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Haque R, Kurien SP, Setty H, Salzberg Y, Stelzer G, Litvak E, Gingold H, Rechavi O, Oren-Suissa M. Sex-specific developmental gene expression atlas unveils dimorphic gene networks in C. elegans. Nat Commun 2024; 15:4273. [PMID: 38769103 PMCID: PMC11106331 DOI: 10.1038/s41467-024-48369-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Accepted: 04/24/2024] [Indexed: 05/22/2024] Open
Abstract
Sex-specific traits and behaviors emerge during development by the acquisition of unique properties in the nervous system of each sex. However, the genetic events responsible for introducing these sex-specific features remain poorly understood. In this study, we create a comprehensive gene expression atlas of pure populations of hermaphrodites and males of the nematode Caenorhabditis elegans across development. We discover numerous differentially expressed genes, including neuronal gene families like transcription factors, neuropeptides, and G protein-coupled receptors. We identify INS-39, an insulin-like peptide, as a prominent male-biased gene expressed specifically in ciliated sensory neurons. We show that INS-39 serves as an early-stage male marker, facilitating the effective isolation of males in high-throughput experiments. Through complex and sex-specific regulation, ins-39 plays pleiotropic sexually dimorphic roles in various behaviors, while also playing a shared, dimorphic role in early life stress. This study offers a comparative sexual and developmental gene expression database for C. elegans. Furthermore, it highlights conserved genes that may underlie the sexually dimorphic manifestation of different human diseases.
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Affiliation(s)
- Rizwanul Haque
- Department of Brain Sciences, Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
| | - Sonu Peedikayil Kurien
- Department of Brain Sciences, Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
| | - Hagar Setty
- Department of Brain Sciences, Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
| | - Yehuda Salzberg
- Department of Brain Sciences, Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel
| | - Gil Stelzer
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Einav Litvak
- Department of Brain Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Hila Gingold
- Department of Neurobiology, Wise Faculty of Life Sciences & Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Oded Rechavi
- Department of Neurobiology, Wise Faculty of Life Sciences & Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Meital Oren-Suissa
- Department of Brain Sciences, Weizmann Institute of Science, Rehovot, Israel.
- Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot, Israel.
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2
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Bista B, Wu Z, Literman R, Valenzuela N. Thermosensitive sex chromosome dosage compensation in ZZ/ZW softshell turtles, Apalone spinifera. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200101. [PMID: 34304598 DOI: 10.1098/rstb.2020.0101] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Sex chromosome dosage compensation (SCDC) overcomes gene-dose imbalances that disturb transcriptional networks, as when ZW females or XY males are hemizygous for Z/X genes. Mounting data from non-model organisms reveal diverse SCDC mechanisms, yet their evolution remains obscure, because most informative lineages with variable sex chromosomes are unstudied. Here, we discovered SCDC in turtles and an unprecedented thermosensitive SCDC in eukaryotes. We contrasted RNA-seq expression of Z-genes, their autosomal orthologues, and control autosomal genes in Apalone spinifera (ZZ/ZW) and Chrysemys picta turtles with temperature-dependent sex determination (TSD) (proxy for ancestral expression). This approach disentangled chromosomal context effects on Z-linked and autosomal expression, from lineage effects owing to selection or drift. Embryonic Apalone SCDC is tissue- and age-dependent, regulated gene-by-gene, complete in females via Z-upregulation in both sexes (Type IV) but partial and environmentally plastic via Z-downregulation in males (accentuated at colder temperature), present in female hatchlings and a weakly suggestive in adult liver (Type I). Results indicate that embryonic SCDC evolved with/after sex chromosomes in Apalone's family Tryonichidae, while co-opting Z-gene upregulation present in the TSD ancestor. Notably, Apalone's SCDC resembles pygmy snake's, and differs from the full-SCDC of Anolis lizards who share homologous sex chromosomes (XY), advancing our understanding of how XX/XY and ZZ/ZW systems compensate gene-dose imbalance. This article is part of the theme issue 'Challenging the paradigm in sex chromosome evolution: empirical and theoretical insights with a focus on vertebrates (Part II)'.
