2021 February: Congratulations to Xu-Kai, Wei and Li for their contribution to a method paper published in Methods. Well done!
2021 February: Fang and Li has contributed an article in Methods. Congratulations to Fang and Li!
2021 January: Congratulations to Wei, Xu-Kai and Li for their contribution to a review article published in Sci. China Life Sci. Well done!
Fig 1. Computational pipelines and biology of circRNAs.
1. Genome-wide profiling and characterization of functional circRNAs
Although only about 2% of the human genome encode protein sequences, recent advances in genome-wide analyses have revealed that the majority of the human genome are transcribed, largely from noncoding segments that were used to be considered as “junk sequences” or “dark matter” of the human genome. Besides well-characterized housekeeping noncoding RNAs (ncRNAs, such as tRNA, rRNA, snRNA and snoRNA) and small regulatory ncRNAs, the transcriptome has become even more complex with pervasively transcribed lncRNAs (at least 200 nt long without coding potential). By collaborating with experimental biologists, we have pioneered in developing poly(A)– RNA-seq and revealed a series of novel types of lncRNAs with specific structural features, including snoRNA-related lncRNAs (sno-lncRNAs; Yin et al 2012 Mol Cell; Zhang et al 2014 BMC Genomics), circular intronic RNAs (ciRNAs; Zhang et al 2013 Mol Cell), 5’ snoRNA-capped and 3’-polyadenylated lncRNAs (SPAs; Wu et al 2016 Mol Cell) and covalently-closed circRNAs produced from back-splicing of exons (circRNAs; Zhang et al 2014 Cell). Here, I mainly summarize systematic findings and our current understanding of circRNA biogenesis and functions, identified in my lab with collaboration (Fig.1).
Fig 2. From editing biology to editing technology.
2. Nucleotide editing modification and genome base editing technologies
Biochemical editing/modification on DNA/RNA not only expands the number of functions encoded by our genomes but also provides additional mechanisms of gene regulation. Over 100 different types of RNA editing/modifications have been identified transcriptome-wide. The most predominant form of such editing/modifications in higher eukaryotes is adenosine-to-inosine (A-to-I) editing on RNA, catalyzed by members of adenosine deaminases acting on RNA (ADAR) enzyme family. As the resulting I preferentially bases pair with cytidine (C) and is therefore functionally guanosine (G), A-to-I editing can have profound effects on downstream RNA processing and function, including recoding of open reading frames, altering the pattern of alternative splicing, interfering with microRNA function, modulating RNAi activity, and playing other roles in gene regulation. In addition to adenosine deaminases, cytidine deaminases are also known to be responsible for cytidine deamination on both single strand DNA (ssDNA) and RNA, catalyze by the apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like/activation-induced cytidine deaminase (APOBEC/AID) family of enzymes. Another major focus of my lab is developing new computational pipelines to globally profile nucleobase editing/modification events and to inspect potential crosstalk between different types of editing/modifications (Xiang et al 2018 Mol Cell). Importantly, by underscoring a previously underappreciated linkage between APOBECs with clustered regularly interspaced short palindromic repeat (CRISPR)-CRISPR associated system (Cas) 9-generated DNA breaks, my lab has contributed in the genome editing field by generating a variety of base editing systems to perform C-to-T changes at target genomic sites in broad genome backgrounds (Lei et al 2018 Nat Struct Mol Biol; Li et al 2018 Nat Biotechnol; Wang et al 2018 Nat Biotechnol; Wang et al 2019 Genome Biol; Wang et al 2020 Cell Rep) (Fig. 2).
The completion of the human genome project (HGP) in the beginning of this century and the application of affordable high-throughput sequencing technologies in the past decade have led life science researches to the post-genome era. The resulting wealth of deep-sequencing datasets at genome (including epi-genome) and transcriptome (including epi-transcriptome) levels challenges us to fully understand how functional genomic elements are transcribed and regulated, thus leading to human health and/or diseases. Importantly, the advent of novel genome editing technologies provides us powerful methods to change genetic information at desired target sites at single nucleotide resolution, which benefits not only basic research aiming to decipher how different genotypes result in distinct phenotypes but also pre-clinical study potential to cure human diseases caused by genetic mutations. Since established in 2011, my lab has continuously developed and applied novel computational strategies, together with the-state-of-the-art deep-sequencing technologies and diverse biochemical methods, to dissect complex expression, novel function and potential application of long noncoding RNAs (lncRNAs), especially structured ones such as covalently-closed circular RNAs (circRNAs) from back-splicing. In addition, a new research interest in my lab has been focusing on the invention of novel base editing technologies, along with distinct mechanisms of their unintended off-target effects for further improvement. These research findings shed new light on the functional potential of previously-underappreciated circRNAs, and provide powerful genome editing systems to achieve precise genetic changes in the application of biomedical research, biotechnology and therapeutics.
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