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Salzler HR, Vandadi V, Matera AG. Set2 and H3K36 regulate the Drosophila male X chromosome in a context-specific manner, independent from MSL complex spreading. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.03.592390. [PMID: 38766267 PMCID: PMC11100620 DOI: 10.1101/2024.05.03.592390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Dosage compensation in Drosophila involves upregulating male X-genes two-fold. This process is carried out by the MSL (male-specific lethal) complex, which binds high-affinity sites and spreads to surrounding genes. Current models of MSL spreading focus on interactions of MSL3 (male-specific lethal 3) with histone marks; in particular, Set2-dependent H3 lysine-36 trimethylation (H3K36me3). However, Set2 might affect DC via another target, or there could be redundancy between canonical H3.2 and variant H3.3 histones. Further, it is difficult to parse male-specific effects from those that are simply X-specific. To discriminate among these possibilities, we employed genomic approaches in H3K36 (residue) and Set2 (writer) mutants. The results confirm a role for Set2 in X-gene regulation, but show that expression trends in males are often mirrored in females. Instead of global male-specific reduction of X-genes in Set2/H3K36 mutants, the effects were heterogeneous. We identified cohorts of genes whose expression was significantly altered following loss of H3K36 or Set2, but the changes were in opposite directions, suggesting that H3K36me states have reciprocal functions. In contrast to H4K16R controls, analysis of combined H3.2K36R/H3.3K36R mutants neither showed consistent reduction in X-gene expression, nor any correlation with MSL3 binding. Examination of other developmental stages/tissues revealed additional layers of context-dependence. Our studies implicate BEAF-32 and other insulator proteins in Set2/H3K36-dependent regulation. Overall, the data are inconsistent with the prevailing model wherein H3K36me3 directly recruits the MSL complex. We propose that Set2 and H3K36 support DC indirectly, via processes that are utilized by MSL but common to both sexes.
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Affiliation(s)
- Harmony R. Salzler
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC, USA
| | - Vasudha Vandadi
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC, USA
| | - A. Gregory Matera
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC, USA
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
- Department of Biology, University of North Carolina, Chapel Hill, NC, USA
- RNA Discovery and Lineberger Comprehensive Cancer Centers, University of North Carolina, Chapel Hill, NC, USA
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2
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Tikhonova EA, Georgiev PG, Maksimenko OG. Functional Role of C-terminal Domains in the MSL2 Protein of Drosophila melanogaster. BIOCHEMISTRY. BIOKHIMIIA 2024; 89:663-673. [PMID: 38831503 DOI: 10.1134/s0006297924040060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 12/11/2023] [Accepted: 12/12/2023] [Indexed: 06/05/2024]
Abstract
Dosage compensation complex (DCC), which consists of five proteins and two non-coding RNAs roX, specifically binds to the X chromosome in males, providing a higher level of gene expression necessary to compensate for the monosomy of the sex chromosome in male Drosophila compared to the two X chromosomes in females. The MSL2 protein contains the N-terminal RING domain, which acts as an E3 ligase in ubiquitination of proteins and is the only subunit of the complex expressed only in males. Functional role of the two C-terminal domains of the MSL2 protein, enriched with proline (P-domain) and basic amino acids (B-domain), was investigated. As a result, it was shown that the B-domain destabilizes the MSL2 protein, which is associated with the presence of two lysines ubiquitination of which is under control of the RING domain of MSL2. The unstructured proline-rich domain stimulates transcription of the roX2 gene, which is necessary for effective formation of the dosage compensation complex.
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Affiliation(s)
| | - Pavel G Georgiev
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia
| | - Oksana G Maksimenko
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia.
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3
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Kalita AI, Marois E, Kozielska M, Weissing FJ, Jaouen E, Möckel MM, Rühle F, Butter F, Basilicata MF, Keller Valsecchi CI. The sex-specific factor SOA controls dosage compensation in Anopheles mosquitoes. Nature 2023; 623:175-182. [PMID: 37769784 PMCID: PMC10620080 DOI: 10.1038/s41586-023-06641-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 09/13/2023] [Indexed: 10/03/2023]
Abstract
The Anopheles mosquito is one of thousands of species in which sex differences play a central part in their biology, as only females need a blood meal to produce eggs. Sex differentiation is regulated by sex chromosomes, but their presence creates a dosage imbalance between males (XY) and females (XX). Dosage compensation (DC) can re-equilibrate the expression of sex chromosomal genes. However, because DC mechanisms have only been fully characterized in a few model organisms, key questions about its evolutionary diversity and functional necessity remain unresolved1. Here we report the discovery of a previously uncharacterized gene (sex chromosome activation (SOA)) as a master regulator of DC in the malaria mosquito Anopheles gambiae. Sex-specific alternative splicing prevents functional SOA protein expression in females. The male isoform encodes a DNA-binding protein that binds the promoters of active X chromosomal genes. Expressing male SOA is sufficient to induce DC in female cells. Male mosquitoes lacking SOA or female mosquitoes ectopically expressing the male isoform exhibit X chromosome misregulation, which is compatible with viability but causes developmental delay. Thus, our molecular analyses of a DC master regulator in a non-model organism elucidates the evolutionary steps that lead to the establishment of a chromosome-specific fine-tuning mechanism.
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Affiliation(s)
| | - Eric Marois
- INSERM U1257, CNRS UPR9022, Université de Strasbourg, Strasbourg, France
| | - Magdalena Kozielska
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, Netherlands
| | - Franz J Weissing
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, Netherlands
| | - Etienne Jaouen
- INSERM U1257, CNRS UPR9022, Université de Strasbourg, Strasbourg, France
| | | | - Frank Rühle
- Institute of Molecular Biology (IMB), Mainz, Germany
| | - Falk Butter
- Institute of Molecular Biology (IMB), Mainz, Germany
- Institute of Molecular Virology and Cell Biology, Friedrich Loeffler Institute, Greifswald, Germany
| | - M Felicia Basilicata
- Institute of Molecular Biology (IMB), Mainz, Germany
- Institute of Human Genetics, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
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4
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Jalloh B, Lancaster CL, Rounds JC, Brown BE, Leung SW, Banerjee A, Morton DJ, Bienkowski RS, Fasken MB, Kremsky IJ, Tegowski M, Meyer K, Corbett A, Moberg K. The Drosophila Nab2 RNA binding protein inhibits m 6A methylation and male-specific splicing of Sex lethal transcript in female neuronal tissue. eLife 2023; 12:e64904. [PMID: 37458420 PMCID: PMC10351920 DOI: 10.7554/elife.64904] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Accepted: 06/23/2023] [Indexed: 07/20/2023] Open
Abstract
The Drosophila polyadenosine RNA binding protein Nab2, which is orthologous to a human protein lost in a form of inherited intellectual disability, controls adult locomotion, axon projection, dendritic arborization, and memory through a largely undefined set of target RNAs. Here, we show a specific role for Nab2 in regulating splicing of ~150 exons/introns in the head transcriptome and focus on retention of a male-specific exon in the sex determination factor Sex-lethal (Sxl) that is enriched in female neurons. Previous studies have revealed that this splicing event is regulated in females by N6-methyladenosine (m6A) modification by the Mettl3 complex. At a molecular level, Nab2 associates with Sxl pre-mRNA in neurons and limits Sxl m6A methylation at specific sites. In parallel, reducing expression of the Mettl3, Mettl3 complex components, or the m6A reader Ythdc1 rescues mutant phenotypes in Nab2 flies. Overall, these data identify Nab2 as an inhibitor of m6A methylation and imply significant overlap between Nab2 and Mettl3 regulated RNAs in neuronal tissue.
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Affiliation(s)
- Binta Jalloh
- Department of Biology, Emory UniversityAtlantaUnited States
- Department of Cell Biology Emory University School of MedicineAtlantaUnited States
- Graduate Program in Genetics and Molecular Biology, Emory UniversityAtlantaUnited States
| | - Carly L Lancaster
- Department of Biology, Emory UniversityAtlantaUnited States
- Department of Cell Biology Emory University School of MedicineAtlantaUnited States
- Graduate Program in Biochemistry, Cell and Developmental Biology, Emory UniversityAtlantaUnited States
| | - J Christopher Rounds
- Department of Biology, Emory UniversityAtlantaUnited States
- Department of Cell Biology Emory University School of MedicineAtlantaUnited States
- Graduate Program in Genetics and Molecular Biology, Emory UniversityAtlantaUnited States
| | - Brianna E Brown
- Department of Biology, Emory UniversityAtlantaUnited States
- Department of Cell Biology Emory University School of MedicineAtlantaUnited States
| | - Sara W Leung
- Department of Biology, Emory UniversityAtlantaUnited States
| | - Ayan Banerjee
- Department of Biology, Emory UniversityAtlantaUnited States
| | - Derrick J Morton
- Department of Biology, Emory UniversityAtlantaUnited States
- Emory Institutional Research and Academic Career Development Award (IRACDA), Fellowships in Research and Science Teaching (FIRST) Postdoctoral FellowshipAtlantaUnited States
| | - Rick S Bienkowski
- Department of Biology, Emory UniversityAtlantaUnited States
- Department of Cell Biology Emory University School of MedicineAtlantaUnited States
- Graduate Program in Genetics and Molecular Biology, Emory UniversityAtlantaUnited States
| | - Milo B Fasken
- Department of Biology, Emory UniversityAtlantaUnited States
| | | | - Matthew Tegowski
- Department of Biochemistry, Duke University School of MedicineDurhamUnited States
| | - Kate Meyer
- Department of Biochemistry, Duke University School of MedicineDurhamUnited States
- Department of Neurobiology, Duke University School of MedicineDurhamUnited States
| | - Anita Corbett
- Department of Biology, Emory UniversityAtlantaUnited States
| | - Ken Moberg
- Department of Cell Biology Emory University School of MedicineAtlantaUnited States
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5
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Forbes Beadle L, Zhou H, Rattray M, Ashe HL. Modulation of transcription burst amplitude underpins dosage compensation in the Drosophila embryo. Cell Rep 2023; 42:112382. [PMID: 37060568 PMCID: PMC10283159 DOI: 10.1016/j.celrep.2023.112382] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 02/03/2023] [Accepted: 03/27/2023] [Indexed: 04/16/2023] Open
Abstract
Dosage compensation, the balancing of X-linked gene expression between sexes and to the autosomes, is critical to an organism's fitness and survival. In Drosophila, dosage compensation involves hypertranscription of the male X chromosome. Here, we use quantitative live imaging and modeling at single-cell resolution to study X chromosome dosage compensation in Drosophila. We show that the four X chromosome genes studied undergo transcriptional bursting in male and female embryos. Mechanistically, our data reveal that transcriptional upregulation of male X chromosome genes is primarily mediated by a higher RNA polymerase II initiation rate and burst amplitude across the expression domain. In contrast, burst frequency is spatially modulated in nuclei within the expression domain in response to different transcription factor concentrations to tune the transcriptional response. Together, these data show how the local and global regulation of distinct burst parameters can establish the complex transcriptional outputs underpinning developmental patterning.
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Affiliation(s)
- Lauren Forbes Beadle
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, UK
| | - Hongpeng Zhou
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, UK
| | - Magnus Rattray
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, UK.
| | - Hilary L Ashe
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, UK.