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Affiliation(s)
- Basanta Bista
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | - Zhiqiang Wu
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA.,Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, People's Republic of China
| | - Robert Literman
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | - Nicole Valenzuela
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
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3
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Li X, Itani OA, Haataja L, Dumas KJ, Yang J, Cha J, Flibotte S, Shih HJ, Delaney CE, Xu J, Qi L, Arvan P, Liu M, Hu PJ. Requirement for translocon-associated protein (TRAP) α in insulin biogenesis. SCIENCE ADVANCES 2019; 5:eaax0292. [PMID: 31840061 PMCID: PMC6892615 DOI: 10.1126/sciadv.aax0292] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 10/07/2019] [Indexed: 05/26/2023]
Abstract
The mechanistic basis for the biogenesis of peptide hormones and growth factors is poorly understood. Here, we show that the conserved endoplasmic reticulum membrane translocon-associated protein α (TRAPα), also known as signal sequence receptor 1, plays a critical role in the biosynthesis of insulin. Genetic analysis in the nematode Caenorhabditis elegans and biochemical studies in pancreatic β cells reveal that TRAPα deletion impairs preproinsulin translocation while unexpectedly disrupting distal steps in insulin biogenesis including proinsulin processing and secretion. The association of common intronic single-nucleotide variants in the human TRAPα gene with susceptibility to type 2 diabetes and pancreatic β cell dysfunction suggests that impairment of preproinsulin translocation and proinsulin trafficking may contribute to the pathogenesis of type 2 diabetes.
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Affiliation(s)
- Xin Li
- Department of Endocrinology and Metabolism, Tianjin Medical University General Hospital, Tianjin, China
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Omar A. Itani
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Leena Haataja
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
- Division of Metabolism, Endocrinology and Diabetes, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Kathleen J. Dumas
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Jing Yang
- Department of Endocrinology and Metabolism, Tianjin Medical University General Hospital, Tianjin, China
| | - Jeeyeon Cha
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Division of Diabetes, Endocrinology and Metabolism, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Stephane Flibotte
- Departments of Zoology and Cellular and Physiological Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Hung-Jen Shih
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Colin E. Delaney
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Jialu Xu
- Department of Endocrinology and Metabolism, Tianjin Medical University General Hospital, Tianjin, China
| | - Ling Qi
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
- Division of Metabolism, Endocrinology and Diabetes, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Peter Arvan
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
- Division of Metabolism, Endocrinology and Diabetes, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Ming Liu
- Department of Endocrinology and Metabolism, Tianjin Medical University General Hospital, Tianjin, China
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
- Division of Metabolism, Endocrinology and Diabetes, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Patrick J. Hu
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, USA
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Cell and Developmental Biology, Vanderbilt University Medical Center, Nashville, TN, USA
- Division of Hematology and Oncology, Vanderbilt University Medical Center, Nashville, TN, USA
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4
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Brejc K, Bian Q, Uzawa S, Wheeler BS, Anderson EC, King DS, Kranzusch PJ, Preston CG, Meyer BJ. Dynamic Control of X Chromosome Conformation and Repression by a Histone H4K20 Demethylase. Cell 2017; 171:85-102.e23. [PMID: 28867287 PMCID: PMC5678999 DOI: 10.1016/j.cell.2017.07.041] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Revised: 06/25/2017] [Accepted: 07/25/2017] [Indexed: 02/07/2023]
Abstract
Chromatin modification and higher-order chromosome structure play key roles in gene regulation, but their functional interplay in controlling gene expression is elusive. We have discovered the machinery and mechanism underlying the dynamic enrichment of histone modification H4K20me1 on hermaphrodite X chromosomes during C. elegans dosage compensation and demonstrated H4K20me1's pivotal role in regulating higher-order chromosome structure and X-chromosome-wide gene expression. The structure and the activity of the dosage compensation complex (DCC) subunit DPY-21 define a Jumonji demethylase subfamily that converts H4K20me2 to H4K20me1 in worms and mammals. Selective inactivation of demethylase activity eliminates H4K20me1 enrichment in somatic cells, elevates X-linked gene expression, reduces X chromosome compaction, and disrupts X chromosome conformation by diminishing the formation of topologically associating domains (TADs). Unexpectedly, DPY-21 also associates with autosomes of germ cells in a DCC-independent manner to enrich H4K20me1 and trigger chromosome compaction. Our findings demonstrate the direct link between chromatin modification and higher-order chromosome structure in long-range regulation of gene expression.
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Affiliation(s)
- Katjuša Brejc
- Howard Hughes Medical Institute and Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720-3204, USA
| | - Qian Bian
- Howard Hughes Medical Institute and Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720-3204, USA
| | - Satoru Uzawa
- Howard Hughes Medical Institute and Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720-3204, USA
| | - Bayly S Wheeler
- Howard Hughes Medical Institute and Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720-3204, USA
| | - Erika C Anderson
- Howard Hughes Medical Institute and Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720-3204, USA
| | - David S King
- HHMI Mass Spectrometry Laboratory, University of California, Berkeley, Berkeley, California 94720-3204, USA
| | - Philip J Kranzusch
- Howard Hughes Medical Institute and Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720-3204, USA
| | - Christine G Preston
- Howard Hughes Medical Institute and Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720-3204, USA
| | - Barbara J Meyer
- Howard Hughes Medical Institute and Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720-3204, USA.
