Biology subjects

Georgiades, E.

Publications and source records attributed to Georgiades, E..

4 recordsLinked to original sources

bioRxiv2024

Deciphering cis-regulatory elements using REgulamentary

With the boom in Genome-Wide Association Studies (GWAS), it has become apparent that many disease-associated genetic variants lie in the non-coding regions of the genome. In order to prioritise these variants and disentangle their functional significance, it is important to be able to accurately classify cis-regulatory elements within these non-coding regions of the genome. Historically, the classification of cis-regulatory elements relied purely on the presence of characteristic histone marks, with recent advancements in their classification using more sophisticated Hidden Markov Model (HMM)-based approaches. The limitation of the HMM-based approaches is that the output of these models is an arbitrary chromatin state, which then requires the user to manually assign these states to a particular class of cis-regulatory elements. Here we present a new tool, REgulamentary, which enables de novo genome-wide annotation of cis-regulatory elements in a cell-type specific manner. We benchmarked REgulamentary against GenoSTAN, the most popular existing published chromatin annotation and regulatory element identification tool, to demonstrate the advancements REgulamentary can provide in assigning chromatin states. Finally, as an example of REgulamentarys utility in solving complex disease trait loci, we applied REgulamentary to published GWAS data to demonstrate how this tool can be used to prioritise likely causal variants.

bioinformatics↗

bioRxiv2023

Active regulatory elements recruit cohesin to establish cell-specific chromatin domains.

As the structure of the genome is analysed at ever increasing resolution it is becoming clear that there is considerable variation in the 3D chromatin architecture across different cell types. It has been proposed that this may, in part, be due to increased recruitment of cohesin to activated cis-elements (enhancers and promoters) leading to cell-type specific loop extrusion underlying the formation of new subTADs. Here we show that cohesin correlates well with the presence of active enhancers and this varies in an allele-specific manner with the presence or absence of polymorphic enhancers which vary from one individual to another. Using the alpha globin cluster as a model, we show that when all enhancers are removed, peaks of cohesin disappear from these regions and the erythroid specific subTAD is no longer formed. Re-insertion of the major alpha globin enhancer (R2) is associated with the appearance of a new peak of cohesin at the site of insertion. In complementary experiments insertion of R2 into a "neutral" region of the genome recruits cohesin, induces transcription and creates a new large (75kb) erythroid specific domain. Together these findings support the proposal that active enhancers recruit cohesin, stimulate loop extrusion and promote the formation of cell specific subTADs.

genomics↗

bioRxiv2023

Loop extrusion by cohesin plays a key role in enhancer-activated gene expression during differentiation

Enhancers and their target promoters often come into close physical proximity when activated. This proximity may be explained by a variety of mechanisms; most recently via cohesin-mediated chromatin loop extrusion. Despite this compelling hypothesis, acute depletion of cohesin does not cause widespread changes in gene expression. We have tested the role of cohesin-mediated loop extrusion on gene expression at the mouse alpha-globin locus during erythropoiesis. Acute depletion of cohesin downregulates alpha-globin expression at early but not late stages of differentiation. When single or multiple CTCF sites are placed between the alpha-globin enhancers and promoters, alpha-gene expression is downregulated. Importantly, the orientation of the CTCF site plays a critical role, suggesting that within this activated domain, cohesin predominantly but not exclusively translocates from the enhancers to the promoters. We find that loop extrusion does play an important role in establishing enhancer-promoter proximity and consequent expression of inducible genes during differentiation.

molecular biology↗

bioRxiv2019

Dissection of the 4D chromatin structure of the α-globin locus through in vivo erythroid differentiation with extreme spatial and temporal resolution

Mammalian gene expression patterns are controlled by regulatory elements, which interact within Topologically Associating Domains (TADs). The relationship between activation of regulatory elements, formation of structural chromatin interactions and gene expression during development is unclear. We developed Tiled-C, a low-input Chromosome Conformation Capture (3C) approach, to study chromatin architecture at high spatial and temporal resolution through in vivo mouse erythroid differentiation. Integrated analysis of matched chromatin accessibility and single-cell expression data shows that regulatory elements gradually become accessible within pre-existing TADs during early differentiation. This is followed by structural re-organization within the TAD and formation of specific contacts between enhancers and promoters. In contrast to previous reports, our high-resolution data show that these enhancer-promoter interactions are not established prior to gene expression, but formed gradually during differentiation, concomitant with progressive upregulation of gene activity. Together, these results provide new insight into the close, interdependent relationship between chromatin architecture and gene regulation during development.

genomics↗