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6
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Laslo M, Just J, Angelini DR. Theme and variation in the evolution of insect sex determination. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART B, MOLECULAR AND DEVELOPMENTAL EVOLUTION 2023; 340:162-181. [PMID: 35239250 PMCID: PMC10078687 DOI: 10.1002/jez.b.23125] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Revised: 11/24/2021] [Accepted: 01/03/2022] [Indexed: 11/07/2022]
Abstract
The development of dimorphic adult sexes is a critical process for most animals, one that is subject to intense selection. Work in vertebrate and insect model species has revealed that sex determination mechanisms vary widely among animal groups. However, this variation is not uniform, with a limited number of conserved factors. Therefore, sex determination offers an excellent context to consider themes and variations in gene network evolution. Here we review the literature describing sex determination in diverse insects. We have screened public genomic sequence databases for orthologs and duplicates of 25 genes involved in insect sex determination, identifying patterns of presence and absence. These genes and a 3.5 reference set of 43 others were used to infer phylogenies and compared to accepted organismal relationships to examine patterns of congruence and divergence. The function of candidate genes for roles in sex determination (virilizer, female-lethal-2-d, transformer-2) and sex chromosome dosage compensation (male specific lethal-1, msl-2, msl-3) were tested using RNA interference in the milkweed bug, Oncopeltus fasciatus. None of these candidate genes exhibited conserved roles in these processes. Amidst this variation we wish to highlight the following themes for the evolution of sex determination: (1) Unique features within taxa influence network evolution. (2) Their position in the network influences a component's evolution. Our analyses also suggest an inverse association of protein sequence conservation with functional conservation.
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Affiliation(s)
- Mara Laslo
- Department of Cell Biology, Curriculum Fellows ProgramHarvard Medical School25 Shattuck StBostonMassachusettsUSA
| | - Josefine Just
- Department of Organismic and Evolutionary BiologyHarvard University26 Oxford StCambridgeMassachusettsUSA
- Department of BiologyColby College5734 Mayflower Hill DrWatervilleMaineUSA
| | - David R. Angelini
- Department of BiologyColby College5734 Mayflower Hill DrWatervilleMaineUSA
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7
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Cheng FP, Hu XF, Pan LX, Gong ZX, Qin KX, Li Z, Wang ZL. Transcriptome changes of Apis mellifera female embryos with fem gene knockout by CRISPR/Cas9. Int J Biol Macromol 2023; 229:260-267. [PMID: 36587640 DOI: 10.1016/j.ijbiomac.2022.12.229] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 12/11/2022] [Accepted: 12/15/2022] [Indexed: 12/31/2022]
Abstract
The sex of honey bees is decided by a regulatory cascade comprising of csd, fem and Amdsx. In order to further identify other genes involved in sex determination and differentiation of honey bees in the early stages of embryo development, the CRISPR/Cas9 method was used to knock out fem gene in the embryonic stage of diploid western honey bees, and RNA-seq was used to analyze gene expression changes in the embryo after fem knockout. Finally, we found that the bees had undergone gender changes due to fem knockout. A total of 155 differentially expressed genes (DEGs) were obtained, with 48 up-regulated and 107 down-regulated DEGs in the mutant group compared to the control group. Of them, many genes are related to sex development or differentiation. In addition, 1502 differentially expressed alternative splicing events (DEASEs) related to 1011 genes, including the main honey bee sex-determining genes csd, tra2, fem, and Amdsx, were identified between the mutant group and control group, indicating that fem regulates alternative splicing of a large number of downstream genes. Our results provide valuable clues for further investigating the molecular mechanism of sex determination and differentiation in honey bees.
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Affiliation(s)
- Fu-Ping Cheng
- Honeybee Research Institute, Jiangxi Agricultural University, Nanchang 330045, China; Jiangxi Province Key Laboratory of Honeybee Biology and Beekeeping, Nanchang 330045, PR China
| | - Xiao-Fen Hu
- Honeybee Research Institute, Jiangxi Agricultural University, Nanchang 330045, China; Jiangxi Province Key Laboratory of Honeybee Biology and Beekeeping, Nanchang 330045, PR China
| | - Lu-Xia Pan
- Honeybee Research Institute, Jiangxi Agricultural University, Nanchang 330045, China; Jiangxi Province Key Laboratory of Honeybee Biology and Beekeeping, Nanchang 330045, PR China
| | - Zhi-Xian Gong
- Honeybee Research Institute, Jiangxi Agricultural University, Nanchang 330045, China; Jiangxi Province Key Laboratory of Honeybee Biology and Beekeeping, Nanchang 330045, PR China
| | - Kai-Xin Qin
- Honeybee Research Institute, Jiangxi Agricultural University, Nanchang 330045, China; Jiangxi Province Key Laboratory of Honeybee Biology and Beekeeping, Nanchang 330045, PR China
| | - Zhen Li
- Honeybee Research Institute, Jiangxi Agricultural University, Nanchang 330045, China; Jiangxi Province Key Laboratory of Honeybee Biology and Beekeeping, Nanchang 330045, PR China
| | - Zi-Long Wang
- Honeybee Research Institute, Jiangxi Agricultural University, Nanchang 330045, China; Jiangxi Province Key Laboratory of Honeybee Biology and Beekeeping, Nanchang 330045, PR China.
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8
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Nanni AV, Martinez N, Graze R, Morse A, Newman JRB, Jain V, Vlaho S, Signor S, Nuzhdin SV, Renne R, McIntyre LM. Sex-biased expression is associated with chromatin state in D. melanogaster and D. simulans. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.13.523946. [PMID: 36711631 PMCID: PMC9882225 DOI: 10.1101/2023.01.13.523946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
We propose a new model for the association of chromatin state and sex-bias in expression. We hypothesize enrichment of open chromatin in the sex where we see expression bias (OS) and closed chromatin in the opposite sex (CO). In this study of D. melanogaster and D. simulans head tissue, sex-bias in expression is associated with H3K4me3 (open mark) in males for male-biased genes and in females for female-biased genes in both species. Sex-bias in expression is also largely conserved in direction and magnitude between the two species on the X and autosomes. In male-biased orthologs, the sex-bias ratio is more divergent between species if both species have H3K27me2me3 marks in females compared to when either or neither species has H3K27me2me3 in females. H3K27me2me3 marks in females are associated with male-bias in expression on the autosomes in both species, but on the X only in D. melanogaster . In female-biased orthologs the relationship between the species for the sex-bias ratio is similar regardless of the H3K27me2me3 marks in males. Female-biased orthologs are more similar in the ratio of sex-bias than male-biased orthologs and there is an excess of male-bias in expression in orthologs that gain/lose sex-bias. There is an excess of male-bias in sex-limited expression in both species suggesting excess male-bias is due to rapid evolution between the species. The X chromosome has an enrichment in male-limited H3K4me3 in both species and an enrichment of sex-bias in expression compared to the autosomes.
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Affiliation(s)
- Adalena V Nanni
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL
- University of Florida Genetics Institute, University of Florida, Gainesville, FL, USA
| | - Natalie Martinez
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL
| | - Rita Graze
- Department of Biological Sciences, Auburn University, Auburn, AL, USA
| | - Alison Morse
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL
- University of Florida Genetics Institute, University of Florida, Gainesville, FL, USA
| | - Jeremy R B Newman
- University of Florida Genetics Institute, University of Florida, Gainesville, FL, USA
| | - Vaibhav Jain
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL
| | - Srna Vlaho
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Sarah Signor
- Department of Biological Sciences, North Dakota State University, Fargo, ND, USA
| | - Sergey V Nuzhdin
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Rolf Renne
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL
- University of Florida Genetics Institute, University of Florida, Gainesville, FL, USA
| | - Lauren M McIntyre
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL
- University of Florida Genetics Institute, University of Florida, Gainesville, FL, USA
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9
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Dosage Compensation in Drosophila: Its Canonical and Non-Canonical Mechanisms. Int J Mol Sci 2022; 23:ijms231810976. [PMID: 36142884 PMCID: PMC9506574 DOI: 10.3390/ijms231810976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 09/16/2022] [Accepted: 09/17/2022] [Indexed: 11/17/2022] Open
Abstract
Dosage compensation equalizes gene expression in a single male X chromosome with that in the pairs of autosomes and female X chromosomes. In the fruit fly Drosophila, canonical dosage compensation is implemented by the male-specific lethal (MSL) complex functioning in all male somatic cells. This complex contains acetyl transferase males absent on the first (MOF), which performs H4K16 hyperacetylation specifically in the male X chromosome, thus facilitating transcription of the X-linked genes. However, accumulating evidence points to an existence of additional, non-canonical dosage compensation mechanisms operating in somatic and germline cells. In this review, we discuss current advances in the understanding of both canonical and non-canonical mechanisms of dosage compensation in Drosophila.
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10
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Tikhonova E, Mariasina S, Efimov S, Polshakov V, Maksimenko O, Georgiev P, Bonchuk A. Structural basis for interaction between CLAMP and MSL2 proteins involved in the specific recruitment of the dosage compensation complex in Drosophila. Nucleic Acids Res 2022; 50:6521-6531. [PMID: 35648444 PMCID: PMC9226498 DOI: 10.1093/nar/gkac455] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 04/26/2022] [Accepted: 05/30/2022] [Indexed: 12/02/2022] Open
Abstract
Transcriptional regulators select their targets from a large pool of similar genomic sites. The binding of the Drosophila dosage compensation complex (DCC) exclusively to the male X chromosome provides insight into binding site selectivity rules. Previous studies showed that the male-specific organizer of the complex, MSL2, and ubiquitous DNA-binding protein CLAMP directly interact and play an important role in the specificity of X chromosome binding. Here, we studied the highly specific interaction between the intrinsically disordered region of MSL2 and the N-terminal zinc-finger C2H2-type (C2H2) domain of CLAMP. We obtained the NMR structure of the CLAMP N-terminal C2H2 zinc finger, which has a classic C2H2 zinc-finger fold with a rather unusual distribution of residues typically used in DNA recognition. Substitutions of residues in this C2H2 domain had the same effect on the viability of males and females, suggesting that it plays a general role in CLAMP activity. The N-terminal C2H2 domain of CLAMP is highly conserved in insects. However, the MSL2 region involved in the interaction is conserved only within the Drosophila genus, suggesting that this interaction emerged during the evolution of a mechanism for the specific recruitment of the DCC on the male X chromosome in Drosophilidae.
