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Hodkinson LJ, Gross J, Schmidt CA, Diaz-Saldana PP, Aoki T, Rieder LE. Sequence reliance of the Drosophila context-dependent transcription factor CLAMP. Genetics 2024:iyae060. [PMID: 38775472 DOI: 10.1093/genetics/iyae060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Accepted: 03/19/2024] [Indexed: 06/04/2024] Open
Abstract
Despite binding similar cis elements in multiple locations, a single transcription factor (TF) often performs context-dependent functions at different loci. How factors integrate cis sequence and genomic context is still poorly understood and has implications for off-target effects in genetic engineering. The Drosophila context-dependent TF chromatin-linked adaptor for male-specific lethal proteins (CLAMP) targets similar GA-rich cis elements on the X-chromosome and at the histone gene locus but recruits very different, locus-specific factors. We discover that CLAMP leverages information from both cis element and local sequence to perform context-specific functions. Our observations imply the importance of other cues, including protein-protein interactions and the presence of additional cofactors.
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Affiliation(s)
- Lauren J Hodkinson
- Genetics and Molecular Biology Graduate Program, Emory University, Atlanta, GA 30322, USA
| | - Julia Gross
- Immunology and Molecular Pathogenesis Graduate Program, Emory University, Atlanta, GA 30322, USA
| | - Casey A Schmidt
- Department of Biology, Emory University, Atlanta, GA 30322, USA
| | | | - Tsutomo Aoki
- Department of Molecular Biology, Princeton University, Princeton, NJ 08540, USA
| | - Leila E Rieder
- Department of Biology, Emory University, Atlanta, GA 30322, USA
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2
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Hodkinson LJ, Gross J, Schmidt CA, Diaz-Saldana PP, Aoki T, Rieder LE. Sequence reliance of a Drosophila context-dependent transcription factor. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.07.570650. [PMID: 38106168 PMCID: PMC10723421 DOI: 10.1101/2023.12.07.570650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Despite binding similar cis elements in multiple locations, a single transcription factor often performs context-dependent functions at different loci. How factors integrate cis sequence and genomic context is still poorly understood and has implications for off-target effects in genetic engineering. The Drosophila context-dependent transcription factor CLAMP targets similar GA-rich cis elements on the X-chromosome and at the histone gene locus but recruits very different, loci-specific factors. We discover that CLAMP leverages information from both cis element and local sequence to perform context-specific functions. Our observations imply the importance of other cues, including protein-protein interactions and the presence of additional cofactors.
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Affiliation(s)
- Lauren J. Hodkinson
- Genetics and Molecular Biology Graduate Program, Emory University, Atlanta, GA 30322 USA
| | - Julia Gross
- Immunology and Molecular Pathogenesis Graduate Program, Emory University, Atlanta, GA 30322 USA
| | | | | | - Tsutomo Aoki
- Department of Molecular Biology, Princeton University, Princeton, NJ 08540 USA
| | - Leila E. Rieder
- Department of Biology Emory University, Atlanta, GA 30322 USA
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3
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Sorkaç A, Moșneanu RA, Crown AM, Savaş D, Okoro AM, Memiş E, Talay M, Barnea G. retro-Tango enables versatile retrograde circuit tracing in Drosophila. eLife 2023; 12:e85041. [PMID: 37166114 PMCID: PMC10208638 DOI: 10.7554/elife.85041] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Accepted: 05/11/2023] [Indexed: 05/12/2023] Open
Abstract
Transsynaptic tracing methods are crucial tools in studying neural circuits. Although a couple of anterograde tracing methods and a targeted retrograde tool have been developed in Drosophila melanogaster, there is still need for an unbiased, user-friendly, and flexible retrograde tracing system. Here, we describe retro-Tango, a method for transsynaptic, retrograde circuit tracing and manipulation in Drosophila. In this genetically encoded system, a ligand-receptor interaction at the synapse triggers an intracellular signaling cascade that results in reporter gene expression in presynaptic neurons. Importantly, panneuronal expression of the elements of the cascade renders this method versatile, enabling its use not only to test hypotheses but also to generate them. We validate retro-Tango in various circuits and benchmark it by comparing our findings with the electron microscopy reconstruction of the Drosophila hemibrain. Our experiments establish retro-Tango as a key method for circuit tracing in neuroscience research.
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Affiliation(s)
- Altar Sorkaç
- Department of Neuroscience, Brown UniversityProvidenceUnited States
- Carney Institute for Brain Science, Brown UniversityProvidenceUnited States
| | - Rareș A Moșneanu
- Department of Neuroscience, Brown UniversityProvidenceUnited States
- Carney Institute for Brain Science, Brown UniversityProvidenceUnited States
| | - Anthony M Crown
- Department of Neuroscience, Brown UniversityProvidenceUnited States
- Carney Institute for Brain Science, Brown UniversityProvidenceUnited States
| | - Doruk Savaş
- Department of Neuroscience, Brown UniversityProvidenceUnited States
- Carney Institute for Brain Science, Brown UniversityProvidenceUnited States
| | - Angel M Okoro
- Department of Neuroscience, Brown UniversityProvidenceUnited States
- Carney Institute for Brain Science, Brown UniversityProvidenceUnited States
| | - Ezgi Memiş
- Department of Neuroscience, Brown UniversityProvidenceUnited States
- Carney Institute for Brain Science, Brown UniversityProvidenceUnited States
| | - Mustafa Talay
- Department of Neuroscience, Brown UniversityProvidenceUnited States
- Carney Institute for Brain Science, Brown UniversityProvidenceUnited States
| | - Gilad Barnea
- Department of Neuroscience, Brown UniversityProvidenceUnited States
- Carney Institute for Brain Science, Brown UniversityProvidenceUnited States
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4
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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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5
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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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6
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Drosophila Dosage Compensation Loci Associate with a Boundary-Forming Insulator Complex. Mol Cell Biol 2017; 37:MCB.00253-17. [PMID: 28784719 DOI: 10.1128/mcb.00253-17] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 07/10/2017] [Indexed: 12/18/2022] Open
Abstract
Chromatin entry sites (CES) are 100- to 1,500-bp elements that recruit male-specific lethal (MSL) complexes to the X chromosome to upregulate expression of X-linked genes in male flies. CES contain one or more ∼20-bp GA-rich sequences called MSL recognition elements (MREs) that are critical for dosage compensation. Recent studies indicate that CES also correspond to boundaries of X-chromosomal topologically associated domains (TADs). Here, we show that an ∼1,000-kDa complex called the late boundary complex (LBC), which is required for the functioning of the Bithorax complex boundary Fab-7, interacts specifically with a special class of CES that contain multiple MREs. Mutations in the MRE sequences of three of these CES that disrupt function in vivo abrogate interactions with the LBC. Moreover, reducing the levels of two LBC components compromises MSL recruitment. Finally, we show that several of the CES that are physically linked to each other in vivo are LBC interactors.
