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Profiling of circular RNA N^(6)-methyladenosine in moso bamboo(Phyllostachys edulis)using nanopore-based direct RNA sequencing

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Journal of Integrative Plant Biology 2020年第12期62卷 1823-1838页

作者： Yongsheng Wang Huihui Wang Feihu Xi Huiyuan Wang Ximei Han Wentao Wei Hangxiao Zhang Qianyue Zhang Yushan Zheng Qiang Zhu Markus V.Kohnen Anireddy S.N.Reddy Lianfeng Gu basic forestry and proteomics research center College of life scienceFujian Agriculture and Forestry UniversityFuzhou 350002China basic forestry and proteomics research center College of ForestryFujian Agriculture and Forestry UniversityFuzhou 350002China College of forestry Fujian Agriculture and Forestry UniversityFuzhou 350002China Department of Biology and Program in Cell and Molecular Biology Colorado State UniversityFort CollinsColoradoUSA

N6-methyladenosine(m^(6)A)is a prevalent modification in messenger RNAs and circular RNAs that play important roles in regulating various aspects of RNA ***,the occurrence of the m^(6)A modification in plant circular RNAs has not been reported.A widely used method to identify m^(6)A modifications relies on m^(6)A-specific antibodies followed by next-generation sequencing of precipitated RNAs(MeRIP-Seq).However,one limitation of MeRIP-Seq is that it does not provide the precise location of m^(6)A at single-nucleotide *** more recent sequencing techniques such as Nanopore-based direct RNA sequencing(DRS)can overcome such limitations,the technology does not allow sequencing of circular RNAs,as these molecules lack a poly(A)***,we developed a novel method to detect the precise location of m^(6)A modifications in circular RNAs using Nanopore *** first enriched our samples for circular RNAs,which we then fragmented and sequenced on the Nanopore platform with a customized *** this method,we identified 470 unique circular RNAs from DRS reads based on the back-spliced junction *** exonic circular RNAs,about 10%contained m^(6)A sites,which mainly occurred around acceptor and donor splice *** study demonstrates the utility of our antibody-independent method in identifying total and methylated circular RNAs using Nanopore *** method has the additional advantage of providing the exact location of m^(6)A sites at single-base resolution in circular RNAs or linear transcripts from non-coding RNA without poly(A)tails.

关键词： circular precise overcome

Genome-wide profiling of circular RNAs,alternative splicing,and R-loops in stem-differentiating xylem of Populus trichocarpa

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Journal of Integrative Plant Biology 2021年第7期63卷 1294-1308页

作者： Xuqing Liu Yubang Gao Jiakai Liao Miao Miao Kai Chen Feihu Xi Wentao Wei Huihui Wang Yongsheng Wang XiXu Anireddy S.N.Reddy Lianfeng Gu basic forestry and proteomics research center College of ForestryFujian Provincial Key Laboratory of Haixia Applied Plant Systems BiologyFujian Agriculture and Forestry UniversityFuzhou 350002China basic forestry and proteomics research center College of Life ScienceFujian Agriculture and Forestry UniversityFuzhou 350002China Department of Biology and Program in Cell and Molecular Biology Colorado State UniversityFort CollinsColorado 80523USA

Circular RNAs(circRNAs)are a recently dis-covered type of non‐coding RNA derived from pre‐mRNAs.R‐loops consist of a DNA:RNA hybrid andthe associated single‐stranded ***-dopsis thaliana,circRNA:DNA R‐loops regulatealternative splicing(AS)ofSEPALLATA3(SEP3).However,the occurrence and functions ofcircRNAs and R‐loops inPopulus trichocarpaarelargely ***,we performed circRNA‐enriched sequencing in the stem‐differentiatingxylem(SDX)*** identified 2,742distinct circRNAs,including circ‐CESA4,circ‐IRX7,and circ‐GUX1,which are generated from genesinvolved in cellulose,and hemicellulose biosyn-thesis,*** investigate the roles ofcircRNAs in modulating alternative splicing(AS),we detected 7,836 AS events using PacBio Iso‐Seq and identified 634 circRNAs that overlappedwith 699 AS ***,using DNA:RNAhybrid immunoprecipitation followed by se-quencing(DRIP‐seq),we identified 8,932 R‐looppeaks that overlapped with 181 circRNAs and 672AS ***,several SDX‐related circRNAsoverlapped with R‐loop peaks,pointing to theirpossible roles in modulating AS in ***,overexpressing circ‐IRX7increased the levels ofR‐loop structures and decreased the frequency ofintron retention in *** provides a valuable R‐loop atlas resourceand uncovers the interplay between circRNAs andAS in SDX ***.