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Affiliation(s)
- Evgeniya Tikhonova
- Department of the Control of Genetic Processes, Institute of Gene Biology, Moscow 119334, Russia
| | - Sofia Mariasina
- Center for Magnetic Tomography and Spectroscopy, Faculty of Fundamental Medicine, M.V. Lomonosov Moscow State University, Moscow 119991, Russia
| | - Sergey Efimov
- NMR Laboratory, Institute of Physics, Kazan Federal University, Kazan 420008, Russia
| | - Vladimir Polshakov
- Center for Magnetic Tomography and Spectroscopy, Faculty of Fundamental Medicine, M.V. Lomonosov Moscow State University, Moscow 119991, Russia
| | - Oksana Maksimenko
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Moscow 119334, Russia
| | - Pavel Georgiev
- Department of the Control of Genetic Processes, Institute of Gene Biology, Moscow 119334, Russia
| | - Artem Bonchuk
- Department of the Control of Genetic Processes, Institute of Gene Biology, Moscow 119334, Russia.,Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Moscow 119334, Russia
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11
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Tomihara K, Katsuma S, Kiuchi T. Transcriptome analysis in the silkworm Bombyx mori overexpressing piRNA-resistant Masculinizer gene. Biochem Biophys Res Commun 2022; 616:104-109. [PMID: 35653824 DOI: 10.1016/j.bbrc.2022.05.073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 05/21/2022] [Indexed: 11/02/2022]
Abstract
Dosage compensation is a process that produces a similar expression of sex-linked and autosomal genes. In the silkworm Bombyx mori with a WZ sex-determination system, the expression from the single Z in WZ females matches that of ZZ males due to the suppression of Z-linked genes in males. A primary maleness determinant gene, Masculinizer (Masc), is also required for dosage compensation. In females, silkworm Piwi is complexed with the W chromosome-derived female-specific Feminizer (Fem) PIWI-interacting RNA (piRNA) and cleaves Masc mRNA. When Fem piRNA-resistant Masc cDNA (Masc-R) is overexpressed in both sexes, only female larvae are dead during the larval stage. In this study, transcriptome analysis was performed in neonate larvae to examine the effects of Masc-R overexpression on a global gene expression profile. Z-linked genes were globally repressed in Masc-R-overexpressing females due to force-driven dosage compensation. In contrast, Masc-R overexpression had little effect on the expression of Z-linked genes and the male-specific isoform of B. mori insulin-like growth factor II mRNA-binding protein in males, indicating that excessive Masc expression strengthens neither dosage compensation nor maleness in males. Fourteen genes were differentially expressed between Masc-R-overexpressing and control neonate larvae in both sexes, suggesting Masc functions other than dosage compensation and masculinization.
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Affiliation(s)
- Kenta Tomihara
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Susumu Katsuma
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8657, Japan.
| | - Takashi Kiuchi
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8657, Japan.
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12
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Sex-specific regulation of development, growth and metabolism. Semin Cell Dev Biol 2022; 138:117-127. [PMID: 35469676 DOI: 10.1016/j.semcdb.2022.04.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 03/07/2022] [Accepted: 04/14/2022] [Indexed: 12/13/2022]
Abstract
Adult females and males of most species differ in many aspects of their morphology, physiology and behavior, in response to sex-specific selective pressures that maximize fitness. While we have an increasingly good understanding of the genetic mechanisms that initiate these differences, the sex-specific developmental trajectories that generate them are much less well understood. Here we review recent advances in the sex-specific regulation of development focusing on two models where this development is increasingly well understood: Sexual dimorphism of body size in the fruit fly Drosophila melanogaster and sexual dimorphism of horns in the horned beetle Onthophagus taurus. Because growth and development are also supported by metabolism, the regulation of sex-specific metabolism during and after development is an important aspect of the generation of female and male phenotypes. Hitherto, the study of sex-specific development has largely been independent of the study of sex-specific metabolism. Nevertheless, as we discuss in this review, recent research has begun to reveal considerable overlap in the cellular and physiological mechanisms that regulate sex-specific development and metabolism.
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13
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Noncanonical function of the Sex lethal gene controls the protogyny phenotype in Drosophila melanogaster. Sci Rep 2022; 12:1455. [PMID: 35087103 PMCID: PMC8795210 DOI: 10.1038/s41598-022-05147-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 12/31/2021] [Indexed: 12/01/2022] Open
Abstract
Drosophila melanogaster females eclose on average 4 h faster than males owing to sexual differences in the pupal period, referred to as the protogyny phenotype. Here, to elucidate the mechanism underlying the protogyny phenotype, we used our newly developed Drosophila Individual Activity Monitoring and Detecting System (DIAMonDS) that detects the precise timing of both pupariation and eclosion in individual flies. Although sex transformation induced by tra-2, tra alteration, or msl-2 knockdown-mediated disruption of dosage compensation showed no effect on the protogyny phenotype, stage-specific whole-body knockdown and mutation of the Drosophila master sex switch gene, Sxl, was found to disrupt the protogyny phenotype. Thus, Sxl establishes the protogyny phenotype through a noncanonical pathway in D. melanogaster.
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14
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When Down Is Up: Heterochromatin, Nuclear Organization and X Upregulation. Cells 2021; 10:cells10123416. [PMID: 34943924 PMCID: PMC8700316 DOI: 10.3390/cells10123416] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 11/29/2021] [Accepted: 12/01/2021] [Indexed: 12/21/2022] Open
Abstract
Organisms with highly differentiated sex chromosomes face an imbalance in X-linked gene dosage. Male Drosophila solve this problem by increasing expression from virtually every gene on their single X chromosome, a process known as dosage compensation. This involves a ribonucleoprotein complex that is recruited to active, X-linked genes to remodel chromatin and increase expression. Interestingly, the male X chromosome is also enriched for several proteins associated with heterochromatin. Furthermore, the polytenized male X is selectively disrupted by the loss of factors involved in repression, silencing, heterochromatin formation or chromatin remodeling. Mutations in many of these factors preferentially reduce male survival or enhance the lethality of mutations that prevent normal recognition of the X chromosome. The involvement of primarily repressive factors in a process that elevates expression has long been puzzling. Interestingly, recent work suggests that the siRNA pathway, often associated with heterochromatin formation and repression, also helps the dosage compensation machinery identify the X chromosome. In light of this finding, we revisit the evidence that links nuclear organization and heterochromatin to regulation of the male X chromosome.
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15
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Topoisomerase II is regulated by translationally controlled tumor protein for cell survival during organ growth in Drosophila. Cell Death Dis 2021; 12:811. [PMID: 34453033 PMCID: PMC8397738 DOI: 10.1038/s41419-021-04091-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 07/28/2021] [Accepted: 08/12/2021] [Indexed: 11/08/2022]
Abstract
Regulation of cell survival is critical for organ development. Translationally controlled tumor protein (TCTP) is a conserved protein family implicated in the control of cell survival during normal development and tumorigenesis. Previously, we have identified a human Topoisomerase II (TOP2) as a TCTP partner, but its role in vivo has been unknown. To determine the significance of this interaction, we examined their roles in developing Drosophila organs. Top2 RNAi in the wing disc leads to tissue reduction and caspase activation, indicating the essential role of Top2 for cell survival. Top2 RNAi in the eye disc also causes loss of eye and head tissues. Tctp RNAi enhances the phenotypes of Top2 RNAi. The depletion of Tctp reduces Top2 levels in the wing disc and vice versa. Wing size is reduced by Top2 overexpression, implying that proper regulation of Top2 level is important for normal organ development. The wing phenotype of Tctp RNAi is partially suppressed by Top2 overexpression. This study suggests that mutual regulation of Tctp and Top2 protein levels is critical for cell survival during organ development.
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16
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Villa R, Jagtap PKA, Thomae AW, Campos Sparr A, Forné I, Hennig J, Straub T, Becker PB. Divergent evolution toward sex chromosome-specific gene regulation in Drosophila. Genes Dev 2021; 35:1055-1070. [PMID: 34140353 PMCID: PMC8247607 DOI: 10.1101/gad.348411.121] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 05/04/2021] [Indexed: 02/07/2023]
Abstract
The dosage compensation complex (DCC) of Drosophila identifies its X-chromosomal binding sites with exquisite selectivity. The principles that assure this vital targeting are known from the D. melanogaster model: DCC-intrinsic specificity of DNA binding, cooperativity with the CLAMP protein, and noncoding roX2 RNA transcribed from the X chromosome. We found that in D. virilis, a species separated from melanogaster by 40 million years of evolution, all principles are active but contribute differently to X specificity. In melanogaster, the DCC subunit MSL2 evolved intrinsic DNA-binding selectivity for rare PionX sites, which mark the X chromosome. In virilis, PionX motifs are abundant and not X-enriched. Accordingly, MSL2 lacks specific recognition. Here, roX2 RNA plays a more instructive role, counteracting a nonproductive interaction of CLAMP and modulating DCC binding selectivity. Remarkably, roX2 triggers a stable chromatin binding mode characteristic of DCC. Evidently, X-specific regulation is achieved by divergent evolution of protein, DNA, and RNA components.
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Affiliation(s)
- Raffaella Villa
- Molecular Biology Division, Biomedical Center, Ludwig-Maximilians-University Munich, 82152 Planegg-Martinsried, Germany
| | - Pravin Kumar Ankush Jagtap
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Andreas W Thomae
- Molecular Biology Division, Biomedical Center, Ludwig-Maximilians-University Munich, 82152 Planegg-Martinsried, Germany.,Core Facility Bioimaging, Biomedical Center, Ludwig-Maximilians-University Munich, 82152 Planegg-Martinsried, Germany
| | - Aline Campos Sparr
- Molecular Biology Division, Biomedical Center, Ludwig-Maximilians-University Munich, 82152 Planegg-Martinsried, Germany
| | - Ignasi Forné
- Protein Analysis Unit, Biomedical Center, Ludwig-Maximilians-University Munich, 82152 Planegg-Martinsried, Germany
| | - Janosch Hennig
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Tobias Straub
- Bioinformatics Unit, Biomedical Center, Ludwig-Maximilians-University Munich, 82152 Planegg-Martinsried, Germany
| | - Peter B Becker
- Molecular Biology Division, Biomedical Center, Ludwig-Maximilians-University Munich, 82152 Planegg-Martinsried, Germany
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17
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Genomic and cDNA selection-amplification identifies transcriptome-wide binding sites for the Drosophila protein sex-lethal. PLoS One 2021; 16:e0250592. [PMID: 34029324 PMCID: PMC8143406 DOI: 10.1371/journal.pone.0250592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 04/11/2021] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Downstream targets for a large number of RNA-binding proteins remain to be identified. The Drosophila master sex-switch protein Sex-lethal (SXL) is an RNA-binding protein that controls splicing, polyadenylation, or translation of certain mRNAs to mediate female-specific sexual differentiation. Whereas some targets of SXL are known, previous studies indicate that additional targets of SXL have escaped genetic screens. METHODOLOGY/PRINCIPAL FINDINGS Here, we have used an alternative molecular approach of GEnomic Selective Enrichment of Ligands by Exponential enrichment (GESELEX) using both the genomic DNA and cDNA pools from several Drosophila developmental stages to identify new potential targets of SXL. Our systematic analysis provides a comprehensive view of the Drosophila transcriptome for potential SXL-binding sites. CONCLUSION/SIGNIFICANCE We have successfully identified new SXL-binding sites in the Drosophila transcriptome. We discuss the significance of our analysis and that the newly identified binding sites and sequences could serve as a useful resource for the research community. This approach should also be applicable to other RNA-binding proteins for which downstream targets are unknown.
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18
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Absence of X-chromosome dosage compensation in the primordial germ cells of Drosophila embryos. Sci Rep 2021; 11:4890. [PMID: 33649478 PMCID: PMC7921590 DOI: 10.1038/s41598-021-84402-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 02/16/2021] [Indexed: 01/31/2023] Open
Abstract
Dosage compensation is a mechanism that equalizes sex chromosome gene expression between the sexes. In Drosophila, individuals with two X chromosomes (XX) become female, whereas males have one X chromosome (XY). In males, dosage compensation of the X chromosome in the soma is achieved by five proteins and two non-coding RNAs, which assemble into the male-specific lethal (MSL) complex to upregulate X-linked genes twofold. By contrast, it remains unclear whether dosage compensation occurs in the germline. To address this issue, we performed transcriptome analysis of male and female primordial germ cells (PGCs). We found that the expression levels of X-linked genes were approximately twofold higher in female PGCs than in male PGCs. Acetylation of lysine residue 16 on histone H4 (H4K16ac), which is catalyzed by the MSL complex, was undetectable in these cells. In male PGCs, hyperactivation of X-linked genes and H4K16ac were induced by overexpression of the essential components of the MSL complex, which were expressed at very low levels in PGCs. Together, these findings indicate that failure of MSL complex formation results in the absence of X-chromosome dosage compensation in male PGCs.
