个人简介

Ph.D. University of Toronto B.Sc. University of Waterloo

研究领域

Bioinformatics & Computational Biology Functional Genomics Genetics Molecular Biology

Our research investigates how the genome is folded and organised in the nucleus and how this organisation influences regulation of gene expression. We often think about transcription as occurring on a particular gene in a linear manner whereas the nucleus is a three dimension organelle into which the genome is folded and organised. Recent work has shown that all transcription occurs at discreet compartments within the nucleus, termed transcription factories, with genes moving in and out of these compartments as they are expressed and silenced. Furthermore, distal enhancers have been shown to physically contact the genes they regulate forming tissue-specific chromatin loops. Our lab uses a combination of Molecular Biology and Cellular Imaging Techniques combined with genome-wide approaches and bioinformatics analysis to investigate the mechanisms that underlie tissue-specific regulation of gene expression and genome folding.

近期论文

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Chromatin Dynamics in Lineage Commitment and Cellular Reprogramming.Shchuka VM, Malek-Gilani N, Singh G, Langroudi L, Dhaliwal NK, Moorthy SD, Davidson S, Macpherson NN, Mitchell JA.Genes (Basel) 2015;6(3):641-61 pubmed The pluripotent regulatory circuitry connecting promoters to their long-range interacting elements.Schoenfelder S, Furlan-Magaril M, Mifsud B, Tavares-Cadete F, Sugar R, Javierre BM, Nagano T, Katsman Y, Sakthidevi M, Wingett SW, Dimitrova E, Dimond A, Edelman LB, Elderkin S, Tabbada K, Darbo E, Andrews S, Herman B, Higgs A, LeProust E, Osborne CS, Mitchell JA, Luscombe NM, Fraser P.Genome Res. 2015 Apr;25(4):582-97 pubmed A Sox2 distal enhancer cluster regulates embryonic stem cell differentiation potential.Zhou HY, Katsman Y, Dhaliwal NK, Davidson S, Macpherson NN, Sakthidevi M, Collura F, Mitchell JA.Genes Dev. 2014 Dec;28(24):2699-711 pubmed Nuclear organization of RNA polymerase II transcription.Davidson S, Macpherson N, Mitchell JA.Biochem. Cell Biol. 2013 Feb;91(1):22-30 pubmed Upstream distal regulatory elements contact the Lmo2 promoter in mouse erythroid cells.Bhattacharya A, Chen CY, Ho S, Mitchell JA.PLoS ONE 2012;7(12):e52880 pubmed Nuclear RNA sequencing of the mouse erythroid cell transcriptome.Mitchell JA, Clay I, Umlauf D, Chen CY, Moir CA, Eskiw CH, Schoenfelder S, Chakalova L, Nagano T, Fraser P.PLoS ONE 2012;7(11):e49274 pubmed Sensitive detection of chromatin coassociations using enhanced chromosome conformation capture on chip.Sexton T, Kurukuti S, Mitchell JA, Umlauf D, Nagano T, Fraser P.Nat Protoc 2012 Jul;7(7):1335-50 pubmed Enhancer identification in mouse embryonic stem cells using integrative modeling of chromatin and genomic features.Chen CY, Morris Q, Mitchell JA.BMC Genomics 2012;13:152 pubmed Preferential associations between co-regulated genes reveal a transcriptional interactome in erythroid cells.Schoenfelder S, Sexton T, Chakalova L, Cope NF, Horton A, Andrews S, Kurukuti S, Mitchell JA, Umlauf D, Dimitrova DS, Eskiw CH, Luo Y, Wei CL, Ruan Y, Bieker JJ, Fraser P.Nat. Genet. 2010 Jan;42(1):53-61 pubmed The Air noncoding RNA epigenetically silences transcription by targeting G9a to chromatin.Nagano T, Mitchell JA, Sanz LA, Pauler FM, Ferguson-Smith AC, Feil R, Fraser P.Science 2008 Dec;322(5908):1717-20 pubmed Transcription factories are nuclear subcompartments that remain in the absence of transcription.Mitchell JA, Fraser P.Genes Dev. 2008 Jan;22(1):20-5 pubmed