Publications by authors named "Ling-Ling Chen"

237 Publications

Long noncoding RNA and protein abundance in lncRNPs.

RNA 2021 Sep 15. Epub 2021 Sep 15.

CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Bio

Although long noncoding RNAs (lncRNAs) are generally expressed at low levels, emerging evidence has revealed that many play important roles in gene regulation by a variety of mechanisms as they engage with proteins. Given that the abundance of proteins often greatly exceeds that of their interacting lncRNAs, quantification of the relative abundance, or even the exact stoichiometry in some cases, within lncRNA-protein complexes is helpful for understanding of the mechanism(s) of action of lncRNAs. We discuss methods used to examine lncRNA and protein expression at the single cell, sub-cellular and sub-organelle levels, the average and local lncRNA concentration in cells, as well as how lncRNAs can modulate the functions of their interacting proteins even at a low stoichiometric concentration.
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http://dx.doi.org/10.1261/rna.078971.121DOI Listing
September 2021

Linking circular intronic RNA degradation and function in transcription by RNase H1.

Sci China Life Sci 2021 Aug 25. Epub 2021 Aug 25.

School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310024, China.

Circular intronic RNAs (ciRNAs) escaping from DBR1 debranching of intron lariats are co-transcriptionally produced from pre-mRNA splicing, but their turnover and mechanism of action have remained elusive. We report that RNase H1 degrades a subgroup of ciRNAs in human cells. Many 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. One ciRNA, ciankrd52, shows a stronger ability of R-loop formation than that of its cognate pre-mRNA by maintaining a locally open RNA structure in vitro. This allows the release of pre-mRNA from R-loops by ci-ankrd52 replacement and subsequent ciRNA removal via RNase H1 for efficient transcriptional elongation. We propose that such an R-loop dependent ciRNA degradation likely represents a mechanism that on one hand limits ciRNA accumulation by recruiting RNase H1 and on the other hand resolves R-loops for transcriptional elongation at some GC-rich ciRNA-producing loci.
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http://dx.doi.org/10.1007/s11427-021-1993-6DOI Listing
August 2021

Characterization of Circular RNAs.

Methods Mol Biol 2021 ;2372:179-192

School of Life Science and Technology, ShanghaiTech University, Shanghai, China.

Accumulated lines of evidence have revealed that a large number of circular RNAs are produced in transcriptomes from fruit fly to mouse and human. Unlike linear RNAs shaped with 5' cap and 3' tail, circular RNAs are characterized by covalently closed loop structures without open terminals, thus required specific treatments for their identification and validation. Here, we describe a detailed pipeline for the characterization of circular RNAs. It has been successfully applied to the study of circular intronic RNAs (ciRNAs) derived from intron lariats and circular RNAs (circRNAs) produced from back spliced exons in human.
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http://dx.doi.org/10.1007/978-1-0716-1697-0_16DOI Listing
January 2021

SCAPTURE: a deep learning-embedded pipeline that captures polyadenylation information from 3' tag-based RNA-seq of single cells.

Genome Biol 2021 08 10;22(1):221. Epub 2021 Aug 10.

CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China.

Single-cell RNA-seq (scRNA-seq) profiles gene expression with high resolution. Here, we develop a stepwise computational method-called SCAPTURE to identify, evaluate, and quantify cleavage and polyadenylation sites (PASs) from 3' tag-based scRNA-seq. SCAPTURE detects PASs de novo in single cells with high sensitivity and accuracy, enabling detection of previously unannotated PASs. Quantified alternative PAS transcripts refine cell identity analysis beyond gene expression, enriching information extracted from scRNA-seq data. Using SCAPTURE, we show changes of PAS usage in PBMCs from infected versus healthy individuals at single-cell resolution.
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http://dx.doi.org/10.1186/s13059-021-02437-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8353616PMC
August 2021

Phasing analysis of the transcriptome and epigenome in a rice hybrid reveals the inheritance and difference in DNA methylation and allelic transcription regulation.

Plant Commun 2021 Jul 15;2(4):100185. Epub 2021 Apr 15.

National Key Laboratory of Crop Genetic Improvement, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China.

