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695 results for “heterochromatin”
Heterochromatin-dependent transcription of satellite DNAs in the Drosophila melanogaster female germline
<p>Large blocks of tandemly repeated DNAs—satellite DNAs (satDNAs)—play important roles in heterochromatin formation and chromosome segregation. We know little about how satDNAs are regulated, however their misregulation is associated with genomic instability and human diseases. We use the <i>Drosophila melanogaster</i> germline as a model to study the regulation of satDNA transcription and chromatin. Here we show that complex satDNAs (>100-bp repeat units) are transcribed into long noncoding RNAs and processed into piRNAs (PIWI interacting RNAs). This satDNA piRNA production depends on the Rhino-Deadlock-Cutoff complex and the transcription factor Moonshiner—a previously-described non-canonical pathway that licenses heterochromatin-dependent transcription of dual-strand piRNA clusters. We show that this pathway is important for establishing heterochromatin at satDNAs. Therefore, satDNAs are regulated by piRNAs originating from their own genomic loci. This novel mechanism of satDNA regulation provides insight into the role of piRNA pathways in heterochromatin formation and genome stability.</p>
Heterochromatin-dependent transcription of satellite DNAs in the Drosophila melanogaster female germline
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Data from: Hierarchical interactions between nucleolar and heterochromatin condensates are mediated by a dual-affinity protein
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Data from: Heterochromatin-enriched assemblies reveal the sequence and organization of the Drosophila melanogaster Y chromosome
Heterochromatic regions of the genome are repeat-rich and poor in protein coding genes, and are therefore underrepresented in even the best genome assemblies. One of the most difficult regions of the genome to assemble are sex-limited chromosomes. The Drosophila melanogaster Y chromosome is entirely heterochromatic, yet has wide-ranging effects on male fertility, fitness, and genome-wide gene expression. The genetic basis of this phenotypic variation is difficult to study, in part because we do not know the detailed organization of the Y chromosome. To study Y chromosome organization in D. melanogaster, we develop an assembly strategy involving the in silico enrichment of heterochromatic long single-molecule reads and use these reads to create targeted de novo assemblies of heterochromatic sequences. We assigned contigs to the Y chromosome using Illumina reads to identify male-specific sequences. Our pipeline extends the D. melanogaster reference genome by 11.9 Mb, closes 43.8% of the gaps, and improves overall contiguity. The addition of 10.6 MB of Y-linked sequence permitted us to study the organization of repeats and genes along the Y chromosome. We detected a high rate of duplication to the pericentric regions of the Y chromosome from other regions in the genome. Most of these duplicated genes exist in multiple copies. We detail the evolutionary history of one sex-linked gene family—crystal-Stellate. While the Y chromosome does not undergo crossing over, we observed high gene conversion rates within and between members of the crystal-Stellate gene family, Su(Ste), and PCKR, compared to genome-wide estimates. Our results suggest that gene conversion and gene duplication play an important role in the evolution of Y-linked genes.
Molecular Dynamics simulation dataset for : Hypoxia increases the methylated histones to prevent histone clipping and redistribution of heterochromatin during Raf-induced senescence.
<p>Files are Initial structures of Cathepsin L(CTSL) with histone H3 peptides (naive and K23me3) and their Molecular Dynamics simulation trajectories. AutoDock Vina and Charmm were used in H3 peptide docking. </p> <p>Wild type CTSL was modeled with apo-Cathepsin L C25A mutant(PDB ID : 3K24) using Charmm-GUI. Trimethylated histone H3 peptide was generated with PyMol. H3 peptide Molecular Dynamics simulations were performed with GPU-accelerated OpenMM.</p>
FIGURE 5 in C-heterochromatin variation in the karyotype reflects species level distinction between Erinaceus roumanicus and E. concolor (Eulipotyphla: Erinaceidae) in Turkey
FIGURE 5. NORs distribution in karyotypes of Turkish hedgehogs. A, female of E. concolor from Sinop in northern Anatolia; B, male of E. concolor from Konya and Antalya in central and southern Anatolia; C. male of E. roumanicus from Edirne in Thrace.
FIGURE 4. C in C-heterochromatin variation in the karyotype reflects species level distinction between Erinaceus roumanicus and E. concolor (Eulipotyphla: Erinaceidae) in Turkey
FIGURE 4. C-banded karyotypes of Turkish hedgehogs. A, male of Erinaceus concolor from Konya in central Anatolia; B, male of E. roumanicus from Edirne in Thrace.
FIGURE 1 in C-heterochromatin variation in the karyotype reflects species level distinction between Erinaceus roumanicus and E. concolor (Eulipotyphla: Erinaceidae) in Turkey
FIGURE 1. Collecting localities. () 1. Sinop, 2. Trabzon (north-eastern Turkey – northern Anatolia); () 3, K₁r₁kkale, 4. Konya, 5. Antalya, 6. Gaziantep, 7. Şanl₁urfa (central and southern Anatolia); () 8. Edirne, 9. Tekirdaǧ (European Turkey –Thrace).
