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Highly structured RNA molecules usually interact with each other, and associate with various RNA-binding proteins, to regulate critical biological processes. However, RNA structures and interactions in intact cells remain largely unknown. Here, by coupling proximity ligation mediated by RNA-binding proteins with deep sequencing, we report an RNA in situ conformation sequencing (RIC-seq) technology for the global profiling of intra- and intermolecular RNA-RNA interactions. This technique not only recapitulates known RNA secondary structures and tertiary interactions, but also facilitates the generation of three-dimensional (3D) interaction maps of RNA in human cells. Using these maps, we identify noncoding RNA targets globally, and discern RNA topological domains and trans-interacting hubs. We reveal that the functional connectivity of enhancers and promoters can be assigned using their pairwise-interacting RNAs. Furthermore, we show that CCAT1-5L--a super-enhancer hub RNA--interacts with the RNA-binding protein hnRNPK, as well as RNA derived from the MYC promoter and enhancer, to boost MYC transcription by modulating chromatin looping. Our study demonstrates the power and applicability of RIC-seq in discovering the 3D structures, interactions and regulatory roles of RNA. RNA in situ conformation sequencing (RIC-seq) enables the generation of three-dimensional interaction maps of RNA in cells, which sheds light on the interactions and regulatory functions of RNA., Author(s): Zhaokui Cai [sup.1] [sup.2] , Changchang Cao [sup.1] , Lei Ji [sup.1] , Rong Ye [sup.1] [sup.2] , Di Wang [sup.1] [sup.2] , Cong Xia [sup.3] , Sui Wang [...]

H2S is an endogenous gas signaling molecule and its multiple biological effects have been demonstrated. The abnormal level of H2S is closely related to the occurrence and development of many diseases, and H2S donors has important pharmacological implications. In recent years, H2S donors represented by ADTOH (5-(4-hydroxyphenyl)-3H-1,2-dithiole-3-thione) are often used to synthesize new 'conjugate' compounds that can release H2S and parent drugs. These hybrids retain the pharmacological activity of the parent drugs and H2S and have a synergistic effect. ADTOH and parent drug hybrids have become one of the important strategies for the development of H2S donor conjugate drugs. This review summarizes molecular hybrids between ADTOH and clinical drugs to provide new ideas for the study of H2S donor drug design. [ABSTRACT FROM AUTHOR]

Background & Aims: The molecular mechanism underlying metabolic dysfunction-associated steatotic liver disease (MASLD) is elusive and whether non-coding RNAs can serve as biomarkers and therapeutic targets of MASLD is less defined., Methods: Exon capture RNA sequencing analysis was used to identify read-through circRNAs (rt-circRNAs) in livers from three MASLD patients and three patients without MASLD. Hepatocyte-specific deletion or overexpression of rt-circRNA RCRIN were utilized to study MASLD pathogenesis., Results: We identified 1126 rt-circRNAs in the liver tissues from MASLD patients. RCRIN was highly expressed in normal livers and was downregulated in MASLD livers. Rcrin deletion in hepatocytes caused lipid accumulation and MASLD development, while Rcrin overexpression suppressed the MASLD progression. Mechanistically, in normal hepatocytes, highly expressed RCRIN bound to RPL8 protein to recruit RNF2 for its degradation, reducing RPL8-contained ribosome numbers and lipid accumulation. In MASLD livers, lowerly expressed RCRIN released RPL8 protein to promote RPL8-contained ribosome numbers and lipid synthesis, leading to higher lipid accumulation and ER stress. We synthesized RCRIN and N-acetylgalactosamine (GalNAc)-Rpl8 siRNA to treat established MASLD in mice, both of which suppressed MASLD pathogenesis., Conclusions: Our findings provide an in vivo function of rt-circRNA RCRIN, show its inhibitory effects in MASLD pathogenesis, indicating RCRIN and RPL8 may be therapeutic targets and candidate nucleic acid drugs for treating MASLD., Impact and Implications: Our finds reveal a novel mechanism connecting a read-through circRNA RCRIN, ribosome heterogeneity and MASLD pathogenesis. In normal hepatocytes, RCRIN exerts its role by reducing liver lipid accumulation and ER stress through promotion of RPL8 degradation. In MASLD patients, lower RCRIN releases RPL8 to form RPL8-contained ribosomes to promote lipid accumulation and ER stress. RCRIN overexpression and RPL8 depletion dramatically suppresses MASLD development and progression. Our findings indicate that RCRIN and RPL8 might be potential therapeutic targets for treatment of MASLD patients., Competing Interests: Declaration of Competing Interest: All of the authors declare no competing financial interests., (Copyright © 2024 Institute of Biophysics, Chinese Academy of Sciences. Published by Elsevier B.V. All rights reserved.)

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.)

H 2 S is an endogenous gas signaling molecule and its multiple biological effects have been demonstrated. The abnormal level of H 2 S is closely related to the occurrence and development of many diseases, and H 2 S donors has important pharmacological implications. In recent years, H 2 S donors represented by ADTOH (5-(4-hydroxyphenyl)-3H-1,2-dithiole-3-thione) are often used to synthesize new 'conjugate' compounds that can release H 2 S and parent drugs. These hybrids retain the pharmacological activity of the parent drugs and H 2 S and have a synergistic effect. ADTOH and parent drug hybrids have become one of the important strategies for the development of H 2 S donor conjugate drugs. This review summarizes molecular hybrids between ADTOH and clinical drugs to provide new ideas for the study of H 2 S donor drug design.