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7
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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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Gerland TA, Sun B, Smialowski P, Lukacs A, Thomae AW, Imhof A. The Drosophila speciation factor HMR localizes to genomic insulator sites. PLoS One 2017; 12:e0171798. [PMID: 28207793 PMCID: PMC5312933 DOI: 10.1371/journal.pone.0171798] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 01/26/2017] [Indexed: 12/22/2022] Open
Abstract
Hybrid incompatibility between Drosophila melanogaster and D. simulans is caused by a lethal interaction of the proteins encoded by the Hmr and Lhr genes. In D. melanogaster the loss of HMR results in mitotic defects, an increase in transcription of transposable elements and a deregulation of heterochromatic genes. To better understand the molecular mechanisms that mediate HMR’s function, we measured genome-wide localization of HMR in D. melanogaster tissue culture cells by chromatin immunoprecipitation. Interestingly, we find HMR localizing to genomic insulator sites that can be classified into two groups. One group belongs to gypsy insulators and another one borders HP1a bound regions at active genes. The transcription of the latter group genes is strongly affected in larvae and ovaries of Hmr mutant flies. Our data suggest a novel link between HMR and insulator proteins, a finding that implicates a potential role for genome organization in the formation of species.
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Affiliation(s)
- Thomas Andreas Gerland
- Biomedical Center, Histone Modifications Group, Department of Molecular Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
- Center for Integrated Protein Science Munich (CIPSM), Ludwig-Maximilians-Universität München, Munich, Germany
| | - Bo Sun
- Biomedical Center, Histone Modifications Group, Department of Molecular Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Pawel Smialowski
- Biomedical Center, Histone Modifications Group, Department of Molecular Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
- Biomedical Center, Core Facility Computational Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Andrea Lukacs
- Biomedical Center, Histone Modifications Group, Department of Molecular Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Andreas Walter Thomae
- Biomedical Center, Histone Modifications Group, Department of Molecular Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
- Biomedical Center, Core Facility Bioimaging, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Axel Imhof
- Biomedical Center, Histone Modifications Group, Department of Molecular Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
- Center for Integrated Protein Science Munich (CIPSM), Ludwig-Maximilians-Universität München, Munich, Germany
- * E-mail:
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9
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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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10
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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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11
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Abstract
Dosage compensation in Drosophila increases the transcription of genes on the single X chromosome in males to equal that of both X chromosomes in females. Site-specific histone acetylation by the male-specific lethal (MSL) complex is thought to play a fundamental role in the increased transcriptional output of the male X. Nucleation and sequence-independent spreading of the complex to active genes serves as a model for understanding the targeting and function of epigenetic chromatin-modifying complexes. Interestingly, two noncoding RNAs are key for MSL assembly and spreading to active genes along the length of the X chromosome.
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Affiliation(s)
- John C Lucchesi
- Department of Biology, O. W. Rollins Research Center, Emory University, Atlanta, Georgia 30322
| | - Mitzi I Kuroda
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115
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12
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Zheng S, Villa R, Wang J, Feng Y, Wang J, Becker PB, Ye K. Structural basis of X chromosome DNA recognition by the MSL2 CXC domain during Drosophila dosage compensation. Genes Dev 2015; 28:2652-62. [PMID: 25452275 PMCID: PMC4248295 DOI: 10.1101/gad.250936.114] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The male-specific lethal dosage compensation complex (MSL-DCC) selectively assembles on the X chromosome in Drosophila and activates gene transcription by twofold through histone acetylation. An MSL recognition element (MRE) sequence motif nucleates the initial MSL association. Here, Zheng et al. identified the CXC domain of MSL2 specifically recognizing the MRE motif and determined its crystal structure bound to specific and nonspecific DNAs. Specific DNA-binding mutants of MSL2 are impaired in MRE binding and X chromosome localization in vivo. The male-specific lethal dosage compensation complex (MSL-DCC) selectively assembles on the X chromosome in Drosophila males and activates gene transcription by twofold through histone acetylation. An MSL recognition element (MRE) sequence motif nucleates the initial MSL association, but how it is recognized remains unknown. Here, we identified the CXC domain of MSL2 specifically recognizing the MRE motif and determined its crystal structure bound to specific and nonspecific DNAs. The CXC domain primarily contacts one strand of DNA duplex and employs a single arginine to directly read out dinucleotide sequences from the minor groove. The arginine is flexible when bound to nonspecific sequences. The core region of the MRE motif harbors two binding sites on opposite strands that can cooperatively recruit a CXC dimer. Specific DNA-binding mutants of MSL2 are impaired in MRE binding and X chromosome localization in vivo. Our results reveal multiple dynamic DNA-binding modes of the CXC domain that target the MSL-DCC to X chromosomes.
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Affiliation(s)
- Sanduo Zheng
- Department of Biochemistry and Molecular Biology, College of Life Sciences, Beijing Normal University, Beijing 100875, China; National Institute of Biological Sciences, Beijing 102206, China
| | - Raffaella Villa
- Molecular Biology Unit, Adolf Butenandt Institute, Center for Integrated Protein Science, Ludwig-Maximilians University, 80336 Munich, Germany
| | - Jia Wang
- Department of Biochemistry and Molecular Biology, College of Life Sciences, Beijing Normal University, Beijing 100875, China; National Institute of Biological Sciences, Beijing 102206, China
| | - Yingang Feng
- Qingdao Engineering Laboratory of Single Cell Oil, Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shangdong 266101, China
| | | | - Peter B Becker
- Molecular Biology Unit, Adolf Butenandt Institute, Center for Integrated Protein Science, Ludwig-Maximilians University, 80336 Munich, Germany
| | - Keqiong Ye
- National Institute of Biological Sciences, Beijing 102206, China; Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
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13
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Abstract
In many animals, males have one X and females have two X chromosomes. The difference in X chromosome dosage between the two sexes is compensated by mechanisms that regulate X chromosome transcription. Recent advances in genomic techniques have provided new insights into the molecular mechanisms of X chromosome dosage compensation. In this review, I summarize our current understanding of dosage imbalance in general, and then review the molecular mechanisms of X chromosome dosage compensation with an emphasis on the parallels and differences between the three well-studied model systems, M. musculus, D. melanogaster and C. elegans.