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5
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Delaney CE, Chen AT, Graniel JV, Dumas KJ, Hu PJ. A histone H4 lysine 20 methyltransferase couples environmental cues to sensory neuron control of developmental plasticity. Development 2017; 144:1273-1282. [PMID: 28209779 PMCID: PMC5399626 DOI: 10.1242/dev.145722] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2016] [Accepted: 02/02/2017] [Indexed: 01/23/2023]
Abstract
Animals change developmental fates in response to external cues. In the nematode Caenorhabditis elegans, unfavorable environmental conditions induce a state of diapause known as dauer by inhibiting the conserved DAF-2 insulin-like signaling (ILS) pathway through incompletely understood mechanisms. We have previously established a role for the C. elegans dosage compensation protein DPY-21 in the control of dauer arrest and DAF-2 ILS. Here, we show that the histone H4 lysine 20 methyltransferase SET-4, which also influences dosage compensation, promotes dauer arrest in part by repressing the X-linked ins-9 gene, which encodes a new agonist insulin-like peptide (ILP) expressed specifically in the paired ASI sensory neurons that are required for dauer bypass. ins-9 repression in dauer-constitutive mutants requires DPY-21, SET-4 and the FoxO transcription factor DAF-16, which is the main target of DAF-2 ILS. By contrast, autosomal genes encoding major agonist ILPs that promote reproductive development are not repressed by DPY-21, SET-4 or DAF-16/FoxO. Our results implicate SET-4 as a sensory rheostat that reinforces developmental fates in response to environmental cues by modulating autocrine and paracrine DAF-2 ILS.
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Affiliation(s)
- Colin E Delaney
- Departments of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Albert T Chen
- Internal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Jacqueline V Graniel
- Internal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Kathleen J Dumas
- Internal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Patrick J Hu
- Departments of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA .,Internal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, USA.,Institute of Gerontology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
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6
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N-Ethyl-N-Nitrosourea (ENU) Mutagenesis Reveals an Intronic Residue Critical for Caenorhabditis elegans 3' Splice Site Function in Vivo. G3-GENES GENOMES GENETICS 2016; 6:1751-6. [PMID: 27172199 PMCID: PMC4889670 DOI: 10.1534/g3.116.028662] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Metazoan introns contain a polypyrimidine tract immediately upstream of the AG dinucleotide that defines the 3' splice site. In the nematode Caenorhabditis elegans, 3' splice sites are characterized by a highly conserved UUUUCAG/R octamer motif. While the conservation of pyrimidines in this motif is strongly suggestive of their importance in pre-mRNA splicing, in vivo evidence in support of this is lacking. In an N-ethyl-N-nitrosourea (ENU) mutagenesis screen in Caenorhabditis elegans, we have isolated a strain containing a point mutation in the octamer motif of a 3' splice site in the daf-12 gene. This mutation, a single base T-to-G transversion at the -5 position relative to the splice site, causes a strong daf-12 loss-of-function phenotype by abrogating splicing. The resulting transcript is predicted to encode a truncated DAF-12 protein generated by translation into the retained intron, which contains an in-frame stop codon. Other than the perfectly conserved AG dinucleotide at the site of splicing, G at the -5 position of the octamer motif is the most uncommon base in C. elegans 3' splice sites, occurring at closely paired sites where the better match to the splicing consensus is a few bases downstream. Our results highlight both the biological importance of the highly conserved -5 uridine residue in the C. elegans 3' splice site octamer motif as well as the utility of using ENU as a mutagen to study the function of polypyrimidine tracts and other AU- or AT-rich motifs in vivo.
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7
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Itani OA, Flibotte S, Dumas KJ, Moerman DG, Hu PJ. Chromoanasynthetic Genomic Rearrangement Identified in a N-Ethyl-N-Nitrosourea (ENU) Mutagenesis Screen in Caenorhabditis elegans. G3 (BETHESDA, MD.) 2015; 6:351-6. [PMID: 26628482 PMCID: PMC4751554 DOI: 10.1534/g3.115.024257] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 11/28/2015] [Indexed: 12/18/2022]
Abstract
Chromoanasynthesis is a recently discovered phenomenon in humans with congenital diseases that is characterized by complex genomic rearrangements (CGRs) resulting from aberrant repair of catastrophic chromosomal damage. How these CGRs are induced is not known. Here, we describe the structure and function of dpDp667, a causative CGR that emerged from a Caenorhabditis elegans dauer suppressor screen in which animals were treated with the point mutagen N-ethyl-N-nitrosourea (ENU). dpDp667 comprises nearly 3 Mb of sequence on the right arm of the X chromosome, contains three duplications and one triplication, and is devoid of deletions. Sequences from three out of the four breakpoint junctions in dpDp667 reveal microhomologies that are hallmarks of chromoanasynthetic CGRs. Our findings suggest that environmental insults and physiological processes that cause point mutations may give rise to chromoanasynthetic rearrangements associated with congenital disease. The relatively subtle phenotype of animals harboring dpDp667 suggests that the prevalence of CGRs in the genomes of mutant and/or phenotypically unremarkable animals may be grossly underestimated.
