Supplementary Information for Tilford CA, Kuroda-Kawaguchi T, Skaletsky H, Rozen S, Brown LG, Rosenberg M, McPherson JD, Wylie K, Sekhon M, Kucaba TA, Waterston RH, Page DC. A physical map of the human Y chromosome. Nature 409, 943 (2001)
Supplementary Information for Wang PJ, McCarrey JR, Yang F, Page DC. An abundance of X-linked genes expressed in spermatogonia. Nature Genetics 27, 422 (2001)
Supplementary Information
for Tomoko Kuroda-Kawaguchi, Helen Skaletsky, Laura G. Brown,
Patrick J. Minx, Holland S. Cordum, Robert H. Waterston,
Richard K. Wilson, Sherman Silber, Robert Oates, Steve Rozen
& David C. Page.
The AZFc region of the Y chromosome
features massive palindromes and uniform
recurrent deletions
in infertile men, Nat. Genet. 29:279-286 (2001)
Supplementary Information
for Steve Rozen, Helen Skaletsky, Janet D. Marszalek, Patrick J. Minx, Holland
S. Cordum, Robert H. Waterston, Richard K. Wilson, & David C. Page. Abundant gene conversion between arms of palindromes in human and ape Y chromosomes.Nature 423:873-876 (2003)
Supplementary Information for Skaletsky, H., Kuroda-Kawaguchi, T., Minx, P.J., Cordum, H.S., Hillier, L.,
Brown, L.G., Repping, S., Pyntikova, T., Ali, J., Bieri, T., Chinwalla, A.,
Delehaunty, A., Delehaunty, K., Du, H., Fewell, G., Fulton, L., Fulton, R.,
Graves, T., Hou, S.-F., Latrielle, P., Leonard, S., Mardis, E., Maupin, R.,
McPherson, J., Miner, T., Nash, W., Nguyen, C., Ozersky, P., Pepin, K.,
Rock, S., Rohlfing, T., Scott, K., Schultz, B., Strong, C., Tin-Wollam, A.,
Yang, S.-P., Waterston, R.H., Wilson, R.K., Rozen, S., and Page, D.C.
The Male Specific Region of the Human Y Chromosome is a Mosaic of Discrete Sequence Classes . Nature 423: 825-837 (2003)
Supplementary Information for Repping S, Skaletsky H, Brown L, van Daalen SK, Korver CM, Pyntikova T, Kuroda-Kawaguchi T, de Vries JW, Oates RD, Silber S, van der Veen F, Page DC, Rozen S. Polymorphism for a 1.6-Mb deletion of the human Y chromosome persists through balance between recurrent mutation and haploid selection. Nature Genetics 35, 247 (2003)
Supplementary Information for Julie Bradley, Andrew Baltus, Helen Skaletsky, Morgan Royce-Tolland, Ken Dewar, & David C. Page. An X-to-autosome retrogene is required for spermatogenesis in mice . Nature Genetics 36 (2004)
Supplementary Information for Hughes, J.F., Skaletsky, H., Pyntikova, T., Minx, P.J., Graves, T., Rozen, S., Wilson, R.K., Page, D.C. Conservation of Y-linked genes during human evolution revealed by comparative sequencing in chimpanzee. Nature 437: 100-3 (2005)
Supplementary Information for Hughes, J.F., Skaletsky, H., Rozen, S., Wilson, R.K., Page, D.C. Has the chimpanzee Y chromosome been sequenced?Nature Genetics 38: 853-4 (2006)
Supplementary Information for Lin Y, Page DC. Dazl deficiency leads to embryonic arrest of germ cell development in XY C57BL/6 mice. Developmental Biology 288, 309 (2005)
Supplementary Information for Koubova J, Menke DB, Zhou Q, Capel B, Griswold MD, Page DC. Retinoic acid regulates sex-specific timing of meiotic initiation in mice. PNAS 103, 2474 (2006)
Supplementary Information for 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. High mutation rates have driven widespread architectural polymorphism among human Y chromosomes. Nature Genetics 38, 463 (2006)
Supplementary Information for Baltus AE, Menke DB, Hu Y, Goodheart ML, Carpenter AE, de Rooij DG, Page DC. In germ cells of mouse embryonic ovaries, the decision to enter meiosis precedes premeiotic DNA replication. Nature Genetics 38, 1430 (2006)
Supplementary Information for Cheng Y, Buffone MG, Kouadio M, Goodheart M, Page DC, Gerton GL, Davidson I, Wang PJ. Abnormal sperm in mice lacking the Taf7l gene. Molecular & Cell Biology 27, 2582 (2007)
Supplementary Information for Yang F, Gull K, van Heijden GW, Eckardt S, Leu NA, Page DC, Benavente R, Her C, Hoog C, McLaughlin KJ, Wang PJ. Meiotic failure in male mice lacking an X-linked factor. Genes & Development 22, 682 (2008)
Supplementary Information for Mueller JL, Mahadevaiah SK, Park PJ, Warburton PE, Page DC, Turner JM. The mouse X chromosome is enriched for multicopy testis genes showing postmeiotic expression. Nature Genetics 40, 794 (2008)
Supplementary Information for Lin Y, Gill ME, Koubova J, Page DC. Germ cell–intrinsic and –extrinsic factors govern meiotic initiation in mouse embryos. Science 322, 1685 (2008)
Supplementary Information for Rozen S, Marszalek JD, Alagappan RK, Skaletsky H, Page DC. Remarkably little variation in proteins encoded by the Y chromosome's single-copy genes, implying effective purifying selection American Journal of Human Genetics 85, 923 (2009)
Supplementary Information for 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. Chimpanzee and human Y chromosomes are remarkably divergent in structure and gene content.Nature 463: 536-9 (2010)
Supplementary Information for Lange, J., Skaletsky, H., van Daalen, S.K.M., Embry, S.L., Korver, C.M., Brown, L.G., Oates, R.D., Silber, S., Repping, S., Page, D.C. Isodicentric Y Chromosomes and Sex Disorders as Byproducts of Homologous Recombination That Maintains Palindromes. Cell 138: 855-869 (4 September 2009)
Supplementary Information for Bellott, D.W., Skaletsky, H., Pyntikova, T., Mardis, E.R., Graves, T., Kremitzki, C., Brown, L.G., Rozen, S., Warren, W.C., Wilson, R.K., Page, D.C. Convergent Evolution of Chicken Z and Human X Chromosomes by Expansion and Gene Acquisition. Nature 466: 612-616 (29 July 2010)
Supplementary Information for Gill ME, Hu Y, Lin Y, Page DC. Licensing of gametogenesis, dependent on RNA binding protein DAZL, as a gateway to sexual differentiation of fetal germ cells. PNAS 108, 7443 (2011)
Supplementary Information for Dawlaty MM, Ganz K, Powell BE, Hu YC, Markoulaki S, Cheng AW, Gao Q, Kim J, Choi SW, Page DC, Jaenisch R. Tet1 is dispensable for maintaining pluripotency and its loss is compatible with embryonic and postnatal development. Cell Stem Cell 9(2), 166 (2011)
Supplementary Information for Medeiros LA, Dennis LM, Gill ME, Houbaviy H, Markoulaki S, Fu D, White AC, Kirak O, Sharp PA, Page DC, Jaenisch R. Mir-290-295 deficiency in mice results in partially penetrant embryonic lethality and germ cells defects. PNAS 108, 14163 (2011)
Supplementary Information for Jennifer F. Hughes, Helen Skaletsky, Laura G. Brown, Tatyana Pyntikova, Tina Graves, Robert S. Fulton, Shannon Dugan, Yan Ding, Christian J. Buhay, Colin Kremitzki, Qiaoyan Wang, Hua Shen, Michael Holder,3 Donna Villasana, Lynne V. Nazareth, Andrew Cree, Laura Courtney, Joelle Veizer, Holland Kotkiewicz, Ting-Jan Cho, Natalia Koutseva, Steve Rozen, Donna M. Muzny, Wesley C. Warren, Richard A. Gibbs, Richard K. Wilson & David C. Page Strict evolutionary conservation followed rapid gene loss on human and rhesus Y chromosomes. Nature 482: (23 February 2012)
Supplementary Information for Heaney JD, Anderson EL, Michelson MV, Zechel JL, Conrad PA, Page DC, Nadeau JH. Germ cell pluripotency, premature differentiation and susceptibility to testicular teratomas in mice. Development 139, 1577 (2012)
Supplementary Information for Buganim Y, Itskovich E, Hu YC, Cheng AW, Ganz K, Sarkar S, Fu D, Welstead G, Page DC, Jaenisch R. Direct reprogramming of fibroblasts into embryonic Sertoli-like cells by defined factors. Cell Stem Cell 11, 373 (2012)
Supplementary Information for Hughes JF, Skaletsky H, Page DC. Sequencing of rhesus macaque Y chromosome clarifies origins and evolution of the DAZ (Deleted in AZoospermia) genes. Bioessays 34, 1035 (2012)
Supplementary Information for Lange J, Noordam MJ, van Daalen SK, Skaletsky H, Clark BA, Macville MV, Page DC, Repping S. Intrachromosomal homologous recombination between inverted repeat amplicons on opposing Y-chromosome arms. Genomics 102, 257 (2013)
Supplementary Information for Wang H, Hu YC, Markoulaki S, Welstead GG, Cheng AW, Shivalila CS, Pyntikova T, Dadon DB, Voytas DF, Bogdanove AJ, Page DC, Jaenisch R. TALEN-mediated editing of the mouse Y chromosome. Nature Biotechnology 31, 530 (2013)
Supplementary Information for Dokshin GA, Baltus AE, Eppig JJ, Page DC. Oocyte differentiation is genetically dissociable from meiosis in mice. Nature Genetics 45, 877 (2013)
Supplementary Information for Hu YC, Okumura LM, Page DC. Gata4 is required for formation of the genital ridge in mice. PLOS Genetics 9, e1003629 (2013)
Supplementary Information for Hu YC, de Rooij DG, Page DC. Tumor suppressor gene Rb is required for self-renewal of spermatogonial stem cells in mice. PNAS 110, 12685 (2013)
Supplementary Information for Mueller JL, Skaletsky H, Brown LG, Zaghlul S, Rock S, Graves T, Auger K, Warren WC, Wilson RK, Page DC. Independent specialization of the human and mouse X chromosomes for the male germ line. Nature Genetics 45, 1083 (2013)
Supplementary Information for Lesch BJ, Dokshin GA, Young RA, McCarrey JR, Page DC. A set of genes critical to development is epigenetically poised in mouse germ cells from fetal stages through completion of meiosis. PNAS 110, 16061 (2013)
Supplementary information for Daniel W. Bellott, Jennifer F. Hughes, Helen Skaletsky, Laura G. Brown, Tatyana Pyntikova, Ting-Jan Cho, Natalia Koutseva, Sara Zaghlul, Tina Graves, Susie Rock, Colin Kremitzki, Robert S. Fulton, Shannon Dugan, Yan Ding, Donna Morton, Ziad Khan, Lora Lewis, Christian Buhay, Qiaoyan Wang, Jennifer Watt, Michael Holder, Sandy Lee, Lynne Nazareth, Jessica Alfoldi, Steve Rozen, Donna M. Muzny, Wesley C. Warren, Richard A. Gibbs, Richard K. Wilson & David C. Page Mammalian Y chromosomes retain widely expressed dosage-sensitive regulators. Nature 494: (24 April 2014)
Supplementary information for Alpatov R, Lesch BJ, Nakamoto-Kinoshita M, Blanco A, Chen S, Stutzer A, Armache KJ, Simon MD, Xu C, Ali M, Murn J, Prisic S, Kutateladze TG, Vakoc CR, Min J, Kingston RE, Rischle W, Warren ST, Page DC, Shi Y. A chromatin-dependent role of the fragile X mental retardation protein FMRP in the DNA damage response Cell 157, 869 (2014)
