Skip to main content
SpringerLink
Log in

FISH analysis of Drosophila melanogaster heterochromatin using BACs and P elements

  • Original Article
  • Published:
Chromosoma Aims and scope Submit manuscript

Abstract

The heterochromatin of chromosomes 2 and 3 of Drosophila melanogaster contains about 30 essential genes defined by genetic analysis. In the last decade only a few of these genes have been molecularly characterized and found to correspond to protein-coding genes involved in important cellular functions. Moreover, several predicted genes have been identified by annotation of genomic sequence that are associated with polytene chromosome divisions 40, 41 and 80 but their locations on the cytogenetic map of the heterochromatin are still uncertain. To expand our current knowledge of the genetic functions located in heterochromatin, we have performed fluorescence in situ hybridization (FISH) mapping to mitotic chromosomes of nine bacterial artificial chromosomes (BACs) carrying several predicted genes and of 13 P  element insertions assigned to the proximal regions of 2R and 3L. We found that 22 predicted genes map to the h46 region of 2R and eight map to the h47 regions of 3L. This amounts to at least 30 predicted genes located in these heterochromatic regions, whereas previous studies detected only seven vital genes. Finally, another 58 genes localize either in the euchromatin-heterochromatin transition regions or in the proximal euchromatin of 2R and 3L.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Subscribe and save

Springer+ Basic
$34.99 /Month
  • Get 10 units per month
  • Download Article/Chapter or eBook
  • 1 Unit = 1 Article or 1 Chapter
  • Cancel anytime
Subscribe now

Buy Now

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1.
Fig. 2A–O.
Fig. 3.
Fig. 4.
Fig. 5A–J.

Similar content being viewed by others

References

  • Adams MD, Celniker SE, Holt RA, Evans CA, Gocayne JD et al (2000) The genome sequence of Drosophila melanogaster. Science 287:2185–2195

    Article  PubMed  Google Scholar 

  • Ashburner M, Misra S, Roote J, Lewis SE, Blazej R et al (1999) An exploration of the sequence of a 2.9-Mb region of the genome of Drosophila melanogaster: The Adh region. Genetics 153:179–219

    CAS  PubMed  Google Scholar 

  • Berghella L, Dimitri P (1996) The heterochromatic rolled gene of Drosophila melanogaster is extensively polytenized and transcriptionally active in the salivary gland chromocenter. Genetics 144:117–125

    CAS  PubMed  Google Scholar 

  • Bier E, Vaessin H, Shepherd S, Lee K, McCall K et al (1989) Searching for pattern and mutation in the Drosophila genome with a P-lacZ vector. Genes Dev 3:1273–1287

    CAS  PubMed  Google Scholar 

  • Biggs HW, Zavitz HK, Dikinson B, Van Der Straten A, Brunner D et al (1994) The Drosophila rolled locus encodes a MAP kinase required in the sevenless signal transduction pathway. EMBO J 13:1628–1635

    CAS  PubMed  Google Scholar 

  • Carmena M, Gonzalez C (1995) Transposable elements map in a conserved pattern of distribution extending from beta-heterochromatin to centromeres in Drosophila melanogaster. Chromosoma 103:676–684

    Article  CAS  Google Scholar 

  • Carvalho AB, Bridget AD, Vibranovsky MD, Clark AG (2002) Identification of five new genes on the Y chromosome of Drosophila melanogaster: Proc Natl Acad Sci U S A 98:13225–13230

    Google Scholar 

  • Castillo-Davis CI, Mekhedov SL, Hartl DL, Koonin EV, Kondrashov FA (2002) Selection for short introns in highly expressed genes. Nat Genet 31:415–418

    CAS  PubMed  Google Scholar 

  • Cenci G, Belloni G, Dimitri P (2003) l(2)41Aa, a heterochromatic gene of Drosophila melanogaster, is required for mitotic and meiotic chromosome condensation. Genet Res 81:15–24

    Article  CAS  PubMed  Google Scholar 

  • Devlin RH, Bingham B, Wakimoto BT (1990) The organization and expression of the light gene, a heterochromatic gene of Drosophila melanogaster. Genetics 125:129–140

    CAS  PubMed  Google Scholar 

  • Dimitri P (1991) Cytogenetic analysis of the second chromosome heterochromatin of Drosophila melanogaster. Genetics 127:553–564

    CAS  PubMed  Google Scholar 

  • Dimitri P (1997) Constitutive heterochromatin and transposable elements in Drosophila melanogaster. Genetica 100:85–93

    CAS  Google Scholar 

  • Dimitri P (2003) Fluorescent in situ hybridization with transposable element probes to mitotic chromosome heterochromatin of Drosophila. In: Capy P, Miller W (eds) Mobile genetic elements: protocols and genomic applications. Humana Press, in press

