Possible Rotation Projects:
HiChIP analysis
Nuclear lamina in metabolic disease
Foxa2 in ligand activation of nuclear receptors (ChIP-Seq)
Training Technologies Used:
Microarray
ChIP-on-ChIP Sequencing: GAI, GAII, Illmina HiSeq, ChIP-seq, RNA-Seq
- BS., Engineering, Chemical Engineering, Princeton University- 2001
- Ph.D.,Genomics and Computational Biology, University of Pennsylvania-2008
- Postdoctoral Fellow, Department of Genetics and Institute for Diabetes, Obesity and Metabolism, Perelman School of Medicine-2010
- Postdoctoral Fellow, Department of Biochemistry, Albert Einstein College of Medicine-2011
- Postdoctoral Fellow, Broad Institute of MIT and Harvard-2014
Bochkis, I.M., Rubins, N.E., White, P., Furth, E. E., Friedman, J.R., Kaestner, K.H. Hepatocyte-specific ablation of Foxa2 alters bile acid homeostasis and results in ER stress. 2008 Nature Medicine Aug;14(8):828-36. PMID:18660816
Bochkis, I.M., Schug, J., Rubins, N.E., Kaestner, K.H. Foxa2-dependent hepatic gene regulatory networks depend on physiological state. 2009 Physiological Genomics. Jul 9;38(2):186-95 PMID:19417011|
Bochkis, I.M., Schug, J., Ye, D.Z., Stratton, S.A., Barton, M.C., Kaestner, K.H. Genome-wide location analysis reveals distinct transcriptional circuitry by paralogous regulators Foxa1 and Foxa2. 2012 PLoS Genetics 8(6) PMID:22737085
Bochkis, I.M., Shin, S., Kaestner, K. H. Bile acid-induced inflammatory signaling in Foxa2-deficient mice leads to activation of mTOR and age-onset obesity. Molecular Metabolism 2013 2(4):447-56. PMID:24327960|
Bochkis, I.M.*, Przybylski, D., Chen, J., Regev, A. Changes in nucleosome occupancy associated with metabolic alterations in aged mammalian liver. Cell Reports 2014 Nov 9(3):996-1006
Whitton, H., Singh, L., Patrick, M.A., Osorio, F.G., López-Otín C, Bochkis, I.M. Changes at the nuclear lamina are required to increase binding of pioneer factor Foxa2 in aged liver. Aging Cell 2018 Jun;17(3):e12742| PMID:29484800
Price, A. J., Manjegowda, M.C., Bochkis, I.M. Hdac3, Setdb1, and Kap1 mark H3K9me3/H3K13ac bivalent regions in young and aged liver. Aging Cell. 2020 Feb;19(2):e13092. doi: 10.1111/acel.13092. Epub 2019 Dec 19. PMID: 31858687
Kain, J.*, Wei, X.*, Reddy, N.A., Price, A.J., Woods, C., Bochkis I.M. Pioneer factor Foxa2 enables ligand-dependent activation of type II nuclear receptors FXR and LXRα. Mol Metab. 2021 Jul 8;53:101291. doi: 10.1016/j.molmet.2021.101291 *equal contribution PMID: 34246806
Wei X, Murphy MA, Reddy NA, Hao Y, Eggertsen TG, Saucerman JJ, Bochkis IM. Redistribution of lamina-associated domains reshapes binding of pioneer factor FOXA2 in development of nonalcoholic fatty liver disease. Genome Research 2022 Nov-Dec;32(11-12):1981-1992. doi: 10.1101/gr.277149.122. Epub 2022 Dec 15. | PMID: 36522168.
Hao Y, Han L, Wu A, Bochkis IM, Pioneer factor Foxa2 mediates chromatin conformation changes for activation of bile acid targets of FXR. Cell Mol Gastroenterol Hepatol. 2023 Oct 23:S2352-345X(23)00188-1. doi: 10.1016/j.jcmgh.2023.10.009. Epub ahead of print. PMID: 37879405.
Schinderle, JD, Bochkis IM. Sequential ChIP-Seq. Methods in molecular biology (Clifton, N.J.)vol. 2846 (2024): 109-121. doi:10.1007/978-1-0716-4071-5_7 Invited Chapter
Schinderle JD, Wu A, Bochkis IM. Reduced ZMPSTE24 expression leads to prelamin accumulation and development of steatosis in MASLD patients. Sci Rep. 2025 Nov 26;15(1):45429. doi: 10.1038/s41598-025-30052-y. PMID: 41298941; PMCID: PMC12748725
Our ongoing studies are investigating how cellular processes govern proper metabolic function and how abnormal physiology leads to metabolic disease. We are focusing on understanding how genome-wide chromatin and transcriptional changes, which include chromatin accessibility, nuclear localization and dynamics, and genome organization, lead to physiological dysfunction. We employ a variety of genomic tools, including ATAC-Seq, ChIP-Seq, and RNA-Seq. Recently we have implemented both the experimental protocol and analysis pipeline for HiChIP, a combination of Hi-C and ChIP to study long-range genomic interactions facilitated by binding of a transcription factor.
Our projects including studying the role of pioneer factor Foxa2 in liver metabolism, investigating the function of nuclear lamina in liver disease, and exploring chromatin changes in models of metabolic dysfunction.
