About

John Tamkun is a Professor of Molecular, Cell & Developmental Biology at UCSC. He holds a B.A. from the University of South Florida and a Ph.D. from the Massachusetts Institute of Technology. His research focuses on the regulation of chromatin structure and gene expression, particularly through the study of nucleosomes and chromatin-remodeling complexes. Tamkun's laboratory uses the fruit fly Drosophila melanogaster as a model organism to investigate how chromatin-remodeling complexes are regulated, targeted to specific genes, and interact with histone-modifying enzymes and other regulatory proteins to modulate chromatin structure and transcription. His work emphasizes understanding the roles of chromatin remodeling in transcriptional regulation, higher-order chromatin structure maintenance, and cell fate specification. The research is highly relevant to human health, as conserved counterparts of Drosophila chromatin-remodeling factors are present in humans, and mutations in related genes are associated with cancer and other diseases.

Research topics

• Biology
• Genetics
• Cell biology
• Molecular biology
• Computational biology

Selected publications

• A genetic screen for regulators of <i>Drosophila</i> histone H1 binding and chromosome structure in vivo

  Genetics · 2026-02-07

  articleOpen accessSenior author

  Histone H1 and related linker histones play critical roles in chromosome organization in eukaryotic cells. Although histone H1 is essential for compacting nucleosomes into chromatin fibers and is a major structural component of chromosomes, its association with chromatin is highly dynamic. Histone H1 exchange modulates the accessibility of regulatory proteins to DNA and has been implicated in the regulation of gene expression and cellular pluripotency. Relatively little is known, however, about how histone H1 binding, exchange, and function are regulated in vivo. In this study, we investigated the regulation of histone H1 function in Drosophila using live analysis and confocal microscopy. A gain-of-function genetic screen identified several factors that affect chromosome structure, histone H1 binding, or histone H1 exchange, including the ATP-dependent chromatin-remodeling factor XNP, the hypoxia-induced factor Scylla, the winged helix transcription factor Jumeau, and the microRNA bantam. Our findings show that altered expression of single factors can have surprisingly global effects on higher-order chromatin structure and histone H1 binding in vivo, with the potential to trigger large-scale changes in genome organization and accessibility.

  PublisherDOI

• Polycomb and Trithorax Group Genes in <i>Drosophila</i>

  Genetics · 2017-08-01 · 238 citations

  reviewOpen accessSenior author

  Abstract Polycomb group (PcG) and Trithorax group (TrxG) genes encode important regulators of development and differentiation in metazoans. These two groups of genes were discovered in Drosophila by their opposing effects on homeotic gene (Hox) expression. PcG genes collectively behave as genetic repressors of Hox genes, while the TrxG genes are necessary for HOX gene expression or function. Biochemical studies showed that many PcG proteins are present in two protein complexes, Polycomb repressive complexes 1 and 2, which repress transcription via chromatin modifications. TrxG proteins activate transcription via a variety of mechanisms. Here we summarize the large body of genetic and biochemical experiments in Drosophila on these two important groups of genes.

  PublisherOA PDFDOI

• A Novel Approach for Studying Histone H1 Function <i>in Vivo</i>

  Genetics · 2015-03-23 · 3 citations

  articleOpen accessSenior authorCorresponding

  In this report, we investigate the mechanisms that regulate Drosophila histone H1 expression and its association with chromatin in vivo. We show that histone H1 is subject to negative autoregulation and exploit this result to examine the effects of mutations of the main phosphorylation site of histone H1.

  PublisherOA PDFDOI

• Transcriptional Regulation by Trithorax-Group Proteins

  Cold Spring Harbor Perspectives in Biology · 2014-10-01 · 124 citations

  reviewOpen accessSenior author

  The trithorax group of genes (trxG) was identified in mutational screens that examined developmental phenotypes and suppression of Polycomb mutant phenotypes. The protein products of these genes are primarily involved in gene activation, although some can also have repressive effects. There is no central function for these proteins. Some move nucleosomes about on the genome in an ATP-dependent manner, some covalently modify histones such as methylating lysine 4 of histone H3, and some directly interact with the transcription machinery or are a part of that machinery. It is interesting to consider why these specific members of large families of functionally related proteins have strong developmental phenotypes. Outline 1 Introduction 2 Connections between trxG proteins and chromatin 3 Connections between trxG proteins and the general transcription machinery 4 Connections between trxG proteins and cohesin 5 Biochemical functions of other trxG proteins 6 Functional interactions between trxG and PcG proteins 7 Noncoding RNAs and the trxG 8 trxG proteins and human disease 9 Conclusion and outlook