Hybrids are always a focus of botanical research and have a high practical value in agricultural production. To better understand allele regulation and differences in DNA methylation in hybrids, we developed a phasing pipeline for hybrid rice based on two parental genomes (PP2PG), which is applicable for Iso-Seq, RNA-Seq, and Bisulfite sequencing (BS-Seq). Using PP2PG, we analyzed differences in gene transcription, alternative splicing, and DNA methylation in an allele-specific manner between parents and progeny or different progeny alleles. The phasing of Iso-Seq data provided a great advantage in separating the whole gene structure and producing a significantly higher separation ratio than RNA-Seq. The interaction of hybrid alleles was studied by constructing an allele co-expression network that revealed the dominant allele effect in the network. The expression variation between parents and the parental alleles in progeny showed tissue- or environment-specific patterns, which implied a preference for -acting regulation under different conditions. In addition, by comparing allele-specific DNA methylation, we found that CG methylation was more likely to be inherited than CHG and CHH methylation, and its enrichment in genic regions was connected to gene structure. In addition to an effective phasing pipeline, we also identified differentiation in gene structure that may have led to the expansion of allele functions in hybrids. In summary, we developed a phasing pipeline and provided valuable insights into alternative splicing, interaction networks, acting regulation, and the inheritance of DNA methylation in hybrid rice.
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http://dx.doi.org/10.1016/j.xplc.2021.100185DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8299081PMC
July 2021

lncRNA controls phase separation of FC/DFCs to facilitate Pol I transcription.

Science 2021 07;373(6554):547-555

State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, China.

RNA polymerase I (Pol I) transcription takes place at the border of the fibrillar center (FC) and the dense fibrillar component (DFC) in the nucleolus. Here, we report that individual spherical FC/DFC units are coated by the DEAD-box RNA helicase DDX21 in human cells. The long noncoding RNA (lncRNA) binds to DDX21 RecA domains to promote DDX21 to adopt a closed conformation at a substoichiometric ratio through a molecular chaperone-like mechanism resulting in the formation of hypomultimerized and loose DDX21 clusters that coat DFCs, which is required for proper FC/DFC liquidity and Pol I processivity. Our results suggest that is an RNA regulator that controls the biophysical properties of FC/DFCs and thus ribosomal RNA production.
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http://dx.doi.org/10.1126/science.abf6582DOI Listing
July 2021

CRISPR-Cereal: a guide RNA design tool integrating regulome and genomic variation for wheat, maize and rice.

Plant Biotechnol J 2021 Jul 26. Epub 2021 Jul 26.

National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China.

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http://dx.doi.org/10.1111/pbi.13675DOI Listing
July 2021

Development of a Novel Multi-Epitope Vaccine Against Crimean-Congo Hemorrhagic Fever Virus: An Integrated Reverse Vaccinology, Vaccine Informatics and Biophysics Approach.

Front Immunol 2021 16;12:669812. Epub 2021 Jun 16.

College of Life Science and Technology, Guangxi University, Nanning, China.

Crimean-Congo hemorrhagic fever (CCHF) is a highly severe and virulent viral disease of zoonotic origin, caused by a tick-born CCHF virus (CCHFV). The virus is endemic in many countries and has a mortality rate between 10% and 40%. As there is no licensed vaccine or therapeutic options available to treat CCHF, the present study was designed to focus on application of modern computational approaches to propose a multi-epitope vaccine (MEV) expressing antigenic determinants prioritized from the CCHFV genome. Integrated computational analyses revealed the presence of 9 immunodominant epitopes from Nucleoprotein (N), RNA dependent RNA polymerase (RdRp), Glycoprotein N (Gn/G2), and Glycoprotein C (Gc/G1). Together these epitopes were observed to cover 99.74% of the world populations. The epitopes demonstrated excellent binding affinity for the B- and T-cell reference set of alleles, the high antigenic potential, non-allergenic nature, excellent solubility, zero percent toxicity and interferon-gamma induction potential. The epitopes were engineered into an MEV through suitable linkers and adjuvating with an appropriate adjuvant molecule. The recombinant vaccine sequence revealed all favorable physicochemical properties allowing the ease of experimental analysis and . The vaccine 3D structure was established . Furthermore, the vaccine displayed excellent binding affinity for critical innate immune receptors: TLR2 (-14.33 kcal/mol) and TLR3 (-6.95 kcal/mol). Vaccine binding with these receptors was dynamically analyzed in terms of complex stability and interaction energetics. Finally, we speculate the vaccine sequence reported here has excellent potential to evoke protective and specific immune responses subject to evaluation of downstream experimental analysis.
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http://dx.doi.org/10.3389/fimmu.2021.669812DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8242340PMC
June 2021

An inferred functional impact map of genetic variants in rice.

Mol Plant 2021 Sep 29;14(9):1584-1599. Epub 2021 Jun 29.

