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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 frontiers.Beijing 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 activities.On 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

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 5.Until 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 deaths.Based on IRV and EpiFluDB database,425 parts of A H1N1 flu virus sequence were achieved,followed by sequenced comparison and evolution analysis.The 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 genome.In 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

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 composition.Previous studies have revealed a decreasing GC gradient from the 5′-end to 3′-end of coding regions in various organisms.We confirmed that this gradient is universal in eukaryotic genes,but the decrease only starts from the~25th codon.This trend is mostly found in nonsynonymous(ns)sites at which the GC gradient is universal across the eukaryotic genome.Increased GC contents at ns sites result in cheaper amino acids,indicating a universal selection for energy efficiency toward the N-termini of encoded proteins.Within a genome,the decreasing GC gradient is intensified from lowly to highly expressed genes(more and more protein products),further supporting this hypothesis.This reveals a conserved selective constraint for cheaper amino acids at the translation start that drives the increased GC contents at ns sites.Elevated GC contents can facilitate transcription but result in a more stable local secondary structure around the start codon and subsequently impede translation initiation.Conversely,the GC gradients at four-fold and two-fold synonymous sites vary across species.They could decrease or increase,suggesting different constraints acting at the GC contents of different codon sites in different species.This 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

Micro RNA profiles and potential regulatory pattern during the early stage of spermatogenesis in mice

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Science China(Life Sciences) 2015年第11期58卷 442-450页

作者： LUO MengMeng HAO LiLi hu Fen DONG YaNan GOU LiXia ZHANG WenDian WANG Xin ZHAO Yuhui JIA MengChun HU SongNian ZHANG XiuJun College of Life Sciences College of Psychology Hebei United University CAS Key Laboratory of Genome Sciences and Information Beijing Institute of Genomics Chinese Academy of Sciences Hebei Normal University for Nationalities Department of Reproductive Endocrinology National Research Institute for Family Planning

Spermatogenesis is a complicated and poorly understood process that relies on the precise regulation of the self-renewal and differentiation of spermatogonia. In many organisms, micro RNAs(mi RNAs) are involved in multiple developmental processes as critical regulators of transcriptional and post-transcriptional gene silencing. This study investigated the expression pattern of mi RNAs in type B spermatogonia cells(BSc) and primary spermatocytes(PSc) of mice, using a high-throughput small RNA sequencing system. The results revealed that the expression levels of Let-7 family mi RNAs were remarkably high in both cell types. Furthermore, the expression levels of mi R-21, mi R-140-3p, mi R-103, mi R-30 a, mi R-101 b and mi R-99 b were decreased during the transformation from BSc to PSc. These mi RNAs target vital genes that participate in apoptosis, cell proliferation and differentiation, junction assembly and cell cycle regulation. These results highlight the indispensable role of mi RNAs in spermatogenesis.

关键词：微小RNA 精子发生监管模式小鼠转录后基因沉默 miRNA 早期初级精母细胞

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Long Non-coding RNAs and Their Biological Roles in Plants

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Genomics, Proteomics & Bioinformatics 2015年第3期13卷 137-147页

作者： Xue Liu Lili Hao Dayong Li Lihuang Zhu songnian hu CAS Key Laboratory of Genome Sciences and Information Beijing Institute of GenomicsChinese Academy of Sciences State Key Laboratory of Plant Genomics and National Center for Plant Gene Research Institute of Genetics and Developmental BiologyChinese Academy of Sciences

With the development of genomics and bioinformatics, especially the extensive applications of high-throughput sequencing technology, more transcriptional units with little or no protein-coding potential have been discovered. Such RNA molecules are called non- protein-coding RNAs （npcRNAs or ncRNAs）. Among them, long npcRNAs or ncRNAs 0npcRNAs or lncRNAs） represent diverse classes of transcripts longer than 200 nucleotides. In recent years, the lncRNAs have been considered as important regulators in many essential biological processes. In plants, although a large number of lncRNA transcripts have been predicted and identified in few species, our current knowledge of their biological functions is still limited. Here, we have summarized recent studies on their identification, characteristics, classification, bioinformatics, resources, and current exploration of their biological functions in olants.