  PublisherOA PDFDOI

• The trithorax group proteins Kismet and ASH1 promote H3K36 dimethylation to counteract Polycomb group repression in<i>Drosophila</i>

  Development · 2013-09-05 · 94 citations

  articleOpen accessSenior author

  Members of the Polycomb group of repressors and trithorax group of activators maintain heritable states of transcription by modifying nucleosomal histones or remodeling chromatin. Although tremendous progress has been made toward defining the biochemical activities of Polycomb and trithorax group proteins, much remains to be learned about how they interact with each other and the general transcription machinery to maintain on or off states of gene expression. The trithorax group protein Kismet (KIS) is related to the SWI/SNF and CHD families of chromatin remodeling factors. KIS promotes transcription elongation, facilitates the binding of the trithorax group histone methyltransferases ASH1 and TRX to active genes, and counteracts repressive methylation of histone H3 on lysine 27 (H3K27) by Polycomb group proteins. Here, we sought to clarify the mechanism of action of KIS and how it interacts with ASH1 to antagonize H3K27 methylation in Drosophila. We present evidence that KIS promotes transcription elongation and counteracts Polycomb group repression via distinct mechanisms. A chemical inhibitor of transcription elongation, DRB, had no effect on ASH1 recruitment or H3K27 methylation. Conversely, loss of ASH1 function had no effect on transcription elongation. Mutations in kis cause a global reduction in the di- and tri-methylation of histone H3 on lysine 36 (H3K36) - modifications that antagonize H3K27 methylation in vitro. Furthermore, loss of ASH1 significantly decreases H3K36 dimethylation, providing further evidence that ASH1 is an H3K36 dimethylase in vivo. These and other findings suggest that KIS antagonizes Polycomb group repression by facilitating ASH1-dependent H3K36 dimethylation.

  PublisherOA PDFDOI

• A Histone Timer for Zygotic Genome Activation

  Developmental Cell · 2013-09-01

  letterOpen accessSenior authorCorresponding
  PublisherOA PDFDOI

• The Drosophila Mi-2 Chromatin-Remodeling Factor Regulates Higher-Order Chromatin Structure and Cohesin Dynamics In Vivo

  PLoS Genetics · 2012-08-09 · 38 citations

  articleOpen accessSenior authorCorresponding

  dMi-2 is a highly conserved ATP-dependent chromatin-remodeling factor that regulates transcription and cell fates by altering the structure or positioning of nucleosomes. Here we report an unanticipated role for dMi-2 in the regulation of higher-order chromatin structure in Drosophila. Loss of dMi-2 function causes salivary gland polytene chromosomes to lose their characteristic banding pattern and appear more condensed than normal. Conversely, increased expression of dMi-2 triggers decondensation of polytene chromosomes accompanied by a significant increase in nuclear volume; this effect is relatively rapid and is dependent on the ATPase activity of dMi-2. Live analysis revealed that dMi-2 disrupts interactions between the aligned chromatids of salivary gland polytene chromosomes. dMi-2 and the cohesin complex are enriched at sites of active transcription; fluorescence-recovery after photobleaching (FRAP) assays showed that dMi-2 decreases stable association of cohesin with polytene chromosomes. These findings demonstrate that dMi-2 is an important regulator of both chromosome condensation and cohesin binding in interphase cells.

  PublisherOA PDFDOI

• Drosophila ISWI Regulates the Association of Histone H1 With Interphase Chromosomes<i>in Vivo</i>

  Genetics · 2009-04-21 · 39 citations

  articleOpen accessSenior authorCorresponding

  Although tremendous progress has been made toward identifying factors that regulate nucleosome structure and positioning, the mechanisms that regulate higher-order chromatin structure remain poorly understood. Recent studies suggest that the ISWI chromatin-remodeling factor plays a key role in this process by promoting the assembly of chromatin containing histone H1. To test this hypothesis, we investigated the function of H1 in Drosophila. The association of H1 with salivary gland polytene chromosomes is regulated by a dynamic, ATP-dependent process. Reducing cellular ATP levels triggers the dissociation of H1 from polytene chromosomes and causes chromosome defects similar to those resulting from the loss of ISWI function. H1 knockdown causes even more severe defects in chromosome structure and a reduction in nucleosome repeat length, presumably due to the failure to incorporate H1 during replication-dependent chromatin assembly. Our findings suggest that ISWI regulates higher-order chromatin structure by modulating the interaction of H1 with interphase chromosomes.