National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China; Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China. Electronic address:

Interpreting the functional impacts of genetic variants (GVs) is an important challenge for functional genomic studies in crops and next-generation breeding. Previous studies in rice (Oryza sativa) have focused mainly on the identification of GVs, whereas systematic functional annotation of GVs has not yet been performed. Here, we present a functional impact map of GVs in rice. We curated haplotype information for 17 397 026 GVs from sequencing data of 4726 rice accessions. We quantitatively evaluated the effects of missense mutations in coding regions in each haplotype based on the conservation of amino acid residues and obtained the effects of 918 848 non-redundant missense GVs. Furthermore, we generated high-quality chromatin accessibility (CA) data from six representative rice tissues and used these data to train deep convolutional neural network models to predict the impacts of 5 067 405 GVs for CA in regulatory regions. We characterized the functional properties and tissue specificity of the GV effects and found that large-effect GVs in coding and regulatory regions may be subject to selection in different directions. Finally, we demonstrated how the functional impact map could be used to prioritize causal variants in mapping populations. This impact map will be a useful resource for accelerating gene cloning and functional studies in rice, and can be freely queried in RiceVarMap V2.0 (http://ricevarmap.ncpgr.cn).
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http://dx.doi.org/10.1016/j.molp.2021.06.025DOI Listing
September 2021

Alteration of Intestinal Microbiota Composition in Oral Sensitized C3H/HeJ Mice Is Associated With Changes in Dendritic Cells and T Cells in Mesenteric Lymph Nodes.

Front Immunol 2021 10;12:631494. Epub 2021 Jun 10.

Beijing Key Laboratory of Environmental Toxicology, School of Public Health, Capital Medical University, Beijing, China.

This research aimed to investigate the allergic reaction of C3H/HeJ mice after sensitization with ovalbumin (OVA) without any adjuvant and to analyze the association between intestinal microbiota and allergy-related immune cells in mesenteric lymph nodes (MLN). The allergic responses of C3H/HeJ mice orally sensitized with OVA were evaluated, and immune cell subsets in spleen and MLN and cytokines were also detected. The intestinal bacterial community structure was analyzed, followed by Spearman correlation analysis between changed gut microbiota species and allergic parameters. Sensitization induced a noticeable allergic response to the gavage of OVA without adjuvant. Increased levels of Th2, IL-4, CD103CD86 DC, and MHCIICD86 DC and decreased levels of Th1, Treg, IFN-γ, TGF-β1, and CD11CCD103 DC were observed in allergic mice. Furthermore, families of , , , and , all of which belonging to the order , were positively related to Treg and CD11CCD103 DC, while they were negatively related to an allergic reaction, levels of Th2, CD103CD86 DC, and MHCIICD86 DC in MLN. The family of belonging to the order was similarly correlated with allergic reaction and immune cells in MLN of mice. To sum up, allergic reactions and intestinal flora disturbances could be induced by OVA oral administration alone. The orders of and in intestinal flora are positively correlated with levels of Treg and CD11CCD103 DC in MLN of mice.
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http://dx.doi.org/10.3389/fimmu.2021.631494DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8222730PMC
September 2021

RNA structure probing uncovers RNA structure-dependent biological functions.

Nat Chem Biol 2021 07 25;17(7):755-766. Epub 2021 Jun 25.

MOE Key Laboratory of Bioinformatics, Beijing Advanced Innovation Center for Structural Biology and Frontier Research Center for Biological Structure, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, China.

RNA molecules fold into complex structures that enable their diverse functions in cells. Recent revolutionary innovations in transcriptome-wide RNA structural probing of living cells have ushered in a new era in understanding RNA functions. Here, we summarize the latest technological advances for probing RNA secondary structures and discuss striking discoveries that have linked RNA regulation and biological processes through interrogation of RNA structures. In particular, we highlight how different long noncoding RNAs form into distinct secondary structures that determine their modes of interactions with protein partners to realize their unique functions. These dynamic structures mediate RNA regulatory functions through altering interactions with proteins and other RNAs. We also outline current methodological hurdles and speculate about future directions for development of the next generation of RNA structure-probing technologies of higher sensitivity and resolution, which could then be applied in increasingly physiologically relevant studies.
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http://dx.doi.org/10.1038/s41589-021-00805-7DOI Listing
July 2021

Two gap-free reference genomes and a global view of the centromere architecture in rice.

Mol Plant 2021 Jun 24. Epub 2021 Jun 24.

