The Drosophila Dot Chromosome: Where Genes Flourish Amidst Repeats

Abstract

The F element of the Drosophila karyotype (the fourth chromosome in Drosophila melanogaster) is often referred to as the “dot chromosome” because of its appearance in a metaphase chromosome spread. This chromosome is distinct from other Drosophila autosomes in possessing both a high level of repetitious sequences (in particular, remnants of transposable elements) and a gene density similar to that found in the other chromosome arms, ∼80 genes distributed throughout its 1.3-Mb “long arm.” The dot chromosome is notorious for its lack of recombination and is often neglected as a consequence. This and other features suggest that the F element is packaged as heterochromatin throughout. F element genes have distinct characteristics (e.g., low codon bias, and larger size due both to larger introns and an increased number of exons), but exhibit expression levels comparable to genes found in euchromatin. Mapping experiments show the presence of appropriate chromatin modifications for the formation of DNaseI hypersensitive sites and transcript initiation at the 5′ ends of active genes, but, in most cases, high levels of heterochromatin proteins are observed over the body of these genes. These various features raise many interesting questions about the relationships of chromatin structures with gene and chromosome function. The apparent evolution of the F element as an autosome from an ancestral sex chromosome also raises intriguing questions. The findings argue that the F element is a unique chromosome that occupies its own space in the nucleus. Further study of the F element should provide new insights into chromosome structure and function.

Molecular and genetic organization of bands and interbands in the dot chromosome of Drosophila melanogaster

“…POF can enhance transcription or RNA transport through nuclear pores by binding to nascent RNA (Johansson et al 2012 ). Thus, an interactive network of epigenetic chromatin regulation, unique for this autosome, including dSETDB1, HP1a, and POF, is involved in maintaining the activity of the fourth chromosome genes in the heterochromatic environment (Seum et al 2007 ; Tzeng et al 2007 ; Brower-Toland et al 2009 ) (for more details about the fourth chromosome organization, see Riddle and Elgin ( 2018 )). We were interested to know whether the band organization of the fourth chromosome is influenced by the combination of characteristics mentioned above that distinguish the chromosome under investigation from other Drosophila autosomes.…”

The X chromosome of the German cockroach, Blattella germanica, is homologous to a fly X chromosome despite 400 million years divergence

“…Element F has reverted to an autosome in D. melanogaster, where it is also known as chromosome 4 or the "dot" chromosome. The dot chromosome is enriched for heterochromatin and has fewer than 100 genes [33].…”

Unpredictable effects of the genetic background of transgenic lines in physiological quantitative traits

“…Specifically, the compound balancer 4 th chromosome increased branching. Since the 4 th chromosome is small, largely heterochromatic and encompasses approximately 100 genes (Riddle and Elgin, 2018), it would be interesting to assess if any of these plays a role in terminal branching. Initial Gene Ontology (GO) analysis of the 4 th chromosome genes, indicates that three of them (ci, an effector of the Hh pathway, pan, an effector of the Wg pathway, and zyx, a cytoskeletal protein) function in the trachea and zyx is involved in terminal branching morphology and tracheal air filling (Merabet et al, 2005;Renfranz et al, 2010).…”