关键词： Long non-coding RNA（IncRNA） Long non-coding naturalantisense transcripts（lncNATs） Epigenetic Small RNA MicroRNA Target mimicry

Identification and analysis of mouse non-coding RNA using transcriptome data

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Science China(Life Sciences) 2016年第9期59卷 589-603页

作者： Yuhui Zhao Wanfei Liu Jingyao Zeng Shoucheng Liu Xinyu Tan Hasanawad Aljohi songnian hu CAS Key Laboratory of Genome Sciences and Information Beijing Institute of Genomics Chinese Academy of Sciences Beijing 100101 China University of Chinese Academy of Sciences Beijing 100049 China Joint Center for Genomics Research (JCGR) King Abdulaziz City for Science and Technology and Chinese Academy of Sciences Riyadh 11442 Saudi Arabia

Transcripts are expressed spatially and temporally and they are very complicated, precise and specific; however, most studies are focused on protein-coding related genes. Recently, massively parallel c DNA sequencing(RNA-seq) has emerged to be a new and promising tool for transcriptome research, and numbers of non-coding RNAs, especially linc RNAs, have been widely identified and well characterized as important regulators of diverse biological processes. In this study, we used ultra-deep RNA-seq data from 15 mouse tissues to study the diversity and dynamic of non-coding RNAs in mouse. Using our own criteria, we identified totally 16,249 non-coding genes(21,569 non-coding RNAs) in mouse. We annotated these non-coding RNAs by diverse properties and found non-coding RNAs are generally shorter, have fewer exons, express in lower level and are more strikingly tissue-specific compared with protein-coding genes. Moreover, these non-coding RNAs show significant enrichment with transcriptional initiation and elongation signals including histone modifications(H3K4me3, H3K27me3 and H3K36me3), RNAPII binding sites and CAGE tags. The gene set enrichment analysis(GSEA) result revealed several sets of linc RNAs associated with diverse biological processes such as immune effector process, muscle development and sexual reproduction. Taken together, this study provides a more comprehensive annotation of mouse non-coding RNAs and gives an opportunity for future functional and evolutionary study of mouse non-coding RNAs.

关键词：非编码RNA 转录表达小鼠蛋白编码基因组织特异性识别组数生物过程

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Transcriptomic analysis reveals key regulators of mammogenesis and the pregnancy-lactation cycle

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Science China(Life Sciences) 2014年第3期57卷 340-355页

作者： ZHOU YuanYuan GONG Wei XIAO JingFa WU JiaYan PAN LinLin LI XiaoNuan WANG XuMin WANG WeiWei HU SongNian YU Jun Beijing Key Laboratory of Genome and Precision Medicine Technologies CAS Key Laboratory of Genome Sciences and InformationBeijing Institute of GenomicsChinese Academy of Sciences University of Chinese Academy of Sciences Division of Gastroenterology Department of MedicineUniversity of Alberta

An organ unique to mammals,the mammary gland develops 90%of its mass after birth and experiences the pregnancy-lactation-involution cycle(PL cycle)during reproduction.To understand mammogenesis at the transcriptomic level and using a ribo-minus RNA-seq protocol,we acquired greater than 50 million reads each for the mouse mammary gland during pregnancy(day 12 of pregnancy),lactation(day 14 of lactation),and involution(day 7 of involution).The pregnancy-,lactation-and involution-related sequencing reads were assembled into 17344,10160,and 13739 protein-coding transcripts and1803,828,and 1288 non-coding RNAs(ncRNAs),respectively.Differentially expressed genes(DEGs)were defined in the three samples,which comprised 4843 DEGs(749 up-regulated and 4094 down-regulated)from pregnancy to lactation and4926 DEGs(4706 up-regulated and 220 down-regulated)from lactation to involution.Besides the obvious and substantive upand down-regulation of the DEGs,we observe that lysosomal enzymes were highly expressed and that their expression coincided with milk secretion.Further analysis of transcription factors such as Trps1,Gtf2i,Tcf7l2,Nupr1,Vdr,Rb1,and Aebp1,and ncRNAs such as mir-125b,Let7,mir-146a,and mir-15 has enabled us to identify key regulators in mammary gland development and the PL cycle.

关键词：转录水平哺乳期周期怀孕差异表达基因非编码RNA 组分动物乳腺

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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