scholarly journals Epigenomic and genomic landscape of Drosophila melanogaster heterochromatic genes

2017 ◽  
Author(s):  
Parna Saha ◽  
Divya Tej Sowpati ◽  
Rakesh K Mishra
Keyword(s):  
Drosophila Melanogaster ◽  
Transcriptional Repression ◽  
Developmental Stages ◽  
Meta Analysis ◽  
Genomic Landscape ◽  
Intergenic Sequences ◽  
Sequence Elements ◽  
Intergenic Regions ◽  
Regulatory Dna ◽  
Heterochromatic Genes

AbstractHeterochromatin is associated with transcriptional repression. In contrast, several genes in the pericentromeric regions of Drosophila melanogaster are dependent on this heterochromatic environment for their expression. Heterochromatic genes encode proteins involved in various developmental processes. Several studies have shown that a variety of epigenetic modifications is associated with these genes. Here we present a comprehensive analysis of the epigenetic landscape of heterochromatic genes across all the developmental stages of Drosophila using the available histone modification and expression data from modENCODE. We find that heterochromatic genes exhibit combinations of active and inactive histone marks that correspond to their level of expression during development. Thus, we classified these genes into three groups based on the combinations of histone modifications present. We also looked for potential regulatory DNA sequence elements in the genomic neighborhood of these genes. Our results show that Nuclear Matrix Associated Regions (MARs) are prominently present in the intergenic regions of heterochromatic genes during embryonic stages suggesting their plausible role in pericentromeric genome organization. We also find that the intergenic sequences in the heterochromatic regions have binding sites for transcription factors known to modulate epigenetic status. Taken together, our meta-analysis of the various genomic datasets suggest that the epigenomic and genomic landscape of the heterochromatic genes are distinct from that of euchromatic genes. These features could be contributing to the unusual regulatory status of the heterochromatic genes as opposed to the surrounding heterochromatin, which is repressive in nature.

scholarly journals Epigenomic and genomic landscape of Drosophila melanogaster heterochromatic genes

Genomics ◽  
2019 ◽  
Vol 111 (2) ◽  
pp. 177-185 ◽  
Author(s):  
Parna Saha ◽  
Divya Tej Sowpati ◽  
Rakesh K. Mishra
Keyword(s):  
Drosophila Melanogaster ◽  
Genomic Landscape ◽  
Heterochromatic Genes

Genetic characterization of ms (3) K81, a paternal effect gene of Drosophila melanogaster.

Genetics ◽  
1995 ◽  
Vol 140 (1) ◽  
pp. 219-229 ◽  
Author(s):  
G K Yasuda ◽  
G Schubiger ◽  
B T Wakimoto
Keyword(s):  
Drosophila Melanogaster ◽  
Developmental Stages ◽  
Normal Function ◽  
Loss Of Function ◽  
Male Sterile ◽  
Specific Product ◽  
Paternal Effect ◽  
Developmental Arrest ◽  
Effect Gene

Abstract The vast majority of known male sterile mutants of Drosophila melanogaster fail to produce mature sperm or mate properly. The ms(3) K81(1) mutation is one of a rare class of male sterile mutations in which sterility is caused by developmental arrest after sperm entry into the egg. Previous studies showed that males homozygous for the K81(1) mutation produce progeny that arrest at either of two developmental stages. Most embryos arrest during early nuclear cycles, whereas the remainder are haploid embryos that arrest at a later stage. This description of the mutant phenotype was based on the analysis of a single allele isolated from a natural population. It was therefore unclear whether this unique paternal effect phenotype reflected the normal function of the gene. The genetic analysis and initial molecular characterization of five new K81 mutations are described here. Hemizygous conditions and heteroallelic combinations of the alleles were associated with male sterility caused by defects in embryogenesis. No other mutant phenotypes were observed. Thus, the K81 gene acted as a strict paternal effect gene. Moreover, the biphasic pattern of developmental arrest was common to all the alleles. These findings strongly suggested that the unusual embryonic phenotype caused by all five new alleles was due to loss of function of the K81+ gene. The K81 gene is therefore the first clear example of a strict paternal effect gene in Drosophila. Based on the embryonic lethal phenotypes, we suggest that the K81+ gene encodes a sperm-specific product that is essential for the male pronucleus to participate in the first few embryonic nuclear divisions.

