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Toward A New Paradigm of genomics Research——Celebration of the 20th Anniversary of Beijing institute of genomics

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genomics, Proteomics & Bioinformatics 2023年第5期21卷 904-909页

作者： Zhang Zhang Songnian Hu Jun Yu National genomics Data Center Beijing Institute of GenomicsChinese Academy of Sciences and China National Center for BioinformationBeijing 100101China CAS Key Laboratory of Genome Sciences and Information Beijing Institute of GenomicsChinese Academy of Sciences and China National Center for BioinformationBeijing 100101China University of Chinese Academy of Sciences Beijing 100049China State Key Laboratory of Microbial Resources Institute of MicrobiologyChinese Academy of SciencesBeijing 100101China

Twenty years after the completion and forty years after the proposal of the Human Genome Project(HGP),genomics,together with its twin field-bioinformatics,has entered a new paradigm,where its bioscience-related,discipline-centric applications have been creating many new research *** institute of genomics(BIG),now also known as China National Center for Bioinformation(CNCB),will play key roles in supporting and participating in these frontier research *** the 20th anniversary of the establishment of BIG,we provide a brief retrospective of its historic events and ascertain strategic research directions with a broader vision for future genomics,where digital genome,digital medicine,and digital health are so structured to meet the needs of human life and healthcare,as well as their related metaverses.

关键词： genomics Bioinformatics BIG CNCB NGDC

The plant cell wall: Biosynthesis, construction, and functions

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Journal of Integrative Plant Biology 2021年第1期63卷 251-272页

作者： Baocai Zhang Yihong Gao Lanjun Zhang Yihua Zhou State Key Laboratory of Plant genomics Institute of Genetics and Developmental BiologyThe Innovative Academy of Seed DesignChinese Academy of SciencesBeiing 100101China University of Chinese Academy of Sciences Bejig 100049China

The plant cell wall is composed of multiple biopolymers, representing one of the most complex structural networks in nature. Hundreds of genes are involved in building such a natural masterpiece. However, the plant cell wall is the least understood cellular structure in plants. Due to great progress in plant functional genomics,manyachievementshavebeenmadein uncovering cell wall biosynthesis, assembly, and architecture, as well as cell wall regulation and signaling. Such information has significantly advanced our understanding of the roles of the cell wall in many biological and physiological processes and has enhanced our utilization of cell wall materials. The use of cutting-edge technologies such as single-molecule imaging,nuclear magnetic resonance spectroscopy, and atomic force microscopy has provided much insight into the plant cell wall as an intricate nanoscale network, opening up unprecedented possibilities for cell wall research. In this review,we summarize the major advances made in understanding the cell wall in this era of functional genomics, including the latest findings on the biosynthesis, construction, and functions of the cell wall.

关键词： biosynthesis cell wall construction function

Phase separation of S-RNase promotes self-incompatibility in Petunia hybrida

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Journal of Integrative Plant Biology 2024年第5期66卷 986-1006页

作者： Huayang Tian Hongkui Zhang Huaqiu Huang Yu'e Zhang Yongbiao Xue The State Key Laboratory of Plant Cell and Chromosome Engineering Institute of Genetics and Developmental Biologythe Chinese Academy of SciencesBeijing 100101China University of the Chinese Academy of Sciences Beijing 100049China beiing institute of genomics Chinese Academy of SciencesNational Center for BioinformationBeijing 100101China

