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Genome-wide analysis of distribution of RNA Helicase Maleless (MLE) in Drosophila Melanogaster early female embryo, before (0-2 Hr) and after (2-4 Hr) maternal to zygotic transition (MZT)

ABSTRACT: Genome-wide analysis of distribution of RNA Helicase Maleless (MLE) in Drosophila Melanogaster early female embryo, before (0-2 Hr) and after (2-4 Hr) maternal to zygotic transition (MZT)

PROVIDER: PRJNA912201 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR22739281_1.fastq.gz	Fastqsanger.gz
	SRR22739281_2.fastq.gz	Fastqsanger.gz
	SRR22739282_1.fastq.gz	Fastqsanger.gz
	SRR22739282_2.fastq.gz	Fastqsanger.gz
	SRR22739283_1.fastq.gz	Fastqsanger.gz

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Genome-wide analysis of distribution of RNA Helicase Maleless (MLE) in Drosophila Melanogaster early female embryo, before (0-2 Hr) and after (2-4 Hr) maternal to zygotic transition (MZT)

Project description:Transcription factor CLAMP associates with RNA helicase, Maleless MLE as part of Male-specific MSL complex in males, which regulates dosage compensation in males. Both CLAMP and MLE are maternally deposited proteins (protein expression detectd in 0- Hr embryo, before zygotic genome activation) and MLE is also a conserved component of spliceosome. Moreover, CLAMP too associates with many other RNA binding protein compoments of spliceosomes. Both these proteins are well expressed in females, but apart from that might influence splicing in females, not much is known if they have any female-specific function. Furthermore, whether they regulate each other's function in females is not known as well, especially before zygotic genome activation starts, in a pre-MZT embryo (0-2 Hr Embryo). Therefore, we performed CutnRun assay to detrmine MLE binding sites on chromatin in female embryos before (0-2 Hr) and after MZT (2-4 Hr). And then identify, in absence of maternal CLAMP, whether there is change is distribution of control MLE female peaks. We identified regions on chromatin where MLE binds during 0-2 Hr pre-MZT and 2-4 Hr post-MZT embryonic stages in females. CLAMP unlike to males do not affect MLE distribution on chromatin in females.

2023-12-31 | GSE220981 | GEO

Genome-wide distribution analysis of RNA Helicase Maleless (MLE) in Drosophila Melanogaster early male embryo, before (0-2 Hr) and after (2-4 Hr) maternal to zygotic transition (MZT) and in absence of CLAMP

Project description:Purpose: Study how maternal Pioneer Transcription factor CLAMP affects sex-specifc splicing during initial embryonic development by regulating occupancy of spliceosome component Maleless (MLE), a RNA helicase on chromatin Method: Cut and Run (CUT&RUN) DNA libraries (Uyehara and McKay 2019) using anti-MLE antibody were generated from male embryos at 0-2 Hr pre-MZT and 2-4 hr post-MZT stages in presence and absence of maternal CLAMP. Maternal CLAMP was depleted by driving UAS-CLAMPRNAi in the ovaries using MTD-GAL4 maternal triple driver. As a control UAS-GFPRNAI was driven using the MTD-GAL4. Embryos were sexed using the meiotic drive system that produces sperm with only Y chromosomes (Reider et al 2017), resulting in progeny of only male genotypes. Results: We identified regions on chromatin where MLE binds during 0-2 Hr pre-MZTand 2-4 Hr post-MZT embryonic stages in males. In 0-2 Hr and 2-4 Hr old control embryos 28,279 and 24,910 MLE peaks were detected. After depletion of maternal CLAMP, 41.97% of 0-2 Hr peaks (22183 remaining, 6096 lost) and 59.1% of 2-4 Hr peaks (15735 remaining, 9175 lost) are lost. We also found loss of maternal CLAMP resulted in 26% and 35.25% new MLE peaks at 0-2 hr pre-MZT and 2-4 Hr post-MZT embryonic stages. Our motif search shows presence of putative motifs for MLE binding on chromatin which needs further validation. Conclusion: This is the first study showing genome-wide MLE occupancy in sexed embryos during 0-2 hr pre-MZT and 2-4 hr post-MZT stages. We show that the maternally deposited transcription factor CLAMP affects MLE occupancy on chromatin in early embryos. Thus, we conclude that maternal transcription factors can affect spliceosome function by regulating occupancy of their components on chromatin.