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Affiliation(s)
- Sevinç Ercan
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA
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14
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Soruco MML, Larschan E. A new player in X identification: the CLAMP protein is a key factor in Drosophila dosage compensation. Chromosome Res 2014; 22:505-15. [PMID: 25102930 DOI: 10.1007/s10577-014-9438-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Revised: 06/29/2014] [Accepted: 07/22/2014] [Indexed: 10/24/2022]
Abstract
Dosage compensation adjusts the expression levels of genes on one or both targeted sex chromosomes in heterogametic species. This process results in the normalized transcriptional output of important and essential gene families encoded on multiple chromosomes. The mechanisms of dosage compensation have been studied in many model organisms, including Drosophila melanogaster (fly), Caenorhabditis elegans (worm), and Mus musculus (mouse). Although the mechanisms of dosage compensations differ among these species, all of these processes rely on the initial discrimination of the X chromosome from autosomes. Recently, a new paradigm for how the X chromosome is targeted for regulation was identified in Drosophila. This mechanism involves a newly identified zinc finger protein, CLAMP. Here, we review important factors involved in dosage compensation across species with special focus on the fly. Understanding how the newly identified CLAMP protein is involved in X targeting in the fly could provide key insights into how the X chromosome is initially identified across species.
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Affiliation(s)
- Marcela M L Soruco
- Department of Molecular Biology, Cellular Biology and Biochemistry, Brown University, Providence, RI, 02912, USA
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15
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Stanton KP, Parisi F, Strino F, Rabin N, Asp P, Kluger Y. Arpeggio: harmonic compression of ChIP-seq data reveals protein-chromatin interaction signatures. Nucleic Acids Res 2013; 41:e161. [PMID: 23873955 PMCID: PMC3763565 DOI: 10.1093/nar/gkt627] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Researchers generating new genome-wide data in an exploratory sequencing study can gain biological insights by comparing their data with well-annotated data sets possessing similar genomic patterns. Data compression techniques are needed for efficient comparisons of a new genomic experiment with large repositories of publicly available profiles. Furthermore, data representations that allow comparisons of genomic signals from different platforms and across species enhance our ability to leverage these large repositories. Here, we present a signal processing approach that characterizes protein–chromatin interaction patterns at length scales of several kilobases. This allows us to efficiently compare numerous chromatin-immunoprecipitation sequencing (ChIP-seq) data sets consisting of many types of DNA-binding proteins collected from a variety of cells, conditions and organisms. Importantly, these interaction patterns broadly reflect the biological properties of the binding events. To generate these profiles, termed Arpeggio profiles, we applied harmonic deconvolution techniques to the autocorrelation profiles of the ChIP-seq signals. We used 806 publicly available ChIP-seq experiments and showed that Arpeggio profiles with similar spectral densities shared biological properties. Arpeggio profiles of ChIP-seq data sets revealed characteristics that are not easily detected by standard peak finders. They also allowed us to relate sequencing data sets from different genomes, experimental platforms and protocols. Arpeggio is freely available at http://sourceforge.net/p/arpeggio/wiki/Home/.
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Affiliation(s)
- Kelly Patrick Stanton
- Department of Pathology, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520, USA, Department of Exact Sciences, Afeka - Tel-Aviv Academic College of Engineering, Tel-Aviv 69107, Israel, Department Of Liver Transplant, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, NY 10467, USA and NYU Center for Health Informatics and Bioinformatics, New York University Langone Medical Center, 227 East 30th Street, New York, NY 10016, USA
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16
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Wang CI, Alekseyenko AA, LeRoy G, Elia AEH, Gorchakov AA, Britton LMP, Elledge SJ, Kharchenko PV, Garcia BA, Kuroda MI. Chromatin proteins captured by ChIP-mass spectrometry are linked to dosage compensation in Drosophila. Nat Struct Mol Biol 2013; 20:202-9. [PMID: 23295261 DOI: 10.1038/nsmb.2477] [Citation(s) in RCA: 94] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2012] [Accepted: 11/21/2012] [Indexed: 12/28/2022]
Abstract
X-chromosome dosage compensation by the MSL (male-specific lethal) complex is required in Drosophila melanogaster to increase gene expression from the single male X to equal that of both female X chromosomes. Instead of focusing solely on protein complexes released from DNA, here we used chromatin-interacting protein MS (ChIP-MS) to identify MSL interactions on cross-linked chromatin. We identified MSL-enriched histone modifications, including histone H4 Lys16 acetylation and histone H3 Lys36 methylation, and CG4747, a putative Lys36-trimethylated histone H3 (H3K36me3)-binding protein. CG4747 is associated with the bodies of active genes, coincident with H3K36me3, and is mislocalized in the Set2 mutant lacking H3K36me3. CG4747 loss of function in vivo results in partial mislocalization of the MSL complex to autosomes, and RNA interference experiments confirm that CG4747 and Set2 function together to facilitate targeting of the MSL complex to active genes, validating the ChIP-MS approach.
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Affiliation(s)
- Charlotte I Wang
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
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17
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Meisel RP, Malone JH, Clark AG. Faster-X evolution of gene expression in Drosophila. PLoS Genet 2012; 8:e1003013. [PMID: 23071459 PMCID: PMC3469423 DOI: 10.1371/journal.pgen.1003013] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2012] [Accepted: 08/22/2012] [Indexed: 01/01/2023] Open
Abstract
DNA sequences on X chromosomes often have a faster rate of evolution when compared to similar loci on the autosomes, and well articulated models provide reasons why the X-linked mode of inheritance may be responsible for the faster evolution of X-linked genes. We analyzed microarray and RNA-seq data collected from females and males of six Drosophila species and found that the expression levels of X-linked genes also diverge faster than autosomal gene expression, similar to the "faster-X" effect often observed in DNA sequence evolution. Faster-X evolution of gene expression was recently described in mammals, but it was limited to the evolutionary lineages shortly following the creation of the therian X chromosome. In contrast, we detect a faster-X effect along both deep lineages and those on the tips of the Drosophila phylogeny. In Drosophila males, the dosage compensation complex (DCC) binds the X chromosome, creating a unique chromatin environment that promotes the hyper-expression of X-linked genes. We find that DCC binding, chromatin environment, and breadth of expression are all predictive of the rate of gene expression evolution. In addition, estimates of the intraspecific genetic polymorphism underlying gene expression variation suggest that X-linked expression levels are not under relaxed selective constraints. We therefore hypothesize that the faster-X evolution of gene expression is the result of the adaptive fixation of beneficial mutations at X-linked loci that change expression level in cis. This adaptive faster-X evolution of gene expression is limited to genes that are narrowly expressed in a single tissue, suggesting that relaxed pleiotropic constraints permit a faster response to selection. Finally, we present a conceptional framework to explain faster-X expression evolution, and we use this framework to examine differences in the faster-X effect between Drosophila and mammals.
