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The RNA interactomes of Imp and Syp reveal temporal RNA regulatory network in Drosophila brain development

ABSTRACT: The RNA interactomes of Imp and Syp reveal temporal RNA regulatory network in Drosophila brain development

PROVIDER: PRJNA1092058 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR28462262.fastq.gz	Fastqsanger.gz
	SRR28462263.fastq.gz	Fastqsanger.gz
	SRR28462264.fastq.gz	Fastqsanger.gz
	SRR28462265.fastq.gz	Fastqsanger.gz
	SRR28462266.fastq.gz	Fastqsanger.gz

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The RNA interactomes of Imp and Syp reveal temporal RNA regulatory network in Drosophila brain development

Project description:The temporal patterning of neural stem cells is a powerful mechanism to generate neural diversity. In Drosophila, the progression of post-embryonic neurogenesis is driven by RNA-binding proteins Imp (IGF2BP) and Syp (SYNCRIP), however how they achieve their function is not well understood, since little is known about their RNA targets in the brain. Here, we present comprehensive RNA interactomes of Imp and Syp at different time points during larval brain development. Imp and Syp target highly overlapping sets of mRNAs whose encoded proteins impact fate specification, stem cell maintenance and tumourigenesis. Within these transcripts, Imp and Syp footprints exhibit limited overlap, instead we show their binding sites have co-evolved, suggesting a combinatorial or cooperative mode of regulation rather than competitive binding. Further, we identify RNAs dynamically interacting with Imp/Syp across development, consisting of existing and potentially new candidates of the neurogenesis program, and loss of Imp or Syp disrupts expression of key transcripts denotative of early or late-born neurons. Together, our findings highlight a post-transcriptional regulatory network that influences temporal order, and our study is a valuable resource for future studies finely-dissecting molecular mechanisms of neuronal fate specifications.

2025-01-16 | GSE262499 | GEO

Opposite Imp/Syp temporal gradients govern birth time-dependent neuronal fates

Project description:Generating diverse neurons involves spatially distinct neural stem cells that show age dependent developmental fates. Drosophila neuroblasts produce long, diverse yet stereotyped series of distinct neurons, called lineages. We searched for novel temporal factors that could pattern such extended lineages by RNA-sequencing of specific neuroblasts at various developmental times. We found that two RNA-binding proteins, Imp and Syp, display opposing high-to-low and low-to-high temporal gradients with distinct dynamics in specific lineages. Manipulating Imp/Syp levels in mushroom body neuroblasts revealed opposing roles in the specification of early and late temporal fates, primarily via regulation of Chinmo translation. This study implicates the opposing Imp/Syp gradients as temporal morphogens that encode stem cell age and govern birth time-dependent offspring cell fate through post-transcriptional regulation of temporal dentity genes.

2015-10-21 | GSE71103 | GEO

Stem cell intrinsic, Seven-up-triggered temporal factor gradients diversify intermediate neural progenitors

Project description:One neural stem cell can produce multiple transiently amplifying, intermediate neural progenitors (INP), which collectively yield diverse neuronal types. It is unclear if and how serially derived INPs contribute to neuron fate diversification. Drosophila type II neuroblasts, like mammalian neural stem cells, deposit neurons and also glia through INPs. The consecutively born INPs in a given lineage produce morphologically distinct progeny, presumably due to their inheritance of different temporal factors from the INP-producing progenitor. To uncover the underlying temporal fating mechanisms, we profiled type II neuroblasts' transcriptome across time. Our results reveal opposing temporal gradients of Imp and Syp RNA-binding proteins (descending and ascending, respectively). Maintaining high Imp throughout serial INP production expands the number of neurons/glia with early temporal fate at the expense of cells with late fate. Conversely, precocious upregulation of Syp reduces the number of cells with early fate. Further, we reveal that the transcription factor, Seven-up initiates progression of the Imp/Syp gradients. Interestingly, neuroblasts apparently locked in their beginning Imp/Syp levels can still yield progeny with a small range of early fates. We propose that the Seven-up-initiated Imp/Syp gradients create coarse temporal windows within type II neuroblasts to pattern INPs, which subsequently undergo fine-tuned subtemporal patterning.

2018-01-23 | GSE94445 | GEO

Imp/IGF2BP and Syp/SYNCRIP temporal RNA interactomes uncover combinatorial networks of regulators of <i>Drosophila</i> brain development.

Project description:Temporal patterning of neural progenitors is an evolutionarily conserved mechanism generating neural diversity. In Drosophila, postembryonic neurogenesis requires the RNA binding proteins (RBPs) Imp/IGF2BP and Syp/SYNCRIP. However, how they coachieve their function is not well understood. Here, we elucidate the in vivo temporal RNA interactome landscapes of Imp and Syp during larval brain development. Imp and Syp bind a highly overlapping set of conserved mRNAs encoding proteins involved in neurodevelopment. We identify transcripts differentially occupied by Imp/Syp over time, featuring a network of known and previously unknown candidate temporal regulators that are post-transcriptionally regulated by Imp/Syp. Furthermore, the physical and coevolutionary relationships between Imp and Syp binding sites reveal a combinatorial, rather than competitive, mode of molecular interplay. Our study establishes an in vivo framework for dissecting the temporal coregulation of RBP networks as well as providing a resource for understanding neural fate specification.

| S-EPMC11804933 | biostudies-literature

SYP-4 phosphoproteomics characterization

Project description:The deletion of the last 114 amino acids of SYP-4 introduced severe defects in crossover regulation during meiosis I in C. elegans. Many processes during meiosis are regulated by post-translational modifications. Therefore, we aimed at identifying putative phosphorylation sites within the last 114 amino acids of SYP-4 by mass spectrometry to later test their functionality.

2025-05-07 | PXD058372 | Pride

Drosophila Imp iCLIP identifies an RNA assemblage co-ordinating F-actin formation

2015-05-27 | GSE62997 | GEO

E. coli imp fabI(G93V) Mutant Cells: Control (E. coli imp fabI(G93V) ) vs. NTG-treated E. coli imp fabI(G93V)

Project description:Transcriptional profiling of NTG-treated E. coli imp fabI(G93V) cells compared to control cells (E. coli imp fabI(G93V) ) in the absence or presence of sub-lethal concentration of triclosan.

2009-07-31 | GSE17441 | GEO

Adverse effects of SYP-3343 on zebrafish development via ROS-mediated mitochondrial dysfunction

Project description:As a newly-invented and highly-efficiency strobilurin fungicide, pyraoxystrobin (SYP-3343) has been recognized as a highly poisonous toxin for a variety of aquatic organisms. Nevertheless, the developmental toxicity and potential mechanism of SYP-3343 have not been well-documented. The results showed that SYP-3343 was relatively stable and maintained within the range of 20 % in 24 h, and the LC50 value to embryos at 72 hpf was 17.13 μg/L. The zebrafish embryotoxicity induced by 1, 2, 4, and 8 μg/L SYP-3343 is demonstrated by repressive embryo incubation, enhancive mortality rate, abnormal heart rate, malformed morphological characteristic, and impaired spontaneous coiling, indicating SYP-3343 mostly exerted its toxicity in a dose- and time-dependent manner. Besides SYP-3343 was critically involved in regulating cell cycle, mitochondrial membrane potential, and reactive oxygen species production as well as zebrafish primary cells apoptosis, which can be mitigated using antioxidant N-acetyl-L-cysteine. A significant change occurred in total protein content, the biochemical indices, and antioxidant capacities owing to SYP-3343 exposure. Additionally, SYP-3343 altered the mRNA levels of heart development-, mitochondrial function-, and apoptosis-related genes in zebrafish embryos. These results indicated that SYP-3343 induced apoptosis accompanying reactive oxygen species-initiated mitochondrial dysfunction in zebrafish embryos.

2023-02-02 | GSE224231 | GEO

Drosophila Imp iCLIP identifies an RNA assemblage co-ordinating F-actin formation

Project description:In this study, we employed a combination of RIP-seq and short- and long-wave iCLIP technologies to identify transcripts associated with cytoplasmic RNPs containing the RNA-binding protein Drosophila Imp. We also made a Imp knockdown vs luciferase control experiment. Two biological iCLIP-seq, as well as two mRNAseq made on cells harvested on the same day. Two biological PAR-iCLIP-seq. Two biological RIP-seq, as well as two mRNAseq made on cells harvested on the same day. Three biological mRNAseq of imp dsRNA treated cells as well as three control mRNAseq of cells treated with Luciferase dsRNA.

2015-05-27 | E-GEOD-62997 | biostudies-arrayexpress

RNAi knock down of RNA binding IMP proteins in human epithelial (HeLa) cells

Project description:To identify factors and pathways regulated by IMP proteins and obtain leads to the mechanism behind the phenotypic changes, we compared the gene expression profiles of IMP siRNA treated cells with mock treated cells. Triplicate gene expression profiles were generated from both the IMP(1,3)A and IMP(1,3)B siRNA sets and were compared to the mock transfected cells. cRNA was hybridized to Affymetrix human U133A arrays.

2006-09-30 | E-MEXP-548 | biostudies-arrayexpress

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