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Proximity-CLIP provides a snapshot of occupied cis-acting elements on RNA in different subcellular compartments on a transcriptome-wide scale

ABSTRACT: Proximity-CLIP provides a snapshot of occupied cis-acting elements on RNA in different subcellular compartments on a transcriptome-wide scale

PROVIDER: PRJNA433561 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR6701080.fastq.gz	Fastqsanger.gz
	SRR6701090.fastq.gz	Fastqsanger.gz
	SRR6701081.fastq.gz	Fastqsanger.gz
	SRR6701091.fastq.gz	Fastqsanger.gz
	SRR6701082.fastq.gz	Fastqsanger.gz

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Proximity-CLIP provides a snapshot of occupied cis-acting elements on RNA in different subcellular compartments on a transcriptome-wide scale

Project description:Many cellular RNAs localize to specific subcellular compartments. Currently, methods to systematically study subcellular RNA localization are limited and lagging behind proteomic approaches. Here, we combined APEX2-mediated proximity biotinylation of proteins with PAR-CLIP to simultaneously profile the proteome and the transcriptome bound by RNA binding proteins in any given subcellular compartment. Our approach is fractionation-independent and does not rely on additional RNA manipulation and labeling steps, thus making it easy to apply. Furthermore, it enables to study the locali-zation of RNA processing intermediates, as well as the identification of regulatory RNA cis-acting elements occupied in different cellular compartments. In a proof-of-concept study we studied RNA and protein localization in the nucleus, cytoplasm and at cell-cell interfaces using Proximity-CLIP. These experiments revealed among other in-sights frequent transcriptional readthrough continuing for several kilobases down-stream of the canonical cleavage and polyadenylation site, a differential binding pat-tern of nuclear and cytoplasmic mRNAs, as well as the localization of mRNAs contain-ing 3’UTR CUG sequence elements at cell-cell interfaces, of which many encode regulatory proteins.

2018-11-26 | GSE110380 | GEO

Proximity-CLIP provides a snapshot of protein-occupied RNA elements in subcellular compartments.

Project description:Methods for the systematic study of subcellular RNA localization are limited, and their development has lagged behind that of proteomic tools. We combined APEX2-mediated proximity biotinylation of proteins with photoactivatable ribonucleoside-enhanced crosslinking to simultaneously profile the proteome and the transcriptome bound by RNA-binding proteins in any given subcellular compartment. Our approach is fractionation independent and allows study of the localization of RNA processing intermediates, as well as the identification of regulatory RNA cis-acting elements occupied by proteins, in a cellular-compartment-specific manner. We used our method, Proximity-CLIP, to profile RNA and protein in the nucleus, in the cytoplasm, and at cell-cell interfaces. Among other insights, we observed frequent transcriptional readthrough continuing for several kilobases downstream of the canonical cleavage and polyadenylation site and a differential RBP occupancy pattern for mRNAs in the nucleus and cytoplasm. We observed that mRNAs localized to cell-cell interfaces often encoded regulatory proteins and contained protein-occupied CUG sequence elements in their 3' untranslated region.

| S-EPMC6289640 | biostudies-literature

BAP-seq proximity labeling of subcellular compartments

Project description:BAP-seq proximity labeling of subcellular compartments

| PRJNA954517 | ENA

Slamseq of subcellular compartments in neurons

Project description:We performed a SLAMseq Metabolic RNA Labeling on neuronal subcellular compartments, e.g. neurites and soma, derived from Ascl1-induced neurons (iNeurons). This experimental approach provides a snapshot of mRNA kinetics which allows to estimate the half-lives of mRNAs. These data was used to investigate the influence of mRNA degradation machinery in both neuronal compartments.

2023-07-12 | E-MTAB-9400 | biostudies-arrayexpress

Analysis of subcellular transcriptomes by RNA proximity labeling with Halo-seq

Project description:We have developed Halo-seq, an RNA proximity labeling method that allows the quantification of subcellular transcriptomes. We have demonstrated the efficacy of Halo-seq here by using it to quantify chromatin-proximal, nucleolar, and cytoplasmic transcriptomes. In Halo-seq, RNA molecules in close proximity to a spatially restricted protein are specifically marked and biotinylated, facilitating their separation from bulk cellular RNA and their quantification.

2021-04-19 | GSE172281 | GEO

Analysis of subcellular transcriptomes by RNA proximity labeling with Halo-seq

Project description:Analysis of subcellular transcriptomes by RNA proximity labeling with Halo-seq

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A snapshot of Bothrops jararaca snake venom gland subcellular proteome

Project description:The synthesis of snake venom proteins is subjected to finely regulated processes in the specialized secretory epithelium within the venom gland. Such processes occur within a defined time frame in the cell and at specific cellular locations. Thus, the determination of subcellular proteomes allows the characterization of protein groups for which the site may be relevant to their biological roles, thereby allowing the deconvolution of complex biological circuits into functional information. In the case of snake venom glands, subcellular proteome analysis could help understand the molecular basis of venom variability. Consequently, knowing the functional implications of such phenotypic plasticity could prove relevant in envenoming treatment and biological research. In this regard, we performed subcellular fractionation of proteins from B. jararaca snake venom gland, focusing on nuclear proteins since this cellular compartment comprises key effectors that shape gene expression. Our results provided a snapshot of B. jararaca's subcellular venom gland proteome. They pointed to a 'conserved' proteome core among different life stages (newborn and adult) and between genders (adult male and female).

2023-09-30 | PXD040239 | Pride

BAP-seq proximity labeling of subcellular compartments

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2024-04-05 | GSE229451 | GEO

Slamseq of subcellular compartments in neurons

Project description:Slamseq of subcellular compartments in neurons

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SlamSeq of subcellular compartments in mouse primary cortical neurons

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2023-07-12 | E-MTAB-12888 | biostudies-arrayexpress

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