National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; College of Life Science and Technology, Guangxi University, Nanning 530004, China. Electronic address:

Rice (Oryza sativa), a major staple throughout the world and a model system for plant genomics and breeding, was the first crop genome sequenced almost two decades ago. However, reference genomes for all higher organisms to date contain gaps and missing sequences. Here, we report the assembly and analysis of gap-free reference genome sequences for two elite O. sativa xian/indica rice varieties, Zhenshan 97 and Minghui 63, which are being used as a model system for studying heterosis and yield. Gap-free reference genomes provide the opportunity for a global view of the structure and function of centromeres. We show that all rice centromeric regions share conserved centromere-specific satellite motifs with different copy numbers and structures. In addition, the similarity of CentO repeats in the same chromosome is higher than across chromosomes, supporting a model of local expansion and homogenization. Both genomes have over 395 non-TE genes located in centromere regions, of which ∼41% are actively transcribed. Two large structural variants at the end of chromosome 11 affect the copy number of resistance genes between the two genomes. The availability of the two gap-free genomes lays a solid foundation for further understanding genome structure and function in plants and breeding climate-resilient varieties.
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http://dx.doi.org/10.1016/j.molp.2021.06.018DOI Listing
June 2021

Early combined rehabilitation intervention to improve the short-term prognosis of premature infants.

BMC Pediatr 2021 06 9;21(1):269. Epub 2021 Jun 9.

Department of Neonatology, Sichuan Provincial Maternity and Child Health Care Hospital, No. 290 West Second Street, Shayan Road, Chengdu, 610031, Sichuan, China.

Background: To explore the clinical effect of early combined rehabilitation intervention on premature infants in the neonatal intensive care unit (NICU).

Methods: Premature infants with gestational ages less than 32 weeks or birth weights less than 1500 g were included in the present study.The participants were divided into the intervention group and control group. All infants received the current routine treatment based on the clinical guidelines, and the intervention group was additionally treated by visual and auditory stimulation, oral motor function, respiratory function and neurodevelopmental training. The following clinical outcomes were compared: durations of oxygen supplementation and indwelling gastric tube use; incidences of retinopathy of prematurity (ROP) and neonatal necrotizing enterocolitis (NEC); Sliverman scores; incidences of bronchopulmonary dysplasia (BPD) and intraventricular haemorrhage; days of hospitalization; and neurodevelopmental outcomes. Datas were analysed using the following statistical tests: the chi-square test, the independent samples or paired t test, repeated measures ANOVA, and the Wilcoxon rank sum test.

Results: Compared with those in the control group, premature infants in the intervention group had shorter durations of oxygen supplementation and indwelling gastric tube use, fewer hospitalization days and lower incidences of ROP, BPD, and NEC.The intervention group had lower Sliverman scores and higher Ballard neuromuscular scores than the control group.

Conclusion: Early combined rehabilitation intervention can improve the short-term clinical outcomes of premature infants.
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http://dx.doi.org/10.1186/s12887-021-02727-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8188692PMC
June 2021

Human adipose tissue-derived MSCs improve psoriasis-like skin inflammation in mice by negatively regulating ROS.

J Dermatolog Treat 2021 Jun 1:1-8. Epub 2021 Jun 1.

Department of Dermatology and Venereology, Suzhou Municipal Hospital, Suzhou, China.

Background: Psoriasis is chronic incurable skin inflammation. The anti-inflammatory properties of mesenchymal stem cells (MSCs) have been put forward to be involved in several inflammatory diseases. However, little was known about the role of human adipose tissue-derived stem cells (hAD-MSCs) in psoriasis.

Objective: We sought to explore the feasibility of using hAD-MSCs infusion as a therapeutic approach in psoriatic mice.

Methods: We constructed the psoriasis-like model by IMQ implication, treated with hAD-MSCs by subcutaneous injection. To evaluate the efficacy, we examined the histology, CD45 and ROS positive cells by HE and flow cytometry respectively. We also tested the key cytokines with PCR. Moreover, to achieve a better therapeutic effect, we treated the model by combing with vitamin E application.

Results: We found that the classic histological symptoms of psoriasis were relieved after treatment with hAD-MSCs, also, the splenic index, the infiltration of immune cells and several pro-inflammatory cytokines were decreased. Interestingly, we also found that hAD-MSCs could inhibit ROS generation. Moreover, the combination therapy of hAD-MSCs and vitamin E could promote the curative effect with greater ROS inhibition.

Conclusion: These results suggested that hAD-MSCs could be useful for treating psoriasis by negatively regulating ROS.
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http://dx.doi.org/10.1080/09546634.2021.1925622DOI Listing
June 2021

LETN and NPM1 tango in human nucleoli.

Cell Res 2021 Jun;31(6):609-610

State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.

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http://dx.doi.org/10.1038/s41422-021-00471-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8169690PMC
June 2021

Cotton pan-genome retrieves the lost sequences and genes during domestication and selection.

