Fields of Interest: Regulation of nuclear organization and function
Recent advances in probing the nucleus have made it clear that nuclear organization is far more complex and ordered than had earlier been appreciated and that it plays a major role in cell function including gene expression and cell division. Our research is directed towards identifying the molecules defining such nuclear organization, as well as the signal transduction pathways regulating cell cycle-specific changes. Using Drosophila as a model system, a combination of molecular and genetic approaches are being used to analyze genes involved in these processes.
These studies are done in collaboration with Dr. Jorgen Johansen
PROJECT 1: Regulation of Chromatin Structure and gene expression.
The long term objective of my laboratory is to gain a molecular understanding of epigenetic processes that regulate chromatin structure and gene expression. Towards this end we have identified a novel tandem kinase in Drosophila, JIL-1, that localizes specifically to the gene-active interband regions of the larval polytene chromosomes, phosphorylates histone H3S10, and is enriched almost two-fold on the transcriptionally hyperactive male larval polytene X chromosome. In JIL-1 hypomorphs orderly interband regions of polytene chromosomes are disrupted and the chromosome arms highly condensed. Position effect variegation (PEV) in Drosophila has served as a major paradigm for the identification and genetic analysis of evolutionarily conserved determinants of epigenetic regulation of chromatin structure and gene silencing and we provide evidence that loss-of-function alleles of the JIL-1 histone H3S10 kinase can act either as suppressors or enhancers of PEV depending on the chromatin environment of the reporter locus. These effects on PEV were correlated with the spreading of the major heterochromatin markers dmH3K9 and HP1 to ectopic locations on the chromosome arms with the most pronounced upregulation found on the male and female X chromosomes. Based on these findings we propose a model where JIL-1 kinase activity and phosphorylation of histone H3S10 at interphase functions to antagonize heterochromatization by regulating a dynamic balance between factors promoting repression and activation of gene expression.
Gene silencing is a critical developmental process relevant to many human health problems that include cancer. Furthermore, JIL-1 is the Drosophila homolog of the mammalian MSK1 kinase which also functions as a regulator of chromatin structure by phosphorylating the histone H3S10 residue. At present the mammalian studies have been directed towards analyzing histone phosphorylation in the context of immediate early gene transcription. However, our results suggest that the concept of histone phosphorylation should be expanded to be considered in the context of the regulation of gene silencing as well. Thus, our studies will serve to provide general insights into the molecular mechanisms of how kinase activity modulates chromatin structure and gene regulation that are directly relevant to humans.
This Research is funded by the National Institutes of Health
PROJECT 2: Cell cycle roles of nuclear proteins forming the spindle matrix.
The microtubule-based spindle apparatus provides a conserved mechanism to segregate chromosomes during mitosis. However, how this process is coordinated with disassembly and reassembly of nuclear structures during mitotic progression is poorly understood. It is also not clear how cell cycle regulators and other diffusible molecules are localized and confined to the spindle region in the absence of diffusion barriers following nuclear envelope breakdown. Towards answering these questions, in Drosophila we have identified four nuclear proteins, Skeletor, Chromator, Megator, and EAST from two different nuclear compartments that interact with each other and that redistribute during prophase to form a dynamic, gel-like spindle matrix that embeds the microtubule spindle apparatus, stretching from pole-to-pole. This matrix forms prior to nuclear envelope breakdown and specific interactions between spindle matrix molecules are necessary for complex formation and cohesion. When microtubules are depolymerized with colchicine just prior to metaphase the spindle matrix contracts and coalesces around the chromosomes suggesting that microtubules act as "struts" stretching the spindle matrix. Furthermore, in colchicine treated embryos free tubulin accumulates co-extensively with the spindle matrix suggesting that this enrichment is dependent on one or more proteins within the spindle matrix with tubulin binding activity. Moreover, we have demonstrated that Megator and its human homolog Tpr act as spindle matrix proteins that have an evolutionarily conserved function as spatial regulators of spindle assembly checkpoint proteins during open and semi-open mitosis. The goal of our current research is to test the hypothesis that reorganization of nuclear proteins into a spindle matrix serves as a general platform for integrating signaling events leading to nuclear envelope breakdown and cell cycle progression in conjunction with contributing to microtubule spindle assembly and dynamics. We hope that the results will provide a mechanistic framework for understanding how cell cycle factors are physically confined and organized in the spindle region in organisms with open or semi-open mitosis, allowing for spatial and temporal control of mitotic progression and chromosome segregation.
