Stress, novel sex genes, and epigenetic reprogramming orchestrate socially controlled sex change

Ovary-to-testis transformation in a sex-changing fish involves transcriptomic and epigenomic reprogramming. Bluehead wrasses undergo dramatic, socially cued female-to-male sex change. We apply transcriptomic and methylome approaches in this wild coral reef fish to identify the primary trigger and subsequent molecular cascade of gonadal metamorphosis. Our data suggest that the environmental stimulus is exerted via the stress axis and that repression of the aromatase gene (encoding the enzyme converting androgens to estrogens) triggers a cascaded collapse of feminizing gene expression and identifies notable sex-specific gene neofunctionalization. Furthermore, sex change involves distinct epigenetic reprogramming and an intermediate state with altered epigenetic machinery expression akin to the early developmental cells of mammals. These findings reveal at a molecular level how a normally committed developmental process remains plastic and is reversed to completely alter organ structures.

[1]  T. Manousaki,et al.  The Gene Toolkit Implicated in Functional Sex in Sparidae Hermaphrodites: Inferences From Comparative Transcriptomics , 2019, Front. Genet..

[2]  Donna M Bond,et al.  Bio-On-Magnetic-Beads (BOMB): Open platform for high-throughput nucleic acid extraction and manipulation , 2018, bioRxiv.

[3]  B. Capel,et al.  The histone demethylase KDM6B regulates temperature-dependent sex determination in a turtle species , 2018, Science.

[4]  A. Ruzov,et al.  Developmental Functions of the Dynamic DNA Methylome and Hydroxymethylome in the Mouse and Zebrafish: Similarities and Differences , 2018, Front. Cell Dev. Biol..

[5]  N. Gemmell,et al.  Stress and sex: does cortisol mediate sex change in fish? , 2017, Reproduction.

[6]  B. Capel Vertebrate sex determination: evolutionary plasticity of a fundamental switch , 2017, Nature Reviews Genetics.

[7]  Hendrik G. Stunnenberg,et al.  The interplay of epigenetic marks during stem cell differentiation and development , 2017, Nature Reviews Genetics.

[8]  Ira W. Deveson,et al.  Differential intron retention in Jumonji chromatin modifier genes is implicated in reptile temperature-dependent sex determination , 2017, Science Advances.

[9]  T. Hore,et al.  The elephant shark methylome reveals conservation of epigenetic regulation across jawed vertebrates , 2017, F1000Research.

[10]  L. Schärer The varied ways of being male and female , 2017, Molecular reproduction and development.

[11]  Timothy L. Tickle,et al.  A Tissue-Mapped Axolotl De Novo Transcriptome Enables Identification of Limb Regeneration Factors. , 2017, Cell reports.

[12]  J. Baroiller,et al.  The Reversible Sex of Gonochoristic Fish: Insights and Consequences , 2016, Sexual Development.

[13]  N. Gemmell,et al.  Bending Genders: The Biology of Natural Sex Change in Fish , 2016, Sexual Development.

[14]  T. Ravasi,et al.  Sex Change in Clownfish: Molecular Insights from Transcriptome Analysis , 2016, Scientific Reports.

[15]  J. Postlethwait,et al.  Gene evolution and gene expression after whole genome duplication in fish: the PhyloFish database , 2016, BMC Genomics.

[16]  Jorge Cadima,et al.  Principal component analysis: a review and recent developments , 2016, Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences.

[17]  N. Gemmell,et al.  Large-scale transcriptome sequencing reveals novel expression patterns for key sex-related genes in a sex-changing fish , 2015, Biology of Sex Differences.

[18]  Evgeny M. Zdobnov,et al.  BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs , 2015, Bioinform..

[19]  N. Gemmell,et al.  The Need for Speed: Neuroendocrine Regulation of Socially-controlled Sex Change. , 2015, Integrative and comparative biology.

[20]  J. Godwin,et al.  Characterizing the neurotranscriptomic states in alternative stress coping styles , 2015, BMC Genomics.

[21]  Pietro Liò,et al.  The BioMart community portal: an innovative alternative to large, centralized data repositories , 2015, Nucleic Acids Res..

[22]  A. Minkina,et al.  Sexual Cell-Fate Reprogramming in the Ovary by DMRT1 , 2015, Current Biology.

[23]  E. Kulczykowska,et al.  Cortisol modulates vasotocinergic and isotocinergic pathways in the gilthead sea bream , 2015, Journal of Experimental Biology.

[24]  J. Marioni,et al.  Genome-wide Bisulfite Sequencing in Zygotes Identifies Demethylation Targets and Maps the Contribution of TET3 Oxidation , 2014, Cell reports.

