Statistical analysis of genome-wide chromatin organisation using Hi-C

Statistical analysis of genome-wide chromatin organisation using Hi-C

Project details

Hi-C combines chromosome conformation capture with high-throughput sequencing to detect chromatin interactions on a genome-wide scale. The interactions give insight into 3D chromatin organisation and suggest how long-range enhancers can promote or inhibit the expression of particular genes. DNA regions with intense interactions suggest closely packed DNA clusters or topologically associated domains (TADS). This project will develop statistical methods for detecting interactions and TADS and for testing whether TADS are conserved between cell types or experimental conditions. The project will involve advanced statistical methods and R programming.

About our research group

Professor Smyth is a statistical bioinformatician with a long history of developing new statistical techniques for the analysis of genomic data from microarray, RNA-seq, ChIP-seq and Hi-C technology. His laboratory has developed a number of widely used R software packages including limma, edgeR, goseq, csaw, diffHic and Rsubread that have become standards in the field. The diffHic package in particular is designed to process Hi-C data and to test for differential chromatin interactions between experimental conditions (Lun, BMC Bioinformatics 2015 16:258). Professor Smyth and his Lab have an ongoing collaboration with Dr Rhys Allen's Lab to study how global genome architecture controls cell identity (Johanson, PLOS Genetics 2018 14(6):e1007431; Johanson, Nature Immunology 2018 19(11):1257).

Researchers:

Professor Gordon Smyth

Professor Gordon Smyth writing on a whiteboard
Professor
Gordon
Smyth
Joint Division Head
Dr Hannah Coughlan
Dr
Hannah
Coughlan
Bioinformatics division

Dr Rhys Allan

Dr Rhys Allan
Dr
Rhys
Allan
Laboratory Head

Project Type: