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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

multiMotif:a generalized tool for scanning and visualization of diverse and distant multiple motifs

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Journal of Genetics and Genomics 2024年第11期51卷 1342-1345页

作者： Sainan Luo Binghan Xiao Jianing Geng songnian hu State Key Laboratory of Microbial Resources Institute of MicrobiologyChinese Academy of SciencesBeijing 100101China University of Chinese Academy of Sciences Beijing 100101China Sino-Danish College University of Chinese Academy of SciencesBeijing 100101China

Motifs,defined as short,conserved sequences with biological functionality,play a crucial role in various biological *** the same protein family,different subfamilies may contain distinct combinations of motifs,and the composition of multiple motifs in a specific order can characterize the functionality of various proteins(Lu et al.,2020).

关键词： processes conserved generalized

Genome evolution of novel influenza A (H1N1) viruses in humans

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Chinese Science Bulletin 2009年第13期54卷 2159-2163页

作者： KOU Zheng hu songnian LI TianXian State Key Laboratory of Virology Wuhan Institute of Virology Chinese Academy of Sciences Wuhan 430071 China Beijing Institute of Genome Chinese Academy of Sciences Beijing 100029

The epidemic situation of A H1N1 flu arose in North America in April 2009,which rapidly expanded to three continents of Europe,Asia and Africa,with the risk ranking up to *** May 13th,the flu virus of A H1N1 had spread into 33 countries and regions,with a laboratory confirmed case number of 5728,including 61 *** on IRV and EpiFluDB database,425 parts of A H1N1 flu virus sequence were achieved,followed by sequenced comparison and evolution *** results showed that the current predominant A H1N1 flu virus was a kind of triple reassortment A flu virus:(i) HA,NA,MP,NP and NS originated from swine influenza virus;PB2 and PA originated from bird influenza virus;PB1 originated from human influenza virus.(ii) The origin of swine influenza virus could be subdivided as follows:HA,NP and NS originated from classic swine influenza virus of H1N1 subtype;NA and MP originated from bird origin swine influenza virus of H1N1 subtype.(iii) A H1N1 flu virus experienced no significant mutation during the epidemic spread,accompanied with no reassortment of the virus *** the paper,the region of the representative strains for sequence analysis(A/California/04/2009(H1N1) and A/Mexico/4486/2009(H1N1)) included USA and Mexico and was relatively wide,which suggested that the analysis results were convincing.

关键词：禽流感病毒基因组进化人类猪流感病毒生理盐水序列比较病毒亚型鸟类起源

Rice Genomics: over the Past Two Decades and into the Future

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Genomics, Proteomics & Bioinformatics 2018年第6期16卷 397-404页

作者： Shuhui Song Dongmei Tian Zhang Zhang songnian hu Jun Yu BIG Data Center Beijing Institute of GenomicsChinese Academy of SciencesBeijing 100101China CAS Key Laboratory of Genome Sciences and Information Beijing Institute of GenomicsChinese Academy of SciencesBeijing 100101China University of Chinese Academy of Sciences Beijing 100049China

Domestic rice(Oryza sativa L.) is one of the most important cereal crops, feeding a large number of worldwide populations. Along with various high-throughput genome sequencing projects, rice genomics has been making great headway toward direct ?eld applications of basic research advances in understanding the molecular mechanisms of agronomical traits and utilizing diverse germplasm resources. Here, we brie?y review its achievements over the past two decades and present the potential for its bright future.

关键词： Rice genome Genomic diversity Heterosis Domestication

A Brief Review on the Mechanisms of miRNA Regulation

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Genomics, Proteomics & Bioinformatics 2009年第4期7卷 147-154页

作者： Yimei Cai Xiaomin Yu songnian hu Jun Yu Key Laboratory of Genome Sciences and Information Beijing Institute of Genomics Chinese Academy of Sciences Beijing 100029 China.