[25]  E. Matunis,et al.  The Jak-STAT target Chinmo prevents sex transformation of adult stem cells in the Drosophila testis niche. , 2014, Developmental cell.

[26]  W. Huber,et al.  Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 , 2014, Genome Biology.

[27]  J. Godwin,et al.  Limited sex-biased neural gene expression patterns across strains in Zebrafish (Danio rerio) , 2014, BMC Genomics.

[28]  F. Fogolari,et al.  Transcriptomic Analysis Unveils Correlations between Regulative Apoptotic Caspases and Genes of Cholesterol Homeostasis in Human Brain , 2014, PloS one.

[29]  C. Nusbaum,et al.  Comprehensive variation discovery in single human genomes , 2014, Nature Genetics.

[30]  Paul Theodor Pyl,et al.  HTSeq – A Python framework to work with high-throughput sequencing data , 2014, bioRxiv.

[31]  T. Manousaki,et al.  The sex-specific transcriptome of the hermaphrodite sparid sharpsnout seabream (Diplodus puntazzo) , 2014, BMC Genomics.

[32]  S. Neuhauss,et al.  Whole-genome duplication in teleost fishes and its evolutionary consequences , 2014, Molecular Genetics and Genomics.

[33]  W. Reik,et al.  Reprogramming the Methylome: Erasing Memory and Creating Diversity , 2014, Cell stem cell.

[34]  Jun Wang,et al.  Epigenetic modification and inheritance in sexual reversal of fish , 2014, Genome research.

[35]  Björn Usadel,et al.  Trimmomatic: a flexible trimmer for Illumina sequence data , 2014, Bioinform..

[36]  Richard M. Leggett,et al.  NextClip: an analysis and read preparation tool for Nextera Long Mate Pair libraries , 2013, Bioinform..

[37]  M. Grober,et al.  Stress and serial adult metamorphosis: multiple roles for the stress axis in socially regulated sex change , 2013, Front. Neurosci..

[38]  J. I. Fernandino,et al.  Environmental stress-induced testis differentiation: androgen as a by-product of cortisol inactivation. , 2013, General and comparative endocrinology.

[39]  M. Baker,et al.  Evolution of hormone selectivity in glucocorticoid and mineralocorticoid receptors , 2013, The Journal of Steroid Biochemistry and Molecular Biology.

[40]  W. Reik,et al.  FGF Signaling Inhibition in ESCs Drives Rapid Genome-wide Demethylation to the Epigenetic Ground State of Pluripotency , 2013, Clinical Epigenetics.

[41]  Jared T. Simpson,et al.  Exploring genome characteristics and sequence quality without a reference , 2013, Bioinform..

[42]  Colin N. Dewey,et al.  De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis , 2013, Nature Protocols.

[43]  Yang Zhang,et al.  Epigenetic modifications during sex change repress gonadotropin stimulation of cyp19a1a in a teleost ricefield eel (Monopterus albus). , 2013, Endocrinology.

[44]  F. Piferrer Epigenetics of sex determination and gonadogenesis , 2013, Developmental dynamics : an official publication of the American Association of Anatomists.

[45]  Kirsten R. McEwen,et al.  Naïve pluripotency is associated with global DNA hypomethylation , 2013, Nature Structural &Molecular Biology.

[46]  T. Down,et al.  Germline DNA Demethylation Dynamics and Imprint Erasure Through 5-Hydroxymethylcytosine , 2013, Science.

[47]  W. Reik,et al.  The Dynamics of Genome-wide DNA Methylation Reprogramming in Mouse Primordial Germ Cells , 2012, Molecular cell.

[48]  Masaru Nakamura,et al.  Diversity and Plasticity of Sex Determination and Differentiation in Fishes , 2012, Sexual Development.

[49]  S. Tevosian Genetic Control of Ovarian Development , 2012, Sexual Development.

[50]  I. Cancio,et al.  5S rRNA and accompanying proteins in gonads: powerful markers to identify sex and reproductive endocrine disruption in fish. , 2012, Environmental science & technology.

[51]  W. Pirovano,et al.  Toward almost closed genomes with GapFiller , 2012, Genome Biology.

[52]  L. Valente,et al.  Molecular evolution of zebrafish dnmt3 genes and thermal plasticity of their expression during embryonic development. , 2012, Gene.

[53]  H. Yao,et al.  How to Make a Gonad: Cellular Mechanisms Governing Formation of the Testes and Ovaries , 2012, Sexual Development.