Wang, C.,Y. Li, W. Cai, X. Bao, J. Girton, J. Johansen and K.M. Johansen (2014) Histone H3S10 phosphorylation by the JIL-1 kinase in pericentric heterochromatin and on the 4th chromosome creates a composite H3S10phK9me2 epigenetic mark. Chromosoma 123 : 273-280.
Cai, W., C. Wang, Y. Li, C. Yao, L. Shen, S. Liu, X. Bao, P. Schnable, J. Girton, J. Johansen and K.M. Johansen (2014) Genome-wide analysis of regulation of gene expression and H3K9me2 distribution by JIL-1 mediated histone H3S10 phosphorylation in Drosophila. Nucleic Acids Res. 42 : 5456-5467.
Yao, C., C. Wang, Y. Li, Y. Ding, U. Rath, S. Sengupta, J. Girton, K.M. Johansen and J. Johansen (2014) The spindle matrix protein, Chromator, is a novel tubulin binding protein that can interact with both microtubules and free tubulin. PLoS ONE 9 : e103855.
Li, Y., W. Cai, C. Wang, C. Yao, X. Bao, H. Deng, J. Girton, J. Johansen and K.M. Johansen (2013) Domain requirements of the JIL-1 tandem kinase for histone H3 serine10 phosphorylation and chromatin remodeling in vivo. J. Biol. Chem. 288 : 19441-19449.
Wang, C., C. Yao, Y. Li, W. Cai, X. Bao, J. Girton, J. Johansen and K.M. Johansen (2013) Evidence against a role for the JIL-1 kinase in H3S28 phosphorylation and 14-3-3 recruitment to active genes in Drosophila. PLoS ONE 8 : e62484.
Girton, J., C. Wang, J. Johansen and K.M. Johansen (2013) The effect of JIL-1 on position-effect variegation is proportional to the total amount of heterochromatin in the genome. Fly 7: 129-133.
Yao, C., U. Rath, H. Maiato, D. Sharp, J. Girton, K.M. Johansen and J. Johansen (2012) A nuclear-derived proteinaceous matrix embeds the microtubule spindle apparatus during mitosis. Mol. Biol. Cell 23 : 3532-3541. [Supplementary Movies].
Wang, C., W. Cai, Y. Li, J. Girton, J. Johansen and K.M. Johansen (2012) H3S10 phosphorylation by the JIL-1 kinase regulates H3K9 dimethylation and gene expression at the white locus in Drosophila. Fly 6 : 93-97.
Yao, C., Y. Ding, W. Cai, C. Wang, J. Girton, K.M. Johansen and J. Johansen. (2012) The chromodomain-containing NH2-terminus of Chromator interacts with histone H1 and is required for correct targeting to chromatin. Chromosoma 121 : 209-220.
Wang, C., W. Cai, H. Deng, X. Bao, J. Girton, J. Johansen and K.M. Johansen (2011) The epigenetic H3S10ph mark is required for counteracting heterochromatic spreading and gene silencing in Drosophila. J. Cell Sci. 124 : 4309-4317.
Wang, C., J. Girton, J. Johansen and K.M. Johansen (2011) A balance between euchromatic [JIL-1] and heterochromatic [SU(VAR)2-5 and SU(VAR)3-9] factors regulates position-effect variegation in Drosophila. Genetics 188 : 745-748.
Johansen, K.M., A. Forer, C. Yao, J. Girton and J. Johansen (2011) Do nuclear envelope and intranuclear proteins reorganize during mitosis to form an elastic, hydrogel-like spindle matrix? Chromosome Res. 19 : 345-365.
Deng, H., W. Cai, C. Wang, S. Lerach, M. Delattre, J. Girton, J. Johansen and K.M. Johansen (2010) JIL-1 and Su(var)3-7 interact genetically and counterbalance each others' effect on position effect variegation in Drosophila. Genetics 185 : 1183-1192.