A dual, catalytic role for the fission yeast Ccr4-Not complex in gene silencing and heterochromatin spreading
<p>Uploaded under this Zenodo DOI are the followings:</p> <p>1. the Analysis Code used for Flow Cytometry analysis (R script).</p> <p>2. the primary Flow Cytometry data (fcs files).</p> <p>3. the plate decoders (xlsx files).</p> <p> </p>
Data from: Heterochromatin-enriched assemblies reveal the sequence and organization of the Drosophila melanogaster Y chromosome
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Toxic Y chromosome: increased repeat expression and age-associated heterochromatin loss in male Drosophila with a young Y chromosome
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Data from: Functional divergence of a heterochromatin-binding protein during stickleback speciation
Intragenomic conflict, the conflict of interest between different genomic regions within an individual, is proposed as a mechanism driving both the rapid evolution of heterochromatin-related proteins and the establishment of intrinsic genomic incompatibility between species. Although molecular studies of laboratory model organisms have demonstrated the link between heterochromatin evolution and hybrid abnormalities, we know little about their link in natural systems. Previously, we showed that F1 hybrids between the Japan Sea stickleback and the Pacific Ocean stickleback show hybrid male sterility and found a region responsible for hybrid male sterility on the X chromosome, but did not identify any candidate genes. In this study we first screened for genes rapidly evolving under positive selection during the speciation of Japanese sticklebacks to find genes possibly involved in intragenomic conflict. We found that the region responsible for hybrid male sterility contains a rapidly evolving gene encoding a heterochromatin-binding protein TRIM24B. We conducted biochemical experiments and showed that the binding affinity of TRIM24B to a heterochromatin mark found at centromeres and transposons, histone H4 lysine 20 trimethylation (H4K20me3), is reduced in the Japan Sea stickleback. In addition, mRNA expression levels of Trim24b were different between the Japan Sea and the Pacific Ocean testes. Further expression analysis of genes possibly in the TRIM24B-regulated pathway showed that some gypsy retrotransposons are overexpressed in the F1 hybrid testes. We therefore demonstrate that a heterochromatin-binding protein can evolve rapidly under positive selection and functionally diverge during stickleback speciation.
Data from: Heterochromatin suppresses gross chromosomal rearrangements at centromeres by repressing Tfs1/TFIIS-dependent transcription
Heterochromatin that is characterized by histone H3 lysine 9 (H3K9) methylation assembles on repetitive regions including centromeres. Although centromeric heterochromatin is important for faithful segregation of chromosomes, its role in maintaining centromere integrity remains elusive. Here, we found in fission yeast that heterochromatin suppresses gross chromosomal rearrangements (GCRs) at centromeres. Mutations in Clr4/Suv39 methyltransferase increased the formation of isochromosomes whose breakpoints are present in centromere repeats. H3K9A and H3K9R mutations also increased GCRs, suggesting that Clr4 appears to suppress GCRs via H3K9 methylation. Both HP1 homologs, Swi6 and Chp2, and an RNAi component Chp1 were the chromodomain proteins that are essential for full suppression of GCRs. Remarkably, mutations in RNA polymerase II (RNAPII) or the transcription factors including Tfs1/TFIIS which facilitates restart of backtracked RNAPII specifically bypassed the requirement of Clr4 to suppress GCRs. These results demonstrate that heterochromatin suppresses GCRs by repressing Tfs1-dependent transcription of centromere repeats.
Figure 3 in Variations in heterochromatin content reveal important polymorphisms for studies of genetic improvement in garlic (Allium sativum L.)
Figure 3. Double staining with CMA/DAPI in accessions "Sussuapara - PI" (A), "Santo Antônio de Lisboa" (B), "Catetinho do Paraná 1254" (C), "Branco Mineiro - PI" (D). Inserts highlight small CMA+/DAPI- bands. Yellow arrows indicate the CMA+/DAPI- bands more evident in chromosomes and interphase nuclei. Red arrows indicate CMA+ bands in the overlaid chromosome (B). White arrows indicate gaps formed by condensation (D). Dots indicate distended nucleolar organiser regions (NORs) (f). Bar = 10 µm. Figure 2. Double staining with CMA/DAPI in accessions "Cateto Roxo 99" (E), "Roxo de Minas" (F) and "Sergipe" (G). Inserts highlight small CMA+/DAPI- bands. Yellow arrows indicate the CMA+/DAPI- bands more evident in chromosomes and interphase nuclei. Dots indicate distended nucleolar organiser regions (NORs) (F). Bar = 10 µm.
FIGURE 3. G in C-heterochromatin variation in the karyotype reflects species level distinction between Erinaceus roumanicus and E. concolor (Eulipotyphla: Erinaceidae) in Turkey
FIGURE 3. G-banded karyotype of Erinaceus concolor (female from Konya in central Anatolia).
FIGURE 2 in C-heterochromatin variation in the karyotype reflects species level distinction between Erinaceus roumanicus and E. concolor (Eulipotyphla: Erinaceidae) in Turkey
FIGURE 2. Conventional karyotype of Erinaceus roumanicus (male from Edirne in Thrace).
Data from: Heterochromatin Protein 1β (HP1β) has distinct functions and distinct nuclear distribution in pluripotent versus differentiated cells
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Data from: Functional divergence of a heterochromatin-binding protein during stickleback speciation
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Data from: Heterochromatin suppresses gross chromosomal rearrangements at centromeres by repressing Tfs1/TFIIS-dependent transcription
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Nucleation and heterochromatin establishment in Drosophila miranda
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