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Affiliation(s)
- Richard P Meisel
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, USA.
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18
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Alekseyenko AA, Ho JWK, Peng S, Gelbart M, Tolstorukov MY, Plachetka A, Kharchenko PV, Jung YL, Gorchakov AA, Larschan E, Gu T, Minoda A, Riddle NC, Schwartz YB, Elgin SCR, Karpen GH, Pirrotta V, Kuroda MI, Park PJ. Sequence-specific targeting of dosage compensation in Drosophila favors an active chromatin context. PLoS Genet 2012; 8:e1002646. [PMID: 22570616 PMCID: PMC3343056 DOI: 10.1371/journal.pgen.1002646] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2011] [Accepted: 02/22/2012] [Indexed: 11/23/2022] Open
Abstract
The Drosophila MSL complex mediates dosage compensation by increasing transcription of the single X chromosome in males approximately two-fold. This is accomplished through recognition of the X chromosome and subsequent acetylation of histone H4K16 on X-linked genes. Initial binding to the X is thought to occur at “entry sites” that contain a consensus sequence motif (“MSL recognition element” or MRE). However, this motif is only ∼2 fold enriched on X, and only a fraction of the motifs on X are initially targeted. Here we ask whether chromatin context could distinguish between utilized and non-utilized copies of the motif, by comparing their relative enrichment for histone modifications and chromosomal proteins mapped in the modENCODE project. Through a comparative analysis of the chromatin features in male S2 cells (which contain MSL complex) and female Kc cells (which lack the complex), we find that the presence of active chromatin modifications, together with an elevated local GC content in the surrounding sequences, has strong predictive value for functional MSL entry sites, independent of MSL binding. We tested these sites for function in Kc cells by RNAi knockdown of Sxl, resulting in induction of MSL complex. We show that ectopic MSL expression in Kc cells leads to H4K16 acetylation around these sites and a relative increase in X chromosome transcription. Collectively, our results support a model in which a pre-existing active chromatin environment, coincident with H3K36me3, contributes to MSL entry site selection. The consequences of MSL targeting of the male X chromosome include increase in nucleosome lability, enrichment for H4K16 acetylation and JIL-1 kinase, and depletion of linker histone H1 on active X-linked genes. Our analysis can serve as a model for identifying chromatin and local sequence features that may contribute to selection of functional protein binding sites in the genome. The genomes of complex organisms encompass hundreds of millions of base pairs of DNA, and regulatory molecules must distinguish specific targets within this vast landscape. In general, regulatory factors find target genes through sequence-specific interactions with the underlying DNA. However, sequence-specific factors typically bind only a fraction of the candidate genomic regions containing their specific target sequence motif. Here we identify potential roles for chromatin environment and flanking sequence composition in helping regulatory factors find their appropriate binding sites, using targeting of the Drosophila dosage compensation complex as a model. The initial stage of dosage compensation involves binding of the Male Specific Lethal (MSL) complex to a sequence motif called the MSL recognition element [1]. Using data from a large chromatin mapping effort (the modENCODE project), we successfully identify an active chromatin environment as predictive of selective MRE binding by the MSL complex. Our study provides a framework for using genome-wide datasets to analyze and predict functional protein–DNA binding site selection.
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Affiliation(s)
- Artyom A. Alekseyenko
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Joshua W. K. Ho
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Center for Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Shouyong Peng
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Center for Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Marnie Gelbart
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Michael Y. Tolstorukov
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Center for Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Annette Plachetka
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Peter V. Kharchenko
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Center for Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Youngsook L. Jung
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Center for Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Andrey A. Gorchakov
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Erica Larschan
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, Rhode Island, United States of America
| | - Tingting Gu
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - Aki Minoda
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, California, United States of America
- Department of Genome Dynamics, Lawrence Berkeley National Lab, Berkeley, California, United States of America
| | - Nicole C. Riddle
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | | | - Sarah C. R. Elgin
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - Gary H. Karpen
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, California, United States of America
| | - Vincenzo Pirrotta
- Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, New Jersey, United States of America
| | - Mitzi I. Kuroda
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
- * E-mail: (MIK); (PJP)
| | - Peter J. Park
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- Center for Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, United States of America
- * E-mail: (MIK); (PJP)
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19
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Lundberg LE, Figueiredo MLA, Stenberg P, Larsson J. Buffering and proteolysis are induced by segmental monosomy in Drosophila melanogaster. Nucleic Acids Res 2012; 40:5926-37. [PMID: 22434883 PMCID: PMC3401434 DOI: 10.1093/nar/gks245] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Variation in the number of individual chromosomes (chromosomal aneuploidy) or chromosome segments (segmental aneuploidy) is associated with developmental abnormalities and reduced fitness in all species examined; it is the leading cause of miscarriages and mental retardation and a hallmark of cancer. However, despite their documented importance in disease, the effects of aneuploidies on the transcriptome remain largely unknown. We have examined the expression effects of seven heterozygous chromosomal deficiencies, both singly and in all pairwise combinations, in Drosophila melanogaster. The results show that genes in one copy are buffered, i.e. expressed more strongly than the expected 50% of wild-type level, the buffering is general and not influenced by other monosomic regions. Furthermore, long genes are significantly more highly buffered than short genes and gene length appears to be the primary determinant of the buffering degree. For short genes the degree of buffering depends on expression level and expression pattern. Furthermore, the results show that in deficiency heterozygotes the expression of genes involved in proteolysis is enhanced and negatively correlates with the degree of buffering. Thus, enhanced proteolysis appears to be a general response to aneuploidy.
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Affiliation(s)
- Lina E Lundberg
- Department of Molecular Biology, Umeå University, SE-90187 Umeå, Sweden
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20
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Conrad T, Akhtar A. Dosage compensation in Drosophila melanogaster: epigenetic fine-tuning of chromosome-wide transcription. Nat Rev Genet 2012; 13:123-34. [PMID: 22251873 DOI: 10.1038/nrg3124] [Citation(s) in RCA: 179] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Dosage compensation is an epigenetic mechanism that normalizes gene expression from unequal copy numbers of sex chromosomes. Different organisms have evolved alternative molecular solutions to this task. In Drosophila melanogaster, transcription of the single male X chromosome is upregulated by twofold in a process orchestrated by the dosage compensation complex. Despite this conceptual simplicity, dosage compensation involves multiple coordinated steps to recognize and activate the entire X chromosome. We are only beginning to understand the intriguing interplay between multiple levels of local and long-range chromatin regulation required for the fine-tuned transcriptional activation of a heterogeneous gene population. This Review highlights the known facts and open questions of dosage compensation in D. melanogaster.