Self-incompatibility(SI)is an intraspecific reproductive barrier widely present in *** SI system with the broadest occurrence in angiosperms is based on an S-RNase linked to a cluster of multiple S-locus F-box(SLF)genes found in the Solanaceae,Plantaginaceae,Rosaceae,and *** studies reveal that non-self S-RNase is degraded by the Skip Cullin F-box(SCF)SLF-mediated ubiquitin–proteasome system in a collaborative manner in Petunia,but how self-RNase functions largely remains ***,we show that S-RNases form S-RNase condensates(SRCs)in the self-pollen tube cytoplasm through phase separation and the disruption of SRC formation breaks SI in self-incompatible Petunia *** further find that the pistil SI factors of a small asparagine-rich protein HT-B and thioredoxin h together with a reduced state of the pollen tube all promote the expansion of SRCs,which then sequester several actin-binding proteins,including the actin polymerization factor PhABRACL,the actin polymerization activity of which is reduced by S-RNase in ***,we find that S-RNase variants lacking condensation ability fail to recruit PhABRACL and are unable to induce actin foci formation required for pollen tube growth *** together,our results demonstrate that phase separation of S-RNase promotes SI response in ***,revealing a new mode of S-RNase action.

关键词： self-incompatibility S-RNase phase separation

Recent Progress Using High-throughput Sequencing Technologies in Plant Molecular Breeding

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Journal of Integrative Plant Biology 2012年第4期54卷 215-227页

作者： Qiang Gao Guidong Yue Wenqi Li Junyi Wang Jiaohui Xu Ye Yin Beijing genomics institute-Shenzhen Shenzhen 518083China

High-throughput sequencing is a revolutionary technological in- novation in DNA sequencing. This technology has an ultra-low cost per base of sequencing and an overwhelmingly high data output. High-throughput sequencing has brought novel research methods and solutions to the research fields of genomics and post-genomics. Furthermore, this technology is leading to a new molecular breeding revolution that has landmark significance for scientific research and enables us to launch multi-level, multi- faceted, and multi-extent studies in the fields of crop genetics, genomics, and crop breeding. In this paper, we review progress in the application of high-throughput sequencing technologies to plant molecular breeding studies.

关键词： High-throughput sequencing genomics molecular breeding.

Single-cell Transcriptome Study as Big Data

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genomics, Proteomics & Bioinformatics 2016年第1期14卷 21-30页

作者： Pingjian Yu Wei Lin genomics and Bioinformatics Lab Baylor Institute for Immunology Research

The rapid growth of single-cell RNA-seq studies （scRNA-seq） demands efficient data storage, processing, and analysis. Big-data technology provides a framework that facilitates the comprehensive discovery of biological signals from inter-institutional scRNA-seq datasets. The strategies to solve the stochastic and heterogeneous single-cell transcriptome signal are discussed in this article. After extensively reviewing the available big-data applications of next-generation sequencing （NGS）-based studies, we propose a workflow that accounts for the unique characteris- tics of scRNA-seq data and primary objectives of single-cell studies.

关键词： Single-cell RNA -seq Big data TranscriptionaSingle-cell heterogenc-ity SignaSingle-cell normaSingle-cellization

Small RNA in rice genome

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Science China(Life Sciences) 2002年第5期45卷 497-503页

作者：王凯朱小蓬钟兰陈润生 Beijing genomics institute/Center of genomics and Bioinformatics Chinese Academy of Sciences Beijing 101300 China Beijing Genomics Institute/Center of Genomics and Bioinformatics Chinese Academy of Sciences Beijing 101300 China College of Life Sciences Peking University Beijing 100871 China Beijing Genomics Institute/Center of Genomics and Bioinformatics Chinese Academy of Sciences Beijing 101300 China Laboratory of Bioinformatics Institute of Biophysics Chinese Academy of Sciences Beijing 100101 China

Rice has many characteristics of a model plant. The recent completion of the draft of the rice genome represents an important advance in our knowledge of plant biology and also has an important contribution to the understanding of general genomic evolution. Besides the rice genome finishing map, the next urgent step for rice researchers is to annotate the genes and noncoding functional sequences. The recent work shows that noncoding RNAs (ncRNAs) play significant roles in biological systems. We have explored all the known small RNAs (a kind of ncRNA) within rice genome and other six species sequences, including Arabidopsis, maize, yeast, worm, mouse and pig. As a result we find 160 out of 552 small RNAs (sRNAs) in database have homologs in 108 rice scaffolds, and almost all of them (99.41%) locate in intron regions of rice by gene predication. 19 sRNAs only appear in rice. More importantly, we find two special U14 sRNAs: one is located in a set of sRNA ZMU14SNR9(s) which only appears in three plants, 86% sequences of them can be compared as the same sequence in rice, Arabidopsis and maize; the other conserved sRNA XLHS7CU14 has a segment which appears in almost all these species from plants to animals. All these results indicate that sRNA do not have evident borderline between plants and animals.

