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Vavilovskii Zhurnal Genetiki I Selektsii Sep 2021Prognosis of neuropsychiatric disorders in progeny requires consideration of individual (1) parent-of-origin effects (POEs) relying on (2) the nerve cell nuclear 3D...
Prognosis of neuropsychiatric disorders in progeny requires consideration of individual (1) parent-of-origin effects (POEs) relying on (2) the nerve cell nuclear 3D chromatin architecture and (3) impact of parent-specific miRNAs. Additionally, the shaping of cognitive phenotypes in parents depends on both learning acquisition and forgetting, or memory erasure. These processes are independent and controlled by different signal cascades: the first is cAMPdependent, the second relies on actin remodeling by small GTPase Rac1 - LIMK1 (LIM-kinase 1). Simple experimental model systems such as Drosophila help probe the causes and consequences leading to human neurocognitive pathologies. Recently, we have developed a Drosophila model for Williams-Beuren Syndrome (WBS): a mutant of the locus (X:11AB) harboring the gene. The mutation drastically increases the frequency of ectopic contacts (FEC) in specific regions of intercalary heterochromatin, suppresses learning/memory and affects locomotion. As is shown in this study, the polytene X chromosome bands in reciprocal hybrids between and the wild type strain are heterogeneous in modes of FEC regulation depending either on maternal or paternal gene origin. Bioinformatic analysis reveals that FEC between X:11AB and the other X chromosome bands correlates with the occurrence of short (~30 bp) identical DNA fragments partly homologous to Drosophila 372-bp satellite DNA repeat. Although learning acquisition in a conditioned courtship suppression paradigm is similar in hybrids, the middle-term memory formation shows patroclinic inheritance. Seemingly, this depends on changes in miR-974 expression. Several parameters of locomotion demonstrate heterosis. Our data indicate that the locus is capable of trans-regulating gene activity via POEs on the chromatin nuclear organization, thereby affecting behavior.
PubMed: 34595370
DOI: 10.18699/VJ21.054 -
Insects Sep 2021By any measure, such as abundance, species diversity or geographic range, the species group is one of the most successful Palearctic taxa of black flies. To explore...
By any measure, such as abundance, species diversity or geographic range, the species group is one of the most successful Palearctic taxa of black flies. To explore potential diversity in this group in the Tian Shan range of Central Asia, we focused on Kyrgyzstan, in which three nominal morphospecies have been recorded. Among our samples, we morphologically identified Rubtsov and a second possible species tentatively identified as Rubtsov. By analyzing banding patterns of the larval polytene chromosomes, we discovered two fixed inversions, two sex-linked rearrangements, and 19 autosomal rearrangements, including supernumerary B chromosomes. The chromosomal data indicate minimal diversity of only one or two species across the surveyed area of nearly 50,000 km. Mitochondrial DNA (CO1) sequences fell into three distinct clusters, possibly representing separate species. The chromosomal, molecular, and morphological data indicate that Kyrgyz populations are unique within the group, but the data sets are not entirely congruent. Thus, reconciling data sets and assigning existing names is tentative. is linked with undifferentiated sex chromosomes, one of the three CO1 clades, and higher elevations, whereas is tenuously associated with differentiated sex chromosomes, a separate CO1 clade, and lower elevations. These associations leave one Kyrgyz larva, which is in a third CO1 clade, unlinked to a formal species name. Our analyses also indicate that Meigen , contrary to previous reports, does not occur in Kyrgyzstan and should be deleted from the country's faunal list.
PubMed: 34564256
DOI: 10.3390/insects12090817 -
International Journal of Molecular... Aug 2021Chromatin 3D structure plays a crucial role in regulation of gene activity. Previous studies have envisioned spatial contact formations between chromatin domains with...
Chromatin 3D structure plays a crucial role in regulation of gene activity. Previous studies have envisioned spatial contact formations between chromatin domains with different epigenetic properties, protein compositions and transcription activity. This leaves specific DNA sequences that affect chromosome interactions. The polytene chromosomes are involved in non-allelic ectopic pairing. The mutant strain , a model for Williams-Beuren syndrome, has an increased frequency of ectopic contacts (FEC) compared to the wild-type strain (). Ectopic pairing can be mediated by some specific DNA sequences. In this study, using our Homology Segment Analysis software, we estimated the correlation between FEC and frequency of short matching DNA fragments (FMF) for all sections of the X chromosome of and strains. With fragment lengths of 50 nucleotides (nt), showed a specific FEC-FMF correlation for 20% of the sections involved in ectopic contacts. The correlation was unspecific in , which may indicate the alternative epigenetic mechanisms affecting FEC in the mutant strain. Most of the fragments that specifically contributed to FMF were related to 1.688 or 372-bp middle repeats. Thus, middle repetitive DNA may serve as an organizer of ectopic pairing.