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19
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Kwon SY, Jang B, Badenhorst P. The ISWI chromatin remodelling factor NURF is not required for mitotic male X chromosome organisation. MICROPUBLICATION BIOLOGY 2021; 2021:10.17912/micropub.biology.000360. [PMID: 33537560 PMCID: PMC7841436 DOI: 10.17912/micropub.biology.000360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The nucleosome remodelling factor (NURF) is an ISWI-class ATP-dependent chromatin remodeling enzyme required both for gene expression and higher order chromatin organisation. NURF binds to histone modifications that decorate the Drosophila polytene male X chromosome and is required to maintain correct organisation of this chromosome. NURF mutants exhibit distorted and decondensed polytene male X chromosomes dependent on the presence of the male-specific lethal (MSL) complex. Here we tested whether mitotic chromosomes similarly require NURF to maintain correct morphology. Surprisingly, although the MSL complex remains associated with mitotic male X chromosomes, NURF is not required to maintain morphology. While the ISWI subunit of NURF is known to remain associated with mitotic chromosomes we show that the NURF specificity subunit Nurf301/BPTF dissociates from chromatin during both Drosophila and human mitosis, further illuminating that NURF is dispensable for mitotic chromosome organisation.
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Affiliation(s)
- So Yeon Kwon
- Birmingham Centre for Genome Biology and Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, United Kingdom,
Correspondence to: So Yeon Kwon (); Paul Badenhorst ()
| | - Boyun Jang
- Birmingham Centre for Genome Biology and Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, United Kingdom
| | - Paul Badenhorst
- Birmingham Centre for Genome Biology and Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, United Kingdom,
Correspondence to: So Yeon Kwon (); Paul Badenhorst ()
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20
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RNA nucleation by MSL2 induces selective X chromosome compartmentalization. Nature 2020; 589:137-142. [PMID: 33208948 DOI: 10.1038/s41586-020-2935-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 09/04/2020] [Indexed: 12/22/2022]
Abstract
Confinement of the X chromosome to a territory for dosage compensation is a prime example of how subnuclear compartmentalization is used to regulate transcription at the megabase scale. In Drosophila melanogaster, two sex-specific non-coding RNAs (roX1 and roX2) are transcribed from the X chromosome. They associate with the male-specific lethal (MSL) complex1, which acetylates histone H4 lysine 16 and thereby induces an approximately twofold increase in expression of male X-linked genes2,3. Current models suggest that X-over-autosome specificity is achieved by the recognition of cis-regulatory DNA high-affinity sites (HAS) by the MSL2 subunit4,5. However, HAS motifs are also found on autosomes, indicating that additional factors must stabilize the association of the MSL complex with the X chromosome. Here we show that the low-complexity C-terminal domain (CTD) of MSL2 renders its recruitment to the X chromosome sensitive to roX non-coding RNAs. roX non-coding RNAs and the MSL2 CTD form a stably condensed state, and functional analyses in Drosophila and mammalian cells show that their interactions are crucial for dosage compensation in vivo. Replacing the CTD of mammalian MSL2 with that from Drosophila and expressing roX in cis is sufficient to nucleate ectopic dosage compensation in mammalian cells. Thus, the condensing nature of roX-MSL2CTD is the primary determinant for specific compartmentalization of the X chromosome in Drosophila.
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21
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Belyi A, Argyridou E, Parsch J. The Influence of Chromosomal Environment on X-Linked Gene Expression in Drosophila melanogaster. Genome Biol Evol 2020; 12:2391-2402. [PMID: 33104185 PMCID: PMC7719225 DOI: 10.1093/gbe/evaa227] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/21/2020] [Indexed: 12/14/2022] Open
Abstract
Sex chromosomes often differ from autosomes with respect to their gene expression and regulation. In Drosophila melanogaster, X-linked genes are dosage compensated by having their expression upregulated in the male soma, a process mediated by the X-chromosome-specific binding of the dosage compensation complex (DCC). Previous studies of X-linked gene expression found a negative correlation between a gene’s male-to-female expression ratio and its distance to the nearest DCC binding site in somatic tissues, including head and brain, which suggests that dosage compensation influences sex-biased gene expression. A limitation of the previous studies, however, was that they focused on endogenous X-linked genes and, thus, could not disentangle the effects of chromosomal position from those of gene-specific regulation. To overcome this limitation, we examined the expression of an exogenous reporter gene inserted at many locations spanning the X chromosome. We observed a negative correlation between the male-to-female expression ratio of the reporter gene and its distance to the nearest DCC binding site in somatic tissues, but not in gonads. A reporter gene’s location relative to a DCC binding site had greater influence on its expression than the local regulatory elements of neighboring endogenous genes, suggesting that intra-chromosomal variation in the strength of dosage compensation is a major determinant of sex-biased gene expression. Average levels of sex-biased expression did not differ between head and brain, but there was greater positional effect variation in the brain, which may explain the observed excess of endogenous sex-biased genes located on the X chromosome in this tissue.
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Affiliation(s)
- Aleksei Belyi
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Planegg-Martinsried, Germany
| | - Eliza Argyridou
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Planegg-Martinsried, Germany
| | - John Parsch
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, Planegg-Martinsried, Germany
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22
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Müller M, Schauer T, Krause S, Villa R, Thomae AW, Becker PB. Two-step mechanism for selective incorporation of lncRNA into a chromatin modifier. Nucleic Acids Res 2020; 48:7483-7501. [PMID: 32510132 PMCID: PMC7528653 DOI: 10.1093/nar/gkaa492] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 05/25/2020] [Accepted: 05/29/2020] [Indexed: 02/04/2023] Open
Abstract
The MLE DExH helicase and the roX lncRNAs are essential components of the chromatin modifying Dosage Compensation Complex (DCC) in Drosophila. To explore the mechanism of ribonucleoprotein complex assembly, we developed vitRIP, an unbiased, transcriptome-wide in vitro assay that reveals RNA binding specificity. We found that MLE has intrinsic specificity for U-/A-rich sequences and tandem stem-loop structures and binds many RNAs beyond roX in vitro. The selectivity of the helicase for physiological substrates is further enhanced by the core DCC. Unwinding of roX2 by MLE induces a highly selective RNA binding surface in the unstructured C-terminus of the MSL2 subunit and triggers-specific association of MLE and roX2 with the core DCC. The exquisite selectivity of roX2 incorporation into the DCC thus originates from intimate cooperation between the helicase and the core DCC involving two distinct RNA selection principles and their mutual refinement.
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Affiliation(s)
- Marisa Müller
- Molecular Biology Division, Biomedical Center, Ludwig-Maximilians-University Munich, 82152 Planegg-Martinsried, Germany
| | - Tamas Schauer
- Molecular Biology Division, Biomedical Center, Ludwig-Maximilians-University Munich, 82152 Planegg-Martinsried, Germany.,Bioinformatics Unit, Biomedical Center, Ludwig-Maximilians-University Munich, 82152 Planegg-Martinsried, Germany
| | - Silke Krause
- Molecular Biology Division, Biomedical Center, Ludwig-Maximilians-University Munich, 82152 Planegg-Martinsried, Germany
| | - Raffaella Villa
- Molecular Biology Division, Biomedical Center, Ludwig-Maximilians-University Munich, 82152 Planegg-Martinsried, Germany
| | - Andreas W Thomae
- Molecular Biology Division, Biomedical Center, Ludwig-Maximilians-University Munich, 82152 Planegg-Martinsried, Germany.,Core Facility Bioimaging at the Biomedical Center, Ludwig-Maximilians-University Munich, 82152 Planegg-Martinsried, Germany
| | - Peter B Becker
- Molecular Biology Division, Biomedical Center, Ludwig-Maximilians-University Munich, 82152 Planegg-Martinsried, Germany
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23
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Samata M, Alexiadis A, Richard G, Georgiev P, Nuebler J, Kulkarni T, Renschler G, Basilicata MF, Zenk FL, Shvedunova M, Semplicio G, Mirny L, Iovino N, Akhtar A. Intergenerationally Maintained Histone H4 Lysine 16 Acetylation Is Instructive for Future Gene Activation. Cell 2020; 182:127-144.e23. [DOI: 10.1016/j.cell.2020.05.026] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2019] [Revised: 02/22/2020] [Accepted: 05/14/2020] [Indexed: 10/24/2022]
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24
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Demakova OV, Demakov SA, Boldyreva LV, Zykova TY, Levitsky VG, Semeshin VF, Pokholkova GV, Sidorenko DS, Goncharov FP, Belyaeva ES, Zhimulev IF. Faint gray bands in Drosophila melanogaster polytene chromosomes are formed by coding sequences of housekeeping genes. Chromosoma 2019; 129:25-44. [PMID: 31820086 DOI: 10.1007/s00412-019-00728-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 09/04/2019] [Accepted: 10/30/2019] [Indexed: 12/13/2022]
Abstract
In Drosophila melanogaster, the chromatin of interphase polytene chromosomes appears as alternating decondensed interbands and dense black or thin gray bands. Recently, we uncovered four principle chromatin states (4НММ model) in the fruit fly, and these were matched to the structures observed in polytene chromosomes. Ruby/malachite chromatin states form black bands containing developmental genes, whereas aquamarine chromatin corresponds to interbands enriched with 5' regions of ubiquitously expressed genes. Lazurite chromatin supposedly forms faint gray bands and encompasses the bodies of housekeeping genes. In this report, we test this idea using the X chromosome as the model and MSL1 as a protein marker of the lazurite chromatin. Our bioinformatic analysis indicates that in the X chromosome, it is only the lazurite chromatin that is simultaneously enriched for the proteins and histone marks associated with exons, transcription elongation, and dosage compensation. As a result of FISH and EM mapping of a dosage compensation complex subunit, MSL1, we for the first time provide direct evidence that lazurite chromatin forms faint gray bands. Our analysis proves that overall most of housekeeping genes typically span from the interbands (5' region of the gene) to the gray band (gene body). More rarely, active lazurite chromatin and inactive malachite/ruby chromatin may be found within a common band, where both the housekeeping and the developmental genes reside together.
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Affiliation(s)
- Olga V Demakova
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Acad. Lavrentiev Ave. 8/2, Novosibirsk, 630090, Russia
| | - Sergey A Demakov
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Acad. Lavrentiev Ave. 8/2, Novosibirsk, 630090, Russia
| | - Lidiya V Boldyreva
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Acad. Lavrentiev Ave. 8/2, Novosibirsk, 630090, Russia
| | - Tatyana Yu Zykova
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Acad. Lavrentiev Ave. 8/2, Novosibirsk, 630090, Russia
| | - Victor G Levitsky
- Novosibirsk State University, Novosibirsk, 630090, Russia.,Institute of Cytology and Genetics, SB RAS, 630090, Novosibirsk, Russia
| | - Valeriy F Semeshin
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Acad. Lavrentiev Ave. 8/2, Novosibirsk, 630090, Russia
| | - Galina V Pokholkova
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Acad. Lavrentiev Ave. 8/2, Novosibirsk, 630090, Russia
| | - Darya S Sidorenko
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Acad. Lavrentiev Ave. 8/2, Novosibirsk, 630090, Russia
| | - Fedor P Goncharov
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Acad. Lavrentiev Ave. 8/2, Novosibirsk, 630090, Russia
| | - Elena S Belyaeva
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Acad. Lavrentiev Ave. 8/2, Novosibirsk, 630090, Russia
| | - Igor F Zhimulev
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Acad. Lavrentiev Ave. 8/2, Novosibirsk, 630090, Russia. .,Novosibirsk State University, Novosibirsk, 630090, Russia.