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Affiliation(s)
- Omar A Itani
- Institute of Gerontology, University of Michigan Medical School, Ann Arbor, Michigan 48109 Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan 48109 Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, Michigan 48109
| | - Stephane Flibotte
- Department of Zoology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Kathleen J Dumas
- Institute of Gerontology, University of Michigan Medical School, Ann Arbor, Michigan 48109 Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan 48109 Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, Michigan 48109
| | - Donald G Moerman
- Department of Zoology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Patrick J Hu
- Institute of Gerontology, University of Michigan Medical School, Ann Arbor, Michigan 48109 Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan 48109 Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, Michigan 48109
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8
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Tower J. Mitochondrial maintenance failure in aging and role of sexual dimorphism. Arch Biochem Biophys 2015; 576:17-31. [PMID: 25447815 PMCID: PMC4409928 DOI: 10.1016/j.abb.2014.10.008] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Revised: 10/08/2014] [Accepted: 10/18/2014] [Indexed: 12/31/2022]
Abstract
Gene expression changes during aging are partly conserved across species, and suggest that oxidative stress, inflammation and proteotoxicity result from mitochondrial malfunction and abnormal mitochondrial-nuclear signaling. Mitochondrial maintenance failure may result from trade-offs between mitochondrial turnover versus growth and reproduction, sexual antagonistic pleiotropy and genetic conflicts resulting from uni-parental mitochondrial transmission, as well as mitochondrial and nuclear mutations and loss of epigenetic regulation. Aging phenotypes and interventions are often sex-specific, indicating that both male and female sexual differentiation promote mitochondrial failure and aging. Studies in mammals and invertebrates implicate autophagy, apoptosis, AKT, PARP, p53 and FOXO in mediating sex-specific differences in stress resistance and aging. The data support a model where the genes Sxl in Drosophila, sdc-2 in Caenorhabditis elegans, and Xist in mammals regulate mitochondrial maintenance across generations and in aging. Several interventions that increase life span cause a mitochondrial unfolded protein response (UPRmt), and UPRmt is also observed during normal aging, indicating hormesis. The UPRmt may increase life span by stimulating mitochondrial turnover through autophagy, and/or by inhibiting the production of hormones and toxic metabolites. The data suggest that metazoan life span interventions may act through a common hormesis mechanism involving liver UPRmt, mitochondrial maintenance and sexual differentiation.
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Affiliation(s)
- John Tower
- Molecular and Computational Biology Program, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089-2910, United States.
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9
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Lau AC, Csankovszki G. Balancing up and downregulation of the C. elegans X chromosomes. Curr Opin Genet Dev 2015; 31:50-6. [PMID: 25966908 DOI: 10.1016/j.gde.2015.04.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Accepted: 04/02/2015] [Indexed: 02/01/2023]
Abstract
In Caenorhabditis elegans, males have one X chromosome and hermaphrodites have two. Emerging evidence indicates that the male X is transcriptionally more active than autosomes to balance the single X to two sets of autosomes. Because upregulation is not limited to males, hermaphrodites need to strike back and downregulate expression from the two X chromosomes to balance gene expression in their genome. Hermaphrodite-specific downregulation involves binding of the dosage compensation complex to both Xs. Advances in recent years revealed that the action of the dosage compensation complex results in compaction of the X chromosomes, changes in the distribution of histone modifications, and ultimately limiting RNA Polymerase II loading to achieve chromosome-wide gene repression.
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Affiliation(s)
- Alyssa C Lau
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, USA
| | - Györgyi Csankovszki
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, USA.
