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.
Similar content being viewed by others
Abbreviations
- H4K16ac:
-
Histone 4 lysine 16 acetylation
- RNA Pol II:
-
RNA polymerase II
- Xist:
-
X inactive specific transcript
- Enox or Jpx:
-
Expressed neighbor of Xist
- YY1:
-
Ying yang 1
- CTCF:
-
CCCTC-binding factor
- PCR2:
-
Polycomb repressive 2
- H3K27me3:
-
Histone 3 lysine 27 tri-methylation
- Tsix:
-
Antisense to Xist
- DCC:
-
Dosage compensation complex
- rex:
-
Recruitment element on X
- dox:
-
Dependent on X
- MSL:
-
Male specific lethal complex
- roX :
-
RNA on the X
- MRE:
-
MSL recognition elements
- H3K36me3:
-
Histone 3 lysine 36 tri-methylation
- CLAMP:
-
Chromatin-linked adapter for MSL proteins
- MSL1:
-
Male specific lethal 1
- MSL2:
-
Male specific lethal 2
- MSL3:
-
Male specific lethal 3
- MLE:
-
Maleless
- MOF:
-
Males absent on the first
- Sxl:
-
Sex lethal
- H2B:
-
Histone 2B
- HAT:
-
Histone acetyl-transferase
- NSL:
-
Nonspecific lethal
- JIL-1:
-
Serine protein kinase
- H3S10:
-
Histone 3 Serine 10
- NURF301:
-
Nucleosome remodeling factor
- CES:
-
Chromatin entry sites
- modENCODE:
-
Model organism encyclopedia of DNA elements
- ChIP-seq:
-
Chromatin immunoprecipitaiton followed with next gen sequencing
- GAF:
-
GAGA factor
References
Alekseyenko AA, Larschan E, Lai WR, Park PJ, Kuroda MI (2006) High-resolution ChIP-chip analysis reveals that the Drosophila MSL complex selectively identifies active genes on the male X chromosome. Genes Dev 20:848–857
Alekseyenko AA, Peng S, Larschan E, Gorchakov AA, Lee OK, Kharchenko P, McGrath SD, Wang CI, Mardis ER, Park PJ et al (2008) A sequence motif within chromatin entry sites directs MSL establishment on the Drosophila X chromosome. Cell 134:599–609
Alekseyenko AA, Ho JW, Peng S, Gelbart M, Tolstorukov MY, Plachetka A, Kharchenko PV, Jung YL, Gorchakov AA, Larschan E et al (2012) Sequence-specific targeting of dosage compensation in Drosophila favors an active chromatin context. PLoS Genet 8:e1002646
Alekseyenko AA, Ellison CE, Gorchakov AA, Zhou Q, Kaiser VB, Toda N, Walton Z, Peng S, Park PJ, Bachtrog D et al (2013) Conservation and de novo acquisition of dosage compensation on newly evolved sex chromosomes in Drosophila. Genes Dev 27:853–858
Bai X, Alekseyenko AA, Kuroda MI (2004) Sequence-specific targeting of MSL complex regulates transcription of the roX RNA genes. EMBO J 23:2853–2861
Bai X, Larschan E, Kwon SY, Badenhorst P, Kuroda MI (2007) Regional control of chromatin organization by noncoding roX RNAs and the NURF remodeling complex in Drosophila melanogaster. Genetics 176:1491–1499
Beckmann K, Grskovic M, Gebauer F, Hentze MW (2005) A dual inhibitory mechanism restricts msl-2 mRNA translation for dosage compensation in Drosophila. Cell 122:529–540
Belote JM, Lucchesi JC (1980) Male-specific lethal mutations of Drosophila melanogaster. Genetics 96:165–186
Chao W, Huynh KD, Spencer RJ, Davidow LS, Lee JT (2002) CTCF, a candidate trans-acting factor for X-inactivation choice. Science 295:345–347
Charlesworth B (1978) Model for evolution of Y chromosomes and dosage compensation. Proc Natl Acad Sci U S A 75:5618–5622
Copps K, Richman R, Lyman LM, Chang KA, Rampersad-Ammons J, Kuroda MI (1998) Complex formation by the Drosophila MSL proteins: role of the MSL2 RING finger in protein complex assembly. EMBO J 17:5409–5417
Deng X, Meller VH (2006) roX RNAs are required for increased expression of X-linked genes in Drosophila melanogaster males. Genetics 174:1859–1866