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25
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Moschall R, Rass M, Rossbach O, Lehmann G, Kullmann L, Eichner N, Strauss D, Meister G, Schneuwly S, Krahn MP, Medenbach J. Drosophila Sister-of-Sex-lethal reinforces a male-specific gene expression pattern by controlling Sex-lethal alternative splicing. Nucleic Acids Res 2019; 47:2276-2288. [PMID: 30590805 PMCID: PMC6411925 DOI: 10.1093/nar/gky1284] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 12/04/2018] [Accepted: 12/14/2018] [Indexed: 01/14/2023] Open
Abstract
In Drosophila, female development is governed by a single RNA-binding protein, Sex-lethal (Sxl), that controls the expression of key factors involved in dosage compensation, germline homeostasis and the establishment of female morphology and behaviour. Sxl expression in female flies is maintained by an auto-regulatory, positive feedback loop with Sxl controlling splicing of its own mRNA. Until now, it remained unclear how males prevent accidental triggering of the Sxl expression cascade and protect themselves against runaway protein production. Here, we identify the protein Sister-of-Sex-lethal (Ssx) as an inhibitor of Sxl auto-regulatory splicing. Sxl and Ssx have a comparable RNA-binding specificity and compete for binding to RNA regulatory elements present in the Sxl transcript. In cultured Drosophila cells, Sxl-induced changes to alternative splicing can be reverted by the expression of Ssx. Moreover, in adult male flies ablation of the ssx gene results in a low level of productive Sxl mRNA splicing and Sxl protein production in isolated, clonal cell populations. In sum, this demonstrates that Ssx safeguards male animals against Sxl protein production to reinforce a stable, male-specific gene expression pattern.
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Affiliation(s)
- Rebecca Moschall
- Institute of Biochemistry I, University of Regensburg, Universitaetsstrasse 31, D-93053 Regensburg, Germany
| | - Mathias Rass
- Institute of Zoology, University of Regensburg, Universitaetsstrasse 31, D-93053 Regensburg, Germany
| | - Oliver Rossbach
- Institute of Biochemistry, Justus-Liebig-University of Giessen, Heinrich-Buff-Ring 17, D-35392 Giessen, Germany
| | - Gerhard Lehmann
- Institute of Biochemistry I, University of Regensburg, Universitaetsstrasse 31, D-93053 Regensburg, Germany
| | - Lars Kullmann
- Institute for Molecular and Cellular Anatomy, University of Regensburg, Universitaetsstrasse 31, D-93053 Regensburg, Germany
| | - Norbert Eichner
- Institute of Biochemistry I, University of Regensburg, Universitaetsstrasse 31, D-93053 Regensburg, Germany
| | - Daniela Strauss
- Institute of Biochemistry I, University of Regensburg, Universitaetsstrasse 31, D-93053 Regensburg, Germany
| | - Gunter Meister
- Institute of Biochemistry I, University of Regensburg, Universitaetsstrasse 31, D-93053 Regensburg, Germany
| | - Stephan Schneuwly
- Institute of Zoology, University of Regensburg, Universitaetsstrasse 31, D-93053 Regensburg, Germany
| | - Michael P Krahn
- Institute for Molecular and Cellular Anatomy, University of Regensburg, Universitaetsstrasse 31, D-93053 Regensburg, Germany.,Medical Clinic D, University of Muenster, Domagkstrasse 3, D-48149 Muenster, Germany
| | - Jan Medenbach
- Institute of Biochemistry I, University of Regensburg, Universitaetsstrasse 31, D-93053 Regensburg, Germany
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26
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Lv M, Yao Y, Li F, Xu L, Yang L, Gong Q, Xu YZ, Shi Y, Fan YJ, Tang Y. Structural insights reveal the specific recognition of roX RNA by the dsRNA-binding domains of the RNA helicase MLE and its indispensable role in dosage compensation in Drosophila. Nucleic Acids Res 2019; 47:3142-3157. [PMID: 30649456 PMCID: PMC6451107 DOI: 10.1093/nar/gky1308] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 12/19/2018] [Accepted: 12/24/2018] [Indexed: 02/04/2023] Open
Abstract
In Drosophila, dosage compensation globally upregulates the expression of genes located on male single X-chromosome. Maleless (MLE) helicase plays an essential role to incorporate the roX lncRNA into the dosage compensation complex (MSL-DCC), and such function is essentially dependent on its dsRNA-binding domains (dsRBDs). Here, we report a 2.90Å crystal structure of tandem dsRBDs of MLE in complex with a 55mer stem-loop of roX2 (R2H1). MLE dsRBDs bind to R2H1 cooperatively and interact with two successive minor grooves and a major groove of R2H1, respectively. The recognition of R2H1 by MLE dsRBDs involves both shape- and sequence-specificity. Moreover, dsRBD2 displays a stronger RNA affinity than dsRBD1, and mutations of key residues in either MLE dsRBD remarkably reduce their affinities for roX2 both in vitro and in vivo. In Drosophila, the structure-based mle mutations generated using the CRISPR/Cas9 system, are partially male-lethal and indicate the inter-regulation among the components of the MSL-DCC at multiple levels. Hence, our research provides structural insights into the interactions between MLE dsRBDs and R2H1 and facilitates a deeper understanding of the mechanism by which MLE tandem dsRBDs play an indispensable role in specific recognition of roX and the assembly of the MSL-DCC in Drosophila dosage compensation.
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Affiliation(s)
- Mengqi Lv
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Yixiang Yao
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Fudong Li
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Ling Xu
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Lingna Yang
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Qingguo Gong
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Yong-Zhen Xu
- State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Yunyu Shi
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, China.,CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Yu-Jie Fan
- State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China.,Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Yajun Tang
- Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, China
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27
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Qi Y, Wu Y, Saunders R, Chen XG, Mao C, Biedler JK, Tu ZJ. Guy1, a Y-linked embryonic signal, regulates dosage compensation in Anopheles stephensi by increasing X gene expression. eLife 2019; 8:43570. [PMID: 30888319 PMCID: PMC6440743 DOI: 10.7554/elife.43570] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 03/16/2019] [Indexed: 12/22/2022] Open
Abstract
We previously showed that Guy1, a primary signal expressed from the Y chromosome, is a strong candidate for a male-determining factor that confers female-specific lethality in Anopheles stephensi (Criscione et al., 2016). Here, we present evidence that Guy1 increases X gene expression in Guy1-transgenic females from two independent lines, providing a mechanism underlying the Guy1-conferred female lethality. The median level gene expression (MGE) of X-linked genes is significantly higher than autosomal genes in Guy1-transgenic females while there is no significant difference in MGE between X and autosomal genes in wild-type females. Furthermore, Guy1 significantly upregulates at least 40% of the 996 genes across the X chromosome in transgenic females. Guy1-conferred female-specific lethality is remarkably stable and completely penetrant. These findings indicate that Guy1 regulates dosage compensation in An. stephensi and components of dosage compensation may be explored to develop novel strategies to control mosquito-borne diseases.
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Affiliation(s)
- Yumin Qi
- Department of Biochemistry, Virginia Tech, Blacksburg, Virginia, United States.,Fralin Life Science Institute, Virginia Tech, Blacksburg, Virginia, United States
| | - Yang Wu
- Department of Pathogen Biology, School of Public Health, Southern Medical University, Guangdong, China
| | - Randy Saunders
- Department of Biochemistry, Virginia Tech, Blacksburg, Virginia, United States.,Fralin Life Science Institute, Virginia Tech, Blacksburg, Virginia, United States
| | - Xiao-Guang Chen
- Fralin Life Science Institute, Virginia Tech, Blacksburg, Virginia, United States
| | - Chunhong Mao
- Biocomplexity Institute of Virginia Tech, Virginia Tech, Blacksburg, Virginia, United States
| | - James Kite Biedler
- Department of Biochemistry, Virginia Tech, Blacksburg, Virginia, United States.,Fralin Life Science Institute, Virginia Tech, Blacksburg, Virginia, United States
| | - Zhijian Jake Tu
- Department of Biochemistry, Virginia Tech, Blacksburg, Virginia, United States.,Fralin Life Science Institute, Virginia Tech, Blacksburg, Virginia, United States
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28
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Abstract
Sexual size dimorphism (SSD), a sex difference in body size, is widespread throughout the animal kingdom, raising the question of how sex influences existing growth regulatory pathways to bring about SSD. In insects, somatic sexual differentiation has long been considered to be controlled strictly cell-autonomously. Here, we discuss our surprising finding that in Drosophila larvae, the sex determination gene Sex-lethal (Sxl) functions in neurons to non-autonomously specify SSD. We found that Sxl is required in specific neuronal subsets to upregulate female body growth, including in the neurosecretory insulin producing cells, even though insulin-like peptides themselves appear not to be involved. SSD regulation by neuronal Sxl is also independent of its known splicing targets, transformer and msl-2, suggesting that it involves a new molecular mechanism. Interestingly, SSD control by neuronal Sxl is selective for larval, not imaginal tissue types, and operates in addition to cell-autonomous effects of Sxl and Tra, which are present in both larval and imaginal tissues. Overall, our findings add to a small but growing number of studies reporting non-autonomous, likely hormonal, control of sex differences in Drosophila, and suggest that the principles of sexual differentiation in insects and mammals may be more similar than previously thought.
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Affiliation(s)
- Annick Sawala
- a Physiology & Metabolism Laboratory , The Francis Crick Institute , London , UK
| | - Alex P Gould
- a Physiology & Metabolism Laboratory , The Francis Crick Institute , London , UK
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29
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Singh R. A Novel Saturation Mutagenesis Approach: Single Step Characterization of Regulatory Protein Binding Sites in RNA Using Phosphorothioates. J Vis Exp 2018. [PMID: 30199036 DOI: 10.3791/57816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Gene regulation plays an important role in development. Numerous DNA- and RNA-binding proteins bind their target sequences with high specificity to control gene expression. These regulatory proteins control gene expression either at the level of DNA (transcription) or at the level of RNA (pre-mRNA splicing, polyadenylation, mRNA transport, decay, and translation). Identification of regulatory sequences helps understand not only how a gene is switched on or off, but also which downstream genes are regulated by a particular regulatory protein. Here, we describe a one-step approach that allows saturation mutagenesis of a protein binding site in RNA. It involves doping DNA template with non-wild-type nucleotides within the binding site, synthesis of separate RNAs with each phosphorothioate nucleotide, and isolation of the bound fraction following incubation with protein. Interference from non-wild-type nucleotides results in their preferential exclusion from the protein-bound fraction. This is monitored by gel electrophoresis following selective chemical cleavage with iodine of phosphodiester bonds containing phosphorothioates (phosphorothioate mutagenesis or PTM). This single-step saturation mutagenesis approach is applicable to the characterization of any protein binding site in RNA.
