Bio

Bio


Jake Kirkland Ph.D. is a Postdoctoral Scholar in the lab of Dr. Gerald Crabtree. He is interested in the role of Chromatin Regulators in cancer and understanding mechanisms of disease using genome-wide techniques and epigenome editing.

Professional Education


  • Bachelor of Arts, University of California Berkeley (2003)
  • Doctor of Philosophy, University of California Santa Cruz (2013)

Stanford Advisors


Research & Scholarship

Lab Affiliations


Publications

All Publications


  • Dominant-negative SMARCA4 mutants alter the accessibility landscape of tissue-unrestricted enhancers. Nature structural & molecular biology Hodges, H. C., Stanton, B. Z., Cermakova, K., Chang, C. Y., Miller, E. L., Kirkland, J. G., Ku, W. L., Veverka, V., Zhao, K., Crabtree, G. R. 2018; 25 (1): 61?72

    Abstract

    Mutation of SMARCA4 (BRG1), the ATPase of BAF (mSWI/SNF) and PBAF complexes, contributes to a range of malignancies and neurologic disorders. Unfortunately, the effects of SMARCA4 missense mutations have remained uncertain. Here we show that SMARCA4 cancer missense mutations target conserved ATPase surfaces and disrupt the mechanochemical cycle of remodeling. We find that heterozygous expression of mutants alters the open chromatin landscape at thousands of sites across the genome. Loss of DNA accessibility does not directly overlap with Polycomb accumulation, but is enriched in 'A compartments' at active enhancers, which lose H3K27ac but not H3K4me1. Affected positions include hundreds of sites identified as superenhancers in many tissues. Dominant-negative mutation induces pro-oncogenic expression changes, including increased expression of Myc and its target genes. Together, our data suggest that disruption of enhancer accessibility represents a key source of altered function in disorders with SMARCA4 mutations in a wide variety of tissues.

    View details for PubMedID 29323272

  • Rapid and reversible epigenome editing by endogenous chromatin regulators NATURE COMMUNICATIONS Braun, S. G., Kirkland, J. G., Chory, E. J., Husmann, D., Calarco, J. P., Crabtree, G. R. 2017; 8: 560

    Abstract

    Understanding the causal link between epigenetic marks and gene regulation remains a central question in chromatin biology. To edit the epigenome we developed the FIRE-Cas9 system for rapid and reversible recruitment of endogenous chromatin regulators to specific genomic loci. We enhanced the dCas9-MS2 anchor for genome targeting with Fkbp/Frb dimerizing fusion proteins to allow chemical-induced proximity of a desired chromatin regulator. We find that mSWI/SNF (BAF) complex recruitment is sufficient to oppose Polycomb within minutes, leading to activation of bivalent gene transcription in mouse embryonic stem cells. Furthermore, Hp1/Suv39h1 heterochromatin complex recruitment to active promoters deposits H3K9me3 domains, resulting in gene silencing that can be reversed upon washout of the chemical dimerizer. This inducible recruitment strategy provides precise kinetic information to model epigenetic memory and plasticity. It is broadly applicable to mechanistic studies of chromatin in mammalian cells and is particularly suited to the analysis of endogenous multi-subunit chromatin regulator complexes.Understanding the link between epigenetic marks and gene regulation requires the development of new tools to directly manipulate chromatin. Here the authors demonstrate a Cas9-based system to recruit chromatin remodelers to loci of interest, allowing rapid, reversible manipulation of epigenetic states.

    View details for PubMedID 28916764

  • The Many Roles of BAF (mSWI/SNF) and PBAF Complexes in Cancer. Cold Spring Harbor perspectives in medicine Hodges, C., Kirkland, J. G., Crabtree, G. R. 2016; 6 (8)

    Abstract

    During the last decade, a host of epigenetic mechanisms were found to contribute to cancer and other human diseases. Several genomic studies have revealed that ?20% of malignancies have alterations of the subunits of polymorphic BRG-/BRM-associated factor (BAF) and Polybromo-associated BAF (PBAF) complexes, making them among the most frequently mutated complexes in cancer. Recurrent mutations arise in genes encoding several BAF/PBAF subunits, including ARID1A, ARID2, PBRM1, SMARCA4, and SMARCB1 These subunits share some degree of conservation with subunits from related adenosine triphosphate (ATP)-dependent chromatin remodeling complexes in model organisms, in which a large body of work provides insight into their roles in cancer. Here, we review the roles of BAF- and PBAF-like complexes in these organisms, and relate these findings to recent discoveries in cancer epigenomics. We review several roles of BAF and PBAF complexes in cancer, including transcriptional regulation, DNA repair, and regulation of chromatin architecture and topology. More recent results highlight the need for new techniques to study these complexes.

    View details for DOI 10.1101/cshperspect.a026930

    View details for PubMedID 27413115

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