News
2024
October: Zhi-Can, Bao-Qing, Fang, Xu-Kai & Li have published an article in Genome Biology. Awesome job!
This study developed DEMINING, a computational framework using DeepDDR to directly distinguish RNA editing from DNA mutations in RNA-seq, revealing novel mutations and RNA editing events linked to gene expression and neoantigen production in acute myeloid leukemia patients.
July: Pei-Hong and Li have contributed an article in Life Science Alliance. Well done!
June: Guo-Hua and Li have contributed an article in Molecular Cell. Well done!
This study identified that a subset of adenosine (A)-rich circRNAs are restricted in H9 nuclei but exported to cytosols upon differentiation. Such a subcellular relocation of circRNAs is modulated by the poly(A)-binding protein PABPC1. Decreased nuclear PABPC1 upon neuronal differentiation enables the export of (A)-rich circRNAs, including circRTN4(2,3), which is required for neurite outgrowth.
May: Pei-Hong has passed the dissertation defense! Congratulations!
March: Li has been selected as one of the 2023 Most Cited Chinese Researchers (released by Elsevier). Congratulations to Li!
2023
December: Li has been selected as the 2023 Highly Cited Researcher (released by Clarivate). Congratulations to Li!
November: Si-Nan, Xu-Kai and Li have contributed an article in Molecular Cell. Well done!
This study unveiled Integrator subunits 6 (IntS6) over-expression blocks Integrator function by titrating Integrator phosphatase module (PP2A-AC) to modulate premature termination of only a subset of Integrator-regulated genes in Drosophila and PP2A-B subunits (tws/wdb) not normally associated with Integrator can also regulate the efficiency of select premature transcription termination events.
November: Zhi-Can, Jia, Yi-Lin and Li have contributed an article in Cell Stem Cell. Congratulations!
This study effectively induced elevated fetal hemoglobin levels in hematopoietic stem/progenitor cells from both healthy and b-thalassemia patients using the Transformer Base Editor (tBE), with no observed off-target mutations. The persistent therapeutic effects of tBE on repopulating hematopoietic stem cells underscore its potential as a safe and effective strategy for treating b-hemoglobinopathies.
October: Bao-Qing and Li have contributed an article in Nature Protocols. Well done!
This paper describes the experimental protocol and computational pipeline for the design and application of the transformer base editor (tBE) in mammalian cells and in mice.
September: Bao-Qing, Jia and Li have contributed an article in MedComm. Congratulations!
This study used prime editor (PE) to precisely edit ACE2 at structurally selected sites, and demonstrated that residue changes at Q24/D30/K31 and/or K353 of ACE2 could completely ablate the binding of tested viruses while maintaining its physiological role in host angiotensin II conversion.
April: Li has been selected as the 2022 Highly Cited Researcher (released by Clarivate). Congratulations to Li!
April: Li has been selected as one of the 2022 Most Cited Chinese Researchers (released by Elsevier). Congratulations to Li!
March: Pei-Hong and Li have contributed an article in Nature. Congratulations!
This work uses high-resolution live-cell microscopy to screen 200 candidate nucleolar proteins, reveal the superfine structure of the nucleoli, provide insight into the functional sub-nucleolar organization and identify a physiologically essential step in rRNA maturation that requires the static protein URB1 in the phase-separated nucleolus.
February: We celebrate the opening of new Fudan IBS workspace.
2022
December: Guo-Wei and Li have contributed an article in EMBO Reports. Well done!
With uncovering the landscape of neuron-type-specific lincRNAs at single-cell resolution by integrating two scRNA-seq methods, this study characterizes a conserved and previously underappreciated lincRNA CLAP that functionally contributes to histamine-mediated itch transmission possibly through downregulating the expression of type-specific and itch-associated genes.
December: Guo-Hua, Ying and Li have contributed an article in Briefings in Bioinformatics. Congratulations!
This study developed RNAlight to precisely predict nuclear or cytoplasmic localization of mRNAs and lncRNAs, and further identified important k-mer features and RBPs possibly involved in their subcellular localizations.
November: Guo-Wei and Li have contributed an article in Cell Reports. Well done!
This study identified m6A-modified lincRNA Dubr can interact and stabilize YTHDF1/3 through its m6A modification, thereby facilitating the translation of Tau and Calmodulin as well as maintaining subsequent axon elongation and neuronal migration.
November: Guo-Wei has passed the dissertation defense! Congratulations!
