Jennifer Mitchell

faculty_img Academic Title: Associate Professor

Campus: St. George

CSB Appointment: Full

Primary Undergraduate Department:
Cell & Systems Biology

Graduate Programs:
Cell & Systems Biology

Titles and Honors:
CIHR new investigator

Academic or Administrative Appointments:


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

 

Mailing Address
Department of Cell & Systems Biology
University of Toronto
25 Harbord St.
Toronto, ON M5S 3G5
Canada

 

Contact Information
Office phone: 416-978-6711
Office: RW 533A
Lab: RW 532 / 533
Lab phone: 416-978-6715
Email: ja.mitchell@utoronto.ca
URL: http://labs.csb.utoronto.ca/mitchell

 

Research Areas
Bioinformatics & Computational Biology
Functional Genomics
Genetics
Molecular Biology

 

Research

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.

 

Publications

 

 

2016

Top

Enhancers and super-enhancers have an equivalent regulatory role in embryonic stem cells through regulation of single or multiple genesMoorthy SD, Davidson S, Shchuka VM, Singh G, Malek-Gilani N, Langroudi L, Martchenko A, So V, Macpherson NN and Mitchell JA. . Genome Res. 2016 (Nov 28).
pubmed
Generating CRISPR/Cas9 Mediated Monoallelic Deletions to Study Enhancer Function in Mouse Embryonic Stem Cells J Vis Exp 2016, (110), e53552Moorthy SD, Mitchell JA.
pubmed
Nuclear RNA Isolation and Sequencing.Methods Mol Biol. 2016;1402:63-71.Dhaliwal NK, Mitchell JA
pubmed
 

2015

Top

Rapamycin reduces fibroblast proliferation without causing quiescence and induces STAT5A/B-mediated cytokine production. Nucleus 2015, 6(6):490-506.Gillespie ZE, MacKay K, Sander M, Trost B, Dawicki W, Wickramarathna A, Gordon J, Eramian M, Kill IR, Bridger JM, Kusalik A, Mitchell JA, Eskiw CH.
pubmed
Concordance between RNA-sequencing data and DNA microarray data in transcriptome analysis of proliferative and quiescent fibroblasts.Trost B, Moir CA, Gillespie ZE, Kusalik A, Mitchell JA, Eskiw CH. R Soc Open Sci. 2015 Sep 30;2(9):150402
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
 

2014

Top

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
 

2013

Top

Nuclear organization of RNA polymerase II transcription.Davidson S, Macpherson N, Mitchell JA.Biochem. Cell Biol. 2013 Feb;91(1):22-30
pubmed
 

2012

Top

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
 

2010

Top

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
 

2008

Top

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
 

2007

Top

Intergenic transcription, cell-cycle and the developmentally regulated epigenetic profile of the human beta-globin locus.Miles J, Mitchell JA, Chakalova L, Goyenechea B, Osborne CS, O’Neill L, Tanimoto K, Engel JD, Fraser P.PLoS ONE 2007;2(7):e630
pubmed
Myc dynamically and preferentially relocates to a transcription factory occupied by Igh.Osborne CS, Chakalova L, Mitchell JA, Horton A, Wood AL, Bolland DJ, Corcoran AE, Fraser P.PLoS Biol. 2007 Aug;5(8):e192
pubmed
 

2005

Top

Replication and transcription: shaping the landscape of the genome.Chakalova L, Debrand E, Mitchell JA, Osborne CS, Fraser P.Nat. Rev. Genet. 2005 Sep;6(9):669-77
pubmed
Differential activation of the connexin 43 promoter by dimers of activator protein-1 transcription factors in myometrial cells.Mitchell JA, Lye SJ.Endocrinology 2005 Apr;146(4):2048-54
pubmed
 

