Faculty Research Page
Howard Hughes Medical Institute Investigator and Professor of Genetics, Genomics and DevelopmentLab Homepage: http://mcb.berkeley.edu/labs/meyer
Research in our lab explores: (1) epigenetic mechanisms by which information in the genome is expressed in a stable and heritable fashion through cell division; (2) molecular mechanisms by which cells commit to specific fates during animal development; (3) genetic programming for cell fate decisions; (4) mechanisms by which chromosomes adopt the correct structure to achieve faithful segregation during cell division and hence genome stability; (5) the control of recombination during the formation of sperm and eggs. We combine genetic, genomic, proteomic, molecular, biochemical, and cell biological approaches to study these questions in the model organism, Caenorhabditis elegans, a round worm.
Counting Chromosomes to Determine Sex. In many organisms, the decision by an embryo to become a male or female is made by an X-chromosome counting mechanism that distinguishes one X chromosome from two. We have used the nematode Caenorhabditis elegans to dissect such a precise chromosome counting mechanism in molecular detail. In this nematode, the two-fold difference in X-chromosome dose between XO and XX embryos is translated into the "on" or "off" state of the gene xol-1 (XO lethal), a switch that specifies male fate when active and hermaphrodite fate when inactive. Setting xol-1 expression is essential for viability as well as sex determination because xol-1 also controls X-chromosome dosage compensation, a chromosome-wide regulatory process that equalizes X-linked gene expression between the sexes. Five X-linked genes called X-signal elements (XSE) communicate X-chromosome dose by repressing the activity of xol-1, using a combination of at least two mechanisms. One involves transcriptional repression of xol-1 in XX embryos and requires an X-signal element that encodes a nuclear hormone receptor. A second involves the post-transcriptional regulation of xol-1 and requires an X-signal element that encodes an RNA binding protein. This protein represses xol-1 by preventing the RNA processing event that generates the functional xol-1 transcript. Both the transcriptional and RNA processing mechanisms of repression act together to ensure the fidelity of the X-chromosome counting process. Sex is not determined simply by X-chromosome number, but rather by the ratio of X chromosomes to sets of autosomes, the ploidy. We determined that the autosomal signal is composed of discrete autosomal signal element genes (ASE) that oppose the X signal. One ASE encodes a T-box class of transcription factors and the other encodes a protein with glutamine and asparagine-rich repeats, zinc fingers, and a metalloprotease domain. These autosomal elements activate xol-1 by opposing the repression by X signal elements. The mechanisms underlying this molecular war are emerging. Efforts are also directed toward understanding the evolution of the X:A signal.
Epgenetic Control of X-Chromosome Gene Expression: Dosage Compensation. In flies, worms and mammals, specialized dosage compensation complexes are targeted exclusively to the X chromosomes of one sex to modulate transcript levels by altering chromosome architecture. By studying dosage compensation, we are discovering how the expression state of an entire chromosome can be established and maintained through changes in chromatin structure. We have shown that dosage compensation is achieved in C. elegans by a complex of at least ten proteins that acts as a molecular dimmer switch. The complex assembles specifically on both hermaphrodite X chromosomes around the 40-cell stage of embryogenesis to reduce transcript levels by half. Core dosage compensation proteins resemble the mitotic chromosome condensation and segregation machinery (the 13S condensin complex) co-discovered in yeast and frogs, implying the evolutionary recruitment of ancient mitotic proteins to the regulation of gene expression. Although dosage compensation is a sex-specific process, the nematode dosage compensation complex (DCC) contains both dosage compensation-specific proteins and general chromatin-associated proteins that are also active in meiosis or mitosis in both sexes. The multifunctional members of the DCC are differentially commissioned for their roles in dosage compensation or chromosome segregation by their association with different protein partners. The protein complexes specialized for dosage compensation, mitosis, and meiosis are under analysis, along with their mechanisms of action.
The DCC is recruited to X chromosomes by two hermaphrodite-specific genes (sdc-2 and sdc-3) that coordinately control both sex determination and dosage compensation. SDC-2 is central to X-chromosome recognition and confers both X-chromosome specificity and hermaphrodite-specificity to dosage compensation. The biochemistry underlying the function of SDC-2 is currently under investigation.