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Affiliation(s)
- Thomas Conrad
- Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108 Freiburg im Breisgau, Germany
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21
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Maenner S, Müller M, Becker PB. Roles of long, non-coding RNA in chromosome-wide transcription regulation: lessons from two dosage compensation systems. Biochimie 2012; 94:1490-8. [PMID: 22239950 DOI: 10.1016/j.biochi.2011.12.026] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2011] [Accepted: 12/31/2011] [Indexed: 11/17/2022]
Abstract
A large part of higher eukaryotic genomes is transcribed into RNAs lacking any significant open reading frame. This "non-coding part" has been shown to actively contribute to regulating gene expression, but the mechanisms are largely unknown. Particularly instructive examples are provided by the dosage compensation systems, which assure that the single X chromosome in male cells and the two X chromosomes in female cells give rise to similar amounts of gene product. Although this is achieved by very different strategies in mammals and fruit flies, long, non-coding RNAs (lncRNAs) are involved in both cases. Here we summarize recent progress towards unraveling the mechanisms, by which the Xist and roX RNAs mediate the selective association of regulators with individual target chromosomes, to initiate dosage compensation in mammals and fruit flies, respectively.
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Affiliation(s)
- Sylvain Maenner
- Adolf-Butenandt-Institute and Center for Integrated Protein Science (CIPSM), Ludwig Maximilian University Munich, Schillerstrasse 44, 80336 München, Germany.
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22
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Abstract
Long noncoding RNAs (lncRNAs) have important regulatory roles and can function at the level of chromatin. To determine where lncRNAs bind to chromatin, we developed capture hybridization analysis of RNA targets (CHART), a hybridization-based technique that specifically enriches endogenous RNAs along with their targets from reversibly cross-linked chromatin extracts. CHART was used to enrich the DNA and protein targets of endogenous lncRNAs from flies and humans. This analysis was extended to genome-wide mapping of roX2, a well-studied ncRNA involved in dosage compensation in Drosophila. CHART revealed that roX2 binds at specific genomic sites that coincide with the binding sites of proteins from the male-specific lethal complex that affects dosage compensation. These results reveal the genomic targets of roX2 and demonstrate how CHART can be used to study RNAs in a manner analogous to chromatin immunoprecipitation for proteins.
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23
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Petty E, Laughlin E, Csankovszki G. Regulation of DCC localization by HTZ-1/H2A.Z and DPY-30 does not correlate with H3K4 methylation levels. PLoS One 2011; 6:e25973. [PMID: 21998734 PMCID: PMC3187824 DOI: 10.1371/journal.pone.0025973] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2011] [Accepted: 09/14/2011] [Indexed: 12/20/2022] Open
Abstract
Dosage compensation is a specialized form of gene regulation that balances sex-chromosome linked gene expression between the sexes. In C. elegans, dosage compensation is achieved by the activity of the dosage compensation complex (DCC). The DCC binds along both X chromosomes in hermaphrodites to down-regulate gene expression by half, limiting X-linked gene products to levels produced in XO males. Sequence motifs enriched on the X chromosome play an important role in targeting the DCC to the X. However, these motifs are not strictly X-specific and therefore other factors, such as the chromatin environment of the X chromosome, are likely to aid in DCC targeting. Previously, we found that loss of HTZ-1 results in partial disruption of dosage compensation localization to the X chromosomes. We wanted to know whether other chromatin components coordinated with HTZ-1 to regulate DCC localization. One candidate is DPY-30, a protein known to play a role in DCC localization. DPY-30 homologs in yeast, flies, and mammals are highly conserved members of histone H3 lysine 4 (H3K4) methyltransferase Set1/MLL complexes. Therefore, we investigated the hypothesis that the dosage compensation function of DPY-30 involves H3K4 methylation. We found that in dpy-30 animals the DCC fails to stably bind chromatin. Interestingly, of all the C. elegans homologs of Set1/MLL complex subunits, only DPY-30 is required for stable DCC binding to chromatin. Additionally, loss of H3K4 methylation does not enhance DCC mislocalization in htz-1 animals. We conclude that DPY-30 and HTZ-1 have unique functions in DCC localization, both of which are largely independent of H3K4 methylation.
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Affiliation(s)
- Emily Petty
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Emily Laughlin
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Györgyi Csankovszki
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
- * E-mail:
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24
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Laverty C, Li F, Belikoff EJ, Scott MJ. Abnormal dosage compensation of reporter genes driven by the Drosophila glass multiple reporter (GMR) enhancer-promoter. PLoS One 2011; 6:e20455. [PMID: 21655213 PMCID: PMC3105068 DOI: 10.1371/journal.pone.0020455] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2011] [Accepted: 04/26/2011] [Indexed: 11/19/2022] Open
Abstract
In Drosophila melanogaster the male specific lethal (MSL) complex is required for upregulation of expression of most X-linked genes in males, thereby achieving X chromosome dosage compensation. The MSL complex is highly enriched across most active X-linked genes with a bias towards the 3′ end. Previous studies have shown that gene transcription facilitates MSL complex binding but the type of promoter did not appear to be important. We have made the surprising observation that genes driven by the glass multiple reporter (GMR) enhancer-promoter are not dosage compensated at X-linked sites. The GMR promoter is active in all cells in, and posterior to, the morphogenetic furrow of the developing eye disc. Using phiC31 integrase-mediated targeted integration, we measured expression of lacZ reporter genes driven by either the GMR or armadillo (arm) promoters at each of three X-linked sites. At all sites, the arm-lacZ reporter gene was dosage compensated but GMR-lacZ was not. We have investigated why GMR-driven genes are not dosage compensated. Earlier or constitutive expression of GMR-lacZ did not affect the level of compensation. Neither did proximity to a strong MSL binding site. However, replacement of the hsp70 minimal promoter with a minimal promoter from the X-linked 6-Phosphogluconate dehydrogenase gene did restore partial dosage compensation. Similarly, insertion of binding sites for the GAGA and DREF factors upstream of the GMR promoter led to significantly higher lacZ expression in males than females. GAGA and DREF have been implicated to play a role in dosage compensation. We conclude that the gene promoter can affect MSL complex-mediated upregulation and dosage compensation. Further, it appears that the nature of the basal promoter and the presence of binding sites for specific factors influence the ability of a gene promoter to respond to the MSL complex.