[54]  Jennifer Nichols,et al.  The Transcriptional and Epigenomic Foundations of Ground State Pluripotency , 2012, Cell.

[55]  Steven L Salzberg,et al.  Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.

[56]  J. Godwin,et al.  Nonapeptides and Social Behavior in Fishes , 2012, Hormones and Behavior.

[57]  D. Zarkower,et al.  Sex and the singular DM domain: insights into sexual regulation, evolution and plasticity , 2012, Nature Reviews Genetics.

[58]  L. Ribas,et al.  DNA Methylation of the Gonadal Aromatase (cyp19a) Promoter Is Involved in Temperature-Dependent Sex Ratio Shifts in the European Sea Bass , 2011, PLoS genetics.

[59]  M. Taketo,et al.  RSPO1/β-Catenin Signaling Pathway Regulates Oogonia Differentiation and Entry into Meiosis in the Mouse Fetal Ovary , 2011, PloS one.

[60]  Colin N. Dewey,et al.  RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome , 2011, BMC Bioinformatics.

[61]  L. O’Connell,et al.  Genes, hormones, and circuits: An integrative approach to study the evolution of social behavior , 2011, Frontiers in Neuroendocrinology.

[62]  M. Griswold,et al.  DMRT1 prevents female reprogramming in the postnatal mammalian testis , 2011, Nature.

[63]  Matko Bosnjak,et al.  REVIGO Summarizes and Visualizes Long Lists of Gene Ontology Terms , 2011, PloS one.

[64]  Marcel Martin Cutadapt removes adapter sequences from high-throughput sequencing reads , 2011 .

[65]  Felix Krueger,et al.  Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications , 2011, Bioinform..

[66]  W. Pirovano,et al.  Scaffolding pre-assembled contigs using SSPACE , 2011, Bioinform..

[67]  D. Reinberg,et al.  The Polycomb complex PRC2 and its mark in life , 2011, Nature.

[68]  O. Kah,et al.  Aromatase, brain sexualization and plasticity: the fish paradigm , 2010, The European journal of neuroscience.

[69]  S. Nylin,et al.  Sex in an Evolutionary Perspective: Just Another Reaction Norm , 2010, Evolutionary Biology.

[70]  R. Horiguchi,et al.  Expression and localization of forkhead transcriptional factor 2 (Foxl2) in the gonads of protogynous wrasse, Halichoeres trimaculatus , 2010, Biology of Sex Differences.

[71]  J. Godwin Neuroendocrinology of sexual plasticity in teleost fishes , 2010, Frontiers in Neuroendocrinology.

[72]  F. Piferrer,et al.  Ovarian aromatase and estrogens: a pivotal role for gonadal sex differentiation and sex change in fish. , 2010, General and comparative endocrinology.

[73]  Ning Ma,et al.  BLAST+: architecture and applications , 2009, BMC Bioinformatics.

[74]  R. Lovell-Badge,et al.  Somatic Sex Reprogramming of Adult Ovaries to Testes by FOXL2 Ablation , 2009, Cell.

[75]  Hadley Wickham,et al.  ggplot2 - Elegant Graphics for Data Analysis (2nd Edition) , 2017 .

[76]  J. Mank,et al.  Evolutionary Perspectives on Hermaphroditism in Fishes , 2009, Sexual Development.

[77]  J. Godwin Social determination of sex in reef fishes. , 2009, Seminars in cell & developmental biology.

[78]  Masaru Nakamura,et al.  Short term treatment with aromatase inhibitor induces sex change in the protogynous wrasse, Halichoeres trimaculatus. , 2009, General and comparative endocrinology.

[79]  Brad T. Sherman,et al.  Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists , 2008, Nucleic acids research.

[80]  R. Young,et al.  H2AZ Is Enriched at Polycomb Complex Target Genes in ES Cells and Is Necessary for Lineage Commitment , 2008, Cell.

[81]  M. Surani,et al.  Chromatin dynamics during epigenetic reprogramming in the mouse germ line , 2008, Nature.

[82]  J. Klinman The Copper-Enzyme Family of Dopamine β-Monooxygenase and Peptidylglycine α-Hydroxylating Monooxygenase: Resolving the Chemical Pathway for Substrate Hydroxylation* , 2006, Journal of Biological Chemistry.

[83]  P. Munday,et al.  Diversity and flexibility of sex-change strategies in animals. , 2006, Trends in ecology & evolution.

[84]  Thomas D. Wu,et al.  GMAP: a genomic mapping and alignment program for mRNA and EST sequence , 2005, Bioinform..