Genome Biol 2021 04 23;22(1):119. Epub 2021 Apr 23.

National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China.

Background: Millennia of directional human selection has reshaped the genomic architecture of cultivated cotton relative to wild counterparts, but we have limited understanding of the selective retention and fractionation of genomic components.

Results: We construct a comprehensive genomic variome based on 1961 cottons and identify 456 Mb and 357 Mb of sequence with domestication and improvement selection signals and 162 loci, 84 of which are novel, including 47 loci associated with 16 agronomic traits. Using pan-genome analyses, we identify 32,569 and 8851 non-reference genes lost from Gossypium hirsutum and Gossypium barbadense reference genomes respectively, of which 38.2% (39,278) and 14.2% (11,359) of genes exhibit presence/absence variation (PAV). We document the landscape of PAV selection accompanied by asymmetric gene gain and loss and identify 124 PAVs linked to favorable fiber quality and yield loci.

Conclusions: This variation repertoire points to genomic divergence during cotton domestication and improvement, which informs the characterization of favorable gene alleles for improved breeding practice using a pan-genome-based approach.
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http://dx.doi.org/10.1186/s13059-021-02351-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8063427PMC
April 2021

Designing multi-epitope vaccine against Staphylococcus aureus by employing subtractive proteomics, reverse vaccinology and immuno-informatics approaches.

Comput Biol Med 2021 05 15;132:104389. Epub 2021 Apr 15.

College of Life Science and Technology, Guangxi University, Nanning, PR China. Electronic address:

Staphylococcus aureus is a deadly human bacterial pathogen that causes a wide variety of clinical manifestations. Invasive S. aureus infections in hospitals and the community are one of the main causes of mortality and morbidity, as virulent and multi-drug-resistant strains have evolved. There is an unmet and urgent clinical need for immune-based non-antibiotic approaches to treat these infections as the growing antibiotic resistance poses a significant public health danger. Subtractive proteomics assisted reverse vaccinology-based immunoinformatics pipeline was used in this study to target the suitable antigenic proteins for the development of multi-epitope vaccine (MEV). Three essential virulent and antigenic proteins were identified including Glycosyltransferase, Elastin Binding Protein, and Staphylococcal secretory antigen. A variety of immunoinformatics tools have been used to forecast T-cell and B-cell epitopes from target proteins. Seven CTL, five HTL, and eight LBL epitopes, connected through suitable linkers and adjuvant, were employed to design 444 amino acids long MEV construct. The vaccine was paired with the TLR4 agonist 50S ribosomal protein L7/L12 adjuvant to enhance the immune response towards the vaccine. The predicted MEV structure was assessed to be highly antigenic, non-toxic, non-allergenic, flexible, stable, and soluble. Molecular docking simulation of the MEV with the human TLR4 (toll-like receptor 4) and major histocompatibility complex molecules (MHCI and MHCII) was performed to validate the interactions with the receptors. Molecular dynamics (MD) simulation and MMGBSA binding free energy analyses were carried out for the stability evaluation and binding of the MEV docked complexes with TLR4, MHCI and MHCII. To achieve maximal vaccine protein expression with optimal post-translational modifications, MEV was reverse translated, its mRNA structure was analyzed, and finally in silico cloning was performed into E. coli expression host. These rigorous computational analyses supported the effectivity of proposed MEV in protection against infections associated with S. aureus. However, further experimental validations are required to fully evaluate the potential of proposed vaccine candidate.
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http://dx.doi.org/10.1016/j.compbiomed.2021.104389DOI Listing
May 2021

An optimized fixation method containing glyoxal and paraformaldehyde for imaging nuclear bodies.

RNA 2021 Jun 12;27(6):725-733. Epub 2021 Apr 12.

State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China.

The mammalian cell nucleus contains different types of membrane-less nuclear bodies (NBs) consisting of proteins and RNAs. Microscopic imaging has been widely applied to study the organization and structure of NBs. However, current fixation methods are not optimized for such imaging: When a fixation method is chosen to maximize the quality of the RNA fluorescence in situ hybridization (FISH), it often limits the labeling efficiency of proteins or affects the ultrastructure of NBs. Here, we report that addition of glyoxal (GO) into the classical paraformaldehyde (PFA) fixation step not only improves FISH signals for RNAs in NBs via augmented permeability of the fixed nucleus and enhanced accessibility of probes, but also largely preserves protein fluorescent signals during fixation and immunostaining. We also show that GO/PFA fixation enables the covisualization of different types of nuclear bodies with minimal impact on their ultrastructures under super-resolution microscopy.
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http://dx.doi.org/10.1261/rna.078671.120DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8127994PMC
June 2021

Albicanol Alleviates D-Galactose-Induced Aging and Improves Behavioral Ability Via by Alleviating Oxidative Stress-Induced Damage.