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Affiliation(s)
- Corey Laverty
- Institute of Molecular BioSciences, Massey University, Palmerston North, New Zealand
| | - Fang Li
- Institute of Molecular BioSciences, Massey University, Palmerston North, New Zealand
| | - Esther J. Belikoff
- Institute of Molecular BioSciences, Massey University, Palmerston North, New Zealand
| | - Maxwell J. Scott
- Institute of Molecular BioSciences, Massey University, Palmerston North, New Zealand
- * E-mail:
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25
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Abstract
X chromosome inactivation (XCI) is a process in mammals that ensures equal transcript levels between males and females by genetic inactivation of one of the two X chromosomes in females. Central to XCI is the long non-coding RNA Xist, which is highly and specifically expressed from the inactive X chromosome. Xist covers the X chromosome in cis and triggers genetic silencing, but its working mechanism remains elusive. Here, we review current knowledge about Xist regulation, structure, function and conservation and speculate on possible mechanisms by which its action is restricted in cis. We also discuss dosage compensation mechanisms other than XCI and how knowledge from invertebrate species may help to provide a better understanding of the mechanisms of mammalian XCI.
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Affiliation(s)
- Daphne B. Pontier
- Department of Reproduction and Development, Erasmus MC, Dr. Molewaterplein 50, 3015 GE Rotterdam, The Netherlands
| | - Joost Gribnau
- Department of Reproduction and Development, Erasmus MC, Dr. Molewaterplein 50, 3015 GE Rotterdam, The Netherlands
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26
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Transcription modulation chromosome-wide: universal features and principles of dosage compensation in worms and flies. Curr Opin Genet Dev 2011; 21:147-53. [PMID: 21316939 DOI: 10.1016/j.gde.2011.01.012] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2010] [Accepted: 01/18/2011] [Indexed: 11/22/2022]
Abstract
Dosage compensation processes in flies and worms provide a unique opportunity to study common regulatory principles of thousands of genes. Technological advancement in the recent years has allowed for the comprehensive description of key aspects such as the targeting of the regulatory factors, the emerging chromatin structure changes and the ensuing subtle transcriptional alterations. With plenty of data at hand the challenge remains to integrate the findings into coherent models that appreciate the global nature of the underlying principles leaving the experimental anecdotes behind while avoiding the numerical burlesque.
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27
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Johansson AM, Allgardsson A, Stenberg P, Larsson J. msl2 mRNA is bound by free nuclear MSL complex in Drosophila melanogaster. Nucleic Acids Res 2011; 39:6428-39. [PMID: 21551218 PMCID: PMC3159442 DOI: 10.1093/nar/gkr236] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
In Drosophila, the global increase in transcription from the male X chromosome to compensate for its monosomy is mediated by the male-specific lethal (MSL) complex consisting of five proteins and two non-coding RNAs, roX1 and roX2. After an initial sequence-dependent recognition by the MSL complex of 150-300 high affinity sites, the spread to the majority of the X-linked genes depends on local MSL-complex concentration and active transcription. We have explored whether any additional RNA species are associated with the MSL complex. No additional roX RNA species were found, but a strong association was found between a spliced and poly-adenylated msl2 RNA and the MSL complex. Based on our results, we propose a model in which a non-chromatin-associated partial or complete MSL-complex titrates newly transcribed msl2 mRNA and thus regulates the amount of available MSL complex by feedback. This represents a novel mechanism in chromatin structure regulation.
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28
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Stenberg P, Larsson J. Buffering and the evolution of chromosome-wide gene regulation. Chromosoma 2011; 120:213-25. [PMID: 21505791 PMCID: PMC3098985 DOI: 10.1007/s00412-011-0319-8] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2011] [Revised: 03/15/2011] [Accepted: 03/31/2011] [Indexed: 11/30/2022]
Abstract
Copy number variation (CNV) in terms of aneuploidies of both entire chromosomes and chromosomal segments is an important evolutionary driving force, but it is inevitably accompanied by potentially problematic variations in gene doses and genomic instability. Thus, a delicate balance must be maintained between mechanisms that compensate for variations in gene doses (and thus allow such genomic variability) and selection against destabilizing CNVs. In Drosophila, three known compensatory mechanisms have evolved: a general segmental aneuploidy-buffering system and two chromosome-specific systems. The two chromosome-specific systems are the male-specific lethal complex, which is important for dosage compensation of the male X chromosome, and Painting of fourth, which stimulates expression of the fourth chromosome. In this review, we discuss the origin and function of buffering and compensation using Drosophila as a model.
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Affiliation(s)
- Per Stenberg
- Department of Molecular Biology, Umeå University, Sweden
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29
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Georgiev P, Chlamydas S, Akhtar A. Drosophila dosage compensation: males are from Mars, females are from Venus. Fly (Austin) 2011; 5:147-54. [PMID: 21339706 DOI: 10.4161/fly.5.2.14934] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Dosage compensation of X-linked genes is a phenomenon of concerted, chromosome-wide regulation of gene expression underpinned by sustained and tightly regulated histone modifications and chromatin remodeling, coupled with constrains of nuclear architecture. This elaborate process allows the accomplishment of regulated expression of genes on the single male X chromosome to levels comparable to those expressed from the two X chromosomes in females. The ribonucleoprotein Male Specific Lethal (MSL) complex is enriched on the male X chromosome and is intricately involved in this process in Drosophila melanogaster. In this review we discuss the recent advances that highlight the complexity lying behind regulation of gene expression by just two-fold.