关键词： alternative splicing circular RNA R‐loop Populustrichocarpa stem‐differentiating xylem

Uncovering the miRNA-mediated regulatory network involved in Ma bamboo(Dendrocalamus latiflorus)de novo shoot organogenesis

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Horticulture research 2023年第12期10卷 1-13页

作者： Nannan Wang Wenjia Wang Yang Cheng Changyang Cai Qiang Zhu basic forestry and proteomics center(BFPC) College of ForestryHaiXia Institute for Science and TechnologyFujian Agriculture and Forestry UniversityFuzhou 350002China

Bamboo is an important non-timber forest product and is well-known for its reluctance to *** we have established a de novo shoot organogenesis(DNSO)protocol in Ma bamboo(Dendrocalamus latiflorus)and revealed the transcriptomic dynamics during Ma bamboo regeneration,which suggested the potential roles of Ma bamboo microRNAs(DlamiRNAs)in this ***,how DlamiRNAs regulate bamboo DNSO is poorly *** we performed integrated analysis with sRNAome,degradome,and transcriptome sequencing by using samples covering the four stages of the bamboo DNSO process.A total of 727 DlamiRNAs showed differential expression during the bamboo DNSO process,and the core DlamiRNA-DlamRNA-mediated regulatory networks for bamboo DNSO were *** on the results,DlamiR156 was selected for further functional characterization of its potential roles in bamboo *** bamboos with increased DlamiR156 levels exhibited an enhancement in their regeneration ***,when DlamiR156 levels were downregulated,the regeneration efficiencies of transgenic bamboos *** findings show that the DlamiRNA-mediated regulatory pathways are significant in the process of bamboo regeneration and will contribute to our understanding of the molecular mechanisms governing plant organogenesis in a more comprehensive manner.

关键词： bamboo Bamboo covering

Optimizing ABA-based chemically induced proximity for enhanced intracellular transcriptional activation and modification response to ABA

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Science China Life Sciences 2024年第12期67卷 2650-2663页

作者： Zeng Zhou Yue-Qi Wang Xu-Nan Zheng Xiao-Hong Zhang Lu-Yao Ji Jun-You Han Ze-Cheng Zuo Wei-Liang Mo Li Zhang College of Life Sciences Fujian Agriculture and Forestry University basic forestry and proteomics research center Fujian Agriculture and Forestry University Jilin Province Engineering Laboratory of Plant Genetic Improvement College of Plant Science Jilin University

Abscisic acid(ABA)-based chemically induced proximity(CIP) is primarily mediated by the interaction of the ABA receptor pyrabactin resistance 1-like 1(PYL1) and the 2C-type protein phosphatase ABI1, which confers ABA-induced proximity to their fusion proteins, and offers precise temporal control of a wide array of biological processes. However, broad application of ABA-based CIP has been limited by ABA response intensity. In this study, we demonstrated that ABA-induced interaction between another ABA receptor pyrabactin resistance 1(PYR1) and ABI1 exhibited higher ABA response intensity than that between PYL1 and ABI1 in HEK293T cells. We engineered PYR1-ABI1and PYL1-ABI1 into ABA-induced transcriptional activation tools in mammalian cells by integration with CRISPR/d Cas9 and found that the tool based on PYR1-ABI1 demonstrated better ABA response intensity than that based on PYL1-ABI1 for both exogenous and endogenous genes in mammalian cells. We further achieved ABA-induced RNA m6A modification installation and erasure by combining ABA-induced PYR1-ABI1 interaction with CRISPR/d Cas13, successfully inhibiting tumor cell proliferation. We subsequently improved the interaction of PYR1-ABI1 through phage-assisted continuous evolution(PACE), successfully generating a PYR1 mutant(PYR1m) whose interaction with ABI1 exhibited a higher ABA response intensity than that of the wild-type. In addition, we tested the transcriptional activation tool based on PYRm-ABI1 and found that it also showed a higher ABA response intensity than that of the wild type. These results demonstrate that we have developed a novel ABA-based CIP and further improved upon it using PACE, providing a new approach for the modification of other CIP systems.