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Affiliation(s)
- Ravinder Singh
- Department of Molecular, Cellular and Developmental Biology, University of Colorado at Boulder;
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30
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Davis RJ, Belikoff EJ, Scholl EH, Li F, Scott MJ. no blokes Is Essential for Male Viability and X Chromosome Gene Expression in the Australian Sheep Blowfly. Curr Biol 2018; 28:1987-1992.e3. [PMID: 29887311 DOI: 10.1016/j.cub.2018.05.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 03/19/2018] [Accepted: 05/02/2018] [Indexed: 12/30/2022]
Abstract
It has been hypothesized that the Drosophila 4th chromosome is derived from an ancient X chromosome [1]. In the Australian sheep blowfly, Lucilia cuprina, the heterochromatic X chromosome contains few active genes and orthologs of Drosophila X-linked genes are autosomal. Of 8 X-linked genes identified previously in L. cuprina, 6 were orthologs of Drosophila 4th-chromosome genes [2]. The X-linked genes were expressed equally in males and females. Here we identify an additional 51 X-linked genes and show that most are dosage compensated. Orthologs of 49 of the 59 X-linked genes are on the 4th chromosome in D. melanogaster. Because painting of fourth (Pof) is important for expression of Drosophila 4th-chromosome genes [3], we used Cas9 to make a loss-of-function knockin mutation in an L. cuprina Pof ortholog we call no blokes (nbl). Homozygous nbl males derived from homozygous nbl mothers die at the late pupal stage. Homozygous nbl females are viable, fertile, and live longer than heterozygous nbl females. RNA expression of most X-linked genes was reduced in homozygous nbl male pupae and to a lesser extent in nbl females compared to heterozygous siblings. The results suggest that NBL could be important for X chromosome dosage compensation in L. cuprina. NBL may also facilitate gene expression in the heterochromatic environment of the X chromosome in both sexes. This study supports the hypothesis on the origin of the Drosophila 4th chromosome and that a POF-like protein was required for normal gene expression on the ancient X chromosome.
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Affiliation(s)
- Rebecca J Davis
- Department of Entomology and Plant Pathology, North Carolina State University, Campus Box 7613, Raleigh, NC 27695-7613, USA
| | - Esther J Belikoff
- Department of Entomology and Plant Pathology, North Carolina State University, Campus Box 7613, Raleigh, NC 27695-7613, USA
| | - Elizabeth H Scholl
- Bioinformatics Research Center, North Carolina State University, Campus Box 7566, Raleigh, NC 27695-7566, USA
| | - Fang Li
- Department of Entomology and Plant Pathology, North Carolina State University, Campus Box 7613, Raleigh, NC 27695-7613, USA
| | - Maxwell J Scott
- Department of Entomology and Plant Pathology, North Carolina State University, Campus Box 7613, Raleigh, NC 27695-7613, USA.
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31
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Abstract
Several lineages of symbiotic bacteria in insects selfishly manipulate host reproduction to spread in a population 1 , often by distorting host sex ratios. Spiroplasma poulsonii2,3 is a helical and motile, Gram-positive symbiotic bacterium that resides in a wide range of Drosophila species 4 . A notable feature of S. poulsonii is male killing, whereby the sons of infected female hosts are selectively killed during development1,2. Although male killing caused by S. poulsonii has been studied since the 1950s, its underlying mechanism is unknown. Here we identify an S. poulsonii protein, designated Spaid, whose expression induces male killing. Overexpression of Spaid in D. melanogaster kills males but not females, and induces massive apoptosis and neural defects, recapitulating the pathology observed in S. poulsonii-infected male embryos5-11. Our data suggest that Spaid targets the dosage compensation machinery on the male X chromosome to mediate its effects. Spaid contains ankyrin repeats and a deubiquitinase domain, which are required for its subcellular localization and activity. Moreover, we found a laboratory mutant strain of S. poulsonii with reduced male-killing ability and a large deletion in the spaid locus. Our study has uncovered a bacterial protein that affects host cellular machinery in a sex-specific way, which is likely to be the long-searched-for factor responsible for S. poulsonii-induced male killing.
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32
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Samata M, Akhtar A. Dosage Compensation of the X Chromosome: A Complex Epigenetic Assignment Involving Chromatin Regulators and Long Noncoding RNAs. Annu Rev Biochem 2018; 87:323-350. [PMID: 29668306 DOI: 10.1146/annurev-biochem-062917-011816] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
X chromosome regulation represents a prime example of an epigenetic phenomenon where coordinated regulation of a whole chromosome is required. In flies, this is achieved by transcriptional upregulation of X chromosomal genes in males to equalize the gene dosage differences in females. Chromatin-bound proteins and long noncoding RNAs (lncRNAs) constituting a ribonucleoprotein complex known as the male-specific lethal (MSL) complex or the dosage compensation complex mediate this process. MSL complex members decorate the male X chromosome, and their absence leads to male lethality. The male X chromosome is also enriched with histone H4 lysine 16 acetylation (H4K16ac), indicating that the chromatin compaction status of the X chromosome also plays an important role in transcriptional activation. How the X chromosome is specifically targeted and how dosage compensation is mechanistically achieved are central questions for the field. Here, we review recent advances, which reveal a complex interplay among lncRNAs, the chromatin landscape, transcription, and chromosome conformation that fine-tune X chromosome gene expression.
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Affiliation(s)
- Maria Samata
- Department of Chromatin Regulation, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg im Breisgau, Germany; .,Faculty of Biology, University of Freiburg, 79104 Freiburg im Breisgau, Germany
| | - Asifa Akhtar
- Department of Chromatin Regulation, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg im Breisgau, Germany;
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33
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Abstract
Male-killing is one strategy used by maternally transmitted bacterial symbionts to boost transmission and spread in populations. In Drosophila melanogaster, Spiroplasma target males by hijacking an essential, male-limited epigenetic process. A new study reveals clues to the mode of killing.
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34
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Moschall R, Strauss D, García-Beyaert M, Gebauer F, Medenbach J. Drosophila Sister-of-Sex-lethal is a repressor of translation. RNA (NEW YORK, N.Y.) 2018; 24:149-158. [PMID: 29089381 PMCID: PMC5769743 DOI: 10.1261/rna.063776.117] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 10/27/2017] [Indexed: 06/07/2023]
Abstract
The RNA-binding protein Sex-lethal (Sxl) is an important post-transcriptional regulator of sex determination and dosage compensation in female Drosophila To prevent the assembly of the MSL dosage compensation complex in female flies, Sxl acts as a repressor of male-specific lethal-2 (msl-2) mRNA translation. It uses two distinct and mutually reinforcing blocks to translation that operate on the 5' and 3' untranslated regions (UTRs) of msl-2 mRNA, respectively. While 5' UTR-mediated translational control involves an upstream open reading frame, 3' UTR-mediated regulation strictly requires the co-repressor protein Upstream of N-ras (Unr), which is recruited to the transcript by Sxl. We have identified the protein Sister-of-Sex-lethal (Ssx) as a novel repressor of translation with Sxl-like activity. Both proteins have a comparable RNA-binding specificity and can associate with uracil-rich RNA regulatory elements present in msl-2 mRNA. Moreover, both repress translation when bound to the 5' UTR of msl-2 However, Ssx is inactive in 3' UTR-mediated regulation, as it cannot engage the co-repressor protein Unr. The difference in activity maps to the first RNA-recognition motif (RRM) of Ssx. Conversion of three amino acids within this domain into their Sxl counterpart results in a gain of function and repression via the 3' UTR, allowing detailed insights into the evolutionary origin of the two proteins and into the molecular requirements of an important translation regulatory pathway.
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Affiliation(s)
- Rebecca Moschall
- Institute of Biochemistry I, University of Regensburg, D-93053 Regensburg, Germany
| | - Daniela Strauss
- Institute of Biochemistry I, University of Regensburg, D-93053 Regensburg, Germany
| | - Marina García-Beyaert
- Gene Regulation, Stem Cells and Cancer Programme, Centre for Genomic Regulation, Barcelona Institute of Science and Technology, 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Fátima Gebauer
- Gene Regulation, Stem Cells and Cancer Programme, Centre for Genomic Regulation, Barcelona Institute of Science and Technology, 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Jan Medenbach
- Institute of Biochemistry I, University of Regensburg, D-93053 Regensburg, Germany
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35
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Urban J, Kuzu G, Bowman S, Scruggs B, Henriques T, Kingston R, Adelman K, Tolstorukov M, Larschan E. Enhanced chromatin accessibility of the dosage compensated Drosophila male X-chromosome requires the CLAMP zinc finger protein. PLoS One 2017; 12:e0186855. [PMID: 29077765 PMCID: PMC5659772 DOI: 10.1371/journal.pone.0186855] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2017] [Accepted: 10/09/2017] [Indexed: 01/21/2023] Open
Abstract
The essential process of dosage compensation is required to equalize gene expression of X-chromosome genes between males (XY) and females (XX). In Drosophila, the conserved Male-specific lethal (MSL) histone acetyltransferase complex mediates dosage compensation by increasing transcript levels from genes on the single male X-chromosome approximately two-fold. Consistent with its increased levels of transcription, the male X-chromosome has enhanced chromatin accessibility, distinguishing it from the autosomes. Here, we demonstrate that the non-sex-specific CLAMP (Chromatin-linked adaptor for MSL proteins) zinc finger protein that recognizes GA-rich sequences genome-wide promotes the specialized chromatin environment on the male X-chromosome and can act over long genomic distances (~14 kb). Although MSL complex is required for increasing transcript levels of X-linked genes, it is not required for enhancing global male X-chromosome chromatin accessibility, and instead works cooperatively with CLAMP to facilitate an accessible chromatin configuration at its sites of highest occupancy. Furthermore, CLAMP regulates chromatin structure at strong MSL complex binding sites through promoting recruitment of the Nucleosome Remodeling Factor (NURF) complex. In contrast to the X-chromosome, CLAMP regulates chromatin and gene expression on autosomes through a distinct mechanism that does not involve NURF recruitment. Overall, our results support a model where synergy between a non-sex-specific transcription factor (CLAMP) and a sex-specific cofactor (MSL) creates a specialized chromatin domain on the male X-chromosome.
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Affiliation(s)
- Jennifer Urban
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, Rhode Island, United States of America
| | - Guray Kuzu
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Sarah Bowman
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Benjamin Scruggs
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, NIH, North Carolina, United States of America
| | - Telmo Henriques
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, NIH, North Carolina, United States of America
| | - Robert Kingston
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Karen Adelman
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, NIH, North Carolina, United States of America
| | - Michael Tolstorukov
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- * E-mail: (MT); (EL)
| | - Erica Larschan
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, Rhode Island, United States of America
- * E-mail: (MT); (EL)
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36
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Rogell B, Fischer B, Rettel M, Krijgsveld J, Castello A, Hentze MW. Specific RNP capture with antisense LNA/DNA mixmers. RNA (NEW YORK, N.Y.) 2017; 23:1290-1302. [PMID: 28476952 PMCID: PMC5513073 DOI: 10.1261/rna.060798.117] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 04/25/2017] [Indexed: 05/07/2023]
Abstract
RNA-binding proteins (RBPs) play essential roles in RNA biology, responding to cellular and environmental stimuli to regulate gene expression. Important advances have helped to determine the (near) complete repertoires of cellular RBPs. However, identification of RBPs associated with specific transcripts remains a challenge. Here, we describe "specific ribonucleoprotein (RNP) capture," a versatile method for the determination of the proteins bound to specific transcripts in vitro and in cellular systems. Specific RNP capture uses UV irradiation to covalently stabilize protein-RNA interactions taking place at "zero distance." Proteins bound to the target RNA are captured by hybridization with antisense locked nucleic acid (LNA)/DNA oligonucleotides covalently coupled to a magnetic resin. After stringent washing, interacting proteins are identified by quantitative mass spectrometry. Applied to in vitro extracts, specific RNP capture identifies the RBPs bound to a reporter mRNA containing the Sex-lethal (Sxl) binding motifs, revealing that the Sxl homolog sister of Sex lethal (Ssx) displays similar binding preferences. This method also revealed the repertoire of RBPs binding to 18S or 28S rRNAs in HeLa cells, including previously unknown rRNA-binding proteins.