Cai, W., Y. Jin, J. Girton, J. Johansen and K.M. Johansen (2010) Preparation of polytene chromo-some squashes for antibody labeling. J. Vis. Exp. http://www.jove.com/index/Details.stp?ID=1748. [Quicktime Movie] [PDF]
Ding, Y., C. Yao, M. Lince-Faria, U. Rath, W. Cai, H. Maiato, J. Girton, K.M. Johansen and J. Johansen. (2009) Chromator is required for proper microtubule spindle formation and mitosis in Drosophila. Dev. Biol. 334 : 253-263.
Johansen, J. and K.M. Johansen (2009) The spindle matrix through the cell cycle in Drosophila. Fly 3 : 22-29.
Johansen, K.M., W. Cai, H. Deng, X. Bao, W. Zhang, J. Girton and J. Johansen (2009) Methods for studying transcription and epigenetic chromatin modification in Drosophila polytene chromosome squash preparations using antibodies. Methods 48 : 387-397.
Lince-Faria, M., S. Maffini, B. Orr, Y. Ding, C. Florindo, C.E. Sunkel, A. Tavares, J. Johansen, K.M. Johansen and H. Maiato (2009) Spatio-temporal control of mitosis by the conserved spindle matrix protein Megator. J. Cell Biol. 184 : 647-657.
Bao, X., W. Cai, H. Deng, W. Zhang, R. Krencik, J. Girton, J. Johansen and K.M. Johansen (2008) The COOH-terminal domain of the JIL-1 histone H3S10 kinase interacts with histone H3 and is required for correct targeting to chromatin. J. Biol. Chem. 283 : 32741-32750.
Cai, W., X. Bao, H. Deng, Y. Jin, J. Girton, J. Johansen and K.M. Johansen (2008) RNA polymerase II-mediated transcription at active loci does not require histone H3S10 phosphorylation in Drosophila. Development 135 : 2917-2925.
Deng, H., X. Bao, W. Cai, M.J. Blacketer, A.S. Belmont, J. Girton, J. Johansen and K.M. Johansen (2008) Ectopic histone H3S10 phosphorylation causes chromatin structure remodeling in Drosophila. Development 135 : 699-705.
Deng, H., X. Bao, W. Zhang, J. Girton, J. Johansen and K.M. Johansen (2007) Reduced levels of Su(var)3-9 but not Su(var)2-5 (HP1) counteract the effects on chromatin structure and viability in loss-of-function mutants of the JIL-1 histone H3S10 kinase. Genetics 177 : 79-87.
Bao, X., H. Deng, J. Johansen, J. Girton and K.M. Johansen (2007) Loss-of-function alleles of the JIL-1 histone H3S10 kinase enhance position-effect-variegation at pericentric sites in Drosophila heterochromatin. Genetics 176 : 1355-1358.
Bao, X., J. Girton, J. Johansen and K.M. Johansen (2007) The lamin Dm0Ari3 allele acts as an enhancer of position effect variegation at the wm4 locus in Drosophila. Genetica 129 : 339-342.
Fabian, L., X. Xia, D.V. Venkitaramani, K.M. Johansen, J. Johansen D.J. Andrew, and A. Forer (2007) Titin in insect spermatocyte spindle fibres associates with microtubules, actin, myosin and the matrix proteins Skeletor, Megator, and Chromator. J. Cell Sci. 120 : 2190-2204.
Lerach, S., W. Zhang, X. Bao, H. Deng, J. Girton, J. Johansen and K.M. Johansen (2006) Loss-of-function alleles of the JIL-1 kinase are strong suppressors of position effect varigation of the wm4 allele in Drosophila. Genetics 173 : 2403-2406.
Johansen, K.M. and J. Johansen (2006) Regulation of chromatin structure by histone H3S10 phosphorylation. Chromosome Res. 14 : 393-404.
Rath, U., Y. Ding, H. Deng, H. Qi, X. Bao, W. Zhang, J. Girton, J. Johansen, and K.M. Johansen (2006) The chromodomain protein, Chromator, interacts with JIL-1 kinase and regulates the structure of Drosophila polytene chromosomes. J. Cell Sci. 119 : 2332-2341.
Zhang, W., H. Deng, X. Bao, S. Lerach, J. Girton, J. Johansen and K.M. Johansen (2006) The JIL-1 histone H3S10 kinase regulates dimethyl histone H3K9 modifications and heterochromatic spreading in Drosophila. Development 133 : 229-235.