2004

Top

Active genes dynamically colocalize to shared sites of ongoing transcription.Osborne CS, Chakalova L, Brown KE, Carter D, Horton A, Debrand E, Goyenechea B, Mitchell JA, Lopes S, Reik W, Fraser P.Nat. Genet. 2004 Oct;36(10):1065-71
pubmed
Mechanical stretch and progesterone differentially regulate activator protein-1 transcription factors in primary rat myometrial smooth muscle cells.Mitchell JA, Shynlova O, Langille BL, Lye SJ.Am. J. Physiol. Endocrinol. Metab. 2004 Sep;287(3):E439-45
pubmed
Progesterone and gravidity differentially regulate expression of extracellular matrix components in the pregnant rat myometrium.Shynlova O, Mitchell JA, Tsampalieros A, Langille BL, Lye SJ.Biol. Reprod. 2004 Apr;70(4):986-92
pubmed
 

2003

Top

Parathyroid hormone-related protein treatment of pregnant rats delays the increase in connexin 43 and oxytocin receptor expression in the myometrium.Mitchell JA, Ting TC, Wong S, Mitchell BF, Lye SJ.Biol. Reprod. 2003 Aug;69(2):556-62
pubmed
 

2002

Top

Differential expression of activator protein-1 transcription factors in pregnant rat myometrium.Mitchell JA, Lye SJ.Biol. Reprod. 2002 Jul;67(1):240-6
pubmed

 

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2015

Top
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

2014

Top
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

2013

Top
Nuclear organization of RNA polymerase II transcription.Davidson S, Macpherson N, Mitchell JA.Biochem. Cell Biol. 2013 Feb;91(1):22-30
pubmed

2012

Top
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

2010

Top
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

2008

Top
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

2007

Top
Intergenic transcription, cell-cycle and the developmentally regulated epigenetic profile of the human beta-globin locus.Miles J, Mitchell JA, Chakalova L, Goyenechea B, Osborne CS, O'Neill L, Tanimoto K, Engel JD, Fraser P.PLoS ONE 2007;2(7):e630
pubmed
Myc dynamically and preferentially relocates to a transcription factory occupied by Igh.Osborne CS, Chakalova L, Mitchell JA, Horton A, Wood AL, Bolland DJ, Corcoran AE, Fraser P.PLoS Biol. 2007 Aug;5(8):e192
pubmed

2005

Top
Replication and transcription: shaping the landscape of the genome.Chakalova L, Debrand E, Mitchell JA, Osborne CS, Fraser P.Nat. Rev. Genet. 2005 Sep;6(9):669-77
pubmed
Differential activation of the connexin 43 promoter by dimers of activator protein-1 transcription factors in myometrial cells.Mitchell JA, Lye SJ.Endocrinology 2005 Apr;146(4):2048-54
pubmed

2004

Top
Active genes dynamically colocalize to shared sites of ongoing transcription.Osborne CS, Chakalova L, Brown KE, Carter D, Horton A, Debrand E, Goyenechea B, Mitchell JA, Lopes S, Reik W, Fraser P.Nat. Genet. 2004 Oct;36(10):1065-71
pubmed
Mechanical stretch and progesterone differentially regulate activator protein-1 transcription factors in primary rat myometrial smooth muscle cells.Mitchell JA, Shynlova O, Langille BL, Lye SJ.Am. J. Physiol. Endocrinol. Metab. 2004 Sep;287(3):E439-45
pubmed
Progesterone and gravidity differentially regulate expression of extracellular matrix components in the pregnant rat myometrium.Shynlova O, Mitchell JA, Tsampalieros A, Langille BL, Lye SJ.Biol. Reprod. 2004 Apr;70(4):986-92
pubmed

2003

Top
Parathyroid hormone-related protein treatment of pregnant rats delays the increase in connexin 43 and oxytocin receptor expression in the myometrium.Mitchell JA, Ting TC, Wong S, Mitchell BF, Lye SJ.Biol. Reprod. 2003 Aug;69(2):556-62
pubmed

2002

Top
Differential expression of activator protein-1 transcription factors in pregnant rat myometrium.Mitchell JA, Lye SJ.Biol. Reprod. 2002 Jul;67(1):240-6
pubmed

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