October: Li contributed to a special issue published in RNA: Tribute to Sidney (Sid) Altman. Sid is one of the veritable architects of modern RNA research and is widely known as the co-recipient of the 1989 Nobel Prize in Chemistry, an honor shared with Tom Cech for the discovery of catalytic RNAs. Li did his post-doc with Sid in Yale from 2004 to 2006. The whole collection of essays is definitely inspiring.
September: We welcome new graduate students Li and Yu-Yao to join our group!
September: We welcome new postdoctor Mei to join our group! Mei obtained her PhD at the Institute of Biophysics of the Chinese Academy of Sciences.
June: Bao-Qing, Ying and Li have contributed an article in Cell Insight. Congratulations!
This study analyzed metagenomic and bacterial genomic databases to comprehensively screen Cas13 homologies, and further developed CRISPRpalette system to successfully achieve multi-color RNA visualization in living cells.
April: Li has been selected as one of the 2021 Most Cited Chinese Researchers (released by Elsevier). Congratulations to Li!
March: Bao-Qing, Ying, Jia and Li have contributed an article in Nat Commun. Well done!
This study developed spegRNA by introducing same-sense mutations to increase PE’s base-editing efficiency and developed apegRNA by altering the pegRNA secondary structure to increase PE’s indelediting efficiency.
March: Zhi-Can, Ying, Jia and Li have contributed an article in The CRISPR Journal. Congratulations!
This study demonstrates that CRISPR-based PE tools induced no observable genome- or transcriptome-wide pegRNA-independent OT effects in human cells, suggesting a high editing specificity of its RTase moiety.
January: Guo-Wei has obtained President Award (Special Prize) at the 4th Graduate Research Appreciation Day (GRAD), Shanghai Institute of Nutrition and Health (SINH). Congratulations to Guo-Wei.
2021
November: Fang has passed the dissertation defense! Congratulations!
August: Yun-Ni, Wei, Fang, Jia and Li have contributed an article in Sci China Life Sci. Well done!
This study reports that many circular intronic RNAs (ciRNAs) contain high GC% and tend to form DNA:RNA hybrids (R-loops) for RNase H1 cleavage, a process that appears to promote Pol II transcriptional elongation at ciRNA-producing loci.
August: Guo-Wei, Fang, Guo-Hua and Li have contributed an article in Genome Biology. Congratulations to Guo-Wei, Fang, Guo-Hua and Li!
This study developed a method to identify, evaluate, and quantify cleavage and polyadenylation sites(PASs) from 3′ tag-based scRNA-seq.
July: Fang and Li have contributed an article in Science. Well done! Congratulations to Fang and Li! Looking forward to the next masterpiece!
This study report that the sno-lncRNA SLERT is an RNA regulator that controls the biophysical properties of FC/DFCs by DDX21 and thus ribosomal RNA production.
May: Wei has passed the dissertation defense! Congratulations!
May: Congratulations to Wei, Jia, Yun-Ni and Li for their contribution to a work published in Nat Cell Biol. Well done!
This study constructs a transformer BE (tBE) system that induces efficient editing with only background levels of genome-wide and transcriptome-wide OT mutations.
April: Li has been selected as one of the 2020 Highly Cited Chinese Researchers (released by Elsevier). Congratulations to Li!
February: Congratulations to Xu-Kai, Wei and Li for their contribution to a method paper published in Methods. Well done!
This review provides a step-by-step protocol to annotate and quantify circRNAs from RNA-seq datasets, by using a series of CIRCexplorer pipelines.
February: Fang and Li have contributed an article in Methods. Congratulations to Fang and Li!
This method paper describes the experimental protocol and computational pipeline unique for circular RNA secondary structural assembly in living cells.
January: Congratulations to Wei, Xu-Kai and Li for their contribution to a review article published in Sci. China Life Sci. Well done!
This review highlights current understanding of back splicing regulation during nascent RNA synthesis by taking advantage of metabolic tagging nascent RNA sequencing. The faster Pol II transcription, the more back-splicing for circRNA biogenesis.
2020
December: Congratulations to Wei, Yun-Ni, Jia and Li for their contribution to a work published in Nat Methods. Well done!
This study establishs CRISPR–RfxCas13d as a useful tool for the discovery and functional study of circRNAs at both individual and large-scale levels.
December: Xu-Kai has been selected into the "Super Postdoctoral Fellow" program of Shanghai. Congratulations to Xu-Kai.
November: Ying has passed the dissertation defense! Congratulations!
November: Meng-Ran has passed the dissertation defense! Congratulations!
November: Xu-Kai and Li have contributed an article in Chemistry of Life. Congratulations to Xu-Kai and Li .
This paper introduces the study that nonconserved RNA processing of conserved lncRNAs contribute to their functional evolution.
