Gene Regulation, Epigenomics and Transcriptomics Current Students

Cody Aros

Mentor: Brigitte Gomperts
Research project:

Cody is studying the differences and similarities between the mechanisms underlying non-small cell and small cell cancers of the lung.

Publications:

Posttranslational modification of β-catenin is associated with pathogenic fibroblastic changes in bronchopulmonary dysplasia. Sucre JM, Vijayaraj P, Aros CJ, Wilkinson D, Paul M, Dunn B, Guttentag SH, Gomperts BN. Am J Physiol Lung Cell Mol Physiol. 2017 Feb 1;312(2):L186-L195. doi: 10.1152/ajplung.00477.2016. Epub 2016 Dec 9.

Narsis Attar

Mentor: Siavash Kurdistani
Research project:

Narsis’ current research involves investigating a novel function of chromatin in regulating cellular metal homeostasis.

Publications:

Narsis Attar & Siavash Kurdistani. Layered regulation of the epigenome and its link to cellular metabolism and physiology. Am. Assoc. Cancer Res. Educ. Book, April 2014

Endoplasmic reticulum-mitochondria junction is required for iron homeostasis. Xue Y, Schmollinger S, Attar N, Campos O, Vogelauer M, Carey MF, Merchant SS, Kurdistani SK. J Biol Chem. 2017 Jun 21. pii: jbc.M117.784249. doi: 10.1074/jbc.M117.784249. [Epub ahead of print]

Histone deacetylase inhibitors provoke a tumor supportive phenotype in pancreatic cancer associated fibroblasts. Nguyen AH, Elliott IA, Wu N, Matsumura C, Vogelauer M, Attar N, Dann A, Ghukasyan R, Toste PA, Patel SG, Williams JL, Li L, Dawson DW, Radu C, Kurdistani SK, Donahue TR. Oncotarget. 2017 Mar 21;8(12):19074-19088. doi: 10.18632/oncotarget.13572.

Exploitation of EP300 and CREBBP Lysine Acetyltransferases by Cancer. Attar N, Kurdistani SK. Cold Spring Harb Perspect Med. 2017 Mar 1;7(3). pii: a026534. doi: 10.1101/cshperspect.a026534. Review.

Adriana Corvalan

Mentor: Hillary Coller
Research project:

In the Coller Lab we are interested in quiescence, the cells resting state outside it’s proliferation cycle. Adriana is interested in the epigenetic changes that occur as a cell transitions from quiescence to proliferation (and vice versa) and how these epigenetic changes affect proliferation, gene expression, and chromatin compaction.

Nivedita Damodaren

Mentor: Currently rotating

Samantha Edwards

Mentor: Tracy Johnson
Research project:

Samantha is studying how the chromatin environment affects pre-mRNA splicing.

Publications:

Posttranscriptional Regulation of Gcr1 Expression and Activity Is Crucial for Metabolic Adjustment in Response to Glucose Availability. Hossain MA, Claggett JM, Edwards SR, Shi A, Pennebaker SL, Cheng MY, Hasty J, Johnson TL. Mol Cell. 2016 May 5;62(3):346-58. doi: 10.1016/j.molcel.2016.04.012.

Emily Hsu

Mentor: Arnold Berk

Research project:

Transcriptional activation of early viral genes by adenovirus large E1A via interactions with Mediator and p300

Lucia Ichino

Mentor: Currently rotating

Michael Kronenberg

Mentor: Michael Carey

Research Project:

Michael studies how transcription factor binding events at enhancers interact to stimulate enhancer-promoter looping and subsequent gene expression.

Jarrett Miller

Mentor: Kathrin Plath

Research project:

Jarrett is studying super enhancer logic in mouse embryonic stem cells.

Shawntel Okonkwo

Mentor: Tracy Johnson
Research project:

Shawntel studies the enzymatic activity underlying RNAPII CTD modification and its relationship to the splicing machinery.

Katherine Pohl

Mentor: Currently rotating

Kevin Qian

Mentor: Peter Tontonoz

Graham Read

Mentor: Currently rotating

Alex Salisbury (David)

Mentor: Tamer Sallam and Peter Tontonoz

Jaspreet Sandhu

Mentor: Peter Tontonoz
 Research project:

Jaspreet’s research focuses on Nuclear Receptors in Metabolism.

Publications:

Transcriptional regulation of macrophage cholesterol efflux and atherogenesis by a long noncoding RNA – Sallam T, Jones M, Thomas BJ, Wu X, Gilliland T, Qian K, Eskin A, Casero D, Zhang Z, Sandhu J, Salisbury D, Rajbhandari P, Civelek M, Hong C, Ito A, Liu X, Daniel B, Lusis AJ, Whitelegge J, Nagy L, Castrillo A, Smale S, Tontonoz P. Nat Med. 2018 Mar;24(3):304-312. doi: 10.1038/nm.4479. Epub 2018 Feb 12. PubMed PMID: 29431742; PubMed Central PMCID: PMC5839972.

