We explore the evolutionary and developmental origins of sexual dimorphism in the mammalian genome and germline. In particular, we are focused on understanding the biology and evolution of sex chromosomes (X and Y), the role that the X and Y chromosomes play in fundamental sex differences beyond the reproductive tract, and the origins and development of germ cells.
Sexual Dimorphism Beyond the Reproductive Tract
For the past two decades, our laboratory has specialized in sequencing the most structurally complex and most technically challenging target in the genome - the Y chromosome. In 2003, our lab completed the sequence of the human Y chromosome, which was the first sex-specific chromosome to be sequenced from any organism. The ultra-high quality of the human Y chromosome reference sequence has enabled unparalleled insight into the mechanism and kinetics of Y rearrangements, which contribute to spermatogenic failure, gonadoblastoma, and Turner syndrome. In collaboration with the Genome Institute at Washington University and the Human Genome Sequencing Center at Baylor, our laboratory subsequently sequenced the chimpanzee, rhesus macaque, and mouse Y chromosomes, the chicken Z chromosome, and the ampliconic regions of the human X chromosome to the same level of refinement. The technology we invented and developed, Single Haplotype Iterative Mapping and Sequencing (SHIMS), is the only proven technology to accurately assemble large, nearly identical repeats that are frequently found on Y chromosomes. We are currently working to evolve SHIMS, making it cheaper, faster, and more widely adopted, which will revolutionize the way that ultra-high-quality reference-grade sequence is generated in the Page Lab and beyond. We are currently applying the new SHIMS technology to complete the Y chromosome sequences of additional mammals - bull, marmoset, rat, and opossum - as well as the chicken W chromosome.
While previous studies have cemented the Y chromosome's role in male-specific functions (ie. testis differentiation and sperm production), our recent comparative genomic studies revealed that the Y chromosome's influences reach far beyond the reproductive tract. Through a systematic and exhaustive comparison of the Y-chromosome gene contents of eight mammals (see figure), we found that Y-chromosome genes with counterparts on the X chromosome form a functionally coherent group. They are enriched for dosage-sensitive, broadly expressed regulators of transcription, translation, and protein stability. The X and Y (male-specific) versions of these genes encode distinct protein isoforms throughout the body. Therefore, fundamental sexual dimorphism exists at the biochemical and molecular level, which has important implications for understanding the differences between males and females in health and disease.
The Circle of Life
Germ cells, which give rise to differentiated gametes (sperm in males and eggs in females), are the ultimate expression of sexual dimorphism. Our goal is to learn how germ cells initiate the meiotic program and acquire a female or male identity (ultimately oocyte or sperm) through genetic and molecular analysis of germ cell differentiation in the mammalian ovary and testis. Starting in the late 1990's we have used the mouse as an experimental model to genetically dissect the process of meiotic initiation, which is a critical juncture in mammalian development, both female and male. Our initial genetic insight came from the discovery that the Stra8 gene is required for meiotic initiation in germ cells of fetal ovaries. Rapid progress followed, including 1) the identification of retinoic acid (RA) as an extrinsic inducer of Stra8, 2) the discovery that RA and Stra8 govern meiotic initiation in postnatal testes, and 3) the discovery that the Dazl gene encodes a meiotic competence factor, enabling fetal germ cells to respond to the RA signal, express Stra8, and enter meiosis. One of our recent findings overturned the long-held view that germ-cell sex determination is dependent on the timing of meiotic initiation. We found that Stra8-deficient female germ cells, which are blocked from initiating meiosis, still differentiate into oocytes. Our work is now focused on using new tools to expand the genetic regulatory network involved in meiotic initation
The essential function of germ cells is to carry the genome from parent to offspring, thereby providing a continuous link between generations. In order to perform this function, germ cells must complete a complex developmental program, which includes maintaining the diploid genome throughout embryogenesis, halving the genome during meiosis, and preparing the haploid genome for fertilization. Through this process, germ cells undergo extensive cellular differentiation and specialization, but they are still capable of generating a totipotent embryo at fertilization. Our recent studies have pointed to the existence of an epigenetic mechanism that might explain this unique ability of germ cells. We have found that germ cells in mice maintain a poised chromatin state, characterized by simultaneous activating and repressing histone signatures as well as silent transcription, at a subset of developmental regulatory genes. The poised state persists through multiple stages of male and female germ cell development. We postulate that maintenance of a poised chromatin state at promoters of developmental regulatory genes in germ cells plays a fundamental role in the ability of germ cells to re-establish totipotency upon fertilization.
