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RNA-binding proteins (RBPs) bind at different positions of the pre-mRNA molecules to promote or reduce the usage of a particular exon. Seeking to understand the working principle of these positional effects, we develop a capture RIC-seq (CRIC-seq) method to enrich specific RBP-associated in situ proximal RNA-RNA fragments for deep sequencing. We determine hnRNPA1-, SRSF1-, and PTBP1-associated proximal RNA-RNA contacts and regulatory mechanisms in HeLa cells. Unexpectedly, the 3D RNA map analysis shows that PTBP1-associated loops in individual introns preferentially promote cassette exon splicing by accelerating asymmetric intron removal, whereas the loops spanning across cassette exon primarily repress splicing. These "positional rules" can faithfully predict PTBP1-regulated splicing outcomes. We further demonstrate that cancer-related splicing quantitative trait loci can disrupt RNA loops by reducing PTBP1 binding on pre-mRNAs to cause aberrant splicing in tumors. Our study presents a powerful method for exploring the functions of RBP-associated RNA-RNA proximal contacts in gene regulation and disease. [Display omitted] • CRIC-seq maps specific RBP-associated RNA-RNA spatial contacts • Positional rules of PTBP1-associated RNA loops in splicing regulation • PTBP1-associated intronic RNA loops facilitate asymmetrical intron removal • sQTLs disrupt PTBP1-associated RNA loops to promote tumor cell growth Ye et al. have developed a new method, named CRIC-seq, for the global profiling of PTBP1-associated RNA-RNA spatial contacts. The authors unravel the positional mechanisms by which PTBP1-associated RNA loops enhance or repress splicing, demonstrating that cancer-related splicing quantitative trait loci can disrupt PTBP1-associated RNA loops to promote tumor cell growth. [ABSTRACT FROM AUTHOR]

SARS-CoV-2 RNA interacts with host factors to suppress interferon responses and simultaneously induces cytokine release to drive the development of severe coronavirus disease 2019 (COVID-19). However, how SARS-CoV-2 hijacks host RNAs to elicit such imbalanced immune responses remains elusive. Here, we analyzed SARS-CoV-2 RNA in situ structures and interactions in infected cells and patient lung samples using RIC-seq. We discovered that SARS-CoV-2 RNA forms 2,095 potential duplexes with the 3′ UTRs of 205 host mRNAs to increase their stability by recruiting RNA-binding protein YBX3 in A549 cells. Disrupting the SARS-CoV-2-to-host RNA duplex or knocking down YBX3 decreased host mRNA stability and reduced viral replication. Among SARS-CoV-2-stabilized host targets, NFKBIZ was crucial for promoting cytokine production and reducing interferon responses, probably contributing to cytokine storm induction. Our study uncovers the crucial roles of RNA-RNA interactions in the immunopathogenesis of RNA viruses such as SARS-CoV-2 and provides valuable host targets for drug development. [Display omitted] • RIC-seq maps SARS-CoV-2-to-host RNA-RNA interactions in infected cells • SARS-CoV-2 stabilizes host mRNAs via base pairings at 3′ UTRs • SARS-CoV-2 stabilizes host mRNAs by recruiting RNA-binding protein YBX3 • Stabilized NFKBIZ contributes to SARS-CoV-2-elicited immunopathogenesis Zhao et al. use RIC-seq technology for global profiling of SARS-CoV-2-to-host RNA-RNA interactions in infected cells. The authors find that SARS-CoV-2 RNA stabilizes host mRNAs through their 3′ UTRs via base pairings by recruiting RNA-binding protein YBX3. The stabilized host mRNA NFKBIZ may contribute to SARS-CoV-2-elicited immunopathogenesis. [ABSTRACT FROM AUTHOR]

Postnatal cardiac development requires the orchestrated maturation of diverse cellular components for which unifying control mechanisms are still lacking. Using full-length sequencing, we examined the transcriptomic landscape of the maturating mouse heart (E18.5-P28) at single-cell and transcript isoform resolution. We identified dynamically changing intercellular networks as a molecular basis of the maturing heart and alternative splicing (AS) as a common mechanism that distinguished developmental age. Manipulation of RNA-binding proteins (RBPs) remodeled the AS landscape, cardiac cell maturation, and intercellular communication through direct binding of splice targets, which were enriched for functions related to general, as well as cell-type-specific, maturation. Overexpression of an RBP nuclear cap-binding protein subunit 2 (NCBP2) in neonatal hearts repressed cardiac maturation. Together, our data suggest AS regulation by RBPs as an organ-level control mechanism in mammalian postnatal cardiac development and provide insight into the possibility of manipulating RBPs for therapeutic purposes., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2024 Elsevier Inc. All rights reserved.)