The haplolethality paradox of the wupA gene in Drosophila

Autoři: Sergio Casas-Tintó aff001;  Alberto Ferrús aff001
Působiště autorů: Instituto Cajal, Consejo Superior de Investigaciones Científicas, Madrid, Spain aff001
Vyšlo v časopise: The haplolethality paradox of the wupA gene in Drosophila. PLoS Genet 17(3): e1009108. doi:10.1371/journal.pgen.1009108
Kategorie: Research Article


Haplolethals (HL) are regions of diploid genomes that in one dose are fatal for the organism. Their biological meaning is obscure because heterozygous loss-of-function mutations result in dominant lethality (DL) and, consequently, should be under strong negative selection. We report an in depth study of the HL associated to the gene wings up A (wupA). It encodes 13 transcripts (A-M) that yield 11 protein isoforms (A-K) of Troponin I (TnI). They are functionally diverse in their control of muscle contraction, cell polarity and cell proliferation. Isoform K transfers to the nucleus where it increases transcription of the cell proliferation related genes CDK2, CDK4, Rap and Rab5. The nuclear translocation of isoform K is prevented by the co-expression of A or B isoforms, which illustrates isoform interactions. The corresponding DL mutations are, either DNA rearrangements clustered towards the gene 3’ end, thus affecting the genomic organization of all transcripts, or CRISPR-induced mutations in one of the two ATG sites which eliminate a subset of wupA products. The joint elimination of isoforms C, F, G and H, however, do not cause DL phenotypes. Genetically driven expression of single isoforms rescue neither DL nor any of the mutants known in the gene, suggesting that normal function requires properly regulated expression of specific combinations, rather than single, TnI isoforms. We conclude that the wupA associated HL results from the combined haploinsufficiency of a large set of TnI isoforms. The qualitative and quantitative normal expression of which, requires the chromosomal integrity of the wupA genomic region. Since all fly TnI isoforms are encoded in the same gene, its HL condition becomes unavoidable. These wupA features are comparable to those of dpp, the only other HL studied to some extent, and reveal a scenario of strict dosage dependence with implications for gene expression regulation and splitting.

Klíčová slova:

Cell proliferation – DNA transcription – Drosophila melanogaster – Gene regulation – Genomics – Heterozygosity – Invertebrate genomics – Point mutation


1. Huang N, Lee I, Marcotte EM, Hurles ME. Characterising and predicting haploinsufficiency in the human genome. PLoS Genet. 2010. doi: 10.1371/journal.pgen.1001154 20976243

2. Ikuno M, Yamakado H, Akiyama H, Parajuli LK, Taguchi K, Hara J, et al. GBA haploinsufficiency accelerates alpha-synuclein pathology with altered lipid metabolism in a prodromal model of Parkinson’s disease. Hum Mol Genet. 2019. doi: 10.1093/hmg/ddz030 30689867

3. Dutt S, Narla A, Lin K, Mullally A, Abayasekara N, Megerdichian C, et al. Haploinsufficiency for ribosomal protein genes causes selective activation of p53 in human erythroid progenitor cells. Blood. 2011. doi: 10.1182/blood-2010-07-295238 21068437

4. Cole CB, Russler-Germain DA, Ketkar S, Verdoni AM, Smith AM, Bangert C V., et al. Haploinsufficiency for DNA methyltransferase 3A predisposes hematopoietic cells to myeloid malignancies. Journal of Clinical Investigation. 2017. doi: 10.1172/JCI93041 28872462

5. Kaboli S, Miyamoto T, Sunada K, Sasano Y, Sugiyama M, Harashima S. Improved stress resistance and ethanol production by segmental haploidization of the diploid genome in Saccharomyces cerevisiae. J Biosci Bioeng. 2016. doi: 10.1016/j.jbiosc.2015.10.012 26690924

6. Deutschbauer AM, Jaramillo DF, Proctor M, Kumm J, Hillenmeyer ME, Davis RW, et al. Mechanisms of haploinsufficiency revealed by genome-wide profiling in yeast. Genetics. 2005. doi: 10.1534/genetics.104.036871 15716499

7. Giaever G, Nislow C. The yeast deletion collection: A decade of functional genomics. Genetics. 2014. doi: 10.1534/genetics.114.161620 24939991