Lerach, S., W. Zhang, H. Deng, X. Bao, J. Girton, J. Johansen and K.M. Johansen (2005) The JIL-1 kinase, a member of the MSL complex, is necessary for proper dosage compensation of eye pigmentation in Drosophila. Genesis 43 : 213-215.
Bao, X., W. Zhang, R. Krencik, Y. Wang, J. Girton, J. Johansen, and K.M. Johansen (2005) The JIL-1 kinase interacts with lamin Dm0 and regulates nuclear lamina morphology of Drosophila nurse cells. J. Cell Sci. 118 : 5079-5087.
Deng, H., W. Zhang, X. Bao, J.N. Martin, J. Girton, J. Johansen and K.M. Johansen (2005) The JIL-1 kinase regulates the structure of Drosophila polytene chromosomes. Chromosoma 114 : 173-182.
Qi, H., U. Rath, Y. Ding, Y. Ji, M.J. Blacketer, J. Girton, J. Johansen and K.M. Johansen (2005) EAST interacts with Megator and localizes to the putative spindle matrix during mitosis in Drosophila. J. Cell Biochem. 95 : 1284-1291.
Qi, H., U. Rath, D. Wang, Y. Xu, W. Zhang, Y. Ding, M.J. Blacketer, M.R. Paddy, J. Girton, J. Johansen and K.M. Johansen (2004) Megator, an essential coiled-coil protein interacts with the putative spindle matrix during mitosis. Mol. Biol. Cell 15 : 4854-4865.
Rath, U., D. Wang, Y. Ding, Y-Z. Xu, M. Blacketer, J. Girton, J. Johansen and K.M. Johansen (2004) Chromator, an essential chromodomain protein interacts directly with the putative spindle matrix protein Skeletor. J. Cell. Biochem. 93 : 1033-1047.
Zhang, W., Y. Jin, Y. Ji, J. Girton, J. Johansen and K.M. Johansen (2003) Genetic and phenotypic analysis of alleles of the Drosophila chromosomal kinase JIL-1 reveals a functional requirement at multiple developmental stages. Genetics 165 : 1341-1354.
Johansen, K.M. and J. Johansen (2003) Studying nuclear organization in embryos using antibody tools. In Drosophila Cytogenetics Protocols. D.S. Henderson, Ed., Humana Press, Totowa, New Jersey. p. 215-234.
Zhang, W., Y. Wang, J. Long, J. Girton, J. Johansen and K.M. Johansen (2003) A developmentally regulated splice variant from the complex lola locus encoding multiple different zinc-finger domain proteins interacts with the chromosomal kinase JIL-1. J. Biol. Chem. 278 : 11696-11704.
Wang, Y., W. Zhang, Y. Jin, J. Johansen and K.M. Johansen (2001) The JIL-1 tandem kinase mediates histone H3 phosphorylation and is required for maintenance of chromatin structure in Drosophila. Cell 105 : 433-443.
Walker, D.L., D. Wang, Y. Jin, U. Rath, Y. Wang, J. Johansen and K.M. Johansen (2000) Skeletor, a novel chromosomal protein that redistributes during mitosis provides evidence for the formation of a spindle matrix. J. Cell Biol. 151 : 1401-1411.
Jin, Y., Y. Wang, J. Johansen and K.M. Johansen (2000) JIL-1, a chromosomal kinase implicated in regulation of chromatin structure, associates with the MSL dosage compensation complex. J. Cell Biol. 149 : 1005-1010.
Jin, Y., Y. Wang, D.L. Walker, H. Dong, C. Conley, J. Johansen and K.M. Johansen (1999) JIL-1: A novel chromosomal tandem kinase implicated in transcriptional regulation in Drosophila. Mol. Cell 4 : 129-135.
Johansen, K.M., J. Johansen, Y. Jin, D.L. Walker, D. Wang, and Y. Wang (1999) Chromatin structure and nuclear remodeling. Crit. Rev. Eukaryotic Gene Expr. 9 : 267-277.
Dong, H., Y. Jin, J. Johansen and K.M. Johansen (1999) Antibody identification, chromosome map assignment, and sequence analysis of a Rab escort protein homolog in Drosophila. Biochem. Biophys. Acta 1449 : 194-198.