June: Xu-Kai has passed the dissertation defense! Congratulations!
June: Jia-Lin has passed the dissertation defense! Congratulations!
June: Ying, Yi-Chun, Jia and Li has contributed an article in Cell Rep. Congratulations to Ying, Yi-Chun, Jia and Li!
This work reported the development and application of a new base editor system, BEACON, which combines dCas12a with human APOBEC3A or its engineering version. BEACON induced efficient editing in cells and mouse embryos with basal levels of DNA damage response, RNA off-target mutations and unintended side-products. In the study, a new RNA-editing analysis-pipeline to decode all-twelve-types of RNA-editing, referred to as RADAR, was also constructed to decode any RNA editing, predominantly A-to-I, events in RNA-seq datasets, and to evaluate C-to-U off-target editing in the treatment with BEs.
June: Ying and Li has contributed an article in Nat Biotechnol. Congratulations to Ying and Li!
Ying and Li involved in this work to profile clinically-relevant variants in human, which can be potentially targeted by the reported dual adenine and cytosine base editor.
April: He-Na and Li has contributed an article in BMC Biology. Congratulations to He-Na and Li!
This work identifies ~ 1000 candidate m5C sites in the wider transcriptome, most in mRNAs, and further reveals a functional interdependence of cytosine methylation level with mRNA translation.
2019
October: Ying, Yi-Chun, Jia and Li has contributed an article in Genome Biol. Congratulations to Ying, Yi-Chun, Jia and Li!
September: Xu-Kai and Li have contributed an article in Theranostics. Congratulations to Xu-Kai and Li.
August: Congratulations to Li for winning The National Science Fund for Distinguished Young Scholars! Cheers!!!
June: Welcome new Research Associate Shi-Yi to join our group!
May: Yang lab and Chen lab had fun at Shanghai Disneyland on the 520 Day!
April: Fang, Wei, Kai-Ge and Li have contributed an article in Cell. Well done! Congratulations to Fang, Wei, Kai-Ge and Li! Looking forward to the next masterpiece!
March: Wei’s first child was born on 3/22! Congratulations on Wei's sweet angel!
2018
December: Welcome new graduate students Yun-Ni and Pei-Hong to join our group!
November: Zheng has passed the dissertation defense! Congratulations to Zheng!
September: Yang lab and Chen lab had a wonderful time together in the trampoline park.
September: Meng-Ran and Li have contributed an article in Nat Cell Biol. Congratulations to Meng-Ran and Li.
September: Rui, Xu-Kai, Guo-Wei and Li have contributed a database article in Genomics Proteomics Bioinformatics. Congratulations to Rui, Xu-Kai, Guo-Wei and Li.
August: Ying, Jia and Li have contributed an article in Nat Biotechnol. Congratulations to Ying, Jia and Li.
July: Welcome new Research Associate Yi-Chun to join our group!
May: Qin has passed the dissertation defense! Congratulations!
2017
December: Wei, Jia and Li have contributed an article in Nat Struct Mol Biol. Congratulations to Wei, Jia and Li.
October: Our lab participated in city hiking and won the second and forth prizes.
June: Qin, Ying and Li have contributed a mini review in Quantitative Biology. Congratulations to Qin, Ying and Li.
July: Congratulations on our recent Mol Cell paper! Our paper has been selected as “Featured Article” of the issue. Moreover, the first authors of the paper were invited to take part in “Meet the Authors” section on the Mol Cell website to share their experience and the stories behind the paper. Congratulations to Wei again!
May: Rui has passed the dissertation defense! He becomes the Ph.D graduate of our lab! Congratulations to Rui!
2016
December: Rui, Xu-Kai and Li have contributed an article in RNA Biol. Congratulations to Rui, Xu-Kai and Li!
Novermber: Xu-Kai, Zheng and Li took part in the Cold Spring Harbor Asia conference on RNA Biology and Li delivered a presentation.
Novermber: Rui and Wei participated in Cell Symposia Functional RNAs and Rui presented his latest public researches in the poster presentations.
November: Our lab participated in city hiking and won the third prize.
October: Zheng, Jian-Feng and Li have contributed an article in Mol Cell. Congratulations to Zheng, Jian-Feng and Li!