Deng X, Hiatt JB, Nguyen DK, Ercan S, Sturgill D, Hillier LW, Schlesinger F, Davis CA, Reinke VJ, Gingeras TR et al (2011) Evidence for compensatory upregulation of expressed X-linked genes in mammals, Caenorhabditis elegans and Drosophila melanogaster. Nat Genet 43:1179–1185
Deng X, Berletch JB, Ma W, Nguyen DK, Hiatt JB, Noble WS, Shendure J, Disteche CM (2013) Mammalian X upregulation is associated with enhanced transcription initiation, RNA half-life, and MOF-mediated H4K16 acetylation. Dev Cell 25:55–68
Disteche CM (2012) Dosage compensation of the sex chromosomes. Annu Rev Genet 46:537–560
Donohoe ME, Zhang LF, Xu N, Shi Y, Lee JT (2007) Identification of a Ctcf cofactor, Yy1, for the X chromosome binary switch. Mol Cell 25:43–56
Ellison CE, Bachtrog D (2013) Dosage compensation via transposable element mediated rewiring of a regulatory network. Science 342:846–850
Fauth T, Muller-Planitz F, Konig C, Straub T, Becker PB (2010) The DNA binding CXC domain of MSL2 is required for faithful targeting the Dosage Compensation Complex to the X chromosome. Nucleic Acids Res 38:3209–3221
Franke A, Baker BS (1999) The rox1 and rox2 RNAs are essential components of the compensasome, which mediates dosage compensation in Drosophila. Mol Cell 4:117–122
Fukunaga A, Tanaka A, Oishi K (1975) Maleless, a recessive autosomal mutant of Drosophila melanogaster that specifically kills male zygotes. Genetics 81:135–141
Gelbart ME, Larschan E, Peng S, Park PJ, Kuroda MI (2009) Drosophila MSL complex globally acetylates H4K16 on the male X chromosome for dosage compensation. Nat Struct Mol Biol 16:825–832
Gonzalez Nelson AC, Paul KR, Petri M, Flores N, Rogge RA, Cascarina SM, Ross ED (2014) Increasing prion propensity by hydrophobic insertion. PLoS One 9:e89286
Gorchakov AA, Alekseyenko AA, Kharchenko P, Park PJ, Kuroda MI (2009) Long-range spreading of dosage compensation in Drosophila captures transcribed autosomal genes inserted on X. Genes Dev 23:2266–2271
Gorman M, Franke A, Baker BS (1995) Molecular characterization of the male-specific lethal-3 gene and investigations of the regulation of dosage compensation in Drosophila. Development 121:463–475
Gu W, Szauter P, Lucchesi JC (1998) Targeting of MOF, a putative histone acetyl transferase, to the X chromosome of Drosophila melanogaster. Dev Genet 22:56–64
Hallacli E, Lipp M, Georgiev P, Spielman C, Cusack S, Akhtar A, Kadlec J (2012) Msl1-mediated dimerization of the dosage compensation complex is essential for male X-chromosome regulation in Drosophila. Mol Cell 48:587–600
Hilfiker A, Hilfiker-Kleiner D, Pannuti A, Lucchesi JC (1997) mof, a putative acetyl transferase gene related to the Tip60 and MOZ human genes and to the SAS genes of yeast, is required for dosage compensation in Drosophila. EMBO J 16:2054–2060
Ilik IA, Quinn JJ, Georgiev P, Tavares-Cadete F, Maticzka D, Toscano S, Wan Y, Spitale RC, Luscombe N, Backofen R et al (2013) Tandem stem-loops in roX RNAs act together to mediate X chromosome dosage compensation in Drosophila. Mol Cell 51:156–173
Izzo A, Regnard C, Morales V, Kremmer E, Becker PB (2008) Structure-function analysis of the RNA helicase maleless. Nucleic Acids Res 36:950–962
Jans J, Gladden JM, Ralston EJ, Pickle CS, Michel AH, Pferdehirt RR, Eisen MB, Meyer BJ (2009) A condensin-like dosage compensation complex acts at a distance to control expression throughout the genome. Genes Dev 23:602–618