关键词： ABA chemically induced proximity transcriptional activation m6A modification protein evolution

The dark activity of Arabidopsis blue-light receptor CRY2

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Science China Life Sciences 2024年

作者： Gaoping Qu Zeru Zhang Chentao Lin basic forestry and Plant proteomics research center Fujian Agriculture and Forestry University

The functions of photoreceptors have been extensively investigated over the last two decades. However, whether those photoreceptors have any functions in the absence of light remained unclear. Recently, Prof. Hongtao Liu’s team at Shenzhen University reports that Arabidopsis blue-light receptor cryptochrome 2(CRY2) is physiologically functional in darkness (Zeng et al., 2024), solving this long-standing question. These researchers discovered that monomeric CRY2 interacted with transcription factors FL1/3 to suppress FL1/3-dependent cell division in roots in darkness, avoiding excessive energy consumption due to the overgrowth of roots in the absence of *** also discovered that blue light inhibited the CRY2-FL1/3 interaction to promote cell division, root growth, and photomorphogenesis under light conditions.

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Allele-aware chromosome-scale assembly of the allopolyploid genome of hexaploid Ma bamboo(Dendrocalamus latiflorus Munro)

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Journal of Integrative Plant Biology 2022年第3期64卷 649-670页

作者： Yushan Zheng Deming Yang Jundong Rong Liguang Chen Qiang Zhu Tianyou He Lingyan Chen Jing Ye Lili Fan Yubang Gao Hangxiao Zhang Lianfeng Gu College of forestry Fujian Agriculture and Forestry UniversityFuzhou 350002China College of Landscape Architecture Fujian Agriculture and Forestry UniversityFuzhou 350002China basic forestry and proteomics research center College of ForestryFujian Provincial Key Laboratory of Haixia Applied PlantSystems BiologyFujian Agriculture and Forestry UniversityFuzhou 350002China

Dendrocalamus latiflorus Munro is a woody clumping bamboo with rapid shoot *** genetic transformation and clustered regularly interspaced short palindromic repeats(CRISPR)/CRISPR-associated protein 9(Cas9)gene editing techniques are available for ***,enabling reverse genetic ***,*** has the potential to be a model bamboo ***,the genome sequence of *** has remained unreported due to its polyploidy and large genome ***,we sequenced the *** genome and assembled it into three allele-aware subgenomes(AABBCC),representingthe largest genome of a major bamboo *** assembled 70 allelic chromosomes(2,737 Mb)for hexaploid *** using both singlemolecule sequencing from the Pacific Biosciences(Pac Bio)Sequel platform and chromosome conformation capture sequencing(Hi-C).Repetitive sequences comprised 52.65%of the *** *** annotated 135231 protein-coding genes in the genome based on transcriptomes from eight different *** sequencing using RNA-Seq and Pac Bio singlemolecule real-time long-read isoform sequencing revealed highly differential alternative splicing(AS)between non-abortive and abortive shoots,suggesting that AS regulates the abortion rate of bamboo *** high-quality hexaploid genome and comprehensive strand-specific transcriptome datasets for this Poaceae family member will pave the way for bamboo research using *** as a model species.

关键词： alternative splicing bamboo shoots chromosome conformation capture sequencing D.latiflorus genome assembly single-molecular sequencing

Müller cells are activated in response to retinal outer nuclear layer degeneration in rats subjected to simulated weightlessness conditions

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Neural Regeneration research 2025年第7期20卷 2116-2128页

作者： Yuxue Mu Ning Zhang Dongyu Wei Guoqing Yang Lilingxuan Yao Xinyue Xu Yang Li Junhui Xue Zuoming Zhang Tao Chen Aerospace Clinical Medical center School of Aerospace MedicineAir Force Medical UniversityXi’anShaanxi ProvinceChina Department of Aviation Medicine Xijing HospitalAir Force Medical UniversityXi’anShaanxi ProvinceChina Department of Emergency Medicine Wuhan No.1 HospitalWuhanHubei ProvinceChina Third Regiment School of Basic MedicineAir Force Medical UniversityXi’anShaanxi ProvinceChina Fourth Regiment School of Basic MedicineAir Force Medical UniversityXi’anShaanxi ProvinceChina

