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

Pericentromeric heterochromatin in Drosophila generally consists of repetitive DNA, forming the environment associated with gene silencing. Despite the expanding knowledge of the impact of transposable elements (TEs) on the host genome, little is known about the evolution of pericentromeric heterochromatin, its structural composition, and age. During the evolution of the Drosophilidae, hundreds of genes have become embedded within pericentromeric regions yet retained activity. We investigated a pericentromeric heterochromatin fragment found in D. virilis and related species, describing the evolution of genes in this region and the age of TE invasion. Regardless of the heterochromatic environment, the amino acid composition of the genes is under purifying selection. However, the selective pressure affects parts of genes in varying degrees, resulting in expansion of gene introns due to TEs invasion. According to the divergence of TEs, the pericentromeric heterochromatin of the species of virilis group began to form more than 20 million years ago by invasions of retroelements, miniature inverted repeat transposable elements (MITEs), and Helitrons. Importantly, invasions into the heterochromatin continue to occur by TEs that fall under the scope of piRNA silencing. Thus, the pericentromeric heterochromatin, in spite of its ability to induce silencing, has the means for being dynamic, incorporating the regions of active transcription

Structure and expression of two members of the d4 gene family in mouse

The d4 family is a group of unique, evolutionarily conserved zinc finger proteins that are involved in the determination of cell fate. The first member of the d4 family, neuro-d4, was cloned as a neurospecific, developmentally regulated rat gene (Buchman et al. 1992). Multiple neuro-d4 mRNAs generated by alternative splicing give rise to a set of structurally unique proteins. The most characteristic feature of these proteins is a cysteine/histidine-rich C-terminal d4-domain, a double-paired finger motif that consists of two tandemly arranged PHD finger domains. PHD fingers (Cx2CxnCx2Cx4Hx2CxnCx2C) have some structural similarity to the LIM domain and RING fingers and are hallmarks of many transcription co-activators/repressors (Aasland et al. 1995; Saha et al. 1995). A single Kru¨ppel-type zinc finger was found in the N-terminal part of the neuro-d4 protein molecule, but some neurod4 proteins lack this finger along with a nuclear localization signal and a stretch of negatively charged amino acids. Studies of the gene structure and expression suggested that the neuro-d4 proteins are neurospecific nuclear factors, although some of these proteins could have cytoplasmic function(s) (Buchman et al. 1992)

Expression pattern of dd4, a sole member of the d4 family of transcription factors in Drosophila melanogaster

In vertebrates, three members of the d4 gene family code for proteins, which are believed to function as transcription factors and involved in regulation of various intracellular processes. One member of the family, ubi-d4/requiem is ubiquitously expressed gene and two other, neuro-d4 and cer-d4, are expressed predominantly in the neural tissues (Nucleic Acids Res. 20 (1992) 5579; Biochim. Biophys. Acta 14 (1992) 172; Mamm. Genome 11 (2000) 72; Mamm. Genome 12 (2001) 862). Typically, d4 proteins show distinct domain organisation with domain 2/3 in the N-terminal, Krüppel-type zinc finger in the central and two adjacent PHD-fingers (d4-domain) in the C-terminal part of the molecule. However, alternative splicing, which is responsible for complex expression patterns of both neurospecific members of the family, generates multiple protein isoforms lacking certain domains (Nucleic Acids Res. 20 (1992) 5579; Genomics 36 (1996) 174; Mamm. Genome 11 (2000) 72; Mamm. Genome 12 (2001) 862). Exact function of d4 proteins is unclear but their involvement in regulation of differentiation and apoptotic cell death has been proposed (J. Biol. Chem. 269 (1994) 29515; Mamm. Genome 11 (2000) 72; Mamm. Genome 12 (2001) 862). Here we identified a single gene, dd4, in the genome of Drosophila melanogaster, the protein product of which could be assigned to the d4 family. Expression of dd4 is regulated during Drosophila development, and is most prominent in syncytial embryos and later in the embryonic nervous and reproductive systems. In flies dd4 mRNA is found in most tissues but the highest level of expression is detected in ovaries

Cerd4, third member of the d4 gene family: expression and organization of genomic locus

Two members of the d4 family of presumptive transcription modulators, neuro-d4 (Neud4) and ubi-d4/Requiem (Req), have been characterized previously. We cloned and characterized the third member of this gene family, cer-d4 (Cerd4), from chicken and mouse cDNA libraries. The expression patterns of Cerd4 gene in both species are similar and more restricted than expression patterns of other two d4 genes. The main sites of Cerd4 expression are retina and cerebellum, where multiple transcripts could be detected. Two major types of Cerd4 proteins are a full-length isoform possessing all domains characteristic to the d4 family and truncated XZ isoform without C-terminal tandem of PHD fingers. The developmental kinetics of expression of these isoforms is different. The intron/exon structure of human Cerd4 gene is similar to that of neuro-d4 and ubi-d4/Requiem genes, but most introns of Cerd4 gene are much larger than the corresponding introns of the other two genes

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

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.peerReviewe

Spontaneous gain of susceptibility suggests a novel mechanism of resistance to hybrid dysgenesis in Drosophila virilis.