  PublisherOA PDFDOI

• Genetic Identification of a Network of Factors that Functionally Interact with the Nucleosome Remodeling ATPase ISWI

  PLoS Genetics · 2008-06-05 · 36 citations

  articleOpen access

  Nucleosome remodeling and covalent modifications of histones play fundamental roles in chromatin structure and function. However, much remains to be learned about how the action of ATP-dependent chromatin remodeling factors and histone-modifying enzymes is coordinated to modulate chromatin organization and transcription. The evolutionarily conserved ATP-dependent chromatin-remodeling factor ISWI plays essential roles in chromosome organization, DNA replication, and transcription regulation. To gain insight into regulation and mechanism of action of ISWI, we conducted an unbiased genetic screen to identify factors with which it interacts in vivo. We found that ISWI interacts with a network of factors that escaped detection in previous biochemical analyses, including the Sin3A gene. The Sin3A protein and the histone deacetylase Rpd3 are part of a conserved histone deacetylase complex involved in transcriptional repression. ISWI and the Sin3A/Rpd3 complex co-localize at specific chromosome domains. Loss of ISWI activity causes a reduction in the binding of the Sin3A/Rpd3 complex to chromatin. Biochemical analysis showed that the ISWI physically interacts with the histone deacetylase activity of the Sin3A/Rpd3 complex. Consistent with these findings, the acetylation of histone H4 is altered when ISWI activity is perturbed in vivo. These findings suggest that ISWI associates with the Sin3A/Rpd3 complex to support its function in vivo.

  PublisherOA PDFDOI

• Drosophila Kismet Regulates Histone H3 Lysine 27 Methylation and Early Elongation by RNA Polymerase II

  PLoS Genetics · 2008-10-09 · 131 citations

  articleOpen accessSenior authorCorresponding

  Polycomb and trithorax group proteins regulate cellular pluripotency and differentiation by maintaining hereditable states of transcription. Many Polycomb and trithorax group proteins have been implicated in the covalent modification or remodeling of chromatin, but how they interact with each other and the general transcription machinery to regulate transcription is not well understood. The trithorax group protein Kismet-L (KIS-L) is a member of the CHD subfamily of chromatin-remodeling factors that plays a global role in transcription by RNA polymerase II (Pol II). Mutations in CHD7, the human counterpart of kis, are associated with CHARGE syndrome, a developmental disorder affecting multiple tissues and organs. To clarify how KIS-L activates gene expression and counteracts Polycomb group silencing, we characterized defects resulting from the loss of KIS-L function in Drosophila. These studies revealed that KIS-L acts downstream of P-TEFb recruitment to stimulate elongation by Pol II. The presence of two chromodomains in KIS-L suggested that its recruitment or function might be regulated by the methylation of histone H3 lysine 4 by the trithorax group proteins ASH1 and TRX. Although we observed significant overlap between the distributions of KIS-L, ASH1, and TRX on polytene chromosomes, KIS-L did not bind methylated histone tails in vitro, and loss of TRX or ASH1 function did not alter the association of KIS-L with chromatin. By contrast, loss of kis function led to a dramatic reduction in the levels of TRX and ASH1 associated with chromatin and was accompanied by increased histone H3 lysine 27 methylation-a modification required for Polycomb group repression. A similar increase in H3 lysine 27 methylation was observed in ash1 and trx mutant larvae. Our findings suggest that KIS-L promotes early elongation and counteracts Polycomb group repression by recruiting the ASH1 and TRX histone methyltransferases to chromatin.

  PublisherOA PDFDOI

Recent grants

• Genetic and molecular studies of Drosophila chromatin remodeling factors

  NIH · $4.9M · 1993–2015

Frequent coauthors

• Paul A. Khavari

  Stanford University

  38 shared

• Gerald Crabtree

  Stanford University

  36 shared

• Filippo Randazzo

  Bill & Melinda Gates Foundation

  36 shared

• Janet Rossant

  University of Toronto

  36 shared

• James A. Kennison

  Eunice Kennedy Shriver National Institute of Child Health and Human Development

  32 shared

• Richard O. Hynes

  Howard Hughes Medical Institute

  29 shared

• Jennifer A. Armstrong

  Children's Hospital at Westmead

  27 shared

• Ophelia Papoulas

  The University of Texas at Austin

  25 shared