Adaptation of gene loci to heterochromatin in the course of Drosophila evolution is associated with insulator proteins

Abstract

Pericentromeric heterochromatin is generally composed of repetitive DNA forming a transcriptionally repressive environment. Dozens of genes were embedded into pericentromeric heterochromatin during evolution of Drosophilidae lineage while retaining activity. However, factors that contribute to insusceptibility of gene loci to transcriptional silencing remain unknown. Here, we find that the promoter region of genes that can be embedded in both euchromatin and heterochromatin exhibits a conserved structure throughout the Drosophila phylogeny and carries motifs for binding of certain chromatin remodeling factors, including insulator proteins. Using ChIP-seq data, we demonstrate that evolutionary gene relocation between euchromatin and pericentric heterochromatin occurred with preservation of sites of insulation of BEAF-32 in evolutionarily distant species, i.e. D. melanogaster and D. virilis . Moreover, promoters of virtually all protein-coding genes located in heterochromatin in D. melanogaster are enriched with insulator proteins BEAF-32, GAF and dCTCF. Applying RNA-seq of a BEAF-32 mutant, we show that the impairment of BEAF-32 function has a complex effect on gene expression in D. melanogaster, affecting even those genes that lack BEAF-32 association in their promoters. We propose that conserved intrinsic properties of genes, such as sites of insulation near the promoter regions, may contribute to adaptation of genes to the heterochromatic environment and, hence, facilitate the evolutionary relocation of genes loci between euchromatin and heterochromatin.

Evolutionary Dynamics of the Pericentromeric Heterochromatin in Drosophila virilis and Related Species

“…Considering the peculiarities of heterochromatic genes, such as the accumulation of TEs within their introns, one may speculate that heterochromatic genes have become adapted to the heterochromatic environment and are now dependent on heterochromatin-specific proteins that are necessary for the expression of piRNA-clusters [ 5 , 69 , 70 , 73 , 74 ]. Indeed, gene loci relocated to heterochromatin probably retain the transcriptionally active euchromatin-like structure of chromatin capable of efficient transcription in the new location [ 12 , 14 ]. We propose that a euchromatin-like state on promoters and exons and a heterochromatin-like state, with enrichment for H3K9me3 and TEs copies within the introns of genes, are formed simultaneously, allowing both maintenance of gene transcription and piRNA-cluster functioning.…”

“…Although gene-poor, constitutive heterochromatin is not devoid of genes, frequently forming islands of active transcription that are dependent on the local environment and particular cis and trans -acting elements for normal expression [ 11 , 12 , 13 , 14 ]. Despite the repressive environment, hundreds of active genes have been identified in the pericentric heterochromatin of D. melanogaster [ 15 ].…”

The Organization of Pericentromeric Heterochromatin in Polytene Chromosome 3 of the Drosophila melanogaster Line with the Rif11; SuURES Su(var)3-906 Mutations Suppressing Underreplication

“…A number of features differentiate heterochromatin from euchromatin. Some of the most important of them are a relatively permanent condensed state throughout the cell cycle, as is suggested by [ 9 ], late replication, enrichment of various types of repeated and satellite DNA, reduced gene and ORC density, the ability to cause effects of gene position, the presence of specific proteins, histone marks and histone modifications, and differential staining of mitotic chromosome regions (reviews [ 3 , 4 , 11 , 12 , 13 , 15 , 16 , 17 ]). At the level of polytene chromosomes, one of the most common features is late replication and underreplication, resulting in the underrepresentation of entire heterochromatic regions in wild-type chromosomes.…”

“…A substantial part of eukaryotic genomes is represented by heterochromatic regions. Heterochromatin is characterized by a permanently condensed state throughout the cell cycle [ 9 ], a special protein composition, a high concentration of repeated sequences, a low recombination frequency, late replication and inactivation or variegation of euchromatin genes close to it (reviews: [ 10 , 11 , 12 , 13 , 14 , 15 , 16 , 17 ]).…”

Multiple Roles of dXNP and dADD1—Drosophila Orthologs of ATRX Chromatin Remodeler

“…It was recently demonstrated that insulator proteins participate in the expression of heterochromatic genes and may facilitate their normal function. A direct impact of insulator presence on heterochromatic gene expression has been established for the GAGA factor [146]. Although the mechanism of this effect is unknown, it can be assumed that GAF-dependent insulators work in the same way in heterochromatin as in euchromatin.…”