Chromatin Structure and Genome Stability

Nick Gilbert's Lab, Edinburgh

Research Summary

In mammalian cells DNA is wrapped around proteins to form chromatin. This protects DNA from damage and regulates gene transcription. Our lab is studying the protein and epigenetic factors that modify DNA and chromatin structure influencing gene expression and genome stability.

A key goal of our research is to understand how changes in chromatin structure affect gene expression and genome stability in disease. These studies will help us to understand this process and develop future drugs to treat diseases like cancer.


Lay Summary

In every mammalian cell DNA is packaged into chromatin, a massive nucleoprotein complex. As fundamental nuclear processes such as gene transcription, replication and repair occur in this environment it is important for us to understand chromatin and genome architecture. We have recently developed an assay for mapping high resolution DNA topology (folding) and have discovered that DNA in cells is organised into DNA topological domains consisting of over and under wound DNA.

We are investigating these topological domains across the human genome and investigate how they influence gene expression programmes, DNA replication and chromosome stability. In many human diseases including cancer the genome becomes fragile and certain regions of the genome have a propensity to becoming unstable. We are investigating the DNA topology and chromatin organisation of these fragile regions and will identify the factors that make them unstable.

Our research will enable us to characterise the mechanistic basis for many chromosomal aberrations and identify approaches that can be use to reduce the likelihood of genome instability. One of the first steps in cancer is the acquisition of genome instability. Characterising this process will better enable us to comprehend the factors and mechanism involved and may in future enable us to either better detect early changes in cancer or develop new approaches for reducing the likelihood of cancer growth.


Full Research Text

In mammalian cells DNA is packaged with proteins to form chromatin. This serves two key purposes: first to protect the DNA from damage and second to help regulate gene expression. In cells, the folding of chromatin can be considered at three different levels, primary, secondary and tertiary. The primary level of folding is wrapping DNA around a single protein complex called a nucleosome. Under normal cellular conditions chromatin is further wound in a solenoid-like fashion to form the second level of chromatin folding, often called the 30-nm fibre. In the cell nucleus this fibre is further packaged in an uncharacterised manner to form the tertiary or interphase chromatin. We are using novel molecular biology techniques, microscopy and developing new structural probes with the chemistry department to investigate and understand the function of chromatin fibre structure.

For normal cellular function it is important that the genome is stable. One of the key roles of chromatin is to protect the genome from damage however changes in chromatin structure will affect genome stability and this will affect the formation of chromosome breaks and translocations. Chromosomal fragile sites are regions of the genome that have a propensity to break. We are using these as a model system to investigate the relationship between chromatin structure and genome stability.

Gene expression is controlled at a number of levels including conformation of the chromatin fibre and the presence or absence of regulatory proteins. As genes are folded in to chromatin the RNA polymerase has to work around these protein-DNA structures. Many studies suggest that although chromatin structures are highly dynamic they are repressive to gene expression, indicating that chromatin structure can be a regulator of transcription. We are developing new techniques to study the relationship between gene transcription and chromatin structure to better investigate gene regulation and understand the molecular basis for disease.


Key Publications

Articles

Title Journal
SAF-A Regulates Interphase Chromosome Structure through Oligomerization with Chromatin-Associated RNAs. Cell. 169 (7): 1214-1227. 2017
Transcription forms and remodels supercoiling domains unfolding large-scale chromatin structures. Nat. Struct. Mol. Biol. 20: 387-395. 2013
Lactate, a product of glycolytic metabolism, inhibits histone deacetylase activity and promotes changes in gene expression. Nucleic Acids Res. 40: 4794-4803. 2012
Global chromatin fibre compaction in response to DNA damage. Biochem. Biophys. Res. Commun. 414, 820-5. 2011
Analysis of active and inactive X chromosome architecture reveals the independent organisation of 30-nm and large scale chromatin structures Mol. Cell 40, 397-409. 2010
Ring1B compacts chromatin structure and represses gene expression independent of histone ubiquitinylation. Mol. Cell 38, 452-64. 2010
DNA methylation affects nuclear organization, histone modifications, and linker histone binding but not chromatin compaction. J. Cell Biol 177, 401-11. 2007.
The chromatin architecture of the human genome: gene-rich domains are packaged in open chromatin fibres. Cell. 118, 555-66; 2004.
Formation of facultative heterochromatin in the absence of HP1. EMBO J. 22, 5540-50; 2003.
Distinctive higher-order chromatin structure at mammalian centromeres. Proc Natl Acad Sci. 98, 11949-54; 2001.

Reviews

Title Journal
Supercoiling in DNA and Chromatin Current Opinions in Genetics & Development. 25, 15-21: 2014
Divergent RNA transcription: A role in promoter unwinding? Transcription. 4. 2013
Chromatin organisation in the mammalian nucleus. Int. Rev. Cytol. 242, 283-336.
The relationship between chromatin structure and transcriptional activity in mammalian genomes. Brief. Funct. Genomic. Proteomic. 4, 129.