8. Browning VL, Bergstrom RA, Daigle S, Schimenti JC. A halolethal locus uncovered by deletions in the mouse t complex. Genetics. 2002. 11861570

9. Winking H, Silver LM. Characterization of a recombinant mouse t haplotype that expresses a dominant lethal maternal effect. Genetics. 1984. 6510705

10. Howell GR, Munroe RJ, Schimenti JC. Transgenic rescue of the mouse t complex haplolethal locus Thl1. Mamm Genome. 2005;16: 838–846. doi: 10.1007/s00335-005-0045-8 16284799

11. Carmeliet P, Ferreira V, Breier G, Pollefeyt S, Kieckens L, Gertsenstein M, et al. Abnormal blood vessel development and lethality in embryos lacking a single vascular endothelial growth factor allele. Nature. 1996.

12. Dixon J. Increased levels of apoptosis in the prefusion neural folds underlie the craniofacial disorder, Treacher Collins syndrome. Hum Mol Genet. 2000. doi: 10.1093/hmg/9.10.1473 10888597

13. Martin CL, Kirkpatrick BE, Ledbetter DH. Copy Number Variants, Aneuploidies, and Human Disease. Clinics in Perinatology. 2015. doi: 10.1016/j.clp.2015.03.001 26042902

14. Johansson ACV, Feuk L. Characterization of copy number-stable regions in the human genome. Hum Mutat. 2011. doi: 10.1002/humu.21524 21542059

15. Lai HH, Chuang TH, Wong LK, Lee MJ, Hsieh CL, Wang HL, et al. Identification of mosaic and segmental aneuploidies by next-generation sequencing in preimplantation genetic screening can improve clinical outcomes compared to array-comparative genomic hybridization. Mol Cytogenet. 2017. doi: 10.1186/s13039-017-0315-7 28450889

16. Brewer C, Holloway S, Zawalnyski P, Schinzel A, Fitzpatrick D. A chromosomal deletion map of human malformations. Am J Hum Genet. 1998. doi: 10.1086/302041 9758599

17. Redon R, Ishikawa S, Fitch KR, Feuk L, Perry GH, Andrews TD, et al. Global variation in copy number in the human genome. Nature. 2006. doi: 10.1038/nature05329 17122850

18. Conrad DF, Andrews TD, Carter NP, Hurles ME, Pritchard JK. A high-resolution survey of deletion polymorphism in the human genome. Nat Genet. 2006. doi: 10.1038/ng1697 16327808

19. Babariya D, Fragouli E, Alfarawati S, Spath K, Wells D. The incidence and origin of segmental aneuploidy in human oocytes and preimplantation embryos. Hum Reprod. 2017. doi: 10.1093/humrep/dex324 29126206

20. Lindsley DL, Sandler L, Baker BS, Carpenter AT, Denell RE, Hall JC, et al. Segmental aneuploidy and the genetic gross structure of the Drosophila genome. Genetics. 1972. 4624779

21. Cook RK, Christensen SJ, Deal JA, Coburn RA, Deal ME, Gresens JM, et al. The generation of chromosomal deletions to provide extensive coverage and subdivision of the Drosophila melanogaster genome. Genome Biol. 2012. doi: 10.1186/gb-2012-13-3-r21 22445104

22. Hoffmann FM, Goodman W. Identification in transgenic animals of the Drosophila decapentaplegic sequences required for embryonic dorsal pattern formation. Genes Dev. 1987. doi: 10.1101/gad.1.6.615 2824286

23. Newfeld SJ, Takaesu NT. Local transposition of a hobo element within the decapentaplegic locus of Drosophila. Genetics. 1999. 9872958

24. Lee H, Cho DY, Whitworth C, Eisman R, Phelps M, Roote J, et al. Effects of Gene Dose, Chromatin, and Network Topology on Expression in Drosophila melanogaster. PLoS Genet. 2016. doi: 10.1371/journal.pgen.1006295 27599372

25. Malone JH, Cho DY, Mattiuzzo NR, Artieri CG, Jiang L, Dale RK, et al. Mediation of Drosophila autosomal dosage effects and compensation by network interactions. Genome Biol. 2012. doi: 10.1186/gb-2012-13-4-r28 22531030

26. Prado A, Canal I, Ferrús A. The haplolethal region at the 16F gene cluster of Drosophila melanogaster: Structure and function. Genetics. 1999. 9872957

