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Fly brm knockdown MNase-seq

ABSTRACT: Drosophila PBAP complex, a form of SWI/SNF class of complexes, played a important role in metamorphosis. We conducted MNase digestion followed by next-generation sequencing (NGS) to analyse the nucleosome profile in both control and Brm knockdown fly larvae.

INSTRUMENT(S): Illumina HiSeq 2000

ORGANISM(S): Drosophila melanogaster

SUBMITTER: Jiejun Shi

PROVIDER: E-MTAB-1967 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Drosophila Brahma complex remodels nucleosome organizations in multiple aspects.

Shi Jiejun J Zheng Meizhu M Ye Youqiong Y Li Min M Chen Xiaolong X Hu Xinjie X Sun Jin J Zhang Xiaobai X Jiang Cizhong C

Nucleic acids research 20140731 15

ATP-dependent chromatin remodeling complexes regulate nucleosome organizations. In Drosophila, gene Brm encodes the core Brahma complex, the ATPase subunit of SWI/SNF class of chromatin remodelers. Its role in modulating the nucleosome landscape in vivo is unclear. In this study, we knocked down Brm in Drosophila third instar larvae to explore the changes in nucleosome profiles and global gene transcription. The results show that Brm knockdown leads to nucleosome occupancy changes throughout the ...[more]

PMID: 25081211

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fly brm knockdown RNA-seq

Project description:Drosophila PBAP complex, a form of SWI/SNF class of complexes, played a important role in metamorphosis. We conducted next-generation sequencing (NGS) to analyse the expression profile in both control and Brm knockdown fly larvae.

2014-05-08 | E-MTAB-1966 | biostudies-arrayexpress

The E3 Ligase CUL3 physically interacts with TANGO10 protein in vivo

Project description:List of protein scores for putative TANGO10 interactors from mass spectrometry analysis of FLAG-tagged TANGO10 using either elav-GAL4 or tim-GAL4 at both ZT10 and ZT 22, as determined using Proteome Discoverer software (ThermoFisher). Fly heads from GAL4 heterozygotes were used as controls. The hits from FLAG-tagged twenty-four (TYF) proteomics were also excluded from the list to increase TANGO10-specificity. Proteins listed are those present in at least one elav-GAL4 sample and at least one tim-GAL4 sample but no negative controls.

2021-11-02 | PXD029326 | Pride

The faint sausage gene encodes a subunit of the spliceosome-activating Prp19 complex and is required for tracheal branching morphogenesis in Drosophila

Project description:Morphogenesis requires the dynamic regulation of gene expression, including transcription, mRNA maturation and translation. Dysfunction of general components of the splicing machinery can cause surprisingly specific phenotypes, but the basis for these cell-type specific effects is not clear. Here we show that the faint sausage (fas) locus, implicated in epithelial morphogenesis and previously reported to encode a secreted immunoglobulin domain protein, in fact encodes a subunit of the Prp19 complex that is essential for efficient pre-mRNA splicing. Loss of zygotic fas function impairs the efficiency of splicing, associated with widespread retention of introns in mature mRNAs and dramatic changes in gene expression. Surprisingly, despite these general effects, zygotic fas mutants show specific defects in tracheal cell migration. Zygotic fas function becomes essential during late embryogenesis when maternally supplied splicing factors decline. We propose that tracheal branching, which relies on dynamic changes in gene expression, is particularly sensitive for efficient spliceosome function. Our results provide an entry point to study functions of splicing during organogenesis and provide a better understanding of specific disease phenotypes associated with mutations in general splicing factors.

2016-11-18 | E-MTAB-5069 | biostudies-arrayexpress

Functional genomic analysis of the periodic transcriptome in the developing Drosophila wing.

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

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Dm Ladybird over-expression and loss-of-function Expression Profiling

Project description:In order to identify Ladybird mesodermal and heart target genes, we decided to analyse the transcriptional profiling of embryos with a targeted gain and Loss of function approach. Embryos were collected at stages 11 to 15 of embryogenesis corresponding to the lb expression period. Homozygous ectopically expressing or repressing embryos were collected from a large scale cross of UAS-lbe or UAS-RNAi-lbe flies with 24B-Gal4 or Tin-Gal4 flies, in parallel to stage-matched control. Three independent collections were performed. Total RNA was extracted. Ectopically expression and reference samples were hybridized together on GeneChip Drosophila Genome array2. With this approach, we were able to dicover a repertory of genes involved in different aspects of muscle and heart formation showing a multi-step action of this family of identity genes.

2008-02-05 | E-TABM-297 | biostudies-arrayexpress

Transcriptional profiling of Drosophila wing pouch following CR32027 RNAi

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2014-03-15 | E-GEOD-54927 | biostudies-arrayexpress

Neprilysins regulate muscle contraction and heart function via cleavage of SERCA-inhibitory micropeptides

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2022-06-01 | PXD027738 | Pride

RNAi profiling by array of Drosophila salivary glands upon NSL3, MCRS2 and MBDR2 RNAi mediated depletion

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2010-06-25 | E-MEXP-2652 | biostudies-arrayexpress

The effect of Dis3 knockdown on miRNA expression in Drosophila wing imaginal discs.

Project description:We investigated the effect on miRNA expression in Drosophila melanogaster wing imaginal discs following the knockdown of the 3'-5' exoribonuclease Dis3.

2015-06-01 | E-MTAB-3569 | biostudies-arrayexpress

Indentification of Dis3L2 targets in Drosophila melanogaster wing imaginal discs

Project description:We investigated the effect on mRNA expression in Drosophila melanogaster wing imaginal discs following the knockdown of the 3'-5' exoribonuclease Dis3L2.

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