Topics: Animals; Base Pairing; Chromatin; Computational Biology; DNA, Satellite; Disease Models, Animal; Drosophila melanogaster; Humans; Polytene Chromosomes; Software; Williams Syndrome; X Chromosome
PubMed: 34445413
DOI: 10.3390/ijms22168713 -
ELife Jul 2021ATP-dependent chromatin remodelers control the accessibility of genomic DNA through nucleosome mobilization. However, the dynamics of genome exploration by remodelers,...
ATP-dependent chromatin remodelers control the accessibility of genomic DNA through nucleosome mobilization. However, the dynamics of genome exploration by remodelers, and the role of ATP hydrolysis in this process remain unclear. We used live-cell imaging of polytene nuclei to monitor Brahma (BRM) remodeler interactions with its chromosomal targets. In parallel, we measured local chromatin condensation and its effect on BRM association. Surprisingly, only a small portion of BRM is bound to chromatin at any given time. BRM binds decondensed chromatin but is excluded from condensed chromatin, limiting its genomic search space. BRM-chromatin interactions are highly dynamic, whereas histone-exchange is limited and much slower. Intriguingly, loss of ATP hydrolysis enhanced chromatin retention and clustering of BRM, which was associated with reduced histone turnover. Thus, ATP hydrolysis couples nucleosome remodeling to remodeler release, driving a continuous transient probing of the genome.
Topics: Adenosine Triphosphatases; Adenosine Triphosphate; Animals; Cell Cycle Proteins; Cell Line; Chromatin Assembly and Disassembly; Drosophila Proteins; Drosophila melanogaster; Histones; Hydrolysis; Nucleosomes; Ribonucleoprotein, U1 Small Nuclear; Trans-Activators
PubMed: 34313222
DOI: 10.7554/eLife.69424 -
International Journal of Molecular... Apr 2021Chromatin organization is developmentally regulated by epigenetic changes mediated by histone-modifying enzymes and chromatin remodeling complexes. In , the Tip60...
Chromatin organization is developmentally regulated by epigenetic changes mediated by histone-modifying enzymes and chromatin remodeling complexes. In , the Tip60 chromatin remodeling complex (dTip60) play roles in chromatin regulation, which are shared by evolutionarily-related complexes identified in animal and plants. Recently, it was found that most subunits previously assigned to the dTip60 complex are shared by two related complexes, DOM-A.C and DOM-B.C, defined by DOM-A and DOM-B isoforms, respectively. In this work, we combined classical genetics, cell biology, and reverse genetics approaches to further investigate the biological roles played during development by a number of subunits originally assigned to the dTip60 complex.
Topics: Animals; Chromatin; Chromatin Assembly and Disassembly; Drosophila Proteins; Drosophila melanogaster; Epigenesis, Genetic; Histone Acetyltransferases; Histones; Polytene Chromosomes; Transcription Factors
PubMed: 33926075
DOI: 10.3390/ijms22094525 -
Cells Apr 2021The reversible posttranslational -GlcNAc modification of serine or threonine residues of intracellular proteins is involved in many cellular events from signaling...
The reversible posttranslational -GlcNAc modification of serine or threonine residues of intracellular proteins is involved in many cellular events from signaling cascades to epigenetic and transcriptional regulation. -GlcNAcylation is a conserved nutrient-dependent process involving two enzymes, with -GlcNAc transferase (OGT) adding -GlcNAc and with -GlcNAcase (OGA) removing it in a manner that's protein- and context-dependent. -GlcNAcylation is essential for epigenetic regulation of gene expression through its action on Polycomb and Trithorax and COMPASS complexes. However, the important role of -GlcNAc in adult life and health span has been largely unexplored, mainly due the lack of available model systems. Cataloging the -GlcNAc proteome has proven useful in understanding the biology of this modification in vivo. In this study, we leveraged a recently developed knockout fly mutant to identify the -GlcNAcylated proteins in adult . The adult -GlcNAc proteome revealed many proteins related to cell and organismal growth, development, differentiation, and epigenetics. We identified many -GlcNAcylated proteins that play a role in increased growth and decreased longevity, including HCF, SIN3A, LOLA, KISMET, ATX2, SHOT, and FOXO. Interestingly, mutant flies are larger and have a shorter life span compared to wild type flies, suggesting increased -GlcNAc results in increased growth. Our results suggest that -GlcNAc alters the function of many proteins related to transcription, epigenetic modification and signaling pathways that regulate growth rate and longevity. Therefore, our findings highlight the importance of -GlcNAc in growth and life span in adult .
Topics: Animals; Body Size; Drosophila Proteins; Drosophila melanogaster; Female; Gene Ontology; Glycoproteins; Histone-Lysine N-Methyltransferase; Longevity; Male; Mutation; Phenotype; Polytene Chromosomes; Proteome; Wings, Animal; beta-N-Acetylhexosaminidases
PubMed: 33925313
DOI: 10.3390/cells10051026 -
Scientific Reports Apr 2021Micronucleoli are among the structures composing the peculiar scenario of the nucleolus in salivary gland nuclei of dipterans representative of Sciaridae. Micronucleolar...
