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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

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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.

2024-02-21 | GSE225808 | GEO

A Unified Framework for Systematic Identification of Post-Transcriptional Regulatory Modules

Project description:This SuperSeries is composed of the SubSeries listed below.

2024-02-21 | GSE225809 | GEO

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

2024-02-21 | GSE225807 | GEO

A Unified Framework for Systematic Identification of Post-Transcriptional Regulatory Modules [ZNF800_ko]

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A Unified Framework for Systematic Identification of Post-Transcriptional Regulatory Modules [ATAC-Seq]

2024-02-21 | GSE225806 | GEO

Transcriptome sequencing elucidates gene modules in microglia

Project description:Microglia are multifunctional cells that are important for brain development and homeostasis. Despite the growing evidence of their complexity, the field lacks a unified system for categorizing the many microglial states. In an effort to develop a comprehensive classification system, we profiled transcriptomes of mouse microglia in 96 different stimulus conditions. We generated fine-resolution gene modules that are robustly preserved across datasets by employing a two-step clustering approach. These modules served as the basis for a combinatorial code that we then used to characterize microglial activation under inflammatory stimulus conditions in vitro. Many of the modules were preserved in vivo, and were differentially regulated during acute inflammation and in aging. In summary, the microglial gene modules presented here are a novel resource for classifying and characterizing microglial states in health and disease.

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