  • Dimitri P, Corradini N, Rossi F, Vernì F, Cenci G, Belloni G, Zhimulev IF, Koryakov DE (2003) Vital genes in the heterochromatin of chromosomes 2 and 3 of Drosophila melanogaster. Genetica 177:209–215

    Article  Google Scholar 

  • Eberl D, Duyf BJ, Hilliker AH (1993) The role of heterochromatin in the expression of a heterochromatic gene, the rolled gene of Drosophila melanogaster. Genetics 134:277–292

    CAS  PubMed  Google Scholar 

  • Eissenberg JC, Hilliker AJ (2000) Versatility of convinction: heterochromatin as both repressor and an activator of transcription. Genetica 109:19–24

    CAS  PubMed  Google Scholar 

  • Gatti M, Pimpinelli S (1992) Functional elements in Drosophila melanogaster heterochromatin. Annu Rev Genet 26:239–275

    CAS  PubMed  Google Scholar 

  • Gatti M, Bonaccorsi S, Pimpinelli S (1994) Looking at Drosophila mitotic chromosomes. Methods Cell Biol 44:371–391

    CAS  PubMed  Google Scholar 

  • Hagstrom K, Muller M, Schedl P (1996) Fab-7 functions as chromatin domain boundary to ensure proper segment specification by the Drosophila bithorax complex. Genes Dev 10:3202–3215

    CAS  PubMed  Google Scholar 

  • Hilliker AJ (1976) Genetic analysis of the centromeric heterochromatin of chromosome 2 of Drosophila melanogaster: deficiency mapping of EMS-induced lethal complementation groups. Genetics 83:765–782

    CAS  PubMed  Google Scholar 

  • Hoskins RA, Smith CD, Carlson JW, Carvalho AB, Halpern A, et al (2002) Heterochromatic sequences in a Drosophila whole-genome shotgun assembly. Genome Biol 3(12):research 0085.1–0085.16

    Article  Google Scholar 

  • Inoue YH, Glover DM (1998) Involvement of the rolled/MAP kinase gene in Drosophila mitosis: interaction between genes for the MAP kinase cascade and abnormal spindle. Mol Gen Genet 258:334–341

    Article  CAS  PubMed  Google Scholar 

  • John B (1988) The biology of heterochromatin. In: Verma RS (ed) Heterochromatin: molecular and structural aspects, Cambridge University Press, Cambridge, UK, pp 1–128

  • Karpen GH, Spradling AC (1992) Analysis of subtelomeric heterochromatin in the Drosophila minichromosome Dp1187 by single P element insertional mutagenesis. Genetics 132:737–753

    CAS  PubMed  Google Scholar 

  • Koryakov DE, Belyaeva ES, Alekseyenko AA, Zhimulev IF (1996) Alpha and beta heterochromatin in polytene chromosome 2 of Drosophila melanogaster. Chromosoma 105:310–319

    Article  CAS  PubMed  Google Scholar 

  • Koryakov DE, Zhimulev IF, Dimitri P (2002) Cytogenetic analysis of the third chromosome heterochromatin of Drosophila melanogaster. Genetics 160:509–517

    CAS  PubMed  Google Scholar 

  • Kozlova T, Zhimulev IF, Kafatos FC (1997) Molecular organization of an individual Drosophila polytene chromomere: transcribed sequences in the 10A1–2 band. Mol Gen Genet 257:55–61

    Article  CAS  PubMed  Google Scholar 

  • Kurek R, Reugels AM, Lammermann U, Buenemann H (2000) Molecular aspects of intron evolution in dynein encoding mega-genes on the heterochromatic Y chromosome of Drosophila sp. Genetica 109:113–123

    CAS  PubMed  Google Scholar 

  • Lindsley DL, Zimm GG (1992) The genome of Drosophila melanogaster. Academic Press, San Diego, Calif

  • Lohe AR, Hilliker AJ, Roberts PA (1993) Mapping simple repeated DNA sequences in heterochromatin of Drosophila melanogaster. Genetics 134:1149–1174

    CAS  PubMed  Google Scholar 

  • Marchant GE, Holm DG (1988) Genetic analysis of the heterochromatin of chromosome 3 in Drosophila melanogaster. II. Vital loci identified through EMS mutagenesis. Genetics 120:519–532

    CAS  Google Scholar 

  • McKee BD (1998) Pairing sites and the role of chromosome pairing in meiosis and spermatogenesis in male Drosophila. Curr Top Dev Biol 37:77–115

    Google Scholar 

  • Misra S, Crosby MA, Mungall CJ, Matthews BB, Campbell KS, et al (2002) Annotation of the Drosophila melanogaster euchromatic genome: a systematic review. Genome Biology 3(12):research0083.1–0083.22

    Article  PubMed  Google Scholar 

  • Parks S, Wieschaus E (1991) The Drosophila gastrulation gene concertina encodes a Ga-like protein. Cell 64:447–458

