Faculty & Research

Biological Sciences

Richard S. Jones, Ph.D.

Professor

Ph.D. Wesleyan University
DLSB 333
214-768-3810

Lab: DLSB 321
Tel: 214-768-2385

Email: rjones@smu.edu


Research Interests


Epigenetic Gene Regulation by Polycomb-Group Proteins

Gene

Developmental genetics is a field of research concerned with how genes control the process by which a single cell, the fertilized egg, gives rise to an adult organism. Following fertilization, this single cell replicates and divides producing two identical daughter cells. This process is repeated many times, eventually giving rise to all the cells of the body, each containing a complete copy of the genetic information contributed to the fertilized egg by the parents. Along the way, cells begin to exhibit distinguishing characteristics. The specialized characteristics of each cell type is due to the different proteins each is producing. The proteins produced by a cell are determined by which genes are turned on in that cell. Since each cell contains the total complement of genes necessary to make the entire organism, mechanisms must exist by which specific sets of genes are turned on and others are kept off in a given cell type.  In recent years, it has become increasingly clear that epigenetic mechanisms, which include covalent modification of histones, modulation of higher order chromatin structure, and in some, but not all organisms DNA methylation, are essential to gene regulation.

Polycomb-group (PcG) proteins comprise a highly conserved epigenetic system that maintains transcriptional silence of target genes. PcG proteins do not initiate transcriptional repression, but rather take over repression of target genes from gene-specific transcription factors and are then capable of heritably maintaining gene silence through an indefinite number of cell cycles.  First identified as negative regulators of Drosophila Hox genes, they have since been found to regulate numerous developmental and cell cycle regulatory genes in a wide range of species.  Mammalian PcG proteins play a central role in maintaining the pluripotent states of stem cells and their misexpression contributes to a variety of cancers in humans.

The Jones lab uses a combination of genetic, immunological and biochemical experimental approaches to study the mechanisms by which products of a class of Drosophila PcG proteins, repress transcription. Due to the high degree of conservation of PcG proteins, this work is expected to also provide insight into the mechanisms by which they contribute to mammalian development and oncogenesis.  Currently our research is focused on two projects.

Much that has been learned about the in vivo activities of PcGp proteins comes from chromatin immunoprecipitation (ChIP) studies of cell cultures or imaginal discs in which certain target genes are uniformly repressed or active.

These studies have yielded insight into the maintenance phase of PcG-mediated repression; however, little is known about the mechanisms by which PcG proteins initially recognize the repressed state of a target gene and then assume control of its repression.  

To circumvent this technical obstacle, we are using a combination of maternal effect mutations to produce embryos in which a PcG target gene is uniformly repressed.  ChIP analysis of carefully staged embryos will then be performed to examine the molecular and cellular events at this gene as PcG proteins assume control of its repression from a gene-specific transcription factor.

De novo establishment of PcG-mediated silencing

Much that has been learned about the in vivo activities of PcGp proteins comes from chromatin immunoprecipitation (ChIP) studies of cell cultures or imaginal discs in which certain target genes are uniformly repressed or active.  These studies have yielded insight into the maintenance phase of PcG-mediated repression; however, little is known about the mechanisms by which PcG proteins initially recognize the repressed state of a target gene and then assume control of its repression. This is largely due to the heterogeneous expression of PcG target genes in embryos. To circumvent this technical obstacle, we are using a combination of maternal effect mutations to produce embryos in which a PcG target gene is uniformly repressed.  ChIP analysis of carefully staged embryos will then be performed to examine the molecular and cellular events at this gene as PcG proteins assume control of its repression from a gene-specific transcription factor. 

Purification of a novel PcG protein complex

We have identified a novel protein complex (PCLC) in Drosophila larvae that includes the PcG protein Polycomblike (Pcl) (Savla et al., 2008).  We hypothesize that the primary contribution of Pcl to PcG-mediated repression may be to mediate interactions with additional proteins.  In embryos, it may do so as a subunit of the previously characterized PRC2 complex, whereas in larvae it exists in a distinct complex with these other proteins.  We are currently using a combination of ion exchange, gel filtration, and affinity chromatography to purify this protein complex from larval nuclear extracts, which will then be identified by mass spectrometry.  Once these proteins are identified, antibodies against them will be incorporated into our broader studies in order to understand their contributions to PcG-mediated repression in embryos and larvae. 