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Affiliation(s)
- Birgit Rogell
- European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Bernd Fischer
- European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
- German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Mandy Rettel
- European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Jeroen Krijgsveld
- European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
- German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Alfredo Castello
- European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, United Kingdom
| | - Matthias W Hentze
- European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
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37
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Dosage Compensation in Drosophila-a Model for the Coordinate Regulation of Transcription. Genetics 2017; 204:435-450. [PMID: 27729494 DOI: 10.1534/genetics.115.185108] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 07/25/2016] [Indexed: 12/20/2022] Open
Abstract
The sex chromosomes have special significance in the history of genetics. The chromosomal basis of inheritance was firmly established when Calvin Bridges demonstrated that exceptions to Mendel's laws of segregation were accompanied at the cytological level by exceptional sex chromosome segregation. The morphological differences between X and Y exploited in Bridges' experiments arose as a consequence of the evolution of the sex chromosomes. Originally a homologous chromosome pair, the degeneration of the Y chromosome has been accompanied by a requirement for increased expression of the single X chromosome in males. Drosophila has been a model for the study of this dosage compensation and has brought key strengths, including classical genetics, the exceptional cytology of polytene chromosomes, and more recently, comprehensive genomics. The impact of these studies goes beyond sex chromosome regulation, providing valuable insights into mechanisms for the establishment and maintenance of chromatin domains, and for the coordinate regulation of transcription.
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38
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Moschall R, Gaik M, Medenbach J. Promiscuity in post-transcriptional control of gene expression: Drosophila sex-lethal and its regulatory partnerships. FEBS Lett 2017; 591:1471-1488. [PMID: 28391641 PMCID: PMC5488161 DOI: 10.1002/1873-3468.12652] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 03/08/2017] [Accepted: 04/04/2017] [Indexed: 12/28/2022]
Abstract
The Drosophila RNA‐binding protein Sex‐lethal (Sxl) is a potent post‐transcriptional regulator of gene expression that controls female development. It regulates the expression of key factors involved in sex‐specific differences in morphology, behavior, and dosage compensation. Functional Sxl protein is only expressed in female flies, where it binds to U‐rich RNA motifs present in its target mRNAs to regulate their fate. Sxl is a very versatile regulator that, by shuttling between the nucleus and the cytoplasm, can regulate almost all aspects of post‐transcriptional gene expression including RNA processing, nuclear export, and translation. For these functions, Sxl employs multiple interactions to either antagonize RNA‐processing factors or to recruit various coregulators, thus allowing it to establish a female‐specific gene expression pattern. Here, we summarize the current knowledge about Sxl function and review recent mechanistic and structural studies that further our understanding of how such a seemingly ‘simple’ RNA‐binding protein can exert this plethora of different functions.
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Affiliation(s)
| | - Monika Gaik
- Max Planck Research Group at the Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Jan Medenbach
- Institute of Biochemistry I, University of Regensburg, Germany
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39
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Urban JA, Doherty CA, Jordan WT, Bliss JE, Feng J, Soruco MM, Rieder LE, Tsiarli MA, Larschan EN. The essential Drosophila CLAMP protein differentially regulates non-coding roX RNAs in male and females. Chromosome Res 2016; 25:101-113. [PMID: 27995349 DOI: 10.1007/s10577-016-9541-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Revised: 12/06/2016] [Accepted: 12/06/2016] [Indexed: 02/05/2023]
Abstract
Heterogametic species require chromosome-wide gene regulation to compensate for differences in sex chromosome gene dosage. In Drosophila melanogaster, transcriptional output from the single male X-chromosome is equalized to that of XX females by recruitment of the male-specific lethal (MSL) complex, which increases transcript levels of active genes 2-fold. The MSL complex contains several protein components and two non-coding RNA on the X ( roX) RNAs that are transcriptionally activated by the MSL complex. We previously discovered that targeting of the MSL complex to the X-chromosome is dependent on the chromatin-linked adapter for MSL proteins (CLAMP) zinc finger protein. To better understand CLAMP function, we used the CRISPR/Cas9 genome editing system to generate a frameshift mutation in the clamp gene that eliminates expression of the CLAMP protein. We found that clamp null females die at the third instar larval stage, while almost all clamp null males die at earlier developmental stages. Moreover, we found that in clamp null females roX gene expression is activated, whereas in clamp null males roX gene expression is reduced. Therefore, CLAMP regulates roX abundance in a sex-specific manner. Our results provide new insights into sex-specific gene regulation by an essential transcription factor.
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Affiliation(s)
- Jennifer A Urban
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI, 02912, USA
| | - Caroline A Doherty
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI, 02912, USA.,Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA
| | - William T Jordan
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI, 02912, USA
| | - Jacob E Bliss
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI, 02912, USA
| | - Jessica Feng
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI, 02912, USA.,University of Massachusetts Medical School, Worcester, MA, 01655, USA
| | - Marcela M Soruco
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI, 02912, USA.,LGC Biosearch Technologies, Petaluma, CA, 94954, USA
| | - Leila E Rieder
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI, 02912, USA
| | - Maria A Tsiarli
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI, 02912, USA
| | - Erica N Larschan
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI, 02912, USA.
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40
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Male-killing symbiont damages host's dosage-compensated sex chromosome to induce embryonic apoptosis. Nat Commun 2016; 7:12781. [PMID: 27650264 PMCID: PMC5036004 DOI: 10.1038/ncomms12781] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 08/01/2016] [Indexed: 12/02/2022] Open
Abstract
Some symbiotic bacteria are capable of interfering with host reproduction in selfish ways. How such bacteria can manipulate host's sex-related mechanisms is of fundamental interest encompassing cell, developmental and evolutionary biology. Here, we uncover the molecular and cellular mechanisms underlying Spiroplasma-induced embryonic male lethality in Drosophila melanogaster. Transcriptomic analysis reveals that many genes related to DNA damage and apoptosis are up-regulated specifically in infected male embryos. Detailed genetic and cytological analyses demonstrate that male-killing Spiroplasma causes DNA damage on the male X chromosome interacting with the male-specific lethal (MSL) complex. The damaged male X chromosome exhibits a chromatin bridge during mitosis, and bridge breakage triggers sex-specific abnormal apoptosis via p53-dependent pathways. Notably, the MSL complex is not only necessary but also sufficient for this cytotoxic process. These results highlight symbiont's sophisticated strategy to target host's sex chromosome and recruit host's molecular cascades toward massive apoptosis in a sex-specific manner. Symbiotic bacteria are able to interfere with host reproduction in ways that are detrimental to the host organism. Here the authors show that Spiroplasma induces DNA damage on the male X chromosome in Drosophila, causing sex-specific apoptosis.
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41
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Bhadra U, Gandhi SG, Palaparthi R, Balyan MK, Pal-Bhadra M. Drosophila maleless gene counteracts X global aneuploid effects in males. FEBS J 2016; 283:3457-70. [PMID: 27456781 DOI: 10.1111/febs.13818] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Revised: 06/27/2016] [Accepted: 07/22/2016] [Indexed: 11/30/2022]
Abstract
UNLABELLED The loss of the entire X chromosome in Drosophila males generates a genome-wide aneuploid effect. We have employed a systems biology approach (microarray) to investigate the global aneuploid effect of the maleless (mle) mutation that disrupts the binding of male specific lethal (MSL) proteins that function in dosage compensation. A large number of the genes (144) that encode a broad spectrum of cellular transport proteins and transcription factors are located mainly in the autosomes of Drosophila melanogaster. We found several such targets to be sensitive to the aneuploid effect and conserved with the X chromosome in primitive Drosophila species and Anopheles gambiae. During evolution, they shifted gradually from their X-chromosomal positions to the autosomes in the species D. melanogaster, suggesting that the counteraction of trans-acting regulatory modifiers and their targets in two separate chromosomes is evolutionarily advantageous. These findings suggest a remarkable and previously unexpected level of complexity favoring natural compensation for the aneuploid effect. We propose that the MSL complex functions in dosage compensation in two separate steps. Initially, X-linked genes including X-linked trans-acting modifiers are hyperactivated in dosage compensated males. Later, these compensated modifiers eventually mitigate inverse aneuploid effects for the equality in expression of their autosomal targets in males and females. DATABASE Microarray data are available at the Gene Expression Omnibus (GEO) web deposit of National Centre for Biotechnology Information (NCBI) with the accession number GSE78227.
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Affiliation(s)
- Utpal Bhadra
- Functional Genomics and Gene Silencing Group, Centre for Cellular and Molecular Biology, Hyderabad, India.
| | - Sumit G Gandhi
- Functional Genomics and Gene Silencing Group, Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Ramesh Palaparthi
- Functional Genomics and Gene Silencing Group, Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Manoj K Balyan
- Functional Genomics and Gene Silencing Group, Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Manika Pal-Bhadra
- Centre for Chemical Biology, Indian Institute of Chemical Technology, Hyderabad, India.
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Birchler JA. Parallel Universes for Models of X Chromosome Dosage Compensation in Drosophila: A Review. Cytogenet Genome Res 2016; 148:52-67. [PMID: 27166165 DOI: 10.1159/000445924] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/27/2016] [Indexed: 11/19/2022] Open
Abstract
Dosage compensation in Drosophila involves an approximately 2-fold increase in expression of the single X chromosome in males compared to the per gene expression in females with 2 X chromosomes. Two models have been considered for an explanation. One proposes that the male-specific lethal (MSL) complex that is associated with the male X chromosome brings histone modifiers to the sex chromosome to increase its expression. The other proposes that the inverse effect which results from genomic imbalance would tend to upregulate the genome approximately 2-fold, but the MSL complex sequesters histone modifiers from the autosomes to the X to mute this autosomal male-biased expression. On the X, the MSL complex must override the high level of resulting histone modifications to prevent overcompensation of the X chromosome. Each model is evaluated in terms of fitting classical genetic and recent molecular data. Potential paths toward resolving the models are suggested.
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Affiliation(s)
- James A Birchler
- Division of Biological Sciences, University of Missouri, Columbia, Mo., USA
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Cheng B, Kuppanda N, Aldrich JC, Akbari OS, Ferree PM. Male-Killing Spiroplasma Alters Behavior of the Dosage Compensation Complex during Drosophila melanogaster Embryogenesis. Curr Biol 2016; 26:1339-45. [PMID: 27161498 DOI: 10.1016/j.cub.2016.03.050] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Revised: 03/16/2016] [Accepted: 03/21/2016] [Indexed: 01/11/2023]
Abstract
Numerous arthropods harbor maternally transmitted bacteria that induce the preferential death of males [1-7]. This sex-specific lethality benefits the bacteria because males are "dead ends" regarding bacterial transmission, and their absence may result in additional resources for their viable female siblings who can thereby more successfully transmit the bacteria [5]. Although these symbionts disrupt a range of developmental processes [8-10], the underlying cellular mechanisms are largely unknown. It was previously shown that mutations in genes of the dosage compensation pathway of Drosophila melanogaster suppressed male killing caused by the bacterium, Spiroplasma [10]. This result suggested that dosage compensation is a target of Spiroplasma. However, it remains unclear how this pathway is affected, and whether the underlying interactions require the male-specific cellular environment. Here, we investigated the cellular basis of male embryonic lethality in D. melanogaster induced by Spiroplasma. We found that the dosage compensation complex (DCC), which acetylates X chromatin in males [11], becomes mis-localized to ectopic regions of the nucleus immediately prior to the killing phase. This effect was accompanied by inappropriate histone acetylation and genome-wide mis-regulation of gene expression. Artificially induced formation of the DCC in infected females, through transgenic expression of the DCC-specific gene msl-2, resulted in mis-localization of this complex to non-X regions and early Spiroplasma-induced death, mirroring the killing effects in males. These findings strongly suggest that Spiroplasma initiates male killing by targeting the dosage compensation machinery directly and independently of other cellular features characteristic of the male sex.