MicroRNAs （miRNAs） are a class of short, endogenously-initiated non-coding RNAs that post-transcriptionally control gene expression via either translational repression or mRNA degradation. It is becoming evident that miRNAs are playing significant roles in regulatory mechanisms operating in various organisms, including developmental timing and host-pathogen interactions as well as cell differentiation, proliferation, apoptosis and tumorigenesis. Likewise, as a regulatory element, miRNA itself is coordinatively modulated by multifarious effectors when carrying out basic functions, such as SNP, miRNA editing, methylation and circadian clock. This mini-review summarized the current understanding of interactions between miRNAs and their targets, including recent advancements in deciphering the regulatory mechanisms that control the biogenesis and functionality of miRNAs in various cellular processes.

关键词： non-coding RNA miRNA miRNA regulation targets

Characterization of Evolutionarily Conserved MicroRNAs in Amphioxus

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Genomics, Proteomics & Bioinformatics 2010年第1期8卷 10-21页

作者： Lei Wang Lan Jiang songnian hu Yejun Wang Beijing Institute of Genomics Chinese Academy of Sciences Beijing 100029 China Graduate University of Chinese Academy of Sciences Beijing 100049 China Department of Biology the Chinese University of Hong Kong Hongkong China.

Amphioxus is an extant species closest to the ancestry of vertebrates. Observation of microRNA （miRNA） distribution of amphioxus would lend some hints for evolutionary research of vertebrates. In this study, using the publicly available scaffold data of the Florida amphioxus （Branchiostomafloridae） genome, we screened and characterized homologs of miRNAs that had been identified in other species. In total, 68 pieces of such homologs were obtained and classified into 33 families. Most of these miRNAs were distributed as clusters in genome. Inter-species comparison showed that many miRNAs, which had been thought as vertebrate- or mammal-specific before, were also present in amphioxus, while some miRNAs that had been considered as protostome-specific before also existed in amphioxus. Compared with ciona, amphioxus had an apparent miRNA gene expansion, but phylogenetic analysis showed that the duplicated miRNAs or clusters of amphioxus had a higher homology level than those duplicated ones in vertebrates.

关键词： amphioxus microRNA genome evolution

A Modified Enrichment Method to Construct Microsatellite Library from Plateau Pika Genome(Ochotona curzoniae)

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Genomics, Proteomics & Bioinformatics 2010年第1期8卷 72-76页

作者： Jianing Geng Kexin Li Yanming Zhang songnian hu CAS Key Laboratory of Genome Sciences and lnformation Beijing Institute of Genomics Chinese Academy of Sciences Beijing 100029 China Northwest Plateau Institute of Biology Chinese Academy of Sciences Xining 810001 China Graduate University of Chinese Academy of Sciences BeiI＇ing 100049 China.

A microsatellite-enriched library of plateau pika （Ochotona curzoniae） was constructed according to the strong affinity between biotin and streptavidin. Firstly, genomic DNA was fragmented by ultrasonication, which is a major improvement over traditional methods. Linker-ligated DNA fragments were hybridized with biotinylated microsatellite probes, and then were subjected to streptavidin-coated magnetic beads. PCR amplification was performed to obtain double-stranded DNA fragments containing microsatellites. Ligation and transformation were carried out by using the pGEM-T Vector System I and Escherichia coli DH10B competent cells. Sequencing results showed that 80.2% of clones contained microsatellite repeat motif. Several modifications make this protocol time-efficient and technically easier than the traditional ones; particularly, composition and relative abundance of microsatellite repeats in plateau pika genome were truly represented through the optimized PCR conditions. This method has also been successfully applied to construct microsatellite-enriched genomic libraries of Chinese hamster （Cricetulus griseus） and small abalone [Haliotis diversicolor （Reeve）] with high rates of positive clones, demonstrating its feasibility and stability.