2022-05-01 | GSE174781 | GEO

Project description:Genome-wide distribution analysis of RNA Helicase Maleless (MLE) in Drosophila Melanogaster early male embryo, before (0-2 Hr) and after (2-4 Hr) maternal to zygotic transition (MZT) and in absence of CLAMP

| PRJNA731511 | ENA

Structural basis of RNA-induced autoregulation of the DExH-type RNA helicase maleless

Project description:RNA unwinding by DExH-type helicases underlies most RNA metabolism and function. It remains unresolved if and how the basic unwinding reaction of helicases is regulated by auxiliary domains. We explored the interplay between the RecA and auxiliary domains of the RNA helicase maleless (MLE) from Drosophila, using a suite of structural and functional studies. We discovered that MLE exists in a dsRNA bound open conformation and the auxiliary dsRBD2 domain aligns the substrate RNA with the accessible helicase tunnel. In an ATP-dependent manner, dsRBD2 associates with the helicase module, leading to tunnel closure around ssRNA. Furthermore, our structures provide a rationale for blunt ended dsRNA unwinding and 3’-5’ translocation by MLE. Structure-based MLE mutations confirm the functional relevance of our model for RNA unwinding. Our findings contribute to our understanding of fundamental mechanics of auxiliary domains in DExH helicase MLE which serves as model for its human ortholog and potentially therapeutic target, DHX9/RHA.

2023-11-27 | PXD045725 | Pride

Mapping of MLE and MSL2 using iCLIP

Project description:Dosage compensation in Drosophila is an epigenetic phenomenon utilizing proteins and long non-coding RNAs (lncRNAs) for transcriptional up-regulation of the entire X-chromosome. Here, UV cross-linking followed by deep sequencing (iCLIP) show that two enzymes in the Male-Specific Lethal complex, MLE RNA helicase and MSL2 ubiquitin ligase, bind evolutionarily conserved domains containing tandem stem-loops in roX1 and roX2 RNAs in vivo.

2013-07-18 | E-MTAB-1669 | biostudies-arrayexpress

MLE ChIP-seq

Project description:Chromatin immunoprecipitation followed by deep sequencing (ChIP-seq) was carried out on wild-type Schneider (S2) cells using specific MLE antibodies to identify binding sites for MLE in the Drosophila genome

2013-10-30 | E-MTAB-1705 | biostudies-arrayexpress

MLE ChIP-seq

Project description:MLE ChIP-seq

| PRJEB4008 | ENA

The interaction of MLE with CLAMP zinc finger domains is important for dosage compensation in Drosophila melanogaster

Project description:The Drosophila male-specific lethal (MSL) complex binds to the male X chromosome to activate transcription, and consists of five proteins, MSL1, MSL2, MSL3, MOF, MLE, and two roX RNAs. The MLE helicase remodels the roX lncRNAs, enabling the lncRNA-mediated assembly of the Drosophila dosage compensation complex. MSL2 is expressed only in males and interacts with the N-terminal zinc-finger of the transcription factor CLAMP that is important for specific recruitment of the MSL complex on the male X chromosome. Here we found that the unstructured C-terminal region of MLE interacts with 6-7 zinc-finger domains of CLAMP. In vitro 4-5 zinc fingers are critical for specific DNA-binding of CLAMP with GA-repeats, which constitute the core motif at the high affinity binding sites for MSL proteins. Deletion of the Clamp Binding Domain (CBD) in MLE results in decreasing of MSL proteins association with male X chromosome and increasing of male lethality. These results suggest that interactions of unstructured regions in MSL2 and MLE with CLAMP zinc finger domains are important for the specific recruitment of the MSL complex on the male X chromosome.

2024-03-20 | GSE239354 | GEO

MLE HITS-CLIP in Drosophila S2 cells

Project description:HITS-CLIP was carried out on wild-type Schneider (S2) cells using specific MLE antibodies to identify binding sites for MLE in the Drosophila transcriptome

2013-10-30 | E-MTAB-1706 | biostudies-arrayexpress

Phase separation of Ddx3xb helicase regulates maternal-to-zygotic transition in zebrafish

Project description:Phase separation of Ddx3xb helicase regulates maternal-to-zygotic transition in zebrafish

| PRJNA715459 | ENA