Biology subjects

Cao, S.-M.

Publications and source records attributed to Cao, S.-M..

4 recordsLinked to original sources

bioRxiv2026

Chimeric archaeal BHB-human pre-tRNA scaffold HARBOR system enables versatile production of functional circular RNA modalities

Circular RNAs (circRNAs) exhibit superior intrinsic stability and lower immunogenicity compared with linear RNAs, rendering them promising modalities for biomedical and biotechnological applications. Here, we establish the HARBOR (Human-Archaeal RNA Backbone for Overexpression of circular RNA) system, an engineered endogenous circRNA expression platform integrating a human precursor transfer RNA (pre-tRNA) scaffold with an archaeal Bulge-Helix-Bulge (BHB) motif. HARBOR repurposes the endogenous tRNA splicing machinery to generate chimeric pre-tRNA intermediates, which are rapidly degraded following processing, while producing circRNAs ranging from hundreds of nucleotides to 8 knt in cells and in vivo. Notably, it enables robust production of large-sized circRNAs with yields nearly 80-fold than the intronic complementary sequence-mediated back-splicing (3D5) system and can drive protein expression from translatable circRNAs at an efficiency close to 20-fold than the Tornado system. Such prominent properties support diverse applications of HARBOR, including producing therapeutic aptamers targeting PKR-associated neuroinflammation and pathological TDP-43 condensation, as well as protein-coding circRNAs encoding adenine base editors for genome editing and MYOD1 for fibroblast-to-myocyte trans-differentiation. Collectively, HARBOR represents a versatile, scalable, and user-friendly platform that unifies circRNA-based aptamer and protein expression applications, advancing circRNA-enabled engineering and biomedical applications.

molecular biology↗

bioRxiv2024

Pre-rRNA spatial distribution and functional organization of the nucleolus

The self-organized nucleolus is where the pre-ribosomal RNA (pre-rRNA) processing and pre-ribosomal ribonucleoprotein (RNP) assembly take place. Here we present the spatiotemporal distribution of pre-rRNA intermediates in the human nucleolus, revealing a segregated spatial distribution of small subunit (SSU) and large subunit (LSU) precursors. Notably, the 5 external transcribed spacer (5 ETS)-containing SSU pre-rRNAs are retained across FC-DFC-PDFC regions, while the internal transcribed spacer 2 (ITS2)-containing LSU pre-rRNAs move to PDFC-GC regions for processing. Inhibiting 5 ETS processing disrupts the SSU pre-rRNA distribution and the nested FC-DFC sub-nucleolar structure. Cells in amniotes possess a multi-layered nucleolus, whereas anamniotes have only a bipartite structure with a merged FC-DFC. Kinetic labeling of pre-rRNA outflow shows a 7-fold higher pace in tetrapartite nucleoli over that in bipartite nucleoli, indicating that the emergence of the nested FC-DFC may facilitate an efficient SSU pre-rRNA processing over the course of evolution. Collectively, depicting the spatiotemporal distribution of pre-rRNAs reveals a key role of processing steps in organizing the multi-layered nucleolus and suggests a possible evolutionary advantage of the multi-layered structure in amniotes.

molecular biology↗

bioRxiv2020

Screening for functional circular RNAs using the CRISPR-Cas13 system

Circular RNAs (circRNAs) produced from back-spliced exons are widely expressed, but individual circRNA functions remain poorly understood due to inadequate methods, such as RNAi and genome engineering, in distinguishing overlapped exons in circRNAs from those in linear cognate mRNAs1,2. Here we report that the programable RNA-guided, RNA-targeting CRISPR-Cas13, RfxCas13d, effectively and specifically discriminates circRNAs from mRNAs, using guide (g)RNAs targeting sequences spanning the back-splicing junction (BSJ) sites featured in RNA circles. Using a lentiviral library that targets sequences across BSJ sites of highly expressed human circRNAs, we show that a group of circRNAs are important for cell growth mostly in a cell-type specific manner and that a common oncogenic circRNA, circFAM120A, promotes cell proliferation in vitro and in vivo by preventing FAM120A mRNA from binding the translation inhibitor IGF2BP2 for efficient translation. Application of RfxCas13d/BSJ-gRNA screening has also uncovered circMan1a2 with regulatory potential in mouse embryo preimplantation development. Together, these results establish CRISPR-RfxCas13d as a useful tool for the discovery and functional study of circRNAs at both individual and large-scale levels.

molecular biology↗

bioRxiv2018

Genome sequencing analysis identifies high-risk Epstein-Barr virus subtypes for nasopharyngeal carcinoma

Epstein-Barr virus (EBV) infection is ubiquitous worldwide and associated with multiple cancers including nasopharyngeal carcinoma (NPC). The role of EBV viral genomic variation in NPC development and its striking endemicity in southern China has been poorly explored. Through large-scale genome sequencing and association study of EBV isolates from China, we identified two non-synonymous EBV variants within BALF2 strongly associated with NPC risk (conditional P value 1.75x10-6 for SNP162476_C and 3.23x10-13 for SNP163364_T), whose cumulative effects contributed to 83% of the overall risk in southern China. Phylogenetic analysis of the risk variants revealed a unique origin in southern China followed by clonal expansion. EBV BALF2 haplotype carrying the risk variants were shown to reduce viral lytic DNA replication, as a result potentially promoting viral latency. Our discovery has not only provided insight to the unique endemic pattern of NPC occurrence in southern China, but also paved the way for the identification of individuals at high risk of NPC and effective intervention program to reduce the disease burden in southern China.

genetics↗