Jeon Y, Lee JT (2011) YY1 tethers Xist RNA to the inactive X nucleation center. Cell 146:119–133
Jeon Y, Sarma K, Lee JT (2012) New and Xisting regulatory mechanisms of X chromosome inactivation. Curr Opin Genet Dev 22:62–71
Jin Y, Wang Y, Johansen J, Johansen KM (2000) JIL-1, a chromosomal kinase implicated in regulation of chromatin structure, associates with the male specific lethal (MSL) dosage compensation complex. J Cell Biol 149:1005–1010
Jonkers I, Monkhorst K, Rentmeester E, Grootegoed JA, Grosveld F, Gribnau J (2008) Xist RNA is confined to the nuclear territory of the silenced X chromosome throughout the cell cycle. Mol Cell Biol 28:5583–5594
Kadlec J, Hallacli E, Lipp M, Holz H, Sanchez-Weatherby J, Cusack S, Akhtar A (2011) Structural basis for MOF and MSL3 recruitment into the dosage compensation complex by MSL1. Nat Struct Mol Biol 18:142–149
Kato M, Han TW, Xie S, Shi K, Du X, Wu LC, Mirzaei H, Goldsmith EJ, Longgood J, Pei J et al (2012) Cell-free formation of RNA granules: low complexity sequence domains form dynamic fibers within hydrogels. Cell 149:753–767
Kelley RL, Wang J, Bell L, Kuroda MI (1997) Sex lethal controls dosage compensation in Drosophila by a non-splicing mechanism. Nature 387:195–199
Kelley RL, Meller VH, Gordadze PR, Roman G, Davis RL, Kuroda MI (1999) Epigenetic spreading of the Drosophila dosage compensation complex from roX RNA genes into flanking chromatin. Cell 98:513–522
Kelley RL, Lee OK, Shim YK (2008) Transcription rate of noncoding roX1 RNA controls local spreading of the Drosophila MSL chromatin remodeling complex. Mech Dev 125:1009–1019
Kim D, Blus BJ, Chandra V, Huang P, Rastinejad F, Khorasanizadeh S (2010) Corecognition of DNA and a methylated histone tail by the MSL3 chromodomain. Nat Struct Mol Biol 17:1027–1029
Kruesi WS, Core LJ, Waters CT, Lis JT, Meyer BJ (2013) Condensin controls recruitment of RNA polymerase II to achieve nematode X-chromosome dosage compensation. eLife 2:e00808
Lam KC, Muhlpfordt F, Vaquerizas JM, Raja SJ, Holz H, Luscombe NM, Manke T, Akhtar A (2012) The NSL complex regulates housekeeping genes in Drosophila. PLoS Genet 8:e1002736
Larschan E, Alekseyenko AA, Gortchakov AA, Peng S, Li B, Yang P, Workman JL, Park PJ, Kuroda MI (2007) MSL complex is attracted to genes marked by H3K36 trimethylation using a sequence-independent mechanism. Mol Cell 28:121–133
Larschan E, Bishop EP, Kharchenko PV, Core LJ, Lis JT, Park PJ, Kuroda MI (2011) X chromosome dosage compensation via enhanced transcriptional elongation in Drosophila. Nature 471:115–118
Larschan E, Soruco MM, Lee OK, Peng S, Bishop E, Chery J, Goebel K, Feng J, Park PJ, Kuroda MI (2012) Identification of chromatin-associated regulators of MSL complex targeting in Drosophila dosage compensation. PLoS Genet 8:e1002830
Li F, Parry DA, Scott MJ (2005) The amino-terminal region of Drosophila MSL1 contains basic, glycine-rich, and leucine zipper-like motifs that promote X chromosome binding, self-association, and MSL2 binding, respectively. Mol Cell Biol 25:8913–8924
Li F, Schiemann AH, Scott MJ (2008) Incorporation of the noncoding roX RNAs alters the chromatin-binding specificity of the Drosophila MSL1/MSL2 complex. Mol Cell Biol 28:1252–1264
Lim CK, Kelley RL (2012) Autoregulation of the Drosophila noncoding roX1 RNA Gene. PLoS Genet 8:e1002564
Livernois AM, Graves JA, Waters PD (2012) The origin and evolution of vertebrate sex chromosomes and dosage compensation. Heredity 108:50–58
