whether UV-damage repair impacts heterochromatin-specific marks, including macroH2A, H3K27me3, and Xist RNA localization on the inactive X. In addition, we will investigate changes in heterochromatin compaction and accessibility by ATAC-see and monitor X-linked gene silencing by RNA-FISH with X chromosome paint probes. To address the mechanisms for heterochromatin restoration after damage, we will examine the recruitment of histone modifiers, histone chaperones and new histone deposition using the SNAP-tag technology that is well established in our group.

iv. Originality and innovative aspects of the ESR project:

We will use a combination of innovative methodologies and tools to dissect the fundamental mechanisms involved in maintaining higher-order chromatin structures following DNA damage, which is a major unresolved issue.

v. Integration of the ESR project to the overall research programme:

Our ESR will collaborate with the Legube group on the re-establishment of histone marks upon DNA breaks, with the Garinis group and LXRepair on NER-defective mice and UV-damage assays.

The offer

• a comprehensive, interactive and international training programme covering innovative and state-of-the-art approaches to the field of DNA damage and chromatin dynamics.
• a series of research-specific, complementary and soft skills, that involve both the academic and industry sectors and are tailor-made to prepare young researchers for their future careers.
• a competitive salary, which is adjusted for the host country.
• a mobility allowance and a family allowance (where applicable) as part of the employment package.

Applicant details

• The applicants can be of any nationality.
• The applicants should preferably hold an MSc degree in Biological Sciences.
• They should be within four years of the diploma granting them access to doctorate studies at the time of recruitment,
• The applicant must not have resided for more than 12 months prior to the singing her/his contract in the country of the host institute.
• Applicants should be proficient in written and spoken English.

The 15 PhD positions are located in several countries across EU. Please visit the Program website ( http://www.itn-address.gr/ ) for more information on the individual research groups, the Principal Investigators involved and the proposed topic of research offered within each lab.