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10
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Jiang J, Lau AC, Csankovszki G. Pluripotent cells will not dosage compensate. WORM 2014; 3:e29051. [PMID: 25254152 DOI: 10.4161/worm.29051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Revised: 04/17/2014] [Accepted: 04/28/2014] [Indexed: 11/19/2022]
Abstract
Dosage compensation is the mechanism that balances gene expression levels between males and females as well as between the X chromosome and autosomes. In mammals, loss of pluripotency and differentiation are closely linked with the onset of dosage compensation. Pluripotency factors negatively regulate Xist (the non-coding RNA that triggers X chromosome inactivation) and positively regulate Tsix, a repressor of Xist, to inhibit dosage compensation. In addition, X chromosome dose also regulates exit from the pluripotent state. A double dose of X chromosomes in undifferentiated female cells inhibits the MAPK and Gsk3 signaling pathways and activates the Akt pathway, thereby blocking differentiation. Here we review our recent report, which showed that the onset of dosage compensation is also linked to the loss of pluripotency in C. elegans. We discuss these findings in light of what is known about pluripotency and differentiation in this organism.
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Affiliation(s)
- Jianhao Jiang
- Department of Molecular, Cellular and Developmental Biology; University of Michigan; Ann Arbor, MI USA
| | - Alyssa C Lau
- Department of Molecular, Cellular and Developmental Biology; University of Michigan; Ann Arbor, MI USA
| | - Györgyi Csankovszki
- Department of Molecular, Cellular and Developmental Biology; University of Michigan; Ann Arbor, MI USA
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11
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Hu PJ. Whole genome sequencing and the transformation of C. elegans forward genetics. Methods 2014; 68:437-40. [PMID: 24874788 DOI: 10.1016/j.ymeth.2014.05.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Revised: 05/16/2014] [Accepted: 05/17/2014] [Indexed: 11/16/2022] Open
Abstract
Forward genetics has been an undeniably powerful approach in Caenorhabditis elegans and other model organisms. However, the trek from mutant isolation to identification of the causative molecular lesion can be time-consuming and fraught with obstacles. This has changed with the advent of whole genome sequencing (WGS). The widespread availability of high-throughput sequencing technology, coupled with the increasing affordability of WGS, has enabled the routine use of WGS in the analysis of forward genetic screens. The noteworthy development of one-step mapping/sequencing approaches has largely eliminated the bottleneck of conventional high-resolution mapping, greatly accelerating the journey from mutagenesis to gene discovery. By enabling the use of increasingly complex and diverse genetic backgrounds as substrates for mutagenesis, WGS is expanding the landscape of biological problems that can be interrogated using forward genetic approaches in C. elegans and other organisms.
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Affiliation(s)
- Patrick J Hu
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109, United States; Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, United States; Institute of Gerontology, University of Michigan Medical School, Ann Arbor, MI 48109, United States.
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12
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Webster CM, Wu L, Douglas D, Soukas AA. A non-canonical role for the C. elegans dosage compensation complex in growth and metabolic regulation downstream of TOR complex 2. Development 2013; 140:3601-12. [PMID: 23884442 DOI: 10.1242/dev.094292] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The target of rapamycin complex 2 (TORC2) pathway is evolutionarily conserved and regulates cellular energetics, growth and metabolism. Loss of function of the essential TORC2 subunit Rictor (RICT-1) in Caenorhabditis elegans results in slow developmental rate, reduced brood size, small body size, increased fat mass and truncated lifespan. We performed a rict-1 suppressor RNAi screen of genes encoding proteins that possess the phosphorylation sequence of the AGC family kinase SGK, a key downstream effector of TORC2. Only RNAi to dpy-21 suppressed rict-1 slow developmental rate. DPY-21 functions canonically in the ten-protein dosage compensation complex (DCC) to downregulate the expression of X-linked genes only in hermaphroditic worms. However, we find that dpy-21 functions outside of its canonical role, as RNAi to dpy-21 suppresses TORC2 mutant developmental delay in rict-1 males and hermaphrodites. RNAi to dpy-21 normalized brood size and fat storage phenotypes in rict-1 mutants, but failed to restore normal body size and normal lifespan. Further dissection of the DCC via RNAi revealed that other complex members phenocopy the dpy-21 suppression of rict-1, as did RNAi to the DCC effectors set-1 and set-4, which methylate histone 4 on lysine 20 (H4K20). TORC2/rict-1 animals show dysregulation of H4K20 mono- and tri-methyl silencing epigenetic marks, evidence of altered DCC, SET-1 and SET-4 activity. DPY-21 protein physically interacts with the protein kinase SGK-1, suggesting that TORC2 directly regulates the DCC. Together, the data suggest non-canonical, negative regulation of growth and reproduction by DPY-21 via DCC, SET-1 and SET-4 downstream of TORC2 in C. elegans.
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Affiliation(s)
- Christopher M Webster
- Center for Human Genetic Research and Diabetes Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
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