Characterization of a novel Drosophila melanogaster cis -regulatory module that drives gene expression to the larval tracheal system and adult thoracic musculature

genesis ◽  
2018 ◽  
Vol 56 (8) ◽  
pp. e23222
Author(s):  
Jorge Victor Wilfredo Cachay Wester ◽  
Carlos Antonio Couto Lima ◽  
Maiaro Cabral Rosa Machado ◽  
Patrícia Vieira Zampar ◽  
Simone Sakagute Tavares ◽  
...  
Keyword(s):  
Gene Expression ◽  
Drosophila Melanogaster ◽  
Tracheal System ◽  
Regulatory Module

scholarly journals A Gain-of-Function Screen Identifying Genes Required for Growth and Pattern Formation of the Drosophila melanogaster Wing

Genetics ◽  
2009 ◽  
Vol 183 (3) ◽  
pp. 1005-1026 ◽  
Author(s):  
Cristina Cruz ◽  
Alvaro Glavic ◽  
Mar Casado ◽  
Jose F. de Celis
Keyword(s):  
Gene Expression ◽  
Drosophila Melanogaster ◽  
Pattern Formation ◽  
Genetic Control ◽  
Longitudinal Vein ◽  
Gain Of Function ◽  
Ectopic Gene Expression ◽  
Insertion Sites ◽  
Wing Growth

The Drosophila melanogaster wing is a model system for analyzing the genetic control of organ size, shape, and pattern formation. The formation of the wing involves a variety of processes, such as cell growth, proliferation, pattern formation, and differentiation. These developmental processes are under genetic control, and many genes participating in specific aspects of wing development have already being characterized. In this work, we aim to identify novel genes regulating wing growth and patterning. To this end, we have carried out a gain-of-function screen generating novel P-UAS (upstream activating sequences) insertions allowing forced gene expression. We produced 3340 novel P-UAS insertions and isolated 300 that cause a variety of wing phenotypes in combination with a Gal4 driver expressed exclusively in the central domain of the presumptive wing blade. The mapping of these P-UAS insertion sites allowed us to identify the gene that causes the gain-of-function phenotypes. We show that a fraction of these phenotypes are related to the induction of cell death in the domain of ectopic gene expression. Finally, we present a preliminary characterization of a gene identified in the screen, the function of which is required for the development of the L5 longitudinal vein.

scholarly journals Interplay of pericentromeric genome organization and chromatin landscape regulates the expression of Drosophila melanogaster heterochromatic genes

2019 ◽  
Author(s):  
Parna Saha ◽  
Divya Tej Sowpati ◽  
Ishanee Srivastava ◽  
Rakesh Kumar Mishra
Keyword(s):  
Gene Expression ◽  
Drosophila Melanogaster ◽  
Genome Organization ◽  
Constitutive Heterochromatin ◽  
Pericentromeric Heterochromatin ◽  
Chromatin Interactions ◽  
Recent Developments ◽  
Epigenetic Code ◽  
Heterochromatic Genes

AbstractTranscription of heterochromatic genes residing within the constitutive heterochromatin is paradoxical to the tenets of the epigenetic code. Drosophila melanogaster heterochromatic genes serve as an excellent model system to understand the mechanisms of their transcriptional regulation. Recent developments in chromatin conformation techniques have revealed that genome organization regulates the transcriptional outputs. Thus, using 5C-seq in S2 cells, we present a detailed characterization of the hierarchical genome organization of Drosophila pericentromeric heterochromatin and its contribution to heterochromatic gene expression. We show that pericentromeric TAD borders are enriched in nuclear Matrix attachment regions while the intra-TAD interactions are mediated by various insulator binding proteins. Heterochromatic genes of similar expression levels cluster into Het TADs which indicates their transcriptional co-regulation. To elucidate how heterochromatic factors, influence the expression of heterochromatic genes, we performed 5C-seq in the HP1a or Su(var)3-9 depleted cells. HP1a or Su(var)3-9 RNAi results in perturbation of global pericentromeric TAD organization but the expression of the heterochromatic genes is minimally affected. Subset of active heterochromatic genes have been shown to have combination of HP1a/H3K9me3 with H3K36me3 at their exons. Interestingly, the knock-down of dMES-4 (H3K36 methyltransferase), downregulates expression of the heterochromatic genes. This indicates that the local chromatin interactions and the combination of heterochromatic factors (HP1a or H3K9me3) along with the H3K36me3 is crucial to drive the expression of heterochromatic genes. Furthermore, dADD1, present near the TSS of the active heterochromatic genes, can bind to both H3K9me3 or HP1a and facilitate the heterochromatic gene expression by regulating the H3K36me3 levels. Therefore, our findings provide mechanistic insights into the interplay of genome organization and chromatin factors at the pericentromeric heterochromatin that regulates Drosophila melanogaster heterochromatic gene expression.

scholarly journals Genetic Basis of Transcriptome Diversity in Drosophila melanogaster

2015 ◽  
Author(s):  
Wen Huang ◽  
Mary Anna Carbone ◽  
Michael Magwire ◽  
Jason Peiffer ◽  
Richard Lyman ◽  
...  
Keyword(s):  
Gene Expression ◽  
Drosophila Melanogaster ◽  
Quantitative Trait ◽  
Genetic Basis ◽  
Trait Variation ◽  
Regulatory Variants ◽  
Genome Wide ◽  
Mean And Variance ◽  
The Mean

Understanding how DNA sequence variation is translated into variation for complex phenotypes has remained elusive, but is essential for predicting adaptive evolution, selecting agriculturally important animals and crops, and personalized medicine. Here, we quantified genome-wide variation in gene expression in the sequenced inbred lines of the Drosophila melanogaster Genetic Reference Panel (DGRP). We found that a substantial fraction of the Drosophila transcriptome is genetically variable and organized into modules of genetically correlated transcripts, which provide functional context for newly identified transcribed regions. We identified regulatory variants for the mean and variance of gene expression, the latter of which could often be explained by an epistatic model. Expression quantitative trait loci for the mean, but not the variance, of gene expression were concentrated near genes. This comprehensive characterization of population scale diversity of transcriptomes and its genetic basis in the DGRP is critically important for a systems understanding of quantitative trait variation.

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