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Affiliation(s)
- Becky Cheng
- W.M. Keck Science Department, Claremont McKenna, Pitzer and Scripps Colleges, 925 N. Mills Avenue, Claremont, CA 91711, USA
| | - Nitin Kuppanda
- W.M. Keck Science Department, Claremont McKenna, Pitzer and Scripps Colleges, 925 N. Mills Avenue, Claremont, CA 91711, USA
| | - John C Aldrich
- W.M. Keck Science Department, Claremont McKenna, Pitzer and Scripps Colleges, 925 N. Mills Avenue, Claremont, CA 91711, USA
| | - Omar S Akbari
- Department of Entomology and Riverside Center for Disease Vector Research, Institute for Integrative Genome Biology, University of California, Riverside, Riverside, CA 92521, USA.
| | - Patrick M Ferree
- W.M. Keck Science Department, Claremont McKenna, Pitzer and Scripps Colleges, 925 N. Mills Avenue, Claremont, CA 91711, USA.
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The sexual identity of adult intestinal stem cells controls organ size and plasticity. Nature 2016; 530:344-8. [PMID: 26887495 PMCID: PMC4800002 DOI: 10.1038/nature16953] [Citation(s) in RCA: 119] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 12/21/2015] [Indexed: 01/01/2023]
Abstract
Sex differences in physiology and disease susceptibility are commonly attributed to developmental and/or hormonal factors, but there is increasing realisation that cell-intrinsic mechanisms play important and persistent roles1,2. Here we use the Drosophila melanogaster intestine to investigate the nature and significance of cellular sex in an adult somatic organ in vivo. We find that the adult intestinal epithelium is a cellular mosaic of different sex differentiation pathways, and displays extensive sex differences in expression of genes with roles in growth and metabolism. Cell-specific reversals of the sexual identity of adult intestinal stem cells uncover its key roles in controlling organ size, its reproductive plasticity and its response to genetically induced tumours. Unlike previous examples of sexually dimorphic somatic stem cell activity, the sex differences in intestinal stem cell behaviour arise from intrinsic mechanisms, which control cell cycle duration and involve a new doublesex- and fruitless-independent branch of the sex differentiation pathway downstream of transformer. Together, our findings indicate that the plasticity of an adult somatic organ is reversibly controlled by its sexual identity, imparted by a new mechanism that may be active in more tissues than previously recognised.
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Primary Sex Determination in Drosophila melanogaster Does Not Rely on the Male-Specific Lethal Complex. Genetics 2015; 202:541-9. [PMID: 26614741 DOI: 10.1534/genetics.115.182931] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Accepted: 11/21/2015] [Indexed: 11/18/2022] Open
Abstract
It has been proposed that the Male Specific Lethal (MSL) complex is active in Drosophila melanogaster embryos of both sexes prior to the maternal-to-zygotic transition. Elevated gene expression from the two X chromosomes of female embryos is proposed to facilitate the stable establishment of Sex-lethal (Sxl) expression, which determines sex and represses further activity of the MSL complex, leaving it active only in males. Important supporting data included female-lethal genetic interactions between the seven msl genes and either Sxl or scute and sisterlessA, two of the X-signal elements (XSE) that regulate early Sxl expression. Here I report contrary findings that there are no female-lethal genetic interactions between the msl genes and Sxl or its XSE regulators. Fly stocks containing the msl3(1) allele were found to exhibit a maternal-effect interaction with Sxl, scute, and sisterlessA mutations, but genetic complementation experiments showed that msl3 is neither necessary nor sufficient for the female-lethal interactions, which appear to be due to an unidentified maternal regulator of Sxl. Published data cited as evidence for an early function of the MSL complex in females, including a maternal effect of msl2, have been reevaluated and found not to support a maternal, or other effect, of the MSL complex in sex determination. These findings suggest that the MSL complex is not involved in primary sex determination or in X chromosome dosage compensation prior to the maternal-to-zygotic transition.
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LAKHOTIA SUBHASHC. Divergent actions of long noncoding RNAs on X-chromosome remodelling in mammals and Drosophila achieve the same end result: dosage compensation. J Genet 2015; 94:575-84. [DOI: 10.1007/s12041-015-0566-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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Sxl-Dependent, tra/tra2-Independent Alternative Splicing of the Drosophila melanogaster X-Linked Gene found in neurons. G3-GENES GENOMES GENETICS 2015; 5:2865-74. [PMID: 26511498 PMCID: PMC4683657 DOI: 10.1534/g3.115.023721] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Somatic sexual determination and behavior in Drosophila melanogaster are under the control of a genetic cascade initiated by Sex lethal (Sxl). In the female soma, SXL RNA-binding protein regulates the splicing of transformer (tra) transcripts into a female-specific form. The RNA-binding protein TRA and its cofactor TRA2 function in concert in females, whereas SXL, TRA, and TRA2 are thought to not function in males. To better understand sex-specific regulation of gene expression, we analyzed male and female head transcriptome datasets for expression levels and splicing, quantifying sex-biased gene expression via RNA-Seq and qPCR. Our data uncouple the effects of Sxl and tra/tra2 in females in the-sex-biased alternative splicing of head transcripts from the X-linked locus found in neurons (fne), encoding a pan-neuronal RNA-binding protein of the ELAV family. We show that FNE protein levels are downregulated by Sxl in female heads, also independently of tra/tra2. We argue that this regulation may have important sexually dimorphic consequences for the regulation of nervous system development or function.
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Linger RJ, Belikoff EJ, Scott MJ. Dosage Compensation of X-Linked Muller Element F Genes but Not X-Linked Transgenes in the Australian Sheep Blowfly. PLoS One 2015; 10:e0141544. [PMID: 26506426 PMCID: PMC4624761 DOI: 10.1371/journal.pone.0141544] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Accepted: 10/10/2015] [Indexed: 11/25/2022] Open
Abstract
In most animals that have X and Y sex chromosomes, chromosome-wide mechanisms are used to balance X-linked gene expression in males and females. In the fly Drosophila melanogaster, the dosage compensation mechanism also generally extends to X-linked transgenes. Over 70 transgenic lines of the Australian sheep blowfly Lucilia cuprina have been made as part of an effort to develop male-only strains for a genetic control program of this major pest of sheep. All lines carry a constitutively expressed fluorescent protein marker gene. In all 12 X-linked lines, female larvae show brighter fluorescence than male larvae, suggesting the marker gene is not dosage compensated. This has been confirmed by quantitative RT-PCR for selected lines. To determine if endogenous X-linked genes are dosage compensated, we isolated 8 genes that are orthologs of genes that are on the fourth chromosome in D. melanogaster. Recent evidence suggests that the D. melanogaster fourth chromosome, or Muller element F, is the ancestral X chromosome in Diptera that has reverted to an autosome in Drosophila species. We show by quantitative PCR of male and female DNA that 6 of the 8 linkage group F genes reside on the X chromosome in L. cuprina. The other two Muller element F genes were found to be autosomal in L. cuprina, whereas two Muller element B genes were found on the same region of the X chromosome as the L. cuprina orthologs of the D. melanogaster Ephrin and gawky genes. We find that the L. cuprina X chromosome genes are equally expressed in males and females (i.e., fully dosage compensated). Thus, unlike in Drosophila, it appears that the Lucilia dosage compensation system is specific for genes endogenous to the X chromosome and cannot be co-opted by recently arrived transgenes.
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Affiliation(s)
- Rebecca J. Linger
- Department of Entomology, North Carolina State University, Campus Box 7613, Raleigh, NC, 27695–7613, United States of America
| | - Esther J. Belikoff
- Department of Entomology, North Carolina State University, Campus Box 7613, Raleigh, NC, 27695–7613, United States of America
| | - Maxwell J. Scott
- Department of Entomology, North Carolina State University, Campus Box 7613, Raleigh, NC, 27695–7613, United States of America
- * E-mail:
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Modulation of Heterochromatin by Male Specific Lethal Proteins and roX RNA in Drosophila melanogaster Males. PLoS One 2015; 10:e0140259. [PMID: 26468879 PMCID: PMC4607463 DOI: 10.1371/journal.pone.0140259] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Accepted: 08/27/2015] [Indexed: 01/04/2023] Open
Abstract
The ribonucleoprotein Male Specific Lethal (MSL) complex is required for X chromosome dosage compensation in Drosophila melanogaster males. Beginning at 3 h of development the MSL complex binds transcribed X-linked genes and modifies chromatin. A subset of MSL complex proteins, including MSL1 and MSL3, is also necessary for full expression of autosomal heterochromatic genes in males, but not females. Loss of the non-coding roX RNAs, essential components of the MSL complex, lowers the expression of heterochromatic genes and suppresses position effect variegation (PEV) only in males, revealing a sex-limited disruption of heterochromatin. To explore the molecular basis of this observation we examined additional proteins that participate in compensation and found that MLE, but not Jil-1 kinase, contributes to heterochromatic gene expression. To determine if identical regions of roX RNA are required for dosage compensation and heterochromatic silencing, we tested a panel of roX1 transgenes and deletions and find that the X chromosome and heterochromatin functions are separable by some mutations. Chromatin immunoprecipitation of staged embryos revealed widespread autosomal binding of MSL3 before and after localization of the MSL complex to the X chromosome at 3 h AEL. Autosomal MSL3 binding was dependent on MSL1, supporting the idea that a subset of MSL proteins associates with chromatin throughout the genome during early development. The broad localization of these proteins early in embryogenesis supports the idea of direct action at autosomal sites. We postulate that this may contribute to the sex-specific differences in heterochromatin that we, and others, have noted.
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Abstract
The different dose of X chromosomes in males and females produces a potentially fatal imbalance in X-linked gene products. This imbalance is addressed by dosage compensation, a process that modulates expression from an entire X chromosome in one sex. Dosage compensation acts on thousands of genes with disparate expression patterns. Both flies and mammals accomplish this with remarkable specificity by targeting epigenetic chromatin modifications to a single chromosome. Long noncoding RNAs that are expressed from the X chromosome are essential elements of the targeting mechanism in both lineages. We recently discovered that the siRNA pathway, as well as small RNA from satellite repeats that are strikingly enriched on the fly X chromosome, also promote X recognition. In this article we review the current understanding of X recognition in flies and discuss potential mechanisms by which the siRNA pathway, repetitive elements and long noncoding RNAs might cooperate to promote X recognition.
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Affiliation(s)
- Debashish U Menon
- a Department of Genetics ; University of North Carolina ; Chapel Hill , NC USA
| | - Victoria H Meller
- b Department of Biological Sciences ; Wayne State University ; Detroit , MI USA
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