Our Research
The Histone Code
The Histone Code is governed by a dynamic interplay of “writers,” “readers,” and “erasers” that regulate processes like transcription, splicing, and the DNA damage response. Writers, such as histone acetyltransferases and methyltransferases, add specific post-translational modifications (PTMs) to histones, while erasers, like histone deacetylases, remove these marks. Readers, including plant homeodomain (PHD) or chromodomain proteins, recognize and bind to these modifications, influencing chromatin structure and recruiting factors involved in gene regulation, splicing machinery, or DNA repair proteins, thereby orchestrating cellular responses.
We aim to advance our understanding of chromatin engagement by chromatin readers, writers, and erasers and the implications to human biology by addressing two central themes:
a. Understanding histone reader engagement with chromatin in cancer:
Our lab investigates how chromatin-associated regulators govern gene expression, RNA processing, and genomic stability—processes frequently altered in cancer. Central to this work is PHRF1, a multi-domain protein that recognizes specific histone signatures and modulates downstream transcriptional and splicing events. By uncovering how PHRF1 integrates these signals, we aim to clarify how cells maintain proper gene activity and respond to genomic stress.
To accomplish this, we combine structural biology, biochemical analyses, and cutting-edge functional genomics to piece together PHRF1’s regulatory mechanisms. Through these integrated approaches, we are unraveling how PHRF1 influences transcription elongation, shapes RNA splicing patterns, and responds to DNA damage. Our goal is to leverage these insights into new concepts for targeting the dysregulation of gene control mechanisms, ultimately informing innovative strategies for cancer therapy.
Relevant work:
- Kanishk Jain*, Pata-Eting K. Tchara, Amanuel B. Mengistalem, Aidan P. Holland, Christopher N. Bowman, Matthew R. Marunde, Irina K. Popov, Spencer W. Cooke, Krzysztof Krajewski, Michael-Christopher Keogh, Jean-Philippe Lambert, and Brian D. Strahl*. “Histone H3 N-terminal recognition by the PHD finger of PHRF1 is required for proper DNA damage response.” https://doi.org/10.1101/2024.11.20.623956 *denotes co-corresponding authors
- Kanishk Jain, Caroline S. Fraser, Matthew Marunde, Madison M. Parker, Cari Sagum, Jon Burg, Nathan Hall, Irina Popova, Keli Rodriguez, Anup Vadiya, Krzysztof Krajewski, Michael-Christopher Keogh, Mark T. Bedford, and Brian D. Strahl. “Characterization of the plant homeodomain (PHD) reader family for their histone tail interactions.” Epigenetics & Chromatin. 2020 Jan 13:3.
b. Demystifying the complex hierarchy of histone PTMs and their crosstalk
Our lab is also devoted to understanding how the Histone Code shapes gene expression. Building on the approaches and insights we applied to other chromatin factors, we now focus on how enzymes like MLL1-4 (key histone H3 K4 methyltransferases) and arginine methyltransferases (PRMTs) work together or in opposition to place these marks. We’ve shown that acetylation of H3 enhances MLL1 and MLL4 activity on H3 K4, influencing the activity of genes involved in essential cellular processes, while our work on PRMTs is beginning to reveal crosstalk between different histone methylarginine marks.
By exploring these dynamic enzyme interactions, we aim to understand how the interplay of different histone modifications creates unique regulatory environments in the genome. We use a combination of biochemical assays and advanced mass spectrometry to identify which modifications naturally occur together and how they direct the placement of each other’s marks. Ultimately, by deciphering how the MLL family, PRMTs, and related enzymes coordinate their actions on histones and other chromatin associated proteins, our lab seeks to uncover fresh insights into gene control that could guide new strategies for targeting malfunctioning gene regulation in disease.
Relevant work:
- Geoffrey C. Fox, Karl F. Poncha, B. Rutledge Smith, Lara N. van der Maas, Nathaniel N. Robbins, Bria Graham, Jill M. Dowen, Brian D. Strahl*, Nicolas L. Young*, and Kanishk Jain*. “H3K18 & H3K23 acetylation directs establishment of MLL-mediated H3K4 methylation.” Biol. Chem. 2024 Aug; 300(8) 107527 *denotes co-corresponding authors
- Kanishk Jain, Matthew R. Marunde, Jonathan M. Burg, Susan L. Gloor, Faith M. Joseph, Karl F. Poncha, Zachary B. Gillespie, Keli L. Rodriguez, Irina K. Popova, Nathan W. Hall, Anup Vaidya, Sarah A. Howard, Hailey F. Taylor, Laylo Mukhsinova, Ugochi C. Onuoha, Emily F. Patteson, Spencer W. Cooke, Bethany C. Taylor, Ellen N. Weinzapfel, Marcus A. Cheek, Matthew J. Meiners, Geoffrey C. Fox, Kevin E. Namitz, Martis W. Cowles, Krzysztof Krajewski, Zu-Wen Sun, Michael S. Cosgrove, Nicolas Young, Michael-C Keogh, and Brian D. Strahl. “An acetylation-mediated chromatin switch governs H3K4 read-write capability.” eLife. 2023 May 12:e82596. Note: This study was published in eLife through the conventional peer-review method.
- Kanishk Jain and Steven G. Clarke. “PRMT7: a unique member of the protein arginine methyltransferase family.” Archive of Biochemistry and Biophysics. 2019 Apr 665: 36-45.
- Kanishk Jain, Cyrus Y. Jin, and Steven G. Clarke. “Epigenetic control via allosteric regulation of mammalian protein arginine methyltransferases.” PNAS USA. 2017 Sep 114(38):10101-10106.
- Kanishk Jain, Rebeccah A. Warmack, Erik W. Debler, Andrea Hadjikyriacou, Pete Stavropoulos, Günter Blobel, and Steven G. Clarke. “Protein arginine methyltransferase product specificity is mediated by distinct active-site architectures.” Biol. Chem. 2016 Aug 291(35): 18299-308.
- Erik W. Debler, Kanishk Jain, Rebeccah A. Warmack, You Feng, Steven G. Clarke, Gunter Blobel, and Pete Stravropoulos. “A glutamate/aspartate switch controls product specificity in a protein arginine methyltransferase.” PNAS USA. 2016 Feb 113(8): 2068-73.