Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2010 Nov 30;8(11):e1000552.
doi: 10.1371/journal.pbio.1000552.

Neighbourhood continuity is not required for correct testis gene expression in Drosophila

Lisa A Meadows  1 , Yuk Sang Chan, John Roote, Steven Russell
Affiliations

Neighbourhood continuity is not required for correct testis gene expression in Drosophila

Lisa A Meadows et al. PLoS Biol. .

Abstract

It is now widely accepted that gene organisation in eukaryotic genomes is non-random and it is proposed that such organisation may be important for gene expression and genome evolution. In particular, the results of several large-scale gene expression analyses in a range of organisms from yeast to human indicate that sets of genes with similar tissue-specific or temporal expression profiles are clustered within the genome in gene expression neighbourhoods. While the existence of neighbourhoods is clearly established, the underlying reason for this facet of genome organisation is currently unclear and there is little experimental evidence that addresses the genomic requisites for neighbourhood organisation. We report the targeted disruption of three well-defined male-specific gene expression neighbourhoods in the Drosophila genome by the synthesis of precisely mapped chromosomal inversions. We compare gene expression in individuals carrying inverted chromosomes with their non-inverted but otherwise identical progenitors using whole-transcriptome microarray analysis, validating these data with specific quantitative real-time PCR assays. For each neighbourhood we generate and examine multiple inversions. We find no significant differences in the expression of genes that define each of the neighbourhoods. We further show that the inversions spatially separate both halves of a neighbourhood in the nucleus. Thus, models explaining neighbourhood organisation in terms of local sequence interactions, enhancer crosstalk, or short-range chromatin effects are unlikely to account for this facet of genome organisation. Our study challenges the notion that, at least in the case of the testis, expression neighbourhoods are a feature of eukaryotic genome organisation necessary for correct gene expression.

PubMed Disclaimer

Conflict of interest statement

The authors have declared that no competing interests exist.

Figures

Figure 1
Figure 1. Inversions disrupting male-specific gene expression neighbourhoods.
Diagrammatic representation of the seven inversions generated in three expression neighbourhoods. (A) Inversions in the X chromosome neighbourhood at 19F. (B) The Chromosome 2L inversions disrupt the 35F neighbourhood. (C) Inversions disrupting the chromosome 3R neighbourhood at 50B. Each of the three neighbourhoods is represented by the shaded boxes with the arrows indicating relative orientation. The genes in the neighbourhood are indicated underneath with bold text indicating male elevated expression; the gap represents the location of the breakpoint in each neighbourhood. Note that the inversions in the 35F region have two different breakpoints. The chromosomal location of each breakpoint is indicated below the wild type chromosome cartoon. Below the wild type, the structure of each inversion is diagrammed to show how the relative position and orientation of genes in the neighbourhood changes. The grey circles represent the centromeres and the stars represent genes assayed by RT-PCR.
Figure 2
Figure 2. Microarray analysis of gene expression.
(A) 19F, (B) 35F, and (C) 50B. For each neighbourhood the heatmaps display the average log2 expression ratio of each gene in the indicated comparisons according to the colour scale at the bottom. The location of the inversion breakpoint within each neighbourhood is indicated by the arrows. Data from the In(2L)EIN133 inversion and cis male versus female comparisons are shown for each neighbourhood. The “cis” designation is shorthand for the uninverted progenitor chromosome that carries the 2 RS insertions used to direct the recombination event. Grey regions indicate no data. While the male versus female comparisons show strong male biased expression (yellow), when inversion males are compared to their non-inversion progenitors there is very little change in expression (black). T, testis.
Figure 3
Figure 3. Disrupting an embryo gene expression neighbourhood.
(A) In(1)EIN103 disrupts an embryo neighbourhood at 18E; the genes in the neighbourhood and their location in the wild type and inverted chromosomes is indicated. (B) Graph of gene expression ratios from a microarray comparison of In(1)EIN103 and its uninverted progenitor. The y-axis represents log2 expression ratios.
Figure 4
Figure 4. Confirmation by quantitative Real-Time PCR.
(A) Supporting the microarray experiments, four genes in the 35F neighbourhood and two genes flanking the other end of the inversion breakpoint at 23A3 show expected male-specific expression and no change in expression when inversion bearing males are compared with undisrupted progenitors. (B and C) Similar confirmation of the microarray data is seen with homozygous (B) and transheterozygous (C) inversions in the 50B neighbourhood. Note the small change in expression detected in females in (B).
Figure 5
Figure 5. Two colour DNA FISH in spermatocytes
. Confocal microscopy and 3D measurement of separation distances between proximal and distal probes. DNA FISH 3D reconstructed image from confocal stack on spermatocytes of (A) progenitor stock and (B) inverted stock. Proximal probe (A555, yellow arrow), distal probe (A488, blue arrow). Nuclei are counterstained with DAPI. (C) Histogram plot of separation distances between proximal and distal probes in progenitor (n = 29) and inversion (n = 17).
See this image and copyright information in PMC

Similar articles

See all similar articles

Cited by

See all "Cited by" articles

References

    1. Milot E, Strouboulis J, Trimborn T, Wijgerde M, de Boer E, et al. Heterochromatin effects on the frequency and duration of LCR-mediated gene transcription. Cell. 1996;87:105–114. - PubMed
    1. Gierman H. J, Indemans M. H, Koster J, Goetze S, Seppen J, et al. Domain-wide regulation of gene expression in the human genome. Genome Res. 2007;17:1286–1295. - PMC - PubMed
    1. Csink A. K, Bounoutas A, Griffith M. L, Sabl J. F, Sage B. T. Differential gene silencing by trans-heterochromatin in Drosophila melanogaster. Genetics. 2002;160:257–269. - PMC - PubMed
    1. Cho R. J, Campbell M. J, Winzeler E. A, Steinmetz L, Conway A, et al. A genome-wide transcriptional analysis of the mitotic cell cycle. Mol Cell. 1998;2:65–73. - PubMed
    1. Cohen B. A, Mitra R. D, Hughes J. D, Church G. M. A computational analysis of whole-genome expression data reveals chromosomal domains of gene expression. Nat Genet. 2000;26:183–186. - PubMed

Publication types