Xu-Kai Ma

Children's Hospital of Fudan University

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Li Yang

Children's Hospital of Fudan University

Ling‐Ling Chen

Center for Excellence in Molecular Cell Science

Bao‐Qing Gao

Shanghai Institute of Nutrition and Health

Youkui Huang

Center for Excellence in Molecular Cell Science

Quan Meng

Institute of Biophysics

Liang-Zhong Yang

Center for Excellence in Molecular Cell Science

Hao Wu

Center for Excellence in Molecular Cell Science

Yu-Hang Pan

Center for Excellence in Molecular Cell Science

Chu‐Xiao Liu

Center for Excellence in Molecular Cell Science

Rui Dong

Nanjing Medical University

Cooperative Institutions

University of Chinese Academy of Sciences

Chinese Academy of Sciences

Second Military Medical University

Center for Excellence in Molecular Cell Science

Eastern Hepatobiliary Surgery Hospital

Fudan University

Children's Hospital of Fudan University

Shanghai Jiao Tong University

Shanghai Institute of Nutrition and Health

Central South University

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Rapid, Efficient and Durable Fetal Hemoglobin Production Following CS-101 Treatment in Transfusion-Dependent β-Thalassemia Participants: An Autologous, Ex Vivo Edited CD34+ Stem Cell Product Using the Innovative Transformer Base Editor (tBE)

Blood (2024)

Yongrong Lai Rongrong Liu Lijie Wang Xu-Kai Ma Yaliang Li

10.1182/blood-2024-200691

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Citations (0)

CircRNA-derived pseudogenes

Cell Research (2016)

Rui Dong Xiao‐Ou Zhang Yang Zhang Xu-Kai Ma Ling‐Ling Chen

Pseudogene

10.1038/cr.2016.42

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Citations (106)

CIRCexplorer3: A CLEAR Pipeline for Direct Comparison of Circular and Linear RNA Expression

Genomics Proteomics & Bioinformatics (2019)

Xu-Kai Ma Mengran Wang Chu‐Xiao Liu Rui Dong Gordon Carmichael

Abstract Sequences of circular RNAs (circRNAs) produced from back-splicing of exon(s) completely overlap with those from cognate linear RNAs transcribed from the same gene loci with the exception of their back-splicing junction (BSJ) sites. Therefore, examination of global circRNA expression from RNA-seq datasets generally relies on the detection of RNA-seq fragments spanning BSJ sites, which is different from the quantification of linear RNA expression by normalized RNA-seq fragments mapped to whole gene bodies. Thus, direct comparison of circular and linear RNA expression from the same gene loci in a genome-wide manner has remained challenging. Here, we update the previously-reported CIRCexplorer pipeline to version 3 for circular and linear RNA expression analysis from ribosomal-RNA depleted RNA-seq (CIRCexplorer3-CLEAR). A new quantitation parameter, fragments per billion mapped bases (FPB), is applied to evaluate circular and linear RNA expression individually by fragments mapped to circRNA-specific BSJ sites or to linear RNA-specific splicing junction (SJ) sites. Comparison of circular and linear RNA expression levels is directly achieved by dividing FPBcirc by FPBlinear to generate a CIRCscore, which indicates the relative circRNA expression level using linear RNA expression level as the background. Highly-expressed circRNAs with low cognate linear RNA expression background can be readily identified by CIRCexplorer3-CLEAR for further investigation. CIRCexplorer3-CLEAR is publically available at https://github.com/YangLab/CLEAR.

Circular RNA

Expression (computer science)

10.1016/j.gpb.2019.11.004

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Citations (74)

Additional file 3 of Knockout of circRNAs by base editing back-splice sites of circularized exons

Figshare (2022)

Xiang Gao Xu-Kai Ma Xiang Li Guo‐Wei Li Chu‐Xiao Liu

Additional file 3:. Table S2. List of oligonucleotides and primer sequences used in this study. (A) Sequences of oligonucleotides used in sgRNA constructs. (B) On-target primer sequences used in genomic DNA amplification. (C) The gRNA-dependent off-target primer sequences used in genomic DNA amplification. (D) Primer sequences used in RT-qPCR and RT-PCR analysis. (E) Primer sequences used in NB. (F) Sequences of oligonucleotides used in shRNA constructs

splice

Base (topology)