27. Ferrus A, Llamazares S, De La Pompa JL, Tanouye MA, Pongs O. Genetic analysis of the Shaker gene complex of Drosophila melanogaster. Genetics. 1990. 2116353

28. Keppy DO, Denell RE. A mutational analysis of the triplo-lethal region of Drosophila melanogaster. Genetics. 1979. 110655

29. Barbas JA, Galceran J, Krah-Jentgens I, De La Pompa JL, Canal I, Pongs O, et al. Troponin I is encoded in the haplolethal region of the Shaker gene complex of Drosophila. Genes Dev. 1991. doi: 10.1101/gad.5.1.132 1899228

30. Barbas JA, Galceran J, Torroja L, Prado A, Ferrús A. Abnormal muscle development in the heldup3 mutant of Drosophila melanogaster is caused by a splicing defect affecting selected troponin I isoforms. Mol Cell Biol. 1993. doi: 10.1128/mcb.13.3.1433 7680094

31. Marín MC, Rodríguez JR, Ferrús A. Transcription of Drosophila Troponin I Gene is Regulated by Two Conserved, Functionally Identical, Synergistic Elements. Mol Biol Cell. 2004;15: 1185–1196. doi: 10.1091/mbc.e03-09-0663 14718563

32. Sahota VK, Grau BF, Mansilla A, Ferrús A. Troponin I and Tropomyosin regulate chromosomal stability and cell polarity. J Cell Sci. 2009;122: 2623–2631. doi: 10.1242/jcs.050880 19567471

33. Casas-Tintó S, Maraver A, Serrano M, Ferrús A. Troponin-I enhances and is required for oncogenic overgrowth. Oncotarget. 2016. doi: 10.18632/oncotarget.10616 27437768

34. Prado A, Canal I, Barbas JA, Molloy J, Ferrús A. Functional recovery of troponin I in a Drosophila heldup mutant after a second site mutation. Mol Biol Cell. 1995. doi: 10.1091/mbc.6.11.1433 8589447

35. Sarov M, Barz C, Jambor H, Hein MY, Schmied C, Suchold D, et al. A genome-wide resource for the analysis of protein localisation in Drosophila. Elife. 2016. doi: 10.7554/eLife.12068 26896675

36. Gil N, Ulitsky I. Regulation of gene expression by cis-acting long non-coding RNAs. Nature Reviews Genetics. 2020. doi: 10.1038/s41576-019-0184-5 31729473

37. Lefrevre G, Johnson TK. Evidence for a sex linked haplo inviable locus in the cut singed region of Drosophila melanogaster. Genetics. 1973.

38. Homyk T, Emerson CP. Functional interactions between unlinked muscle genes within haploinsufficient regions of the Drosophila genome. Genetics. 1988. 3135237

39. Casas-Tintó S, Ferrús A. Troponin-I mediates the localization of selected apico-basal cell polarity signaling proteins. J Cell Sci. 2019;132. doi: 10.1242/jcs.225243 30872455

40. Read RD, Cavenee WK, Furnari FB, Thomas JB. A Drosophila model for EGFR-Ras and PI3K-dependent human glioma. PLoS Genet. 2009. doi: 10.1371/journal.pgen.1000374 19214224

41. Alevizopoulos K, Vlach J, Hennecke S, Amati B. Cyclin E and c-Myc promote cell proliferation in the presence of p16(INK4a) of hypophosphorylated retinoblastoma family proteins. EMBO J. 1997. doi: 10.1093/emboj/16.17.5322 9311992

42. Elend M, Eilers M. Cell growth: Downstream of Myc—To grow or to cycle? Current Biology. 1999. doi: 10.1016/s0960-9822(00)80109-8 10607581

43. Datar SA, Jacobs HW, De La Cruz AFA, Lehner CF, Edgar BA. The Drosophila Cyclin D-Cdk4 complex promotes cellular growth. EMBO J. 2000. doi: 10.1093/emboj/19.17.4543 10970848

44. Frei C. Cyclin D/Cdk4: New insights from Drosophila. Cell Cycle. 2004. doi: 10.4161/cc.3.5.867 15044855

45. Pimentel AC, Venkatesh TR. rap gene encodes Fizzy-related protein (Fzr) and regulates cell proliferation and pattern formation in the developing Drosophila eye-antennal disc. Dev Biol. 2005. doi: 10.1016/j.ydbio.2005.07.011 16098963