scholarly journals Human PRE-PIK3C2B exhibits long-range intra- and inter-chromosomal interactions with genomic regions enriched in repressive marks

2020 ◽  
Author(s):  
Jayant Maini ◽  
Ankit Kumar Pathak ◽  
Kausik Bhattacharyya ◽  
Narendra Kumar ◽  
Ankita Narang ◽  
...  
Keyword(s):  
Long Range ◽  
Meta Analysis ◽  
Range Interaction ◽  
Dual Nature ◽  
Polycomb Response Element ◽  
Chromatin Interactions ◽  
Long Range Interaction ◽  
Intergenic Regions ◽  
Genomic Regions ◽  
Transcriptional Start Sites

AbstractHuman PRE-PIK3C2B is a dual nature polycomb response element that interacts with both polycomb as well as trithorax members. In the current study, using 4C-Seq (Capturing Circular Chromosomal Conformation-Sequencing), we identified long-range chromatin interactions associated with PRE-PIK3C2B and validated them with 3C-PCR. We identified both intra-as well as inter-chromosomal interactions, a large proportion of which were found to be closely distributed around transcriptional start sites (TSS). A significant number of interactions were also found to be associated with heterochromatic regions. Meta-analysis of ENCODE ChIP-Seq data identified an overall enrichment of YY1, CTCF as well as histone modification such as H3K4me3 and H3K27me marks in different cell lines. Almost 90% interactions were derived from either intronic or intergenic regions. among which large proportions of intronic interactors were either unique sequences or LINE/SINE derived. In case of intergenic interactions, majority of the interaction were associated with LINE/SINE repeats. We further found that genes proximal to the interactor sequences were co-expressed, they showed reduced expression. To the best of our knowledge this is one of the early demonstrations of long-range interaction of PRE sequences in human genome.

Organization of the Drosophila melanogaster hsp70 heat shock regulation unit

1987 ◽  
Vol 7 (3) ◽  
pp. 1055-1062
Author(s):  
J Amin ◽  
R Mestril ◽  
P Schiller ◽  
M Dreano ◽  
R Voellmy
Keyword(s):  
Drosophila Melanogaster ◽  
Heat Shock ◽  
Synergistic Effect ◽  
Consensus Sequence ◽  
Relative Orientation ◽  
Hsp70 Promoter ◽  
Promoter Sequences ◽  
Highly Active ◽  
Sequence Elements ◽  
Five Elements

Expression from the Drosophila melanogaster hsp70 promoter was controlled by a regulatory unit that was composed of two sequence elements that resembled the heat shock consensus sequence. The unit functioned in both orientations and at different distances from downstream promoter sequences. Each element of the unit alone was essentially inactive. Association of two elements resulted in a dramatic increase of transcription from the hsp70 promoter. This synergistic effect was independent of the relative orientation of the elements and, to a large extent, of the distance between them. Duplication of a region containing only one element also yielded a highly active, heat-regulated promoter. Genes with three to five elements were three to four times more active than those with a single regulatory unit.

Morphological and molecular modifications induced by heat shock in Drosophila melanogaster embryos

Development ◽  
1983 ◽  
Vol 77 (1) ◽  
pp. 167-182
Author(s):  
Giorgio Graziosi ◽  
Franco de Cristini ◽  
Angelo di Marcotullio ◽  
Roberto Marzari ◽  
Fulvio Micali ◽  
...  
Keyword(s):  
Drosophila Melanogaster ◽  
Heat Shock ◽  
Dna Synthesis ◽  
Histological Analysis ◽  
Developmental Stages ◽  
Early Embryo ◽  
Direct Relation ◽  
Hsp 70 ◽  
Survival Pattern ◽  
Shock Proteins

