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Understanding principles of DNA recognition in chromatin

English title Understanding principles of DNA recognition in chromatin
Applicant Thomä Nicolas
Number 179541
Funding scheme Project funding (Div. I-III)
Research institution Friedrich Miescher Institute for Biomedical Research
Institution of higher education Institute Friedrich Miescher - FMI
Main discipline Biochemistry
Start/End 01.06.2018 - 31.05.2022
Approved amount 1'008'000.00
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All Disciplines (2)

Discipline
Biochemistry
Molecular Biology

Keywords (5)

Structural Biology; Transcription; DNA binding proteins; Chromatin; DNA repair

Lay Summary (German)

Lead
Strukturelle und funktionelle Einblicke von Proteinen die DNA im Kontext von Chromatin binden
Lay summary
Im Rahmen des Projekts wollen wir untersuchen, wie Proteine DNA umschließen, wenn diese um Nukleosomen gewickelt ist. Nucleosomen sind die zentrale Verpackungseinheit von Säugetier-DNA. Sie dienen der DNA-Kompaktierung und verhindern unspezifische DNA Bindung. Nucleosomale DNA, die auch als Chromatin bezeichnet wird, ist ubiquitär in Säugetierzellen vorhanden. Nukleosomen, wenn sie DNA verdichten, behindern dabei auch den Zugang zu DNA. Unser Fokus wird darauf liegen, wie DNA-Reparaturproteine und Transkriptionsfaktoren Zugang zu DNA in einem chromatinierten Genom erhalten, eine Frage, die derzeit noch nicht beantwortet wird. Wir wollen diese Frage strukturell mit einer Kombination biochemischer, biophysikalischer und zellbiologischer Werkzeuge angehen.



Direct link to Lay Summary Last update: 16.05.2018

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Abstract

Genome regulation at the level of transcription, DNA repair and replication requires highly specific DNA sequence recognition by the proteins involved. In eukaryotes nucleosomes limit access to DNA across a substantial part of the genome. Nucleosomes are comprised of two copies of histones H2A, H2B, H3 and H4 together with ca. 146 bp duplex DNA1-3. When wrapped around the nucleosome, the solvent accessibility of the packaged DNA is severely restricted, and this barrier needs to be overcome for DNA repair, or transcriptional activation, to occur. How DNA binding proteins engage nucleosomal DNA in a sequence-, or DNA damage-dependent manner is an unresolved question, which we will address using a combination of structural techniques, biochemistry and functional assays. We will focus on a diverse subset of DNA repair proteins, and transcription factors, known to bind nucleosomes. We will study the structure (Aim 1) of the UV-DDB DNA repair complex and its mechanism for recognizing UV-light-induced crosslinks of pyrimidine photodimers in nucleosomal DNA. Similarly, we will ask how pioneering transcription factor and transcription factor complexes recognize cognate DNA sequences within a nucleosome (Aim 2); and examine, on the molecular level, how downstream factors such as the histone acetyltransferase CBP/p300, or SWI/SNF chromatin remodellers, recognize protein-nucleosome complexes (Aim 3). The work aims to address the fundamental mechanism how the nucleosomal barrier is overcome to achieve site specific DNA binding in repair and transcriptional regulation.
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