Lucchesi JC, Kelly WG, Panning B (2005) Chromatin remodeling in dosage compensation. Annu Rev Genet 39:615–651
Lyman LM, Copps K, Rastelli L, Kelley RL, Kuroda MI (1997) Drosophila male-specific lethal-2 protein: structure/function analysis and dependence on MSL-1 for chromosome association. Genetics 147:1743–1753
Maenner S, Muller M, Frohlich J, Langer D, Becker PB (2013) ATP-dependent roX RNA remodeling by the helicase maleless enables specific association of MSL proteins. Mol Cell 51:174–184
Meller VH, Rattner BP (2002) The roX genes encode redundant male-specific lethal transcripts required for targeting of the MSL complex. EMBO J 21:1084–1091
Meller VH, Gordadze PR, Park Y, Chu X, Stuckenholz C, Kelley RL, Kuroda MI (2000) Ordered assembly of roX RNAs into MSL complexes on the dosage-compensated X chromosome in Drosophila. Curr Biol 10:136–143
Meyer BJ (2010) Targeting X chromosomes for repression. Curr Opin Genet Dev 20:179–189
Oh H, Park Y, Kuroda MI (2003) Local spreading of MSL complexes from roX genes on the Drosophila X chromosome. Genes Dev 17:1334–1339
Oh H, Bone JR, Kuroda MI (2004) Multiple classes of MSL binding sites target dosage compensation to the X chromosome of Drosophila. Curr Biol 14:481–487
Park Y, Kelley RL, Oh H, Kuroda MI, Meller VH (2002) Extent of chromatin spreading determined by roX RNA recruitment of MSL proteins. Science 298:1620–1623
Park Y, Mengus G, Bai X, Kageyama Y, Meller VH, Becker PB, Kuroda MI (2003) Sequence-specific targeting of Drosophila roX genes by the MSL dosage compensation complex. Mol Cell 11:977–986
Park SW, Oh H, Lin YR, Park Y (2010) MSL cis-spreading from roX gene up-regulates the neighboring genes. Biochem Biophys Res Commun 399:227–231
Payer B, Lee JT (2008) X chromosome dosage compensation: how mammals keep the balance. Annu Rev Genet 42:733–772
Pferdehirt RR, Kruesi WS, Meyer BJ (2011) An MLL/COMPASS subunit functions in the C. elegans dosage compensation complex to target X chromosomes for transcriptional regulation of gene expression. Genes Dev 25:499–515
Plath K, Fang J, Mlynarczyk-Evans SK, Cao R, Worringer KA, Wang H, de la Cruz CC, Otte AP, Panning B, Zhang Y (2003) Role of histone H3 lysine 27 methylation in X inactivation. Science 300:131–135
Prestel M, Feller C, Straub T, Mitlohner H, Becker PB (2010) The activation potential of MOF is constrained for dosage compensation. Mol Cell 38:815–826
Reenan RA, Hanrahan CJ, Ganetzky B (2000) The mle(napts) RNA helicase mutation in Drosophila results in a splicing catastrophe of the para Na+ channel transcript in a region of RNA editing. Neuron 25:139–149
Regnard C, Straub T, Mitterweger A, Dahlsveen IK, Fabian V, Becker PB (2011) Global analysis of the relationship between JIL-1 kinase and transcription. PLoS Genet 7:e1001327
Scott MJ, Pan LL, Cleland SB, Knox AL, Heinrich J (2000) MSL1 plays a central role in assembly of the MSL complex, essential for dosage compensation in Drosophila. EMBO J 19:144–155
Shogren-Knaak M, Ishii H, Sun JM, Pazin MJ, Davie JR, Peterson CL (2006) Histone H4-K16 acetylation controls chromatin structure and protein interactions. Science 311:844–847
Simon MD, Pinter SF, Fang R, Sarma K, Rutenberg-Schoenberg M, Bowman SK, Kesner BA, Maier VK, Kingston RE, Lee JT (2013) High-resolution Xist binding maps reveal two-step spreading during X-chromosome inactivation. Nature 504:465–469