关键词： ncRNA, sRNA, conserved sequences, plant-specific sRNA gene.

Development of a functional cell-based HTS assay for identification of NKCC1-negative modulators

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Chinese Science Bulletin 2014年第7期59卷 630-638页

作者： Yanqiu Bai Lianghui Ma Shiyou Li Beijing institute of genomics Chinese Academy of Sciences University of Chinese Academy of Sciences Laboratory of Disease genomics and Individualized Medicine Beijing Institute of Genomics Chinese Academy of Sciences

Na–K–Cl cotransporter 1(NKCC1) cotransports Na+, K+, and Cl-ions across the plasma membrane into cells. Accumulation of Cl-ions in dorsal root ganglion neurons induces depolarizing GABAA receptors, which mediate presynaptic inhibition and filtration of sensory noise. The activity of the Na–K–Cl cotransporter is modulated by high-dose loop diuretics, such as furosemide and bumetanide. To identify NKCC1 modulators, we developed a functional cell-based assay feasible for highthroughput screening(HTS), in which the activity of NKCC1 was detected by a BTC-AM dye-based thallium transportation assay. We demonstrated that the influx of Tl?was mediated by NKCC1, which required the existence of Cl-ions and could be inhibited by bumetanide and furosemide. Our results demonstrated that the assay was stable, reproducible, and suitable for HTS of negative modulators for NKCC1.

关键词：细胞膜测定法 HTS 调节剂识别背根神经节神经元 GABAA受体转运蛋白

A Putative NES Mediates Cytoplasmic Localization of Apoptin in Normal Cells

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Acta Biochimica et Biophysica Sinica 2004年第12期36卷 817-823页

作者： Qing-Ming WANG*, Guo-Cai FAN, Ji-Zhong CHEN, Hui-Peng CHEN, and Fu-Chu HE* Department of genomics and Proteomics, Beijing institute of Radiation Medicine, Beijing 100850, China Department of genomics and Proteomics Beijing Institute of Radiation MedicineBeijing 100850 China

Apoptin, a protein expressed by chicken anemia virus, is found predominantly in the cytoplasm in normal cells, whereas it localizes in the nucleus in transformed and malignant cells. However, the mecha- nisms that regulate the different subcellular localization of Apoptin in normal and tumor cells have not been fully clarified. In this work, a putative nuclear export signal (NES) in Apoptin was predicted. It was testified that the putative NES (pNES) of Apoptin was not a functional NES, but actually acted as a cytoplasmic retention signal. Deletion of the pNES led to the nuclear accumulation of Apoptin in normal cells. In addition, when a strong nuclear localization signal was introduced into Apoptin, it exclusively translocated to the nucleus in normal cells. These observations indicated that the cytoplasmic localization of Apoptin in normal cells results from the balance between cytoplasmic retention and nuclear import. On the other hand, the pNES was also proved to be necessary for Apoptin multimerization. Mutants lacking the pNES did not form obviously visible globular aggregates in normal or tumor cells.

关键词： Apoptin nuclear localization signal cytoplasmic retention signal nuclear export signal

Making topological protein links using enzymatic reactions

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National Science Review 2024年第3期11卷 50-51页

作者： Roger Castells-Graells Todd O.Yeates Department of Chemistry and Biochemistry University of California UCLA-DOE institute for genomics and Proteomics

Proteins are exceedingly complex molecules though, at their heart, they are essentially linear polymers. Pull at their ends and one obtains an extended backbone. While that is true in most cases, some natural proteins...

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