Fluorescent in situ hybridization (FISH) of mitotic chromosomes from Drosophila larval brain

Cytological heterogeneity of heterochromatin among 10 sequenced Drosophila species

In Drosophila chromosomal rearrangements can be maintained and are associated with karyotypic variability among populations from different geographic localities. The abundance of variability in gene arrangements among chromosomal arms is even greater when comparing more distantly related species and the study of these chromosomal changes has provided insights into the evolutionary history of species in the genus. In addition, the sequencing of genomes of several Drosophila species has offered the opportunity to establish the global pattern of genomic evolution, at both genetic and chromosomal level. The combined approaches of comparative analysis of syntenic blocks and direct physical maps on polytene chromosomes have elucidated changes in the orientation of genomic sequences and the difference between heterochromatic and euchromatic regions. Unfortunately, the centromeric heterochromatic regions cannot be studied using the cytological maps of polytene chromosomes because they are underreplicated and therefore reside in the chromocenter. In Drosophila melanogaster, a cytological map of the heterochromatin has been elaborated using mitotic chromosomes from larval neuroblasts. In the current work, we have expanded on that mapping by producing cytological maps of the mitotic heterochromatin in an additional 10 sequenced Drosophila species. These maps highlight 2 apparently different paths, for the evolution of the pericentric heterochromatin between the subgenera Sophophora and Drosophila. One path leads toward a progressive complexity of the pericentric heterochromatin (Sophophora) and the other toward a progressive simplification (Drosophila). These maps are also useful for a better understanding how karyotypes have been altered by chromosome arm reshuffling during evolution.

Trans-Reactivation: A New Epigenetic Phenomenon Underlying Transcriptional Reactivation of Silenced Genes

In order to study the role played by cellular RNA pools produced by homologous genomic loci in defining the transcriptional state of a silenced gene, we tested the effect of non-functional alleles of the white gene in the presence of a functional copy of white, silenced by heterochromatin. We found that non-functional alleles of white, unable to produce a coding transcript, could reactivate in trans the expression of a wild type copy of the same gene silenced by heterochromatin. This new epigenetic phenomenon of transcriptional trans-reactivation is heritable, relies on the presence of homologous RNA’s and is affected by mutations in genes involved in post-transcriptional gene silencing. Our data suggest a general new unexpected level of gene expression control mediated by homologous RNA molecules in the context of heterochromatic genes.

We discovered a new epigenetic phenomenon we called trans-reactivation. We found that genes, unable to produce a functional coding transcript, but with the potential of transcribing other RNA’s within their gene body, strongly reactivate the transcription of a wildtype copy of the same gene silenced by heterochomatin. This new epigenetic phenomenon is heritable, relies on the presence of diffusible RNAs able to carry and transfer epigenetic information and is affected by mutations in genes involved in Post-Transcriptional Gene Silencing. Our data strongly suggest that homologous non-coding RNA can reactivate the expression of genes silenced by heterochromatin, thus defining a new unpredicted level of gene expression control in the context of heterochromatic genes.

Simple method for fluorescence DNA in situ hybridization to squashed chromosomes

DNA in situ hybridization (DNA ISH) is a commonly used method for mapping sequences to specific chromosome regions. This approach is particularly effective at mapping highly repetitive sequences to heterochromatic regions, where computational approaches face prohibitive challenges. Here we describe a streamlined protocol for DNA ISH that circumvents formamide washes that are standard steps in other DNA ISH protocols. Our protocol is optimized for hybridization with short single strand DNA probes that carry fluorescent dyes, which effectively mark repetitive DNA sequences within heterochromatic chromosomal regions across a number of different insect tissue types. However, applications may be extended to use with larger probes and visualization of single copy (non-repetitive) DNA sequences. We demonstrate this method by mapping several different repetitive sequences to squashed chromosomes from Drosophila melanogaster neural cells and Nasonia vitripennis spermatocytes. We show hybridization patterns for both small, commercially synthesized probes and for a larger probe for comparison. This procedure uses simple laboratory supplies and reagents, and is ideal for investigators who have little experience with performing DNA ISH.

Hybridization to tissues on slides or coverslips for whole-mount FISH in Drosophila

Many Drosophila tissues (other than embryos or egg chambers) are too large, delicate, transparent, or buoyant for manipulation in suspension. Tissues such as spermatocytes, spermatids, and imaginal disks are difficult to handle in suspension and are more appropriately fixed on slides or coverslips for whole-mount fluorescent in situ hybridization (FISH). As described in this protocol, the hybridization reaction can be performed in Coplin jars (which require 50-60 mL of solution to cover the sample), larger staining jars (which require 200 mL), or coverslip-staining jars (which hold ∼7-10 mL). Following hybridization, staining with antibodies or other detection reagents can be performed in a humid chamber and staining solution can be applied directly to the tissue.