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Affiliation(s)
- Plamen Georgiev
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
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30
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Pferdehirt RR, Kruesi WS, Meyer BJ. An MLL/COMPASS subunit functions in the C. elegans dosage compensation complex to target X chromosomes for transcriptional regulation of gene expression. Genes Dev 2011; 25:499-515. [PMID: 21363964 PMCID: PMC3049290 DOI: 10.1101/gad.2016011] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2010] [Accepted: 01/10/2011] [Indexed: 11/24/2022]
Abstract
Here we analyze the essential process of X-chromosome dosage compensation (DC) to elucidate mechanisms that control the assembly, genome-wide binding, and function of gene regulatory complexes that act over large chromosomal territories. We demonstrate that a subunit of Caenorhabditis elegans MLL/COMPASS, a gene activation complex, acts within the DC complex (DCC), a condensin complex, to target the DCC to both X chromosomes of hermaphrodites for chromosome-wide reduction of gene expression. The DCC binds to two categories of sites on X: rex (recruitment element on X) sites that recruit the DCC in an autonomous, sequence-dependent manner, and dox (dependent on X) sites that reside primarily in promoters of expressed genes and bind the DCC robustly only when attached to X. We find that DC mutations that abolish rex site binding greatly reduce dox site binding but do not eliminate it. Instead, binding is diminished to the low level observed at autosomal sites in wild-type animals. Changes in DCC binding to these non-rex sites occur throughout development and correlate directly with transcriptional activity of adjacent genes. Moreover, autosomal DCC binding is enhanced by rex site binding in cis in X-autosome fusion chromosomes. Thus, dox and autosomal sites have similar binding potential but are distinguished by linkage to rex sites. We propose a model for DCC binding in which low-level DCC binding at dox sites is dictated by intrinsic properties correlated with high transcriptional activity. Sex-specific DCC recruitment to rex sites then enhances the magnitude of DCC binding to dox sites in cis, which lack high affinity for the DCC on their own. We also show that the DCC balances X-chromosome gene expression between sexes by controlling transcription.
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Affiliation(s)
- Rebecca R. Pferdehirt
- Howard Hughes Medical Institute, University of California at Berkeley, Berkeley, California 94720, USA and Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, California 94720, USA
| | - William S. Kruesi
- Howard Hughes Medical Institute, University of California at Berkeley, Berkeley, California 94720, USA and Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, California 94720, USA
| | - Barbara J. Meyer
- Howard Hughes Medical Institute, University of California at Berkeley, Berkeley, California 94720, USA and Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, California 94720, USA
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Guertin MJ, Lis JT. Chromatin landscape dictates HSF binding to target DNA elements. PLoS Genet 2010; 6:e1001114. [PMID: 20844575 PMCID: PMC2936546 DOI: 10.1371/journal.pgen.1001114] [Citation(s) in RCA: 160] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2010] [Accepted: 08/05/2010] [Indexed: 11/20/2022] Open
Abstract
Sequence-specific transcription factors (TFs) are critical for specifying patterns and levels of gene expression, but target DNA elements are not sufficient to specify TF binding in vivo. In eukaryotes, the binding of a TF is in competition with a constellation of other proteins, including histones, which package DNA into nucleosomes. We used the ChIP-seq assay to examine the genome-wide distribution of Drosophila Heat Shock Factor (HSF), a TF whose binding activity is mediated by heat shock-induced trimerization. HSF binds to 464 sites after heat shock, the vast majority of which contain HSF Sequence-binding Elements (HSEs). HSF-bound sequence motifs represent only a small fraction of the total HSEs present in the genome. ModENCODE ChIP-chip datasets, generated during non-heat shock conditions, were used to show that inducibly bound HSE motifs are associated with histone acetylation, H3K4 trimethylation, RNA Polymerase II, and coactivators, compared to HSE motifs that remain HSF-free. Furthermore, directly changing the chromatin landscape, from an inactive to an active state, permits inducible HSF binding. There is a strong correlation of bound HSEs to active chromatin marks present prior to induced HSF binding, indicating that an HSE's residence in “active” chromatin is a primary determinant of whether HSF can bind following heat shock. Many Transcription Factors (TFs) have been shown to bind DNA in a sequence-specific manner. However, only a sub-set of possible binding sites are occupied in vivo, and it remains unclear how TFs discriminate between sequences of equal predicted binding affinity. We set out to determine how a specific TF, Heat Shock Factor (HSF), distinguishes between utilized and unused potential binding sites. HSF is uniquely qualified to study this problem, because HSF is inactive and lowly bound to DNA in unstressed cells and upon stress HSF becomes active and strongly binds to DNA. We compared the properties of the unstressed chromatin between the sites that become HSF-bound or remain HSF-free following stress activation. We find that sites that are destined to be bound strongly by HSF after stress are associated with distinct chromatin marks compared to sites that are unoccupied by HSF after heat shock. Furthermore, chromatin landscape can be changed from a restrictive to a permissive state, allowing inducible HSF binding. These finding suggest that TF binding sites can be predicted based on the chromatin signatures present prior to induced TF recruitment.
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Affiliation(s)
- Michael J. Guertin
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - John T. Lis
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
- * E-mail:
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Dosage compensation and demasculinization of X chromosomes in Drosophila. Curr Biol 2010; 20:1476-81. [PMID: 20705467 DOI: 10.1016/j.cub.2010.06.076] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2010] [Revised: 06/22/2010] [Accepted: 06/23/2010] [Indexed: 01/01/2023]
Abstract
The X chromosome of Drosophila shows a deficiency of genes with male-biased expression, whereas mammalian X chromosomes are enriched for spermatogenesis genes expressed premeiosis and multicopy testis genes. Meiotic X-inactivation and sexual antagonism can only partly account for these patterns. Here, we show that dosage compensation (DC) in Drosophila may contribute substantially to the depletion of male genes on the X. To equalize expression between X-linked and autosomal genes in the two sexes, male Drosophila hypertranscribe their single X, whereas female mammals silence one of their two X chromosomes. We combine fine-scale mapping data of dosage compensated regions with genome-wide expression profiles and show that most male-biased genes on the D. melanogaster X are located outside dosage compensated regions. Additionally, X-linked genes that have newly acquired male-biased expression in D. melanogaster are less likely to be dosage compensated, and parental X-linked genes that gave rise to an autosomal male-biased retrocopy are more likely located within compensated regions. This suggests that DC contributes to the observed demasculinization of X chromosomes in Drosophila, both by limiting the emergence of male-biased expression patterns of existing X genes, and by contributing to gene trafficking of male genes off the X.
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Park SW, Oh H, Lin YR, Park Y. MSL cis-spreading from roX gene up-regulates the neighboring genes. Biochem Biophys Res Commun 2010; 399:227-31. [PMID: 20654579 DOI: 10.1016/j.bbrc.2010.07.059] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2010] [Accepted: 07/16/2010] [Indexed: 10/19/2022]
Abstract
The male-specific lethal (MSL) complex in Drosophila melanogaster paints the male X chromosome in a manner that is both cis and trans to induce 2-fold hypertranscription of the X chromosome. To characterize the upregulation of gene expression by MSL cis-spreading, we measured the expressional change of neighboring genes by microarray when the genes were bound by MSL complexes that spread from an autosomal roX transgene. Genes within a 200kb region that includes roX transgenes were upregulated concurrently with MSL cis-spreading. Conversely, there was almost no expressional change in genes from other regions. RT-PCR and ChIP analyses confirmed that the approximately 2-fold gene hypertranscription was due to MSL cis-spreading. We also demonstrated that upregulation of the neighboring gene could rescue haplo-insufficient phenotypes of the Minute mutant, such as short bristle, delayed adult eclosion and decreased viability. These results indicate that the hypertranscription by MSL cis-spreading is a general mechanism that occurs in several tissue types. Our molecular and genetic data suggest that cis-spreading of the MSL complex from high-affinity sites including the roX gene results in upregulation of the neighboring genes, which are targets for dosage compensation in the male X chromosome.