Neurochem Res 2021 May 24;46(5):1058-1067. Epub 2021 Mar 24.

College of Life Sciences, Northeast Agricultural University, Harbin, Heilongjiang Province, China.

Albicanol is a natural terpenoid derived from Dryopteris fragrans. Herein, we assessed the ability of Albicanol to protect against oxidative stress-induced senescence. Using a murine model of D-galactose (D-gal)-induced aging, we determined that Albicanol treatment can reverse D-gal-mediated learning impairments and behavioral changes, while also remediating brain tissue damage in treated mice. We found that serum SOD, CAT, GSH-Px, and T-AOC levels were significantly decreased in aging mice, and that Albicanol treatment significantly increased the serum levels of these antioxidant enzymes. We additionally evaluated the impact of Albicanol treatment on the Keap1/Nrf2/ARE signaling pathway, and found that it was able to decrease Keap1 expression while increasing the expression of Nrf2, thereby activating this signaling pathway, suppressing oxidative damage, and enhancing the expression of downstream target genes including SOD, GSH, GST, HO-1, and NQO1 in this murine aging model system. Albicanol treatment also inhibited the secretion of inflammatory TNF-a and IL-1b. Together, these data indicated that Albicanol can activate Nrf2 pathway-related genes, thereby inhibition of delayed aging by alleviating oxidative stress-induced damage.
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http://dx.doi.org/10.1007/s11064-020-03220-xDOI Listing
May 2021

CharPlant: A De Novo Open Chromatin Region Prediction Tool for Plant Genomes.

Genomics Proteomics Bioinformatics 2021 Mar 1. Epub 2021 Mar 1.

Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China. Electronic address:

Chromatin accessibility is a highly informative structural feature for understanding gene transcription regulation because it indicates the degree to which nuclear macromolecules such as proteins and RNAs can access chromosomal DNA. Studies show that chromatin accessibility is highly dynamic during stress response, stimulus response, and developmental transition. Moreover, physical access to chromosomal DNA in eukaryotes is highly cell-specific. Therefore, current technologies such as DNase-seq, ATAC-seq, and FAIRE-seq reveal only a portion of the open chromatin regions (OCRs) present in a given species. Thus, the genome-wide distribution of OCRs remains unknown. In this study, we developed a bioinformatics tool called CharPlant for the de novo prediction of OCRs in plant genomes. To develop this tool, we constructed a three-layer convolutional neural network (CNN) and subsequently trained the CNN using DNase-seq and ATAC-seq datasets of four plant species. The model simultaneously learns the sequence motifs and regulatory logics, which are jointly used to determine DNA accessibility. All of these steps are integrated into CharPlant, which can be run using a simple command line. The results of data analysis using CharPlant in this study demonstrate its prediction power and computational efficiency. To our knowledge, CharPlant is the first de novo prediction tool that can identify potential OCRs in the whole genome. The source code of CharPlant and supporting files are freely available from https://github.com/Yin-Shen/CharPlant.
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http://dx.doi.org/10.1016/j.gpb.2020.06.021DOI Listing
March 2021

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

Methods 2021 Feb 12. Epub 2021 Feb 12.

CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China; School of Life Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai 201210, China. Electronic address:

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.
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http://dx.doi.org/10.1016/j.ymeth.2021.02.008DOI Listing
February 2021

Mapping circular RNA structures in living cells by SHAPE-MaP.

Methods 2021 Feb 9. Epub 2021 Feb 9.

State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China; School of Life Science and Technology, ShanghaiTech University, 100 Haike Road, Shanghai 201210, China; School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China. Electronic address:

Circular RNAs are produced from back-splicing of exons of precursor mRNAs (pre-mRNAs). The sequences of exons in circular RNAs are identical to their linear cognate mRNAs, but the circular format may confer constraints on their folding and conformation, leading to potentially different functions from their linear RNA cognates. Here, we describe experimental and computational steps that optimize the selective 2'-hydroxyl acylation analyzed by primer extension and mutational profiling (SHAPE-MaP) to probe circular RNA secondary structure at single-nucleotide resolution in living cells.
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http://dx.doi.org/10.1016/j.ymeth.2021.01.011DOI Listing
February 2021

Analysis of Rice Transcriptome Reveals the LncRNA/CircRNA Regulation in Tissue Development.