10.6084/m9.figshare.18132711

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Increased complexity of circRNA expression during species evolution

Figshare (2016)

Rui Dong Xu-Kai Ma Ling‐Ling Chen Li Yang

Circular RNAs (circRNAs) are broadly identified from precursor mRNA (pre-mRNA) back-splicing across various species. Recent studies have suggested a cell-/tissue- specific manner of circRNA expression. However, the distinct expression pattern of circRNAs among species and its underlying mechanism still remain to be explored. Here, we systematically compared circRNA expression from human and mouse, and found that only a small portion of human circRNAs could be determined in parallel mouse samples. The conserved circRNA expression between human and mouse is correlated with the existence of orientation-opposite complementary sequences in introns that flank back-spliced exons in both species, but not the circRNA sequences themselves. Quantification of RNA pairing capacity of orientation-opposite complementary sequences across circRNA-flanking introns by Complementary Sequence Index (CSI) identifies that among all types of complementary sequences, SINEs, especially Alu elements in human, contribute the most for circRNA formation and that their diverse distribution across species leads to the increased complexity of circRNA expression during species evolution. Together, our integrated and comparative reference catalog of circRNAs in different species reveals a species-specific pattern of circRNA expression and suggests a previously under-appreciated impact of fast-evolved SINEs on the regulation of (circRNA) gene expression.

Expression (computer science)

10.6084/m9.figshare.4476377

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IntS6 and the Integrator phosphatase module tune the efficiency of select premature transcription termination events

Molecular Cell (2023)

Rina Fujiwara Si-Nan Zhai Dongming Liang Aayushi Shah Matthew P. Tracey

Transcription

10.1016/j.molcel.2023.10.035

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Citations (9)

A guide to naming eukaryotic circular RNAs

Nature Cell Biology (2023)

Ling‐Ling Chen Albrecht Bindereif Irene Bozzoni Howard Y. Chang A. Gregory Matera

CLARITY

Circular RNA

10.1038/s41556-022-01066-9

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Citations (67)

Additional file 5 of CRISPR-dCas13-tracing reveals transcriptional memory and limited mRNA export in developing zebrafish embryos

Figshare (2023)

Youkui Huang Bao‐Qing Gao Quan Meng Liang-Zhong Yang Xu-Kai Ma

Additional file 5: Table S4. Expression of 15 transcripts containing at least eight repeated sequences at different development time (Related to Fig. 4b).

Tracing

10.6084/m9.figshare.22605976

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CIRCexplorer pipelines for circRNA annotation and quantification from non-polyadenylated RNA-seq datasets

Methods (2021)

Xu-Kai Ma Wei Xue Ling‐Ling Chen Li Yang

Covalently closed circular RNAs (circRNAs) produced by back-splicing of exon(s) are co-expressed with their cognate linear RNAs from the same gene loci. Most circRNAs are fully overlapped with their cognate linear RNAs in sequences except the back-spliced junction (BSJ) site, thus challenging the computational detection, experimental validation and hence functional evaluation of circRNAs. Nevertheless, specific bioinformatic pipelines were developed to identify fragments mapped to circRNA-featured BSJ sites, and circRNAs were pervasively identified from non-polyadenylated RNA-seq datasets in different cell lines/tissues and across species. Precise identification and quantification of circRNAs provide a basis to further understand their functions. Here, we describe detailed computational steps to annotate and quantify circRNAs using a series of CIRCexplorer pipelines.

Circular RNA

10.1016/j.ymeth.2021.02.008

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Citations (27)

Additional file 2 of Knockout of circRNAs by base editing back-splice sites of circularized exons

Figshare (2022)

Xiang Gao Xu-Kai Ma Xiang Li Guo‐Wei Li Chu‐Xiao Liu

Additional file 2:. Table S1. List of high-confidence circRNAs in 293FT Cells. High-confidence circRNAs was determined from ribo–, poly(A)– and RNaseR-treated RNA-seq in 293FT cells, shown by circRNA location, strand, gene symbol, transcript ID, included exons, FPB in ribo–, p(A)– and RNaseR-treated samples, whether can be targeted by hA3A-eBE-Y130F or ABEmax, whether have predominantly bs-exons, and whether have novel bs-exons

splice

Base (topology)

10.6084/m9.figshare.18132708

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