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Affiliation(s)
- Seung-Won Park
- Department of Cell Biology and Molecular Medicine, UMDNJ-New Jersey Medical School, 185 South Orange Ave., Newark, NJ 07103, United States
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Targeting X chromosomes for repression. Curr Opin Genet Dev 2010; 20:179-89. [PMID: 20381335 DOI: 10.1016/j.gde.2010.03.008] [Citation(s) in RCA: 95] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2010] [Revised: 03/12/2010] [Accepted: 03/15/2010] [Indexed: 01/10/2023]
Abstract
Dosage compensation is a chromosome-wide regulatory process that balances X-chromosome gene expression between males and females that have different complements. Recent advances have clarified the molecular nature of the Caenorhabditis elegans sex-determination signal, which tallies X-chromosome number relative to the ploidy and controls both the choice of sexual fate and the process of dosage compensation. Dissecting the sex signal has revealed molecular mechanisms by which small quantitative differences in intracellular signals are translated into dramatically different developmental fates. Recent experiments have also revealed fundamental principles by which C. elegans dosage compensation proteins recognize and bind X chromosomes of XX embryos to reduce gene expression. Dosage compensation proteins function not only in a condensin complex specialized for regulating X-chromosome gene expression, but also in distinct condensin complexes that control other chromosome-wide processes: chromosome segregation and meiotic crossover recombination. The reshuffling of interchangeable molecular parts creates independent machines with similar architecture but distinct biological functions.
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Gallach M, Arnau V, Aldecoa R, Marín I. A sequence motif enriched in regions bound by the Drosophila dosage compensation complex. BMC Genomics 2010; 11:169. [PMID: 20226017 PMCID: PMC2848247 DOI: 10.1186/1471-2164-11-169] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2009] [Accepted: 03/12/2010] [Indexed: 11/29/2022] Open
Abstract
Background In Drosophila melanogaster, dosage compensation is mediated by the action of the dosage compensation complex (DCC). How the DCC recognizes the fly X chromosome is still poorly understood. Characteristic sequence signatures at all DCC binding sites have not hitherto been found. Results In this study, we compare the known binding sites of the DCC with oligonucleotide profiles that measure the specificity of the sequences of the D. melanogaster X chromosome. We show that the X chromosome regions bound by the DCC are enriched for a particular type of short, repetitive sequences. Their distribution suggests that these sequences contribute to chromosome recognition, the generation of DCC binding sites and/or the local spreading of the complex. Comparative data indicate that the same sequences may be involved in dosage compensation in other Drosophila species. Conclusions These results offer an explanation for the wild-type binding of the DCC along the Drosophila X chromosome, contribute to delineate the forces leading to the establishment of dosage compensation and suggest new experimental approaches to understand the precise biochemical features of the dosage compensation system.
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Affiliation(s)
- Miguel Gallach
- Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas (IBV-CSIC), Valencia, Spain
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Laverty C, Lucci J, Akhtar A. The MSL complex: X chromosome and beyond. Curr Opin Genet Dev 2010; 20:171-8. [PMID: 20167472 DOI: 10.1016/j.gde.2010.01.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2009] [Revised: 01/21/2010] [Accepted: 01/24/2010] [Indexed: 12/18/2022]
Abstract
X chromosomal regulation is a process that presents systematic problems of chromosome recognition and coordinated gene regulation. In Drosophila males, the ribonucleoprotein Male-Specific Lethal (MSL) complex plays an important role in hyperactivation of the X-linked genes to equalize gene dosage differences between the sexes. It appears that X chromosome recognition by the MSL complex may be mediated through a combination of sequence-specificity and transcriptional activities. The resulting transcriptional up-regulation also seems to involve several mechanisms, encompassing both gene-specific and chromosome-wide approaches. Interestingly the histone H4 lysine 16 specific MOF histone acetyl transferase, a key MSL member that hyper-acetylates the male X chromosome, is also involved in gene regulation beyond dosage compensation. A comparison of Drosophila and mammalian systems reveals intriguing parallels in MOF behavior, and highlights the multidisciplinary nature of this enzyme.
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Affiliation(s)
- Corey Laverty
- Max-Planck-Institut für Immunbiologie, Freiburg im Breisgau, Germany
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Fauth T, Müller-Planitz F, König C, Straub T, Becker PB. The DNA binding CXC domain of MSL2 is required for faithful targeting the Dosage Compensation Complex to the X chromosome. Nucleic Acids Res 2010; 38:3209-21. [PMID: 20139418 PMCID: PMC2879509 DOI: 10.1093/nar/gkq026] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Dosage compensation in Drosophila melanogaster involves the selective targeting of the male X chromosome by the dosage compensation complex (DCC) and the coordinate, ∼2-fold activation of most genes. The principles that allow the DCC to distinguish the X chromosome from the autosomes are not understood. Targeting presumably involves DNA sequence elements whose combination or enrichment mark the X chromosome. DNA sequences that characterize ‘chromosomal entry sites’ or ‘high-affinity sites’ may serve such a function. However, to date no DNA binding domain that could interpret sequence information has been identified within the subunits of the DCC. Early genetic studies suggested that MSL1 and MSL2 serve to recognize high-affinity sites (HAS) in vivo, but a direct interaction of these DCC subunits with DNA has not been studied. We now show that recombinant MSL2, through its CXC domain, directly binds DNA with low nanomolar affinity. The DNA binding of MSL2 or of an MSL2–MSL1 complex does not discriminate between different sequences in vitro, but in a reporter gene assay in vivo, suggesting the existence of an unknown selectivity cofactor. Reporter gene assays and localization of GFP-fusion proteins confirm the important contribution of the CXC domain for DCC targeting in vivo.
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Affiliation(s)
- Torsten Fauth
- Adolf-Butenandt-Institute and Centre for Integrated Protein Science, Ludwig-Maximilians-University, 80336 Munich, Germany
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