Rice (N Y) 2021 Jan 28;14(1):14. Epub 2021 Jan 28.

National Key Laboratory of Crop Genetic Improvement, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China.

Background: Long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) can play important roles in many biological processes. However, no study of the influence of epigenetics factors or the 3D structure of the genome in their regulation is available in plants.

Results: In the current analysis, we identified a total of 15,122 lncRNAs and 7902 circRNAs in three tissues (root, leaf and panicle) in the rice varieties Minghui 63, Zhenshan 97 and their hybrid Shanyou 63. More than 73% of these lncRNAs and parental genes of circRNAs (P-circRNAs) are shared among Oryza sativa with high expression specificity. We found that, compared with protein-coding genes, the loci of these lncRNAs have higher methylation levels and the loci of circRNAs tend to locate in the middle of genes with high CG and CHG methylation. Meanwhile, the activated lncRNAs and P-circRNAs are mainly transcribed from demethylated regions containing CHH methylation. In addition, ~ 53% lncRNAs and ~ 15% P-circRNAs are associated with transposable elements (TEs), especially miniature inverted-repeat transposable elements and RC/Helitron. We didn't find correlation between the expression of lncRNAs and histone modifications; however, we found that the binding strength and interaction of RNAPII significantly affects lncRNA expression. Interestingly, P-circRNAs tend to combine active histone modifications. Finally, we found that lncRNAs and circRNAs acting as competing-endogenous RNAs have the potential to regulate the expression of genes, such as osa-156 l-5p (related to yield) and osa-miR444a-3p (related to N/P metabolism) confirmed through dual-luciferase reporter assays, with important roles in the growth and development of rice, laying a foundation for future rice breeding analyses.

Conclusions: In conclusion, our study comprehensively analyzed the important regulatory roles of lncRNA/circRNA in the tissue development of Indica rice from multiple perspectives.
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http://dx.doi.org/10.1186/s12284-021-00455-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7843763PMC
January 2021

Author Correction: Gene regulation by long non-coding RNAs and its biological functions.

Nat Rev Mol Cell Biol 2021 Feb;22(2):159

Center for Applied Medical Research, University of Navarra, Pamplona, Spain.

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http://dx.doi.org/10.1038/s41580-021-00330-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8095262PMC
February 2021

Gene regulation by long non-coding RNAs and its biological functions.

Nat Rev Mol Cell Biol 2021 02 22;22(2):96-118. Epub 2020 Dec 22.

Center for Applied Medical Research, University of Navarra, Pamplona, Spain.

Evidence accumulated over the past decade shows that long non-coding RNAs (lncRNAs) are widely expressed and have key roles in gene regulation. Recent studies have begun to unravel how the biogenesis of lncRNAs is distinct from that of mRNAs and is linked with their specific subcellular localizations and functions. Depending on their localization and their specific interactions with DNA, RNA and proteins, lncRNAs can modulate chromatin function, regulate the assembly and function of membraneless nuclear bodies, alter the stability and translation of cytoplasmic mRNAs and interfere with signalling pathways. Many of these functions ultimately affect gene expression in diverse biological and physiopathological contexts, such as in neuronal disorders, immune responses and cancer. Tissue-specific and condition-specific expression patterns suggest that lncRNAs are potential biomarkers and provide a rationale to target them clinically. In this Review, we discuss the mechanisms of lncRNA biogenesis, localization and functions in transcriptional, post-transcriptional and other modes of gene regulation, and their potential therapeutic applications.
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http://dx.doi.org/10.1038/s41580-020-00315-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7754182PMC
February 2021

Designing of a next generation multiepitope based vaccine (MEV) against SARS-COV-2: Immunoinformatics and in silico approaches.

PLoS One 2020 22;15(12):e0244176. Epub 2020 Dec 22.

College of Life Science and Technology, Guangxi University, Nanning, P. R. China.

Coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory coronavirus 2 (SARS-COV-2) is a significant threat to global health security. Till date, no completely effective drug or vaccine is available to cure COVID-19. Therefore, an effective vaccine against SARS-COV-2 is crucially needed. This study was conducted to design an effective multiepitope based vaccine (MEV) against SARS-COV-2. Seven highly antigenic proteins of SARS-COV-2 were selected as targets and different epitopes (B-cell and T-cell) were predicted. Highly antigenic and overlapping epitopes were shortlisted. Selected epitopes indicated significant interactions with the HLA-binding alleles and 99.93% coverage of the world's population. Hence, 505 amino acids long MEV was designed by connecting 16 MHC class I and eleven MHC class II epitopes with suitable linkers and adjuvant. MEV construct was non-allergenic, antigenic, stable and flexible. Furthermore, molecular docking followed by molecular dynamics (MD) simulation analyses, demonstrated a stable and strong binding affinity of MEV with human pathogenic toll-like receptors (TLR), TLR3 and TLR8. Finally, MEV codons were optimized for its in silico cloning into Escherichia coli K-12 system, to ensure its increased expression. Designed MEV in present study could be a potential candidate for further vaccine production process against COVID-19. However, to ensure its safety and immunogenic profile, the proposed MEV needs to be experimentally validated.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0244176PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7755200PMC
January 2021