Soh YQS, Alföldi J, Pyntikova T, Brown LG, Graves T, Minx PJ, Fulton RS, Kremitzki C, Koutseva N, Mueller JL, Rozen S, Hughes JF, Owens E, Womack JE, Murphy WJ, Cao Q, de Jong P, Warren WC, Wilson RK, Skaletsky H, Page DC (2014) Sequencing the mouse Y chromosome reveals convergen gene acquisition and amplification on both sex chromosomes. Cell 159: 800-13
Bellott DW, Hughes JF, Skaletsky H, Brown LG, Pyntikova T, Cho TJ, Koutseva N, Zaghlul S, Graves T, Rock S, Kremitzki C, Fulton RS, Dugan S, Ding Y, Morton D, Khan Z, Lewis L, Buhay C, Wang Q, Watt J, Holder M, Lee S, Nazareth L, Rozen S, Muzny DM, Warren WC, Gibbs RA, Wilson RK, Page DC
(2014) Mammalian Y chromosomes retain widely expressed, dosage-sensitive regulators.
Nature 508: 494-9
Lesch BJ, Dokshin GA, Young RA, McCarrey JR, Page DC (2013) A set a genes critical to development is epigenetically poised in mouse germ cells from fetal stages though completion of meiosis. Proc Natl Acad Sci 110:16061-6
Mueller JL, Skaletsky H, Brown LG, Zaghlul S, Rock S, Grave T, Auger K, Warren WC, Wilson RK, Page DC (2013) Independent specialization of the human and mouse X chromosomes for the male germline. Nat Genet 45:1083-7
Hu YC, de Rooij DG, Page DC (2013) Tumor suppressor gene Rb is required for self-renewal of spermatogonial stem cells in mice. Proc Natl Acad Sci 110:12685-90
Hu YC, Okumura LM, Page DC (2013) Gata4 is required for formation of the genital ridge in mice. PLOS Genet 9:e1003629
Dokshin G, Baltus AE, Eppig JJ, Page DC (2013) Oocyte differentiation is genetically dissociable from meiosis in mice. Nat Genet 8:877-83
Hughes JF, Skaletsky H, Brown LG, Pyntikova T, Graves TA, Fulton RS, Dugan S, Ding Y, Buhay CJ, Kremitzki C, Wang Q, Shen H, Holder M, Villasana D, Nazareth LV, Cree A, Courtney L, Veizer J, Kotkiewicz H, Cho T, Koutseva N, Rozen S, Muzny DM, Warren WC, Gibbs RA, Wilson RK, Page DC
(2012) Strict evolutionary conservation followed rapid gene loss on human and rhesus Y chromosomes. Nature 483: 82-6
Gill ME, Hu Y, Lin Y, Page DC (2011) Licensing of gametogenesis, dependent on RNA binding protein DAZL, as a gateway to sexual differentiation of fetal germ cells. Proc Natl Acad Sci 108: 7443-8
Bellott DW, Skaletsky H, Pyntikova T, Mardis ER, Graves T, Kremitzki C, Brown LG, Rozen S, Warren WC, Wilson RK, Page DC (2010) Convergent evolution of chicken Z and human X chromosomes by expansion and gene acquisition. Nature 466: 612-16
Hughes JF, Skaletsky H, Pyntikova T, Graves TA, van Daalen SK, Minx PJ, Fulton RS, McGrath SD, Locke DP, Friedman C, Trask BJ, Mardis ER, Warren WC, Repping S, Rozen S, Wilson RK, Page DC (2010) Chimpanzee and human Y chromosomes are remarkably divergent in structure and gene content. Nature 463: 536-9
Rozen S, Marszalek JD, Alagappan RK, Skaletsky H, Page DC (2009) Remarkably little variation in proteins encoded by the Y chromosome's single-copy genes, implying effective purifying selection. Am J Hum Genet 85: 923-8
Lange J, Skaletsky H, van Daalen SK, Embry SL, Korver CM, Brown LG, Oates RD, Silber S, Repping S, Page DC (2009) Isodicentric Y chromosomes and sex disorders as byproducts of homologous recombination that maintains palindromes. Cell 138: 855-69
Lin Y, Gill ME, Koubova J, Page DC (2008) Germ cell–intrinsic and –extrinsic factors govern meiotic initiation in mouse embryos. Science 322:1685-7
Anderson E, Baltus AE, Roepers-Gajadien HL, Hassold TJ, de Rooij DG, van Pelt AMM, Page DC (2008) Stra8 and its inducer, retinoic acid, regulate meiotic initiation in both spermatogenesis and oogenesis in mice. Proc Natl Acad Sci 105:14876-80
Baltus AE, Menke DB, Hu Y, Goodheart ML, Carpenter AE, de Rooij DG, Page DC (2006) In germ cells of mouse embryonic ovaries, the decision to enter meiosis precedes premeiotic DNA replication. Nat Genet 38: 1430-4
Repping S, van Daalen SKM, Brown LG, Korver CM, Lange J, Marszalek JD, Pyntikova T, van der Veen F, Skaletsky H, Page DC, Rozen S (2006) High mutation rates have driven widespread architectural polymorphism among human Y chromosomes. Nat Genet 38: 463-7
Hughes JF, Skaletsky H, Pyntikova T, Minx PJ, Graves T, Rozen S, Wilson RK, Page DC (2005) Conservation of Y-linked genes during human evolution revealed by comparative sequencing in chimpanzee. Nature 437: 100-3