46. Chen PI, Kong C, Su X, Stahl PD. Rab5 isoforms differentially regulate the trafficking and degradation of epidermal growth factor receptors. J Biol Chem. 2009. doi: 10.1074/jbc.M109.034546 19723633

47. Wharton KA, Ray RP, Gelbart WM. An activity gradient of decapentaplegic is necessary for the specification of dorsal pattern elements in the Drosophila embryo. Development. 1993. 8330541

48. Farah CS, Reinach FC. The troponin complex and regulation of muscle contraction. FASEB J. 1995. doi: 10.1096/fasebj.9.9.7601340 7601340

49. Caridi CP, Plessner M, Grosse R, Chiolo I. Nuclear actin filaments in DNA repair dynamics. Nature Cell Biology. 2019. doi: 10.1038/s41556-019-0379-1 31481797

50. Capelson M. How Genes Move: Spatial Repositioning of Activated Genes Is Driven by Nuclear Actin-Based Pathway. Dev Cell. 2020. doi: 10.1016/j.devcel.2020.01.019 32049034

51. Wang A, Kolhe JA, Gioacchini N, Baade I, Brieher WM, Peterson CL, et al. Mechanism of Long-Range Chromosome Motion Triggered by Gene Activation. Dev Cell. 2020;52: 309-320.e5. doi: 10.1016/j.devcel.2019.12.007 31902656

52. Foster DB, Noguchi T, VanBuren P, Murphy AM, Van Eyk JE. C-Terminal Truncation of Cardiac Troponin I Causes Divergent Effects on ATPase and Force: Implications for the Pathophysiology of Myocardial Stunning. Circ Res. 2003. doi: 10.1161/01.RES.0000099889.35340.6F 14551240

53. Vylegzhanina A V., Kogan AE, Katrukha IA, Koshkina E V., Bereznikova A V., Filatov VL, et al. Full-size and partially truncated cardiac troponin complexes in the blood of patients with acute myocardial infarction. Clin Chem. 2019. doi: 10.1373/clinchem.2018.301127 30858159

54. Kedar V, McDonough H, Arya R, Li HH, Rockman HA, Patterson C. Muscle-specific RING finger 1 is a bona fide ubiquitin ligase that degrades cardiac troponin I. Proc Natl Acad Sci U S A. 2004. doi: 10.1073/pnas.0404341102 15601779

55. Bin Yu Z, Zhang LF, Jin JP. A Proteolytic NH2-terminal Truncation of Cardiac Troponin I that is Up-regulated in Simulated Microgravity. J Biol Chem. 2001. doi: 10.1074/jbc.M011048200 11278823

56. Bolt CC, Duboule D. The regulatory landscapes of developmental genes. Dev. 2020. doi: 10.1242/dev.171736 32014867

57. Sexton T, Yaffe E, Kenigsberg E, Bantignies F, Leblanc B, Hoichman M, et al. Three-dimensional folding and functional organization principles of the Drosophila genome. Cell. 2012. doi: 10.1016/j.cell.2012.01.010 22265598

58. Lieberman-Aiden E, Van Berkum NL, Williams L, Imakaev M, Ragoczy T, Telling A, et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science (80-). 2009. doi: 10.1126/science.1181369 19815776

59. Ghavi-Helm Y, Jankowski A, Meiers S, Viales RR, Korbel JO, Furlong EEM. Highly rearranged chromosomes reveal uncoupling between genome topology and gene expression. Nat Genet. 2019. doi: 10.1038/s41588-019-0462-3 31308546

60. Bazzini AA, Viso F, Moreno-Mateos MA, Johnstone TG, Vejnar CE, Qin Y, et al. Codon identity regulates mRNA stability and translation efficiency during the maternal-to-zygotic transition. EMBO J. 2016. doi: 10.15252/embj.201694699 27436874

61. Lorent J, Kusnadi EP, Hoef V, Rebello RJ, Leibovitch M, Ristau J, et al. Translational offsetting as a mode of estrogen receptor α-dependent regulation of gene expression. EMBO J. 2019. doi: 10.15252/embj.2018101323 31556460

62. Zarrei M, MacDonald JR, Merico D, Scherer SW. A copy number variation map of the human genome. Nature Reviews Genetics. 2015. doi: 10.1038/nrg3871 25645873