 

Selected Publications

Lee, N., H. Erdjument-Bromage, P. Tempst, R.S. Jones, and Y. Zhang (2009) The H3K4 demethylase Lid associates with and inhibits the histone deacetylase Rpd3. Mol. Cell. Biol. 29:1401-1410.

Joshi, P., E.A. Carrington, L. Wang, C.S. Ketel, E.L. Miller, R.S. Jones, and J.A. Simon (2008) Dominant alleles identify SET domain residues required for histone methyltransferase of Polycomb repressive complex 2. J. Biol. Chem. 283: 27757-27766.

Savla, U., J. Benes, J. Zhang, and R.S. Jones (2008) Recruitment of Drosophila Polycomb-group proteins by Polycomblike, a component of a novel protein complex in larvae. Development. 135: 813-817.

Jones, R.S. (2007) Reversing the irreversible. Nature 450: 357-359.

Lee, N., J. Zhang, R.J. Klose, H. Erdjument-Bromage, P. Tempst, R.S. Jones, and Y. Zhang (2007) The trithorax-group protein Lid is a histone H3 trimethyl-Lys4 demethylase. Nat. Struct. Mol. Biol. 14:341-343.

Wang, J., N. Jahren, M.L. Vargas, E.F. Andersen, J. Benes, J. Zhang, E.L. Miller, R.S. Jones, and J.A. Simon (2006) Alternative ESC and ESC-Like subunits of a Polycomb group histone methyltransferase complex are differentially deployed during Drosophila development. Mol. Cell. Biol. 26:2637-2647.

Wang, H., L. Wang, H. Erdjument-Bromage, M. Vidal, P. Tempst, R.S. Jones, and Y. Zhang (2004) Role of histone H2A ubiquitination in Polycomb silencing. Nature 431:873-878.

Wang, L., J.L. Brown, R. Cao, Y. Zhang, J.A. Kassis, and R.S. Jones (2004) Hierarchical recruitment of Polycomb-group silencing complexes. Molec. Cell 14:637-646.

Sedkov, Y., E. Cho, S. Petruk, L. Cherbas, S.T. Smith, R.S. Jones, P. Cherbas, E. Canaani, J.B. Jaynes, and A. Mazo (2003) Methylation at lysine 4 of histone H3 in ecdysone-dependent development of Drosophila. Nature 426: 78-83.

Cao, R., L. Wang, H. Wang, L. Xia, H. Erdjument-Bromage, P. Tempst, R.S. Jones, and Y. Zhang (2002) Role of histone H3 lysine 27 methylation in Polycomb-group silencing. Science 298:1039-1043.

Wang, L., L. Ding, C.A. Jones, and R.S. Jones (2002) The Drosophila Enhancer of zeste protein directly interacts with dSAP18. Gene 285:119-125.

O’Connell, S., L. Wang, S. Roberts, C.A. Jones, R. Saint, and R.S. Jones (2001) Polycomblike PHD fingers mediate conserved interaction with Enhancer of zeste protein. J. Biol. Chem 276: 43065-43073.

I. Bajusz, L. Sipos, Z. Györgypál, E.A. Carrington, R.S. Jones, J. Gausz, H. Gyurkovics (2001) The Trithorax-mimic allele of Enhancer of zeste renders active domains of target genes accessible to Polycomb-group dependent silencing in Drosophila melanogaster. Genetics 159: 1135-1150.

Sedkov, Y., J.J. Benes, J.R. Berger, K.M. Riker, S. Tillib, R.S. Jones, A. Mazo (1999) Molecular genetic analysis of the Drosophila trithorax-related gene which encodes a novel SET domain protein. Mech. Dev. 82:171-179.

Jones, CA, J. Ng, A.J. Peterson, K. Morgan, J. Simon and R.S. Jones (1998) The Drosophila esc and E(z) proteins are direct partners in Polycomb-group mediated repression. Mol. Cell Biol. 18:2825-2834.

Carrington, E.A and R.S. Jones (1996) The Drosophila Enhancer of zeste gene encodes a chromosomal protein: examination of wild type and mutant protein distribution. Development 122:4073-4083.

 

Support

NIH, R15-GM094737, De novo establishment of Polycomb-group-mediated repression, Role PI.

Texas Higher Education Coordinating Board, Norman Hackerman Advanced Research Program (NHARP), Purification of a novel Polycomb-group protein complex, Role PI.