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Transcriptome analysis on wild type and ddx39a mutant zebrafish embryos by Next Generation Sequencing

ABSTRACT: DEAD box RNA helicase DDX39A has been shown to regulate RNA metabolism; however its role in vertebrate development has not previously been examined. To determine the impact of loss of ddx39a on transcriptome during vertebrate early development, we pursued transcriptome analysis (RNA-Seq) on wild type and ddx39a mutant zebrafish embryos at 24 hour-post-fertilization. And by using RIP-seq to identify targeted RNA which were DDX39A binded.

ORGANISM(S): Danio rerio

PROVIDER: GSE97067 | GEO | 2017/03/28

SECONDARY ACCESSION(S): PRJNA380609

REPOSITORIES: GEO

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Unwinding the roles of DEAD-box RNA helicases DDX39A and DDX39B in alternative RNA splicing

Project description:Dead-box RNA helicases are crucial in mRNA processing, specifically in RNA splicing. Our previous work has shown that DDX39B is responsible for regulating the splicing of IL7R exon 6 and several FOXP3 introns, which rely on DDX39B's helicase and ATPase activities, respectively [this is not accurate since exon 6 also must require the ATPase activity, which is required for helicase activity]. In this study, we aimed to investigate whether DDX39A, a highly homologous paralog of DDX39B, plays a similar role in regulating alternative RNA splicing. We find that DDX39A and DDX39B have significant redundancy in their gene targets, however, DDX39A is incapable of complementing defective splicing of IL7R exon 6 when DDX39B is knockdown. Conversely, overexpressing DDX39A can rescue FOXP3 intron 11 splicing under DDX39B-depleted conditions. In this work we also confirm that introns containing C-rich/U-poor polypyrimidine tract are very sensitive to DDX39B levels. We also observed that cassette exons with C-rich/U-poor py tracts in upstream introns were also sensitive to DDX39B levels and were skipped more upon depletion of DDX39B, but not DDX39A. Among the introns retained more upon DDX39A and DDX39B depletion were DDX39A and DDX39B intron 6, which depend on DDX39A and DDX39B levels, respectively. Therefore, we identified an autoregulatory mechanism through which DDX39A and DDX39B control their respective expression. This study presents evidence that while DDX39A and DDX39B differentially impact certain RNA splicing events, they have many shared targets.

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Unwinding the roles of DEAD-box RNA helicases DDX39A and DDX39B in alternative RNA splicing

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Dynamic Control of RNA-DNA Hybrid Formation Orchestrates DNA2 Activation at Stalled Forks by RNAPII and DDX39A [ChIP-seq]

Project description:The accurate processing of stalled forks by the DNA2 nuclease is pivotal for replication fork restart, as excessive degradation poses a threat to genomic stability. However, the regulation of DNA2 activity at stalled forks remains elusive. Here, we demonstrate that, upon replication stress, RNA polymerase II (RNAPII) is recruited to stalled forks, actively promoting the transient formation of RNA-DNA hybrids. Furthermore, we provide evidence that DDX39A, functioning as an RNA-DNA resolver, unwinds these hybrids, allowing DNA2 access to stalled forks. This orchestrated process facilitates controlled DNA2-dependent stalled fork processing and restart. Nevertheless, premature removal of RNA-DNA hybrids at stalled forks leads to DNA2-dependent excessive degradation of nascent DNA. Finally, we reveal that loss of DDX39A enhances the protection of stalled forks in BRCA1/2-deficient cells, consequently conferring chemoresistance within this specific cellular context. Our results suggest that the dynamic regulation of RNA-DNA hybrid formation at stalled forks by RNAPII and DDX39A precisely governs the timing of DNA2 activation, contributing to stalled fork processing and restart, ultimately promoting genome stability.

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Analysis of DDX39A and DDX56 interacting proteins

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MicroRNA profiling of wild type and p72 knock-out mice embryos

Project description:To examine the effect of DEAD-box RNA helicase subunits on the primary miRNAs processing by Drosha complex, we made knockout mice of p72, DEAD-box RNA helicase, a component of Drosha complex. And we compare the miRNA expression profiles derived from whole mice embryo between wild-type and p72 KO mice.

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Transcriptome analysis of neuroblastoma SH-SY5Y cells upon DDX17 helicase knock-down

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lncRNA-protein interactions in hematopoietic progenitor cells by hybridization capture and mass spectrometry

Project description:Long non-coding RNAs (lncRNAs) exert regulatory functions in a wide spectrum of biological contexts, and certain regulatory functions involve the formation of RNA-protein complexes. Discovering the structure/function of these complexes may unveil important functional insights. The DDX41 gene encoding the DEAD-box RNA helicase 41 protein (DDX41) is subject to extensive germline genetic variation, and certain variants create a predisposition to develop myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML). While the importance of DDX41 for the control of hematopoiesis is established, many questions remain regarding the mechanisms of how DDX41 functions in hematopoietic stem and progenitor cells. Previously, we identified a DDX41-regulated lncRNA, growth arrest-specific 5 (Gas5) (Kim et al.). As Gas5 function in hematopoiesis is unknown, we analyzed protein interactors of Gas5 lncRNA using HyPR-MS (Hybridization Purification of RNA-Protein complexes followed by Mass Spectrometry). 28 proteins were identified as Gas5 lncRNA interactors, five of which were experimentally validated as Gas5 lncRNA interactors by RNA Immunoprecipitation qPCR (RIP-qPCR) analysis. The identification of protein interactors with a DDX41-regulated lncRNA establishes a foundation to guide future mechanistic and biological studies.c

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Interplay between bacterial RNA 5'-termini deNADding protein NudC and DEAD-box RNA helicase CsdA in stress-responses

Project description:Nicotinamide adenine dinucleotide (NAD) "cap" recently discovered in bacteria could have similar functions as eukaryotic 7-methylguanine (m7G) "cap", which protects RNA 5'-terminus from degradation and mediates RNA interactions with proteins involved in its transportation, editing and translation. The only known 5'-NAD-RNA-interacting E. coli protein is Nudix superfamily hydrolase NudC which is responsible for this "cap" hydrolysis. We conducted the search for NudC-interacting proteins and discovered that in vivo and in vitro NudC interacts with RNA helicase DeaD. We also discovered using bacterial two hybrid system that N-terminal parts of both proteins are involved in this interaction, particularly the N-terminal domain and zinc finger motif of NudC and RecA1, RecA2 and dimerization domains of DeaD. Detailed investigation on the hydrolase interactome revealed NudC contacts with at least three proteins involved in formation of RNA degradosome complex, DeaD, Hfq and PNPase, under stress conditions raising the idea that NudC could also function within the RNA degradosome. On the other hand, NudC together with DeaD interacts with 70S ribosome proteins. Thus, NudC is closely related to protein synthesis in ribosomes. Finally, since at least six NudC-interacting partners are involved in cell stress response we think that the helicase could play important role by moduling the cell conditions in response to environment changes.

2022-07-10 | MSV000089861 | MassIVE

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