Targeting the Dosage Compensation Complex to X Chromosomes. One goal has been to identify X chromosome target sites responsible for DCC recruitment and to define molecular features within these recruitment sites critical for target recognition and DCC binding. We first surveyed large regions of X (1-10Mbp) for their ability to recruit the DCC when detached from X. Some detached regions recruited the DCC and others did not, yet the DCC localized to all corresponding regions of the intact X chromosome. These results led to the model that DCC recruitment sites are distributed along X to bind the DCC and to nucleate DCC spreading to X regions lacking recruitment sites. We then identified numerous discrete recruitment elements on X (rex sites) that mark nematode X chromosomes as targets for gene repression by the DCC. These rex sites are widely dispersed along X and reside in promoters, exons, and intergenic regions. rex sites share at least two distinct motifs that act in combination to recruit the DCC. Mutating these motifs severely reduces or abolishes DCC binding in vivo, demonstrating the importance of primary DNA sequence in chromosome-wide regulation. The motifs are not enriched on X, but altering motif numbers within rex sites demonstrates that motif co-occurrence in unusually high densities is essential for optimal DCC recruitment. Thus, X-specific repression can be established through sequences not specific to X. Rather, the distinctive arrangement of common motifs within recruitment regions appears to specify chromosome-wide repression. Current projects involve computational, biochemical, and cell biological approaches to define more precisely the motifs and their arrangements within rex sites responsible for differentiating X chromosomes from autosomes to recruit the DCC. The mechanism of DCC spreading is under investigation, as is the biochemical mechanism by which the DCC can repress X transcript levels by half.
Regulation of Meiotic Crossover Interference in C. elegans. In most organisms, homologous chromosomes must undergo at least one crossover to guarantee proper segregation during meiosis. The number and distribution of crossovers is controlled through the process of crossover interference. In C. elegans, crossover interference is extremely tight, such that only one crossover event occurs per homologous chromosome pair per meiosis. Our recent experiments indicate that several dosage compensation proteins and meiotic condensin components are important for this regulation of crossovers. Mutations in genes encoding these proteins disrupt interference, causing double and triple crossovers per homolog pair and a skewing of the crossover distribution. The mechanism of crossover interference and its relationship to chromatin structure is under investigation.
Clustered DNA Motifs Mark X Chromosomes for Repression by a Dosage Compensation Complex. [P. McDonel, J. Jans, B. Peterson, B. Meyer (2006) Nature 444, 614-618]
Sperm Chromatin Proteomics Identifies Evolutionarily Conserved Fertility Factors. [D. Chu, H. Liu, P. Nix, T. Wu, E. Ralston, J. Yates, B. Meyer (2006) Nature 443, 101-105]
The T-Box Transcription Factor SEA-1 Is an Autosomal Element of the X:A Signal that Determines C. elegans Sex. [J. Powell, M. Jow, B. Meyer (2005) Dev. Cell 3, 339-349]
X-Chromosome dosage compensation. [B. Meyer (2005) In WormBook, editors: The C. elegans Research Community, http://www.wormbook.org]
Condensin Restructures Chromosomes in Preparation for Meiotic Divisions. [R. Chan, A. Severson, B. Meyer (2004) J. Cell Biol. 167, 613-625]
Dissection of the mammalian midbody proteome reveals conserved cytokinesis mechanisms. [A. Skop, H. Liu, J. Yates, B. Meyer, R. Heald (2004) Science 305, 61-66]
Recruitment and spreading of the C. elegans dosage compensation complex along X chromosomes. [G. Csankovszki, P. McDonel, B. Meyer (2004) Science 303, 1182-1185]
Recruitment of C. elegans dosage compensation proteins for gene-specific versus chromosome-wide repression. [S. Yonker and B. Meyer (2003) Development 130, 6519-6532]
Chromosome cohesion is regulated by C. elegans TIM-1, a paralog of the clock protein TIMELESS. [R. Chan, A. Chan, M. Jeon, T. Wu, D. Pasqualone, A. Rougvie, B. Meyer (2003) Nature 423, 1002-1009]
XOL-1, primary determinant of sexual fate in C. elegans is a GHMP kinase family member and a structural prototype for a new class of developmental regulators. [J. Luz, C. Hassig, A. Godzik, C. Pickle, B. Meyer, I. Wilson. (2003) Genes Dev. 17, 977-990]
A molecular link between gene-specific and chromosome-wide transcriptional repression. [D. Chu, H. Dawes, J. Lieb, R. Chan, A. Kuo, B. Meyer (2002) Genes Dev. 16, 796-805]
Last Updated 2007-01-23