General Research Interests

m_f_flies.gifMy research interests are focused on the genetic and molecular analysis of chromosome and chromatin structure in Drosophila melanogaster. Through examining and understanding mutations associated with gene position effects, my work will help elucidate the role that chromosome and chromatin structure plays in regulating gene expression. I am currently concentrating on the cubitus interruptus (ci) locus on Drosophila chromosome 4 and its unusual position effects. I am also involved in the large scale physical mapping of chromosome 4 .

Mapping chromosome 4 of Drosophila melanogaster

bw1chromsmall.jpg The model organism Drosophila melanogaster has two sex chromosomes and 3 autosomes.The smallest chromosome is chromosome 4, ~5 Mbp in length (Locke and McDermid, 1993), which appears as a "dot" chromosome in metaphase spreads. Chromosome 4 has two major regions. The centromeric domain is a-heterochromatic and consists primarily of about ~3-4 Mbp of short, satellite repeats. This region forms part of the highly condensed chromocenter seen in polytene chromosome spreads. The remaining ~1.2 Mbp constitutes cytogenetic regions 101E to 102F on salivary gland chromosomes (the banded region). Of the ~80 genes expected on chromosome 4, only 15-20 of the genes have been mapped and so far all to this domain.

The fourth is an atypical Drosophila chromosome in several respects, all of which relate to the long-standing presumption that this chromosome is, in some ways, heterochromatic in nature. First, the banded region of chromosome 4 often shows a diffuse and poorly defined appearance similar to regions of b -heterochromatin. Second, a similarity to b-heterochromatin is shown in that the chromosomal protein HP1, thought to be an important constituent of heterochromatin, binds to several sites along the chromosome. Third, repetitive DNA sequences normally confined to b -heterochromatin are distributed throughout the banded region of 4. Fourth, further similarities to b -heterochromatin are indicated by the behavior of P element transgenes inserted into this region since they frequently show variegated expression of a white+ marker gene, a characteristic of insertion sites near heterochromatic boundaries.Fifth, chromosome 4 lack crossing over during meiosis.


The loci on chromosome 4 have been shunned in the Drosophila literature. Most genetic screens have been designed to recover mutants on only the X, 2, or 3 and ignored chromosome 4 loci. This evasive action was probably due to its small size and the last feature above, lack of crossing over. Without crossing over was perceived as hard, if not impossible, to characterize chromosome 4 genes. Nevertheless, Hochman in 1976 identified ~ loci and roughly mapped them using the few deletions available at the time.

4th_tip.gifChromosome 4, which constitutes cytogenetic regions 101E to 102F on salivary gland chromosomes, is the region we have decided to map. Beginning with many entry points and many chromosomal walks we have recovered overlapping cosmid and BAC clones that together constitute a contig that spans the length of the "banded region" defined by cytogenetic bands 101E to 102F. Chromosome walking has been hindered by the abundance of moderately repeated sequences dispersed along the chromosome. The clones have been correlated to the cytogenetic map by in situ hybridization to polytene chromosomes. The locations of previously cloned genes have also been mapped on the contig. A minimal tiling set of clones from the contig will provide templates for sequencing this chromosome as part of the Drosophila Genome Project.

Position effects and the ci   locus

Under construction.



wild type vs. ci wing




Recent Publications

Papers: Submitted, in press, or published. (Jan'00)

McFadyen, D. A., Locke, J.
High resolution FISH mapping of the rat a2u-globulin multigene family.
Mammalian Genome (at the Press) 1999.

J. Locke, L.T. Howard, N. Aippersbach, L. Podemski and R.B. Hodgetts (1999)
The characterization of DINE-1, a short, interspersed repetitive element present on chromosome 4 and in the centric heterochromatin of Drosophila melanogaster .
Chromosoma 108:356-366.

Locke, J., L. Podemski , K. Roy, D. Pilgrim and R. Hodgetts (1999)
DNA sequence analysis of two cosmid clones from chromosome 4 of Drosophila melanogaster predicts two new genes amid an unusual arrangement of repeated sequences.
Genome Research 9;137-149

McFadyen, D. A. W. Addison, and J. Locke (1999)
Genomic Organization of the Rat a2u-Globulin Gene Cluster.
Mammalian Genome 10:463-470.

Wang K.S., McFadyen D.A., Locke J, Hodgetts R.B. (1997)
Three subsets of genes whose tissue specific expression is sex and age-dependent can be identified within the rat alpha 2u-globulin family.
Dev. Genet 21:234-244

journals - pullmethods.gif Locke, J. and S. Hanna. (1996)
engrailed gene dosage determines whether certain recessive cubitus interruptus alleles exhibit dominance of the adult wing phenotype in Drosophila.
Dev. Genetics 19:340-349.

Locke, J., Rairdan, G., McDermid, H., Nash, D., Pilgrim, D., Bell, J. Roy, K., and R. Hodgetts. (1996)
Cross-screening: a new method to assemble clones rapidly and unambiguously into contigs.
Genome Research 6:155-165.

Schwartz, C., Locke, J., Nishida, C. and T. Kornberg. (1995)
Analysis of cubitus interruptus regulation in Drosophila embryos and imaginal disks.
Development 121;1625-1635.

Locke, J. and K.D. Tartof (1994).
Molecular analysis of cubitus interruptus (ci) mutations suggests an explanation for the unusual ci-position effect.
Molecular and General Genetics 243: 234-243.

Locke, J. and McDermid, H. E. (1993)
Analysis of Drosophila Chromosome 4 using pulsed field gel electrophoresis.
Chromosoma 102:718-723.

Locke, J. (1993)
Examination of DNA sequences undergoing chromatin changes at a variegating breakpoint in Drosophila melanogaster.
Genetica 92: 33-41.

Locke, J., S. Hanna and D. Kong. (1993).
Evidence for mobilization of hobo transposons in a P-element mutagenesis screen.
Genome 36:1138-1147.

Tartof, K.D. Bishop, C., Jones, M., Hobbs, C.A., and Locke, J. (1989).
Towards an understanding of position effect variegation.
Dev. Genetics 10; 162-176.

Locke, J., Kotarski, M.A., and Tartof, K. D. (1988).
Dosage dependent modifiers of position effect variegation in Drosophila and a mass action model that explains their effect.
Genetics 120;181-198.


Copyright © 1999 John Locke