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A Unified Framework for Systematic Identification of Post-Transcriptional Regulatory Modules [Ribosomal profiling]

ABSTRACT: A Unified Framework for Systematic Identification of Post-Transcriptional Regulatory Modules [Ribosomal profiling]

PROVIDER: PRJNA937656 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR23585000.fastq.gz	Fastqsanger.gz
	SRR23585001.fastq.gz	Fastqsanger.gz
	SRR23585002.fastq.gz	Fastqsanger.gz
	SRR23585003.fastq.gz	Fastqsanger.gz
	SRR23585004.fastq.gz	Fastqsanger.gz

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A Unified Framework for Systematic Identification of Post-Transcriptional Regulatory Modules [Ribosomal profiling]

Project description:RNA-binding proteins (RBPs) are multifunctional regulators of gene expression with complex and context-dependent mechanisms of action, yet the regulatory grammar that underlies RBP-mediated functions remains underexplored. Here, we performed a multi-omic data integration to systematically decipher the context-specific functions of RBPs. First, we report a compendium of in vivo proximity-dependent biotinylation (BioID) datasets of 50 human RBPs, which we used to generate a large-scale map of RBP protein neighborhoods. In parallel, we took advantage of CRISPR-interference with single-cell RNA-seq read-out (Perturb-seq) to capture rich transcriptomic phenotypes downstream of each RBP knockdown. By combining these physical and functional interaction readouts, along with the ENCODE transcriptome-wide atlas of RBP binding sites from eCLIP assays, we generated an integrated map of functional RBP interactions. This map not only captures well-studied post-transcriptional processes, but also reveals numerous previously unknown RBP-mediated regulatory functions. For a number of these cases, we have validated their predicted context-specific RBP functions using biochemical and genetic approaches. By deciphering these complex modes of functional interactions between RBPs, we have taken the first step towards a more comprehensive understanding of post-transcriptional regulatory processes and their underlying molecular grammar.

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