The authors have employed a variety of techniques including RNA immunoprecipitation and deep sequencing to explore the repertoire of snoRNA related lncRNAs. These approaches allowed the authors to identify a type of polycistronic transcript derived lncRNAs that are 5' snoRNA capped and 3' polyadenylated (SPAs). SPA processing is associated with nascent mRNA 3’ processing and kinetic competition between XRN2 trimming and Pol II elongation. Following cleavage/polyadenylation of its upstream gene, the downstream uncapped pre-SPA is trimmed by XRN2 until this exonuclease reaches the co-transcriptionally assembled snoRNP. This snoRNP complex prevents further degradation, generates a novel 5' end and allows continuous Pol II elongation. The imprinted 15q11-q13 encodes two SPAs that are deleted in Prader-Willi syndrome (PWS) patients. These PWS region SPAs, together with previously identified sno-lncRNAs (Yin et al., Mol Cell, 2012) form a nuclear accumulation that is enriched in multiple RNA binding proteins (RBPs) including TDP43, RBFOX2 and hnRNP M. Generation of a human PWS cellular model by depleting these lncRNAs results in altered patterns of RBPs binding and alternative splicing. Prader-Willi Syndrome is a multiple-system human disorder including global developmental delay, mental retardation, morbid obesity, and etc. These findings thus implicated previously unannotated class of lncRNAs in PWS pathogenesis during early embryonic development and adulthood.
October: Zheng, Qin and Li have contributed a preview in Mol Cell. Congratulations to Zheng, Qin and Li.
September: Rui has obtained National Scholarship for Outstanding Graduate Student, Ministry of Education of the People's Republic of China. Congratulations to Rui!
July: Rui took part in the second circular RNA Research Forum and delivered a presentation.
June: Rui and Wei participated in the 2016 joint annual meeting of the RNA Society and the RNA Society of Japan and presented their latest public researches in the poster presentations.
June: We have published a collaborative work with Chen Lab in Genome Res. Congratulations to Xiao-Ou, Rui, Jia-Lin, Zheng and Li.
May: Xiao-Ou has passed the dissertation defense! He becomes the first Ph.D graduate of our lab! Congratulations to Xiao-Ou!
April: Welcome new graduate student Meng-Ran to join our group!
March: Our lab has contributed a letter in Cell Res. Congratulations to Rui, Xiao-Ou, Xu-Kai and Li.
March: Xiao-Ou has obtained 2016 Shanghai outstanding graduates and 2016 Shanghai tri-merit student honor award. Congratulations to Xiao-Ou.
March: Welcome new graduate students Kai-Xuan and Ying to join our group!
2015
December: We welcome new Research Associate Jia to join our group!
August: Li has contributed an article in Genome Res. Congratulations to Li!
August: Xiao-Ou has been selected as a recipient of the 2015 Ray Wu Prize for Excellent in Life Sciences. Congratulations to Xiao-Ou!
July: We have published a collaborative work on haploid embryonic stem cells with Yang Lab in Cell Stem Cell. Congratulations to Rui and Li.
April: We welcome new graduate students Xu-Kai and Jia-Lin to join our group!
April: Our website has been updated with wholly new engine and templates. Cheer Up!
2014
December: Zheng has passed his prelim! Congratulations to Zheng!
September: We have published a collaborative work on circular RNAs with Chen Lab in Cell. Congratulations to Xiao-Ou and Li.
May: We have published a collaborative work on sno-lncRNAs with Chen Lab in BMC Genomics. Congratulations to Xiao-Ou and Li.
May: Rui and Qin of our group have passed the mid-term review. Congratulations to Rui and Qin!
April: Welcome new graduate student Zheng to join our group!
2013
December: Rui and Qin of our group have passed their prelim. Congratulations to Rui and Qin!
October: Hua-Hong has a cute baby boy. Cheer up!
September: We have published a collaborative work on circular intronic RNAs with Chen Lab in Mol Cell. Congratulations to Xiao-Ou, Shanshan and Li.
August: Our sno-lncRNA paper published in Mol Cell was recently selected as one of Best of 2012 by Mol Cell.
June: Xiao-Ou has obtained the Best Poster Awards in The 2013 CAS-MPG Partner Institute for Computational Biology Scientific Exchange Meeting. Congratulations to Xiao-Ou!
March: Xiao-Ou has passed his mid-term evaluation. Congratulations to Xiao-Ou!
April: We have published a collaborative work on RNA editing with Chen Lab in BMC Genomics. Congratulations to Shanshan and Li.
April: We welcome new graduate students Rui and Qin to join our group!
2012
December: Li was invited to give comments on Diffculties in RNA editing study in Nat Biotechnol. Congratulations to Li!
December: Congratulations to Xiao-Ou for passing his prelim!
October: We published a collaborative work on sno-lncRNA with Chen Lab in Mol Cell. Congratulations to Li.
October: Chen Lab and our lab had an enjoyable joint lab retreat in Suzhou.