Investigating a role for the cohesin complex in chromatin looping, gene regulation and development
Lead Research Organisation:
University College London
Department Name: Cancer Biology
Abstract
Cell division poses one of the central questions of biology, namely, how does a single cell manage to replicate and separate its entire genome ensuring that both new cells receive an exact copy of each chromosome. To do this, a specialized group of proteins, known as the cohesins, play a central role ensuring that newly replicated DNA molecules do not prematurely separate, resulting in abnormal chromosome distribution and ultimately cell death. However, recent studies have shown that cohesin proteins do more then simply hold DNA strands together. Evidence from human diseases and animal models have suggested cohesins also control gene expression in the cell. My research will focus on how cohesin proteins, with their unique ability to hold DNA molecules together, influence gene expression during cellular development and if this can be explained by their role in establishing the correct 3-dimensional organization of genes within the cell nucleus.
Technical Summary
Cohesin proteins have a well established role in sister chromatid cohesion. In addition to their structural role, new evidence implicates cohesins in the regulation of gene expression. Cohesin has been shown to colocalise with CTCF on mammalian chromosome arms. CTCF is a sequence-specific DNA binding protein known to function as a transcriptional regulator, chromatin insulator and boundary element. The functional association between CTCF and cohesin provides one way by which cohesins could influence the expression of genes.
Both inter- and intra-chromosomal CTCF-dependent chromatin loops have been described at several loci. It is likely that cohesin proteins could mediate CTCF-dependent chromatin loops due to their unique ability to establish links between chromatin fibres, as well as their colocalization to CTCF sites reported to be involved in chromatin looping. By constraining the conformation of chromatin, cohesins could affect the probability with which distal regulatory elements interact and thus gene expression. The first aim of this proposal is to address whether cohesin proteins, rather then simply behaving as architectural elements, can re-use their ability to tether chromatids to mediate chromatin loop conformations and if these conformations are important for gene function. RNAi and genetic methods will help to establish if these interactions are functional.
The binding of CTCF to chromatin is sensitive to DNA methylation and recent reports indicate that DNA methylation profiles change extensively during development. Indeed, cohesin mapping data reveals cell-type specific patterns of cohesin binding that correlate with differential methylation. The second aim of this proposal is to address whether CTCF-dependent cohesin recruitment to specific sites changes from pluripotent to committed cells. The differential localization of cohesin and CTCF proteins could function to regulate the expression of these genes, possibly through the formation of cell-type specific chromatin loops or through the recruitment of regulatory complexes whose composition changes during development.
I will use readily available molecular and computational biology techniques to study chromatin topology and cohesin localization during development, at both specific loci and genome-wide to gain insight into the role of cohesins in gene regulation.
Cohesins play a key role during cell division to prevent anueploidy. Normal cells are able to sense DNA damage or abnormal chromosome segregation and will cease to divide whereas cancer cells can override these checkpoints and accumulate abnormal DNA. Thus, having a basic understanding of the mechanisms and proteins which facilitate normal chromosome transmission and function will be directly relevant to an understanding of cancer.
Both inter- and intra-chromosomal CTCF-dependent chromatin loops have been described at several loci. It is likely that cohesin proteins could mediate CTCF-dependent chromatin loops due to their unique ability to establish links between chromatin fibres, as well as their colocalization to CTCF sites reported to be involved in chromatin looping. By constraining the conformation of chromatin, cohesins could affect the probability with which distal regulatory elements interact and thus gene expression. The first aim of this proposal is to address whether cohesin proteins, rather then simply behaving as architectural elements, can re-use their ability to tether chromatids to mediate chromatin loop conformations and if these conformations are important for gene function. RNAi and genetic methods will help to establish if these interactions are functional.
The binding of CTCF to chromatin is sensitive to DNA methylation and recent reports indicate that DNA methylation profiles change extensively during development. Indeed, cohesin mapping data reveals cell-type specific patterns of cohesin binding that correlate with differential methylation. The second aim of this proposal is to address whether CTCF-dependent cohesin recruitment to specific sites changes from pluripotent to committed cells. The differential localization of cohesin and CTCF proteins could function to regulate the expression of these genes, possibly through the formation of cell-type specific chromatin loops or through the recruitment of regulatory complexes whose composition changes during development.
I will use readily available molecular and computational biology techniques to study chromatin topology and cohesin localization during development, at both specific loci and genome-wide to gain insight into the role of cohesins in gene regulation.
Cohesins play a key role during cell division to prevent anueploidy. Normal cells are able to sense DNA damage or abnormal chromosome segregation and will cease to divide whereas cancer cells can override these checkpoints and accumulate abnormal DNA. Thus, having a basic understanding of the mechanisms and proteins which facilitate normal chromosome transmission and function will be directly relevant to an understanding of cancer.