Conserved Imprinted Genes between Intra-Subspecies and Inter-Subspecies Are Involved in Energy Metabolism and Seed Development in Rice.

Int J Mol Sci 2020 Dec 17;21(24). Epub 2020 Dec 17.

National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China.

Genomic imprinting is an epigenetic phenomenon in which a subset of genes express dependent on the origin of their parents. In plants, it is unclear whether imprinted genes are conserved between subspecies in rice. Here we identified imprinted genes from embryo and endosperm 5-7 days after pollination from three pairs of reciprocal hybrids, including inter-subspecies, intra-subspecies, and intra-subspecies reciprocal hybrids. A total of 914 imprinted genes, including 546 in inter-subspecies hybrids, 211 in intra-subspecies hybrids, and 286 in intra-subspecies hybrids. In general, the number of maternally expressed genes (MEGs) is more than paternally expressed genes (PEGs). Moreover, imprinted genes tend to be in mini clusters. The number of shared genes by R9N (reciprocal crosses between 9311 and Nipponbare) and R9Z (reciprocal crosses between 9311 and Zhenshan 97), R9N and RZN (reciprocal crosses between Zhonghua11 and Nipponbare), R9Z and RZN was 72, 46, and 16. These genes frequently involved in energy metabolism and seed development. Five imprinted genes (, , , , and ) are commonly detected in all three pairs of reciprocal hybrids and were validated by RT-PCR sequencing. Gene editing of two imprinted genes revealed that both genes conferred grain filling. Moreover, 15 and 27 imprinted genes with diverse functions in rice were shared with Arabidopsis and maize, respectively. This study provided valuable resources for identification of imprinting genes in rice or even in cereals.
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http://dx.doi.org/10.3390/ijms21249618DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7765902PMC
December 2020

Selection of a subspecies-specific diterpene gene cluster implicated in rice disease resistance.

Nat Plants 2020 12 7;6(12):1447-1454. Epub 2020 Dec 7.

National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China.

Diterpenoids are the major group of antimicrobial phytoalexins in rice. Here, we report the discovery of a rice diterpenoid gene cluster on chromosome 7 (DGC7) encoding the entire biosynthetic pathway to 5,10-diketo-casbene, a member of the monocyclic casbene-derived diterpenoids. We revealed that DGC7 is regulated directly by JMJ705 through methyl jasmonate-mediated epigenetic control. Functional characterization of pathway genes revealed OsCYP71Z21 to encode a casbene C10 oxidase, sought after for the biosynthesis of an array of medicinally important diterpenoids. We further show that DGC7 arose relatively recently in the Oryza genus, and that it was partly formed in Oryza rufipogon and positively selected for in japonica during domestication. Casbene-synthesizing enzymes that are functionally equivalent to OsTPS28 are present in several species of Euphorbiaceae but gene tree analysis shows that these and other casbene-modifying enzymes have evolved independently. As such, combining casbene-modifying enzymes from these different families of plants may prove effective in producing a diverse array of bioactive diterpenoid natural products.
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http://dx.doi.org/10.1038/s41477-020-00816-7DOI Listing
December 2020

Screening for functional circular RNAs using the CRISPR-Cas13 system.

Nat Methods 2021 01 7;18(1):51-59. Epub 2020 Dec 7.

State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.

Circular RNAs (circRNAs) produced from back-spliced exons are widely expressed, but individual circRNA functions remain poorly understood owing to the lack of adequate methods for distinguishing circRNAs from cognate messenger RNAs with overlapping exons. Here, we report that CRISPR-RfxCas13d can effectively discriminate circRNAs from mRNAs by using guide RNAs targeting sequences spanning 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 by preventing the mRNA for family with sequence similarity 120A (FAM120A) from binding the translation inhibitor IGF2BP2. Further application of RfxCas13d-BSJ-gRNA screening has uncovered circMan1a2, which has 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.
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http://dx.doi.org/10.1038/s41592-020-01011-4DOI Listing
January 2021
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