Syndromes of hybrid dysgenesis (HD) have been critical for our understanding of the transgenerational maintenance of genome stability by piRNA. HD in D. virilis represents a special case of HD since it includes simultaneous mobilization of a set of TEs that belong to different classes. The standard explanation for HD is that eggs of the responder strains lack an abundant pool of piRNAs corresponding to the asymmetric TE families transmitted solely by sperm. However, there are several strains of D. virilis that lack asymmetric TEs, but exhibit a "neutral" cytotype that confers resistance to HD. To characterize the mechanism of resistance to HD, we performed a comparative analysis of the landscape of ovarian small RNAs in strains that vary in their resistance to HD mediated sterility. We demonstrate that resistance to HD cannot be solely explained by a maternal piRNA pool that matches the assemblage of TEs that likely cause HD. In support of this, we have witnessed a cytotype shift from neutral (N) to susceptible (M) in a strain devoid of all major TEs implicated in HD. This shift occurred in the absence of significant change in TE copy number and expression of piRNAs homologous to asymmetric TEs. Instead, this shift is associated with a change in the chromatin profile of repeat sequences unlikely to be causative of paternal induction. Overall, our data suggest that resistance to TE-mediated sterility during HD may be achieved by mechanisms that are distinct from the canonical syndromes of HD

Early Triassic Monzonite–Granite Series in Eastern Kazakhstan as a Reflection of Siberian Large Igneous Province Activity

We provide the results of studying the internal structure and composition of the rocks of the Semeitau and Delbegetei massifs located in Eastern Kazakhstan. It was previously believed that these massifs have different ages and were formed in different geodynamic settings. The U-Pb zircon age from the monzonites and quartz monzonites was determined to be 249 ± 2 Ma, which showed the same Early Triassic age of the massifs. Both massifs are composed of rocks of the same monzonite–granite series of rocks with a significant proportion of high-silica rocks (leucocratic granites). Intermediate rocks are formed due to the differentiation of subalkaline mafic magmas, and the felsic rocks (rhyolites and granites) are the result of partial melting of crustal substrates. The massif formation model assumes the intrusion of mafic magmas into the crust, their differentiation and mixing with crustal melts, and then the intrusion of various rocks into the upper crustal levels. Analysis of the geological position, age and composition of the rocks allows us to conclude that the Semeitau and Delbegetei massifs were formed in an intraplate geodynamic setting. The activity of the mantle plume is the most probable reason for their formation. The Semeitau and Delbegetei massifs can be included in the southern part of the range of the Early Triassic Siberian Large Igneous Province

Early Triassic Monzonite–Granite Series in Eastern Kazakhstan as a Reflection of Siberian Large Igneous Province Activity

We provide the results of studying the internal structure and composition of the rocks of the Semeitau and Delbegetei massifs located in Eastern Kazakhstan. It was previously believed that these massifs have different ages and were formed in different geodynamic settings. The U-Pb zircon age from the monzonites and quartz monzonites was determined to be 249 ± 2 Ma, which showed the same Early Triassic age of the massifs. Both massifs are composed of rocks of the same monzonite–granite series of rocks with a significant proportion of high-silica rocks (leucocratic granites). Intermediate rocks are formed due to the differentiation of subalkaline mafic magmas, and the felsic rocks (rhyolites and granites) are the result of partial melting of crustal substrates. The massif formation model assumes the intrusion of mafic magmas into the crust, their differentiation and mixing with crustal melts, and then the intrusion of various rocks into the upper crustal levels. Analysis of the geological position, age and composition of the rocks allows us to conclude that the Semeitau and Delbegetei massifs were formed in an intraplate geodynamic setting. The activity of the mantle plume is the most probable reason for their formation. The Semeitau and Delbegetei massifs can be included in the southern part of the range of the Early Triassic Siberian Large Igneous Province

Drosophila Model for the Analysis of Genesis of LIM-kinase 1-Dependent Williams-Beuren Syndrome Cognitive Phenotypes: INDELs, Transposable Elements of the Tc1/Mariner Superfamily and MicroRNAs

Genomic disorders, the syndromes with multiple manifestations, may occur sporadically due to unequal recombination in chromosomal regions with specific architecture. Therefore, each patient may carry an individual structural variant of DNA sequence (SV) with small insertions and deletions (INDELs) sometimes less than 10 bp. The transposable elements of the Tc1/mariner superfamily are often associated with hotspots for homologous recombination involved in human genetic disorders, such as Williams Beuren Syndromes (WBS) with LIM-kinase 1-dependent cognitive defects. The Drosophila melanogaster mutant agnts3 has unusual architecture of the agnostic locus harboring LIMK1: it is a hotspot of chromosome breaks, ectopic contacts, underreplication, and recombination. Here, we present the analysis of LIMK1-containing locus sequencing data in agnts3 and three D. melanogaster wild-type strains—Canton-S, Berlin, and Oregon-R. We found multiple strain-specific SVs, namely, single base changes and small INDEls. The specific feature of agnts3 is 28 bp A/T-rich insertion in intron 1 of LIMK1 and the insertion of mobile S-element from Tc1/mariner superfamily residing ~460 bp downstream LIMK1 3′UTR. Neither of SVs leads to amino acid substitutions in agnts3 LIMK1. However, they apparently affect the nucleosome distribution, non-canonical DNA structure formation and transcriptional factors binding. Interestingly, the overall expression of miRNAs including the biomarkers for human neurological diseases, is drastically reduced in agnts3 relative to the wild-type strains. Thus, LIMK1 DNA structure per se, as well as the pronounced changes in total miRNAs profile, probably lead to LIMK1 dysregulation and complex behavioral dysfunctions observed in agnts3 making this mutant a simple plausible Drosophila model for WBS