About

Kanishk Jain, PhD, is an assistant professor in the Department of Biochemistry, Molecular Biology and Biophysics at the University of Minnesota Twin Cities. His research focuses on combining classical biochemistry with genomic and proteomic approaches to understand the fundamental principles of chromatin engagement by epigenetic machinery and their contributions to human biology and disease. Specifically, he studies how the Histone Code is established and how chromatin is accessed both in vitro and in vivo, aiming to elucidate how these processes influence vital cellular mechanisms such as transcription, splicing, and DNA damage response. His work seeks to deepen the understanding of epigenetic regulation in human health and to develop new therapeutic strategies for cancer.

Research topics

• Genetics
• Biology
• Computational biology
• Cell biology
• Evolutionary biology
• Chemistry
• Botany
• Nanotechnology

Selected publications

• PRMT7 as a unique member of the protein arginine methyltransferase family: A review

  UNC Libraries · 2026-04-11

  articleOpen accessSenior author
  PublisherDOI

• YY1 relieves p300 autoinhibition to promote histone acetylation in advanced prostate cancer, enhancing the oncogenic signaling of Androgen Receptor Splice Variant 7

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-08-06

  preprintOpen access

  Abstract Genetic and epigenetic aberrations often act in concert to establish oncogenic transcriptomic programs in aggressive cancers. For example, the development of castration-resistant prostate cancer (CRPC), an advanced prostate cancer form, is closely associated with over-expression and/or hyper-activation of transcription factors (TFs) such as Androgen Receptor (AR) and Yin Yang 1 (YY1), as well as p300, a prominent histone acetyltransferase. How exactly these cancer-related lesions are coordinated to generate a malignant cell state remains elusive. Here, we demonstrate that YY1, which is frequently over-expressed in advanced prostate cancers, allosterically stimulates the acetyltransferase activity of p300 in cis , leading to the globally elevated acetylation of histone H3 lysine 18 and 27 (H3K18ac and H3K27ac). Mechanistically, YY1’s N-terminal activation domain (AD) directly interacts with p300’s TAZ2 domain, relieving the autoinhibition of p300 to facilitate substrate acetylation. Our integrated genome-wide mapping and transcriptomic studies reveal significant co-localization of genomic binding sites of YY1, androgen receptor splice variant 7 (AR-V7, a constitutively active form of AR) and p300 in CRPC cells, where the YY1-mediated p300 activation and resultant histone acetylation increases promote the oncogenic gene-expression programs downstream of YY1 and AR/AR-V7. Both in vitro and in vivo functional assays demonstrate a critical requirement of the above signaling for the advanced disease progression and drug resistance seen in CRPC. Altogether, this study uncovers that YY1 acts to alleviate p300’s autoinhibition at target genes co-bound by oncogenic TFs (YY1 and/or AR/AR-V7) in CRPC, thereby sustaining tumorigenicity. Additionally, the blockade of YY1-mediated gene activation resensitizes CRPC to treatment to the clinic anti-AR agent (enzalutamide), which provides a rationale for overcoming the therapeutic resistance often seen in advanced prostate cancers.

  PublisherOA PDFDOI

• A SETD2–CDK1–lamin axis maintains nuclear morphology and genome stability

  Nature Cell Biology · 2025-08-01 · 6 citations

  articleOpen access
  PublisherOA PDFDOI

• Histone H3 N-terminal recognition by the PHD finger of PHRF1 is required for proper DNA damage response

  Nucleic Acids Research · 2025-07-08 · 1 citations

  articleOpen access1st authorCorresponding

  Plant homeodomain (PHD) fingers are critical effectors of histone post-translational modifications (PTMs), regulating gene expression and genome integrity, and are frequently implicated in human disease. While most PHD fingers recognize unmodified and methylated states of histone H3 lysine 4 (H3K4), the specific functions of many of the over 100 human PHD finger-containing proteins are poorly understood. Here, we present a comprehensive analysis of one such poorly characterized PHD finger-containing protein, PHRF1. Using biochemical, molecular, and cellular approaches, we demonstrate that PHRF1 robustly binds to histone H3, specifically at its N-terminal region. Through integrating RNA-seq and proteomic analyses, we show that PHRF1 regulates transcription and RNA splicing and plays a critical role in DNA damage response (DDR). Crucially, we show that a cancer-associated mutation in the PHRF1 PHD finger (P221L) abolishes its histone interaction and fails to rescue defective DDR in PHRF1 knockout cells. These findings underscore the importance of the PHRF1-H3 interaction in maintaining genome integrity and provide new insight into how PHD fingers contribute to chromatin biology.