    CAS  PubMed  Google Scholar 

  • Pimpinelli S, Berloco M, Fanti L, Dimitri P, Bonaccorsi S, et al (1995) Transposable elements are stable structural components of Drosophila melanogaster heterochromatin. Proc Natl Acad Sci U S A 92: 3804–3808

    Google Scholar 

  • Rollins RA, Morcillo P, Dorsett D (1999) Nipped-B, a Drosophila homologue of chromosomal adherins, participates in activation by remote enhancers in the cut and Ultrabithorax genes. Genetics 152:577–593

    CAS  PubMed  Google Scholar 

  • Roseman RR, Johnson EA, Rodesh CK, Bjerke M, Nagoshi RN, Geyer PK (1995) A P element containing suppressor of Hairy-wing binding regions has novel properties for mutagenesis in Drosophila melanogaster. Genetics 141:1061–1074

    CAS  PubMed  Google Scholar 

  • Schulze S, Sinclair DA, Silva E, Fitzpatrick KA, Singh M et al (2001) Essential genes in proximal 3L heterochromatin of Drosophila melanogaster. Mol Gen Genet 264:782–789

    Article  CAS  PubMed  Google Scholar 

  • Sinclair DA, Schulze S, Silva E, Fitzpatrick KA, Honda BM (2000) Essential genes in autosomal heterochromatin of Drosophila melanogaster. Genetica 109:9–18

    CAS  PubMed  Google Scholar 

  • Sullivan BA, Blower MD, Karpen GH (2001) Determining centromere identity: cyclical stories and forking paths. Nat Rev Genet 2:584–596

    Article  CAS  PubMed  Google Scholar 

  • Sumner AT (1990) Chromosome banding. Unwin Hyman, London

  • Tulin A, Stewart D, Spradling AC (2002) The Drosophila heterochromatic gene encoding poly (ADP-ribose) polymerase (PARP) is required to modulate chromatin structure during development. Genes Dev 16:2108–2119

    Article  CAS  PubMed  Google Scholar 

  • Wakimoto BT, Hearn MG (1990) The effects of chromosome rearrangements on the expression of heterochromatic genes in chromosome 2L of D. melanogaster. Genetics 125:141–154

    CAS  PubMed  Google Scholar 

  • Warner TS, Sinclair DA, Fitzpatrick KA, Singh M, Devlin RH, Honda BM (1998) The light gene of Drosophila melanogaster encodes a homologue of VPS41, a yeast gene involved in cellular-protein trafficking. Genome 41:236–243

    Article  CAS  PubMed  Google Scholar 

  • Weiler KS, Wakimoto BT (1995) Heterochromatin and gene expression in Drosophila. Annu Rev Genet 29:577–605

    CAS  PubMed  Google Scholar 

  • Yan CM, Dobie KW, Le HD, Konev AY, Karpen GH (2002) Efficient recovery of centric heterochromatin P element insertions in Drosophila melanogaster. Genetics 161:217–229

    CAS  PubMed  Google Scholar 

  • Zhang P, Spradling AC (1994) Insertional mutagenesis of Drosophila heterochromatin with single P elements. Proc Natl Acad Sci U S A 91:3539–3543

    Google Scholar 

  • Zuckerkandl E, Hennig W (1995) Tracking heterochromatin. Chromosoma 104:75–83

    Google Scholar 

Download references

Acknowledgements

We wish to thank Michael Ashburner, Nicolaj Junakovic, Roger Hoskins, Patrizia Lavia and Chris Smith for helpful comments and discussions. We are also gratefull to our friend Igor Zhimulev for his help in the interpretation of polytene chromosome images. We are indebted to Ruggiero Caizzi for the gift of BACs and Martin Muller, Hugo Bellen laboratory and BDGP for providing us with P  element insertion lines. This work was supported by grants from the Ministero dell'Università e della Ricerca Scientifica e Tecnologica and Consiglio Nazionale delle Ricerche.

Author information

Authors and Affiliations

  1. Dipartimento di Genetica e Biologia Molecolare, Università "La Sapienza" , Piazzale A. Moro 5, 00185 Rome, Italy

    Nicoletta Corradini, Fabrizio Rossi, Fiammetta Vernì & Patrizio Dimitri

Authors
  1. Nicoletta Corradini
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Fabrizio Rossi
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Fiammetta Vernì
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Patrizio Dimitri
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Patrizio Dimitri.

Additional information

Edited by: B. McKee

N. Corradini and F. Rossi contributed equally to this work

Rights and permissions

Reprints and permissions

About this article

Cite this article

Corradini, N., Rossi, F., Vernì, F. et al. FISH analysis of Drosophila melanogaster heterochromatin using BACs and P elements. Chromosoma 112, 26–37 (2003). https://doi.org/10.1007/s00412-003-0241-9

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00412-003-0241-9

Keywords

Search

Navigation