Smith ER, Pannuti A, Gu W, Steurnagel A, Cook RG, Allis CD, Lucchesi JC (2000) The drosophila MSL complex acetylates histone H4 at lysine 16, a chromatin modification linked to dosage compensation. Mol Cell Biol 20:312–318
Smith ER, Allis CD, Lucchesi JC (2001) Linking global histone acetylation to the transcription enhancement of X-chromosomal genes in Drosophila males. J Biol Chem 276:31483–31486
Soruco MM, Chery J, Bishop EP, Siggers T, Tolstorukov MY, Leydon AR, Sugden AU, Goebel K, Feng J, Xia P et al (2013) The CLAMP protein links the MSL complex to the X chromosome during Drosophila dosage compensation. Genes Dev 27:1551–1556
Straub T, Grimaud C, Gilfillan GD, Mitterweger A, Becker PB (2008) The chromosomal high-affinity binding sites for the Drosophila dosage compensation complex. PLoS Genet 4:e1000302
Straub T, Zabel A, Gilfillan GD, Feller C, Becker PB (2013) Different chromatin interfaces of the Drosophila dosage compensation complex revealed by high-shear ChIP-seq. Genome Res 23:473–485
Sun L, Fernandez HR, Donohue RC, Li J, Cheng J, Birchler JA (2013) Male-specific lethal complex in Drosophila counteracts histone acetylation and does not mediate dosage compensation. Proc Natl Acad Sci U S A 110:E808–E817
Sural TH, Peng S, Li B, Workman JL, Park PJ, Kuroda MI (2008) The MSL3 chromodomain directs a key targeting step for dosage compensation of the Drosophila melanogaster X chromosome. Nat Struct Mol Biol 15:1318–1325
Tian D, Sun S, Lee JT (2010) The long noncoding RNA, Jpx, is a molecular switch for X chromosome inactivation. Cell 143:390–403
Villa R, Forne I, Muller M, Imhof A, Straub T, Becker PB (2012) MSL2 combines sensor and effector functions in homeostatic control of the Drosophila dosage compensation machinery. Mol Cell 48:647–654
Wang C, Cai W, Li Y, Deng H, Bao X, Girton J, Johansen J, Johansen KM (2011) The epigenetic H3S10 phosphorylation mark is required for counteracting heterochromatic spreading and gene silencing in Drosophila melanogaster. J Cell Sci 124:4309–4317
Wang CI, Alekseyenko AA, LeRoy G, Elia AE, Gorchakov AA, Britton LM, Elledge SJ, Kharchenko PV, Garcia BA, Kuroda MI (2013) Chromatin proteins captured by ChIP-mass spectrometry are linked to dosage compensation in Drosophila. Nat Struct Mol Biol 20:202–209
Wilkins RC, Lis JT (1999) DNA distortion and multimerization: novel functions of the glutamine-rich domain of GAGA factor. J Mol Biol 285:515–525
Wood AJ, Severson AF, Meyer BJ (2010) Condensin and cohesin complexity: the expanding repertoire of functions. Nat Rev Genet 11:391–404
Wu L, Zee BM, Wang Y, Garcia BA, Dou Y (2011) The RING finger protein MSL2 in the MOF complex is an E3 ubiquitin ligase for H2B K34 and is involved in crosstalk with H3 K4 and K79 methylation. Mol Cell 43:132–144
Acknowledgments
We are grateful to Dr. Leila Rieder for insights and critical review of the manuscript.
Conflict of interest
The author declares that they have no conflict of interest.
Author information
Authors and Affiliations
Corresponding author
Additional information
Responsible Editor: Beth A. Sullivan.
Rights and permissions
About this article
Cite this article
Soruco, M.M.L., Larschan, E. A new player in X identification: the CLAMP protein is a key factor in Drosophila dosage compensation. Chromosome Res 22, 505–515 (2014). https://doi.org/10.1007/s10577-014-9438-4
Received:
Revised:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s10577-014-9438-4