  PublisherOA PDFDOI

• Abstract 1798 Histone H3 N-terminal recognition by the PHD finger of PHRF1 is required for proper DNA damage response

  Journal of Biological Chemistry · 2025-05-01

  articleOpen access1st authorCorresponding

  Plant homeodomain (PHD) fingers are critical effectors of histone post-translational modifications (PTMs), acting as regulators of gene expression and genome integrity, and frequently presenting in human disease. While most PHD fingers recognize unmodified and methylated states of histone H3 lysine 4 (H3K4), the specific functions of many of the over 100 PHD finger-containing proteins in humans remain poorly understood, despite their significant implications in disease processes. In this study, we undertook a comprehensive analysis of one such poorly characterized PHD finger-containing protein, PHRF1.

  PublisherOA PDFDOI

• Leveraging Machine Learning for Cardiovascular Risk Prediction: A Comparative Approach

  2025-05-28

  articleSenior author
  PublisherDOI

• Learning What Matters: Prioritized Concept Learning via Relative Error-driven Sample Selection

  arXiv (Cornell University) · 2025-06-01

  preprintOpen access

  Instruction tuning has been central to the success of recent vision-language models (VLMs), but it remains expensive-requiring large-scale datasets, high-quality annotations, and large compute budgets. We propose PRioritized cOncept learninG via Relative Error-driven Sample Selection (PROGRESS), a data- and compute-efficient framework that enables VLMs to dynamically select what to learn next based on their evolving needs during training. At each stage, the model tracks its learning progress across skills and selects the most informative samples-those it has not already mastered and that are not too difficult to learn at the current stage of training. This strategy effectively controls skill acquisition and the order in which skills are learned. Specifically, we sample from skills showing the highest learning progress, prioritizing those with the most rapid improvement. Unlike prior methods, PROGRESS requires no upfront answer annotations, queries answers only on a need basis, avoids reliance on additional supervision from auxiliary VLMs, and does not require compute-heavy gradient computations for data selection. Experiments across multiple instruction-tuning datasets of varying scales demonstrate that PROGRESS consistently outperforms state-of-the-art baselines with much less data and supervision. Additionally, we show strong cross-architecture generalization and transferability to larger models, validating PROGRESS as a scalable solution for efficient learning.

  PublisherOA PDFDOI

• Non-canonical function of histone methyltransferase G9a in the translational regulation of chronic inflammation

  UNC Libraries · 2024-10-19

  articleOpen access
  PublisherDOI

• ACUTE PANCREATITIS MASQUERADING AS ST ELEVATION MYOCARDIAL INFARCTION

  INTERNATIONAL JOURNAL OF SCIENTIFIC RESEARCH · 2024-06-01

  article1st authorCorresponding

  Medicine over centuries has been developed and evolved to make the health and life of an individual easier. It is believed that the brightest minds take up medicine as a major, as it requires dealing with real beings and not just machines. In the past, scientist, researchers and physicians have been able to describe every disease presented before them in the easiest, most elaborative and scientic way possible. However, it is not always so easy, especially when one encounters an atypical presentation of an illness or multiple illnesses presenting at the same time. It is also difcult as sometimes, a disease presentation do not correlate with the tests, on which modern medicine so heavily depends, and doctors frequently require birds eye view in analyzing constellation of signs rather than getting biased on a single investigation. We present a case of 63 year old male presented to ER with chest pain and ECG too suggested STEMI which turned out to be acute pancreatitis.

  PublisherDOI

• Benchmarking Vision Language Models for Cultural Understanding

  2024-01-01 · 26 citations

  articleOpen access

  Shravan Nayak, Kanishk Jain, Rabiul Awal, Siva Reddy, Sjoerd Van Steenkiste, Lisa Anne Hendricks, Karolina Stanczak, Aishwarya Agrawal. Proceedings of the 2024 Conference on Empirical Methods in Natural Language Processing. 2024.

  PublisherOA PDFDOI

Frequent coauthors

• Brian D. Strahl

  University of North Carolina at Chapel Hill

  19 shared

• Krzysztof Krajewski

  11 shared

• Matthew R. Marunde

  EpiCypher (United States)

  9 shared

• Jonathan M. Burg

  EpiCypher (United States)

  7 shared

• Spencer W. Cooke

  University of North Carolina Health Care

  7 shared

• Nathan W. Hall

  EpiCypher (United States)

  7 shared

• Anup Vaidya

  EpiCypher (United States)

  7 shared

• Keli L. Rodriguez

  EpiCypher (United States)

  7 shared

Labs

• The Jain LabPI

Education

• Doctor of Philosophy in Biochemistry and Molecular Biology, Chemistry and Biochemistry

  UCLA Division of Physical Sciences

  2018

Awards & honors

• American Cancer Society Postdoctoral Fellow, 2021-24
• NIH/NCI Postdoctoral T32: Cancer Epigenetics Training Progra…
• NIH/NIGMS Predoctoral T32: Cellular and Molecular Biology Tr…