关键词： microsatellite enriched library magnetic bead ultrasonication

The Most Redundant Sequences in human CpG Island Library Are Derived from Mitochondrial Genome

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Genomics, Proteomics & Bioinformatics 2010年第2期8卷 81-91页

作者： Ximiao He Shu Tao Jing Jin songnian hu Jun Yu CAS Key Laboratory of Genome Sciences and Information BeOing Institute of Genomics Chinese Academy of Sciences Beijing 100029 China Graduate University of Chinese Academy of Sciences Beijing 100049 China Department of Biology University of Science and Technology of China Hefei 230027 China.

An altered pattern of epigenetic modifications, such as DNA methylation and histone modification, is critical to many common human diseases, including cancer. Recently, mitochondrial DNA （mtDNA） was reported to be associated with tumorigenesis through epigenetic regulation of methylation patterns. One of the promising approaches to study DNA methylation and CpG islands （CGIs） is sequencing and analysis of clones derived from the physical library generated by methyl-CpG-binding domain proteins and restriction enzyme MseI. In this study, we observed that the most redundant sequences of 349 clones in a human CGI library were all generated from the human mitochondrial genome. Further analysis indicated that there was a 5,845-bp DNA transfer from mtDNA to chromosome 1, and all the clones should be the products of a 510-bp MseI fragment, which contained a putative CGI of 270 bp. The 510-bp fragment was annotated as part of cytochrome c oxidase subunit II （COXII）, and phylogenetic analysis of homologous sequences containing COXII showed three DNA transfer events from mtDNA to nuclear genome, one of which underwent secondary transfer events between different chromosomes. These results may further our understanding of how the mtDNA regulates DNA methylation in the nucleus.

关键词： human DNA methylation CpG islands nuclear mitochondrial DNA molecular phylogeny

Selection for Cheaper Amino Acids Drives Nucleotide Usage at the Start of Translation in Eukaryotic Genes

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Genomics, Proteomics & Bioinformatics 2021年第6期19卷 949-957页

作者： Na L.Gao Zilong He Qianhui Zhu Puzi Jiang songnian hu Wei-hua Chen Key Laboratory of Molecular Biophysics of the Ministry of Education Hubei Key Laboratory of Bioinformatics and Molecular-imagingDepartment of Bioinformatics and Systems BiologyCollege of Life Science and TechnologyHuazhong University of Science and TechnologyWuhan 430074China Institute for Computer Science and Cluster of Excellence on Plant Sciences Heinrich Heine UniversityD-40225 DuesseldorfGermany CAS Key Laboratory of Genome Sciences and Information Beijing Institute of GenomicsChinese Academy of SciencesBeijing 100101China State Key Laboratory of Microbial Resources Institute of MicrobiologyChinese Academy of SciencesBeijing 100101China Beijing Advanced Innovation Center for Big Data-Based Precision Medicine Interdisciplinary Innovation Institute of Medicine and EngineeringBeihang UniversityBeijing 100191China University of Chinese Academy of Sciences Beijing 100049China

Coding regions have complex interactions among multiple selective forces,which are manifested as biases in nucleotide *** studies have revealed a decreasing GC gradient from the 5′-end to 3′-end of coding regions in various *** confirmed that this gradient is universal in eukaryotic genes,but the decrease only starts from the~25th *** trend is mostly found in nonsynonymous(ns)sites at which the GC gradient is universal across the eukaryotic *** GC contents at ns sites result in cheaper amino acids,indicating a universal selection for energy efficiency toward the N-termini of encoded *** a genome,the decreasing GC gradient is intensified from lowly to highly expressed genes(more and more protein products),further supporting this *** reveals a conserved selective constraint for cheaper amino acids at the translation start that drives the increased GC contents at ns *** GC contents can facilitate transcription but result in a more stable local secondary structure around the start codon and subsequently impede translation ***,the GC gradients at four-fold and two-fold synonymous sites vary across *** could decrease or increase,suggesting different constraints acting at the GC contents of different codon sites in different *** study reveals that the overall GC contents at the translation start are consequences of complex interactions among several major biological processes that shape the nucleotide sequences,especially efficient energy usage.

关键词： Macroevolution Prioritization of selective forces Energy efficiency Transcription Translation initiation