A microgravity environment has been shown to cause ocular damage and affect visual acuity,but the underlying mechanisms remain ***,we established an animal model of weightlessness via tail suspension to examine the pathological changes and molecular mechanisms of retinal damage under *** 4 weeks of tail suspension,there were no notable alterations in retinal function and morphology,while after 8 weeks of tail suspension,significant reductions in retinal function were observed,and the outer nuclear layer was thinner,with abundant apoptotic *** investigate the mechanism underlying the degenerative changes that occurred in the outer nuclear layer of the retina,proteomics was used to analyze differentially expressed proteins in rat retinas after 8 weeks of tail *** results showed that the expression levels of fibroblast growth factor 2(also known as basic fibroblast growth factor)and glial fibrillary acidic protein,which are closely related to Müller cell activation,were significantly *** addition,Müller cell regeneration and Müller cell gliosis were observed after 4 and 8 weeks,respectively,of simulated *** findings indicate that Müller cells play an important regulatory role in retinal outer nuclear layer degeneration during weightlessness.

关键词： glial fibrous acidic protein gliosis Müller cells nerve growth factor neural differentiation neurodegeneration proteomic retinal degeneration retinal outer nuclear layer simulated weightlessness

Video-Driven 2D Character Animation

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Chinese Journal of Electronics 2021年第6期30卷 1038-1048页

作者： YIN Qinran CAO Weiqun School of Information Science and Technology Beijing Forestry University Engineering research center for forestry-oriented Intelligent Information Processing of National forestry and Grassland Administration

Video-driven animation has always been a hot and challenging topic in the field of computer animation. We propose a method of mapping a sequence of human skeletal keypoints in a video onto a two-dimensional character to generate 2 D character animation. For a given two-dimensional character picture, we extract the motion of real human in video data, driving the character deformation. We analyze common two-dimensional human body movements, classify the basic posture of the human body, realize the recognition of skeleton posture based on back propagation network, capture human body motion by automatically tracking the position of the human skeleton keypoints coordinates in the video and redirect the motion data to a 2 D character. Compared with the traditional method, our work is less affected by video data illumination and background complexity. We calibrate human body motion in videos to a 2 D character according to the skeleton topology to avoid motion distortion caused by the difference in skeleton size and ratio. The experimental results show that the proposed algorithm can generate the motion of two-dimensional characters based on the motion of human characters in video data. The animation is natural and smooth, and the algorithm has strong robustness.

关键词： two-dimensional character picture motion distortion skeleton size video data illumination human characters video signal processing computer animation character deformation basic posture two-dimensional human body movements background complexity hot topic motion data video-driven animation computational geometry human skeleton keypoints skeleton topology skeleton posture human skeletal keypoints video-driven 2D character animation capture human body motion

Development of an efficient expression system with large cargo capacity for interrogation of gene function in bamboo based on bamboo mosaic virus

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Journal of Integrative Plant Biology 2023年第6期65卷 1369-1382页

作者： Yandong Jin Baijie Wang Mingchuan Bao Yujie Li Shengwu Xiao Yuhua Wang Jun Zhang Liangzhen Zhao Hangxiao Zhang Yau-Heiu Hsu Mingjie Li Lianfeng Gu College of forestry Fujian Agriculture and Forestry UniversityFuzhou 350002China basic forestry and proteomics research center School of Future TechnologyCollege of ForestryFujian Agriculture and Forestry UniversityFuzhou 350002China Graduate Institute of Biotechnology Chung Hsing UniversityTaichung 40227China College of crop science Fujian Agriculture and Forestry UniversityFuzhou 350002China

Bamboo is one of the fastest growing plants among monocotyledonous species and is grown extensively in subtropical *** bamboo has high economic value and produces much biomass quickly,gene functional research is hindered by the low efficiency of genetic transformation in this *** therefore explored the potential of a bamboo mosaic virus(BaMV)-mediated expression system to investigate genotype-phenotype *** determined that the sites between the triple gene block proteins(TGBps)and the coat protein(CP)of BaMV are the most efficient insertion sites for the expression of exogenous genes in both monopodial and sympodial bamboo ***,we validated this system by individually overexpressing the two endogenous genes ACE1 and DEC1,which resulted in the promotion and suppression of intemode elongation,*** particular,this system was able to drive the expression of three 2A-linked betalain biosynthesis genes(more than 4 kb in length)to produce betalain,indicating that it has high cargo capacity and may provide the prerequisite basis for the development of a DNA-free bamboo genome editing platform in the *** BaMV can infect multiple bamboo species,we anticipate that the system described in this study will greatly contribute to gene function research and further promote the molecular breeding of bamboo.

关键词： ACE1 bamboo BaMV-mediated overexpression DEC1 expression virus-mediated genome editing