Chromatin Human chromosomal DNA is packaged into a string of distinct protein-nucleic acid complexes, called chromatin structures, which are critical for gene regulation, genome stability, and protection against cancer. A chromatin structure is generally considered to belong one of two broad categories: euchromatin or heterochromatin. Euchromatin is permissive towards gene expression while heterochromatin structures are repressive. The cell utilizes "facultative heterochromatin" to turn gene expression off and "constitutive heterochromatin" to maintain genome stability. The mechanisms by which constitutive heterochromatin maintains genome stability are poorly understood. The Marahrens laboratory studies the role of heterochromatin in maintaining genome stability using knockout mice and ex vivo chromatin remodeling systems in conjunction chromatin immunoprecipitation and immunofluorescence imaging which monitor chromatin defects in response to mutations.
Role of repetitive sequences in cancer. Approximately one half of the human genome consists of repetitive sequences or "repeats" which are generally packaged in heterochromatin. The two most abundant repeats are transposable element sequences: LINE-1 elements (15.6% of human genome sequence) and the short but extremely numerous Alu elements (10.1%). In many tumors, the heterochromatin structure of LINE-1 or Alu elements or other repeats is disrupted and the repeats become sites of genome rearrangements. The Marahrens lab investigates the chromatin and gene expression defects in response to mutations that destabilize mouse and human genomes and predispose individuals to cancer using microarray data, bioinformatics, and assays for chromatin structure.
Role of the Xist locus and repetitive sequences in X-inactivation and X chromosome stability. X-inactivation provides a striking example of chromatin remodeling on a very large scale. In a developing human female embryo, homologous pairing between the two X chromosomes leads to chromatin remodeling over more than 150-Mb on only one of the two X chromosomes resulting in a heterochromatic transcriptionally inactive X chromosome. This X-inactivation process reduces X chromosomal gene expression in XX females to the same level as in XY males. LINE-1 elements and other repeats are unusually abundant on the X chromosome and have been implicated in X-inactivation. Also important is the X-linked Xist locus. The Marahrens lab showed that excising Xist from the X chromosomes causes dramatic changes in the chromatin properties of both the inactive and active X chromosomes yet causes remarkable little gene reactivation on the inactive X. Importantly, the lab showed that the loss of Xist causes the X chromosomes to become highly prone to deletions and translocations, with the sites of the rearrangements being concentrated in repeat-rich regions. It therefore appears that Xist maintains repetitive sequences along the X chromosome in a stabilizing heterochromatin structure and we are examining this in more detail. Interestingly, processes closely resembling X-inactivation also occur on one copy of each autosomal pair, but only 8 - 23% of autosomal genes are inactivated. We have shown that autosome-inactivated genes are similarly flanked by high concentrations of LINE-1 and other repeats. Certain autosomal deletions and translocations destabilize the chromosomes raising the possibility that Xist-like chromosome stabilization centers are needed by all chromosomes.
Human genetic diseases that predispose to cancer. Several human genetic diseases are characterized by genome instability and cancer predisposition. We have been linking a number of these disease genes to repetitive sequences and the maintenance of X-inactivation. The picture that is emerging from our research is that a number of proteins are shared in the processes of X-inactivation, meiotic chromosome pairing, and certain types of DNA repair. The common denominator appears to be homology sensing between chromosomes. To strengthen these links, the Marahrens lab also studies DNA repair.
Selected Publications (Pubmed Search)
Eller, C.D., Regelson, M., Merriman, B., Nelson, S., Horvath, S., *Marahrens, Y. Repetitive sequence environment distinguishes housekeeping genes Gene 2007 Apr 1;390(1-2):153-65(*corresponding author)
Dawson, D.W., Hong, J.S., Shen, R.R., French, S.W., Troke, J.J., Wu, Y.Z., Chen, S.S., Gui, D., Regelson, M., Marahrens, Y, Morse, H.C. 3rd, Said, J., Plass, C., Teitell, M.A. Global DNA methylation profiling reveals silencing of a secreted form of Epha7 in mouse and human germinal center B-cell lymphomas. Oncogene. 2007 Jun 21;26(29):4243-52.
Diaz-Perez, S. Ferguson, D.O., Wang, C., Csankovszki, G., Wang, C., Tsai, S-C., Dutta, D, Perez, Vanessa, Kim, S., Eller, C.D., Salstrom, J., Ouyang, Y., Teitell, M.A., Kaltenboeck ,B., Chess, A., Huang, S., *Marahrens, Y A deletion at the mouse Xist gene exposes trans-effects that alter the heterochromatin of the inactive X chromosome and the replication time and DNA stability of both X chromosomes Genetics 2006 Nov;174(3):1115-33. Epub 2006 Sep 15. (*corresponding author)
Goldstine, J.V., Nahas, S., Gamo, K., Gartler, S.M. Hansen, R.S. Roelfsema, J.H., Gatti , R.A., *Marahrens, Y. Constitutive phosphorylation of ATM in lymphoblastoid cell lines from patients with ICF syndrome without downstream kinase activity DNA Repair2006 16; 5(4): 432-443 (*corresponding author)
Regelson, M., Eller, C.D, *Horvath, S., *Marahrens, Y., A Link Between Repetitive Sequences and Gene Replication Time Cytogenetic and Genome Research2006 112:184-193 (*corresponding author)
Ouyang, Y., Kwon, Y.T., An, J. Y., Eller, C.D., Tsai, S-C., Diaz-Perez, S., Troke J.J., Teitell M.A., *Marahrens, Y. Loss of Ubr2, an E3 ubiquitin ligase, leads to chromosome fragility and impaired homologous recombinational repair Mutation Research 2006, 596: 64-75 (*corresponding author)
Henson, S.E., Tsai, S-C., Malone, C.S., Soghomonian, S.V., Ouyang, Y., Wall, R., *Marahrens, Y, *Teitell, M.A., Pir51, a Rad51-Interacting protein with high expression in aggressive lymphoma, controls mitomycin C sensitivity and prevents chromosomal breaks Mutation Research 2006, Oct 10;601(1-2):113-24. (*corresponding author)
Diaz-Perez, S., Ouyang, Y., Perez, V., Cisneros, R., Regelson, M., and *Marahrens, Y. The element(s) at the non-transcribed Xist locus of the active X chromosome controls chromosomal replication timing in the mouse. Genetics 2005 Oct;171(2):663-672 (*corresponding author)
Hernández-Muñoz, I., Lund, A. H., van der Stoop, P., Boutsma, E., Muijrers, I., Verhoeven, E., Nusinow, D. A., Panning, B., Marahrens, Y., and van Lohuizen, M., Stable X-chromosome inactivation requires variant histone MACROH2A, CULLIN3/SPOP dependent ubiquitination and involves dynamic recruitment of the PRC1 polycomb complex. PNAS 2005 May 24; 102(21):7635-7640
Ouyang, Y., Salstrom, J. Diaz-Perez, S., Nahas, S., Matsuno, Y., Dawson, D., Teitell, M. A. Horvath, S., Riggs, A. D., Gatti, R.A., *Marahrens, Y. Inhibition of Atm and/or Atr Disrupts Gene Silencing on the Inactive X Chromosome Biochem Biophys Res Commun. 2005 Nov 25;337(3):875-880 (*corresponding author)