63. Hastings PJ, Lupski JR, Rosenberg SM, Ira G. Mechanisms of change in gene copy number. Nature Reviews Genetics. 2009. doi: 10.1038/nrg2593 19597530

64. Ng PC, Levy S, Huang J, Stockwell TB, Walenz BP, Li K, et al. Genetic variation in an individual human exome. PLoS Genet. 2008. doi: 10.1371/journal.pgen.1000160 18704161

65. Ibn-Salem J, Köhler S, Love MI, Chung HR, Huang N, Hurles ME, et al. Deletions of chromosomal regulatory boundaries are associated with congenital disease. Genome Biol. 2014. doi: 10.1186/s13059-014-0423-1 25315429

66. Ferrus A. Parameters of mitotic recombination in minute mutants of Drosophila melanogaster. Genetics. 1975;79: 589–599. 805750

67. Jishage M, Yu X, Shi Y, Ganesan SJ, Chen WY, Sali A, et al. Architecture of Pol II(G) and molecular mechanism of transcription regulation by Gdown1. Nat Struct Mol Biol. 2018. doi: 10.1038/s41594-018-0118-5 30190596

68. Aoyagi N, Wassarman DA. Genes encoding Drosophila melanogaster RNA polymerase II general transcription factors: Diversity in TFIIA and TFIID components contributes to gene-specific transcriptional regulation. J Cell Biol. 2000. doi: 10.1083/jcb.150.2.f45 10908585

69. Salz HK, Erickson JW. Sex determination in Drosophila: The view from the top. Fly (Austin). 2010. doi: 10.4161/fly.4.1.11277 20160499

70. Meisel RP, Malone JH, Clark AG. Faster-X Evolution of Gene Expression in Drosophila. PLoS Genet. 2012. doi: 10.1371/journal.pgen.1003013 23071459

71. Conrad T, Akhtar A. Dosage compensation in Drosophila melanogaster: Epigenetic fine-tuning of chromosome-wide transcription. Nature Reviews Genetics. 2012. doi: 10.1038/nrg3124 22251873

72. Villa R, Schauer T, Smialowski P, Straub T, Becker PB. PionX sites mark the X chromosome for dosage compensation. Nature. 2016. doi: 10.1038/nature19338 27580037

73. Li X, Liu M, Ren X, Loncle N, Wang Q, Hemba-Waduge RUS, et al. The Mediator CDK8-Cyclin C complex modulates Dpp signaling in Drosophila by stimulating Mad-dependent transcription. PLoS Genet. 2020. doi: 10.1371/journal.pgen.1008832 32463833

74. Venken KJT, Carlson JW, Schulze KL, Pan H, He Y, Spokony R, et al. Versatile P[acman] BAC libraries for transgenesis studies in Drosophila melanogaster. Nat Methods. 2009. doi: 10.1038/nmeth.1331 19465919

75. Ejsmont RK, Sarov M, Winkler S, Lipinski KA, Tomancak P. A toolkit for high-throughput, cross-species gene engineering in Drosophila. Nat Methods. 2009. doi: 10.1038/nmeth.1334 19465918

Článek vyšel v časopise

PLOS Genetics

2021 Číslo 3
Nejčtenější tento týden
Nejčtenější v tomto čísle

Zvyšte si kvalifikaci online z pohodlí domova

Důležitost adherence při depresivním onemocnění
nový kurz
Autoři: MUDr. Eliška Bartečková, Ph.D.

Koncepce osteologické péče pro gynekology a praktické lékaře
Autoři: MUDr. František Šenk

Sekvenční léčba schizofrenie
Autoři: MUDr. Jana Hořínková, Ph.D.

Hypertenze a hypercholesterolémie – synergický efekt léčby
Autoři: prof. MUDr. Hana Rosolová, DrSc.

Multidisciplinární zkušenosti u pacientů s diabetem
Autoři: Prof. MUDr. Martin Haluzík, DrSc., prof. MUDr. Vojtěch Melenovský, CSc., prof. MUDr. Vladimír Tesař, DrSc.

Všechny kurzy
Zapomenuté heslo

Zadejte e-mailovou adresu, se kterou jste vytvářel(a) účet, budou Vám na ni zaslány informace k nastavení nového hesla.


Nemáte účet?  Registrujte se