Micronucleoli are among the structures composing the peculiar scenario of the nucleolus in salivary gland nuclei of dipterans representative of Sciaridae. Micronucleolar bodies contain ribosomal DNA and RNA, are transcriptionally active and may appear free in the nucleoplasm or associated with specific chromosome regions in salivary gland nuclei. This report deals with an extreme case of nucleolar fragmentation/dispersion detected in the salivary gland of Schwenkfeldina sp. Such a phenomenon in this species was found to be restricted to cell types undergoing polyteny and seems to be differentially controlled according to the cell type. Furthermore, transcriptional activity was detected in virtually all the micronucleolar bodies generated in the salivary gland. The relative proportion of the rDNA in polytene and diploid tissues showed that rDNA under-replication did not occur in polytene nuclei suggesting that the nucleolar and concomitant rDNA dispersion in Schwenkfeldina sp. may reflect a previously hypothesised process in order to counterbalance the rDNA loss due to the under-replication. The chromosomal distribution of epigenetic markers for the heterochromatin agreed with early cytological observations in this species suggesting that heterochromatin is spread throughout the chromosome length of Schwenkfeldina sp. A comparison made with results from another sciarid species argues for a role played by the heterochromatin in the establishment of the rDNA topology in polytene nuclei of Sciaridae.
Topics: Animals; Cell Nucleolus; DNA Fragmentation; DNA Replication; DNA, Ribosomal; Diptera; Heterochromatin; Polytene Chromosomes; RNA, Ribosomal; Salivary Glands; Transcription, Genetic
PubMed: 33863925
DOI: 10.1038/s41598-021-87012-5 -
Insects Feb 2021The genome assembly of consists of 2221 scaffolds (N50 = 115,072 bp) and has a size spanning 136.94 Mbp. This assembly represents one of the smallest genomes among...
The genome assembly of consists of 2221 scaffolds (N50 = 115,072 bp) and has a size spanning 136.94 Mbp. This assembly represents one of the smallest genomes among species. genomic DNA fragments of ~37 Kb were cloned, end-sequenced, and used as probes for fluorescence in situ hybridization (FISH) with salivary gland polytene chromosomes. In total, we mapped nine DNA probes to scaffolds and autosomal arms. Comparative analysis of the scaffolds with homologous sequences of the and genomes identified chromosomal rearrangements among these species. Our results confirmed that physical mapping is a useful tool for anchoring genome assemblies to mosquito chromosomes.
PubMed: 33671870
DOI: 10.3390/insects12020164 -
Bio-protocol Jul 2020larval salivary gland polytene chromosome squashes have been used for decades to analyze genome-wide protein-binding patterns, transcriptional activation processes, and...
larval salivary gland polytene chromosome squashes have been used for decades to analyze genome-wide protein-binding patterns, transcriptional activation processes, and changes in chromatin structure at specific genetic loci. There have been many evolutions of the squashing protocol over the years, with sub-optimal reproducibility and low sample success rate as accepted caveats. However, low sample success rates are an obvious disadvantage when polytene chromosomes are used for more high-throughput approaches, such as genetic or antibody screens, or for experiments requiring high-quality chromosome structure preservation. Here we present an exceptionally reproducible squashing and fluorescence staining protocol, which generates high-quality fluorescence images on well-spread chromosomes. This is followed by our novel, semi-automated MATLAB analysis program used to determine correlations between fluorescence signals of interest at a single site on polytene chromosomes, in a pixel-by-pixel manner. In our case, we have used this approach to assess chromatin changes at genomic sites, ectopically targeted by nuclear pore proteins. The use of our analysis program increases the ability to make unbiased conclusions on changes in chromatin structure, or in protein recruitment to chromatin, regardless of sample variation in immunofluorescence staining. As it is simply based upon differences in fluorescence intensity at a defined location, the provided analysis program is not limited to analysis of polytene chromosome, and could be applied to many different contexts where correlation between fluorescent signals at any particular location is of interest.
PubMed: 33659343
DOI: 10.21769/BioProtoc.3673 -
MicroPublication Biology Jan 2021The nucleosome remodelling factor (NURF) is an ISWI-class ATP-dependent chromatin remodeling enzyme required both for gene expression and higher order chromatin...
The nucleosome remodelling factor (NURF) is an ISWI-class ATP-dependent chromatin remodeling enzyme required both for gene expression and higher order chromatin organisation NURF binds to histone modifications that decorate the polytene male X chromosome and is required to maintain correct organisation of this chromosome. NURF mutants exhibit distorted and decondensed polytene male X chromosomes dependent on the presence of the male-specific lethal (MSL) complex. Here we tested whether mitotic chromosomes similarly require NURF to maintain correct morphology. Surprisingly, although the MSL complex remains associated with mitotic male X chromosomes, NURF is not required to maintain morphology. While the ISWI subunit of NURF is known to remain associated with mitotic chromosomes we show that the NURF specificity subunit Nurf301/BPTF dissociates from chromatin during both and human mitosis, further illuminating that NURF is dispensable for mitotic chromosome organisation.
PubMed: 33537560
DOI: 10.17912/micropub.biology.000360