The early embryo of Drosophila melanogaster did not survive treatment at 37 °C (heat shock) for 25 min. The histological analysis of eggs treated in this way showed that the heat shock caused disintegration of nuclei and of cytoplasmic islands, displacement and swelling of nuclei and blocked mitoses. These effects were not observed in embryos treatedafter blastoderm formation. After this stage, we noticed that development was slowed down. The heat shock proteins (hsp 83,70 and 68) were, under shock, synthesized at all developmental stages. There was little or no synthesis of hsp 70 and 68 in unfertilized eggs, but synthesis increased in proportion to the number of nuclei present. Most probably, hsp 70 synthesis was directed by zygotic mRNA. DNA synthesis was not blocked by the heat shock though the overall incorporation of [3H]thymidine was substantially reduced, presumably because of the block of mitoses. We did not find a direct relation between survival pattern and hsp synthesis. We concluded that some, at least, of the heat shock genes can be activated at all developmental stages and that heat shock could be used for synchronizing mitoses.

The effects of chromosome rearrangements on the expression of heterochromatic genes in chromosome 2L of Drosophila melanogaster.

Genetics ◽  
1990 ◽  
Vol 125 (1) ◽  
pp. 141-154 ◽  
Author(s):  
B T Wakimoto ◽  
M G Hearn
Keyword(s):  
Drosophila Melanogaster ◽  
Chromosome Rearrangements ◽  
Centromeric Heterochromatin ◽  
Chromosome 2 ◽  
Regulatory Requirement ◽  
Position Effects ◽  
Heterochromatic Genes

Abstract The light (lt) gene of Drosophila melanogaster is located at the base of the left arm of chromosome 2, within or very near centromeric heterochromatin (2Lh). Chromosome rearrangements that move the lt+ gene from its normal proximal position and place the gene in distal euchromatin result in mosaic or variegated expression of the gene. The cytogenetic and genetic properties of 17 lt-variegated rearrangements are described in this report. We show that five of the heterochromatic genes adjacent to lt are subject to inactivation by these rearrangements and that the euchromatic loci in proximal 2L are not detectably affected. The properties of the rearrangements suggest that proximity to heterochromatin is an important regulatory requirement for at least six 2Lh genes. We discuss how the properties of the position effects on heterochromatic genes relate to other proximity-dependent phenomena such as transvection.

scholarly journals Evidence That Runt Acts as a Counter-Repressor of Groucho During Drosophila melanogaster Primary Sex Determination

2020 ◽  
Vol 10 (7) ◽  
pp. 2487-2496
Author(s):  
Sharvani Mahadeveraju ◽  
Young-Ho Jung ◽  
James W. Erickson
Keyword(s):  
Drosophila Melanogaster ◽  
Sex Determination ◽  
Transcriptional Repression ◽  
Biological Effects ◽  
Regulatory Gene ◽  
Animal Cells ◽  
Interaction Domain ◽  
Link Type ◽  
High Level ◽  
Runx Proteins

Runx proteins are bifunctional transcription factors that both repress and activate transcription in animal cells. Typically, Runx proteins work in concert with other transcriptional regulators, including co-activators and co-repressors to mediate their biological effects. In Drosophila melanogaster the archetypal Runx protein, Runt, functions in numerous processes including segmentation, neurogenesis and sex determination. During primary sex determination Runt acts as one of four X-linked signal element (XSE) proteins that direct female-specific activation of the establishment promoter (Pe) of the master regulatory gene Sex-lethal (Sxl). Successful activation of SxlPe requires that the XSE proteins overcome the repressive effects of maternally deposited Groucho (Gro), a potent co-repressor of the Gro/TLE family. Runx proteins, including Runt, contain a C-terminal peptide, VWRPY, known to bind to Gro/TLE proteins to mediate transcriptional repression. We show that Runt’s VWRPY co-repressor-interaction domain is needed for Runt to activate SxlPe. Deletion of the Gro-interaction domain eliminates Runt-ability to activate SxlPe, whereas replacement with a higher affinity, VWRPW, sequence promotes Runt-mediated transcription. This suggests that Runt may activate SxlPe by antagonizing Gro function, a conclusion consistent with earlier findings that Runt is needed for Sxl expression only in embryonic regions with high Gro activity. Surprisingly we found that Runt is not required for the initial activation of SxlPe. Instead, Runt is needed to keep SxlPe active during the subsequent period of high-level Sxl transcription suggesting that Runt helps amplify the difference between female and male XSE signals by counter-repressing Gro in female, but not in male, embryos.

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