Supplementary information for The Marmoset Genome Sequencing and Analysis Consortium. The common marmoset genome provides insight into primate biology and evolution. Nature Genetics 46, 850 (2014)
Supplementary information for Koubova J, Hu YC, Bhattacharyya T, Soh YQS, Gill ME, Goodheart ML, Hogarth CA, Griswold MD, Page DC. Retinoic acid activates two pathways required for meiosis in mice PLOS Genetics 10, e004541 (2014)
Supplementary information for Koenig PA, Nicholls PK, Schmidt FI, Hagiwara M, Maruyama T, Frydman GH, Watson N, Page DC, Ploegh HL. The E2 ubiquitin conjugating enzyme UBE2J1 is required for spermiogenesis in mice. J Biol Chem 289, 34490 (2014)
Supplementary information for Soh YQS, Alfoldi 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 Sequencing the mouse Y chromosome reveals convergent gene acquisition and amplification on both sex chromosomes. Cell 159: 800 (6 November 2014)
Supplementary information for Yesilaltay A, Dokshin GA, Bussoc D, Wang L, Galiani D, Chavarria T, Vasile E, Quilaqueo L, Orellana JA, Walzer D, Shalgi R, Dekel N, Albertini DF, Rigotti A, Page DC, and Krieger M. Excess cholesterol induces mouse egg activation and may cause female infertility PNAS 111, E1972 (2014)
Supplementary information for Hu YC, Nicholls PK, Soh YQ, Daniele JR, Junker JP, van Oudenaarden A, Page DC. Licensing of primordial germ cells for gametogenesis depends on genital ridge signaling PLOS Genetics 11, e1005019 (2015)
Supplementary information for Endo T, Romer KA, Anderson EL, Baltus AE, de Rooij DG, Page DC. Periodic retinoic acid-STRA8 signaling intersects with periodic germ-cell competencies to regulate spermatogenesis. PNAS 112, E2347 (2015)
Supplementary information for Hughes JF, Skaletsky H, Koutseva N, Pyntikova T, and Page DC. Sex chromosome-to-autosome transposition events counter Y-chromosome gene loss in mammals Genome Biology 16, 104 (2015)
Supplementary information for Yang F, Silber S, Leu NA, Oates RD, Marszalek JD, Skaletsky H, Brown LG, Rozen S, Page DC, Wang PJ. TEX11 is mutated in infertile men with azoospermia and regulates genome-wide recombination rates in mouse. EMBO Mol Med 7, 1198 (2015)
Supplementary information for Warren WC et al., The genome of the vervet (Chlorocebus aethiops sabaeus). Genome Res 25, 1921 (2015)
Supplementary information for Soh YQS, Junker JP, Gill ME, Mueller JL, van Oudenaarden A, Page DC. A gene regulatory program for meiotic prophase in the fetal ovary. PLOS Genet 17, e1005531 (2015)
Supplementary Information for Kern DM, Nicholls PK, Page DC, Cheeseman IM. A mitotic SKAP isoform regulates spindle positioning at astral microtubule plus ends. J Cell Biol 213, 315 (2016)
Supplementary Information for Bluma J Lesch, Sherman J Silber, John R McCarrey & David C Page. Parallel evolution of male germline epigenetic poising and somatic development in animals. Nature Genetics volume 48, pages 888–894 (2016)
Supplementary Information for MA Carmell, GA Dokshin, H Skaletsky, YC Hu, JC von Wolfswinkel, KJ Igarashi, DW Bellott, M Nefedov, PW Reddien, GC Enders, VN Uversky, CC Mello, DC Page. A widely employed germ cell marker is an ancient disordered protein with reproductive functions in diverse eukaryotes.eLife 5, e19993 (2016)