[85]  Jean YH Yang,et al.  Bioconductor: open software development for computational biology and bioinformatics , 2004, Genome Biology.

[86]  J. Godwin,et al.  Multiple mechanisms of phenotype development in the bluehead wrasse , 2004, Hormones and Behavior.

[87]  T. Bestor,et al.  Windows for sex-specific methylation marked by DNA methyltransferase expression profiles in mouse germ cells. , 2004, Developmental biology.

[88]  Stephen M. Mount,et al.  Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies. , 2003, Nucleic acids research.

[89]  Brad T. Sherman,et al.  DAVID: Database for Annotation, Visualization, and Integrated Discovery , 2003, Genome Biology.

[90]  C. H. Summers,et al.  Monoaminergic changes associated with socially induced sex reversal in the saddleback wrasse , 2003, Neuroscience.

[91]  Masaru Nakamura,et al.  Role of steriod hormones in sex change of protogynous wrasse , 2003, Fish Physiology and Biochemistry.

[92]  C. H. Summers,et al.  Monoamines stimulate sex reversal in the saddleback wrasse. , 2003, General and comparative endocrinology.

[93]  S. Wray,et al.  17-β-Estradiol regulates expression of genes that function in macrophage activation and cholesterol homeostasis , 2002, The Journal of Steroid Biochemistry and Molecular Biology.

[94]  R. Devlin,et al.  Sex determination and sex differentiation in fish: an overview of genetic, physiological, and environmental influences , 2002 .

[95]  W. J. Kent,et al.  BLAT--the BLAST-like alignment tool. , 2002, Genome research.

[96]  C. Ponting,et al.  Regulation of chromatin structure by site-specific histone H3 methyltransferases , 2000, Nature.

[97]  M. Ashburner,et al.  Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.

[98]  T. Jinks,et al.  The JAK/STAT signaling pathway is required for the initial choice of sexual identity in Drosophila melanogaster. , 2000, Molecular cell.

[99]  J. Godwin,et al.  Behavioural sex change in the absence of gonads in a coral reef fish , 1996, Proceedings of the Royal Society of London. Series B: Biological Sciences.

[100]  N. Gemmell,et al.  An efficient method for the extraction of DNA from vertebrate tissues. , 1996, Trends in genetics : TIG.

[101]  J. Godwin,et al.  Sex change and steroid profiles in the protandrous anemonefish Amphiprion melanopus (Pomacentridae, Teleostei). , 1993, General and comparative endocrinology.

[102]  R. R. Warner,et al.  Social Control of Sex Change in the Bluehead Wrasse, Thalassoma bifasciatum (Pisces: Labridae). , 1991, The Biological bulletin.

[103]  T. Hourigan,et al.  Histological and ultrastructural evidence for the role of gonadal steroid hormones in sex change in the protogynous wrasse Thalassoma duperrey , 1989, Environmental Biology of Fishes.

[104]  M. Frommer,et al.  CpG islands in vertebrate genomes. , 1987, Journal of molecular biology.

[105]  R. R. Warner Mating Behavior and Hermaphroditism in Coral Reef Fishes , 1984 .

[106]  R. R. Warner The Adaptive Significance of Sequential Hermaphroditism in Animals , 1975, The American Naturalist.

[107]  N. Gemmell,et al.  Female Mimicry by Sneaker Males Has a Transcriptomic Signature in Both the Brain and the Gonad in a Sex-Changing Fish , 2018, Molecular biology and evolution.

[108]  Florian Hahne,et al.  Visualizing Genomic Data Using Gviz and Bioconductor , 2016, Statistical Genomics.

[109]  K. Maruska,et al.  Reproductive- and social-state plasticity of multiple sensory systems in a cichlid fish. , 2021, Integrative and comparative biology.

[110]  R Core Team,et al.  R: A language and environment for statistical computing. , 2014 .

[111]  M. Griswold,et al.  DMRT1 prevents female reprogramming in the postnatal mammalian testis. , 2011, Nature.

[112]  Cedric E. Ginestet ggplot2: Elegant Graphics for Data Analysis , 2011 .

[113]  Claude-Alain H. Roten,et al.  Fast and accurate short read alignment with Burrows–Wheeler transform , 2009, Bioinform..

[114]  Brad T. Sherman,et al.  Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources , 2008, Nature Protocols.

[115]  J. Klinman The copper-enzyme family of dopamine beta-monooxygenase and peptidylglycine alpha-hydroxylating monooxygenase: resolving the chemical pathway for substrate hydroxylation. , 2006, The Journal of biological chemistry.