IL-10 Signaling Remodels Adipose Chromatin Architecture to Limit Thermogenesis and Energy Expenditure – Rajbhandari P, Thomas BJ, Feng AC, Hong C, Wang J, Vergnes L, Sallam T, Wang B, Sandhu J, Seldin MM, Lusis AJ, Fong LG, Katz M, Lee R, Young SG, Reue K, Smale ST, Tontonoz P. Cell. 2018 Jan 11;172(1-2):218-233.e17. doi: 10.1016/j.cell.2017.11.019. Epub 2017 Dec 14. PubMed PMID: 29249357; PubMed Central PMCID: PMC5766418.

Noncoding RNA Discovery in Cardiovascular Disease: Decoding Form to Function – Sallam T, Sandhu J, Tontonoz P. Long. Circ Res. 2018 Jan 5;122(1):155-166. doi: 10.1161/CIRCRESAHA.117.311802. Review. PubMed PMID: 29301847; PubMed Central PMCID: PMC5902384.

Inhibition of cholesterol biosynthesis through RNF145-dependent ubiquitination of SCAP – Zhang L, Rajbhandari P, Priest C, Sandhu J, Wu X, Temel R, Castrillo A, de Aguiar Vallim TQ, Sallam T, Tontonoz P. Elife. 2017 Oct 25;6. pii: e28766. doi: 10.7554/eLife.28766. PubMed PMID: 29068315; PubMed Central PMCID: PMC5656429.

Critical Roles of the Histone Methyltransferase MLL4/KMT2D in Murine Hepatic Steatosis Directed by ABL1 and PPARγ2 – Kim DH, Kim J, Kwon JS, Sandhu J, Tontonoz P, Lee SK, Lee S, Lee JW. Cell Rep. 2016 Nov 1;17(6):1671-1682. doi: 10.1016/j.celrep.2016.10.023.

Feedback modulation of cholesterol metabolism by the lipid-responsive non-coding RNA LeXis – Sallam T, Jones MC, Gilliland T, Zhang L, Wu X, Eskin A, Sandhu J, Casero D, Vallim TQ, Hong C, Katz M, Lee R, Whitelegge J, Tontonoz P. Nature. 2016 May 11;534(7605):124-8. doi: 10.1038/nature17674.

CMF22 is a broadly conserved axonemal protein and is required for propulsive motility in Trypanosoma brucei – Nguyen HT, Sandhu J, Langousis G, Hill KL. Eukaryot Cell 2013 Sep;12(9):1202-13. doi: 10.1128/EC.00068-13. Epub 2013 Jul 12. PubMed PMID: 23851336; PubMed Central PMCID: PMC3811564.

 

Carina Sandoval

Mentor: Oliver Fregoso

Shawn (Ying Xuan) Tan

Mentor: Kathrin Plath
Research project:

Shawn is working on elucidation of the localization and molecular function of the Tsix IncRNA.

Guillaume Urtecho

Mentor: Sri Kosuri

Research project:

Guillaume researches multiplexed library approaches to studying promoter architecture in E. coli.

Publications:

Systematic Dissection of Sequence Elements Controlling σ70 Promoters Using a Genomically-Encoded Multiplexed Reporter Assay in E. coli. Biochemistry. Urtecho G, Tripp AD, Insigne K, Kim H, Kosuri S. Systematic Dissection of Sequence Elements Controlling σ70 Promoters Using a Genomically-Encoded Multiplexed Reporter Assay in E. coli. Biochemistry. February 2018:10.1021/acs.biochem.7b01069. doi:10.1021/acs.biochem.7b01069

Nathan Zemke

Mentor: Arnold Berk
Research project:

Characterizing the mechanisms of adenoviral E1A cellular reprogramming by examining its influence on gene expression and interacting cellular proteins.

Publications:

Adenovirus small E1A employs the lysine acetylases p300/CBP and tumor suppressor Rb to repress select host genes and promote productive virus infection. Ferrari R, Gou D, Jawdekar G, Johnson SA, Nava M, Su T, Yousef AF, Zemke NR, Pellegrini M, Kurdistani SK, Berk AJ. Cell Host Microbe. 2014 Nov 12;16(5):663-76. doi: 10.1016/j.chom.2014.10.004. Epub 2014 Nov 12.

Lingyu Zhan

Mentor: Jae Hoon Sul