Supplementary information for Daniel W. Bellott, Helen Skaletsky, Ting-Jan Cho, Laura Brown, Devin Locke, Nancy Chen, Svetlana Galkina, Tatyana Pyntikova, Natalia Koutseva, Tina Graves, Colin Kremitzki, Wesley C. Warren, Andrew G. Clark, Elena Gaginskaya, Richard K. Wilson & David C Page Avian W and mammalian Y chromosomes convergently retained dosage-sensitive regulators. Nature Genetics 49, 387-394 (2017)
Supplementary information for Tsutomu Endo, Elizaveta Freinkman, Dirk G. de Rooij, and David C. Page. Periodic production of retinoic acid by meiotic and somatic cells coordinates four transitions in mouse spermatogenesis. PNAS 114, E10132 (2017)
Supplementary information for Naqvi S, Bellott DW, Lin KS, Page DC. Conserved microRNA targeting reveals preexisting gene dosage sensitivities that shaped amniote sex chromosome evolution Genome Res 28, 474 (2018)
Supplementary information for Bellott DW, Cho TJ, Hughes JF, Skaletsky H, Page DC. Cost-effective high-throughput single-haplotype iterative mapping and sequencing for complex genomic structures Nat Protoc 13, 787 (2018)
Supplementary Information for Teitz LS, Pyntikova T, Skaletsky H, Page DC.Selection has countered high mutability to preserve the ancestral copy number of Y chromosome amplicons in diverse human lineages Am J Hum Genet 103, 261 (2018)
Supplementary Information for Romer KA, De Rooij DG, Kojima ML, Page DC. Isolating mitotic and meiotic germ cells from male mice by developmental synchronization, staging, and sorting Dev Biol 443, 19 (2018)
Supplementary Information for Kojima ML, de Rooij DG, Page DC. Amplification of a broad transcriptional program by a common factor triggers the meiotic cell cycle in mice eLife 8, e43738 (2019)
Supplementary Information for Ly P, Brunner SF, Shoshani O, Kim DH, Lan W, Pyntikova T, Flanagan AM, Behjati S, Page DC, Campbell PJ, Cleveland DW. Chromosome segregation errors generate a diverse spectrum of simple and complex genomic rearrangements Nat Genet 51, 705 (2019)
Supplementary Information for Nicholls PK, Bellott DW, Cho TJ, Pyntikova T, Page DC. Locating and characterizing a transgene integration site by nanopore sequencing G3 9, 1481 (2019)
Supplementary information for Bluma J Lesch, Zuzana Tothova, Elizabeth A Morgan, Zhicong Liao, Roderick T Bronson, Benjamin L Ebert, David C Page. Intergenerational Epigenetic Inheritance of Cancer Susceptibility in Mammals eLIFE 8, e39380 (2019)
Processed Data and Code for Sahin Naqvi, Alexander K. Godfrey, Jennifer F. Hughes, Mary L. Goodheart, Richard N. Mitchell, & David C. Page Conservation, acquisition, and functional impact of sex-biased gene expression in mammalian tissues Science 365, eaaw7317 (2019) DOI: 10.1126/science.aaw7317
Supplementary Information for Sahin Naqvi, Alexander K. Godfrey, Jennifer F. Hughes, Mary L. Goodheart, Richard N. Mitchell, & David C. Page Conservation, acquisition, and functional impact of sex-biased gene expression in mammalian tissues Science 365, eaaw7317 (2019) DOI: 10.1126/science.aaw7317
Supplementary information for Emily K. Jackson, Daniel W. Bellott, Helen Skaletsky, and David C. Page GC-biased gene conversion in X-chromosome palindromes conserved in human, chimpanzee, and rhesus macaque. G3 epub July 8 (2021)