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Identification of Candidate Transcription Factor Binding Sites in the Cattle Genome

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genomics, proteomics & Bioinformatics 2013年第3期11卷 195-198页

作者： Derek M. Bickhart George E. Liu Bovine functional genomics laboratory United States Department of Agriculture Agricultural Research Service (USDA-ARS) Beltsville Agricultural Research Service

A resource that provides candidate transcription factor binding sites （TFBSs） does not currently exist for cattle. Such data is necessary, as predicted sites may serve as excellent starting locations for future omics studies to develop transcriptional regulation hypotheses. In order to generate this resource, we employed a phylogenetic footprinting approach--using sequence conservation across cattle, human and dog and position-specific scoring matrices to identify 379,333 putative TFBSs upstream of nearly 8000 Mammalian Gene Collection （MGC） annotated genes within the cattle genome. Comparisons of our predictions to known binding site loci within the PCKI, ACTA1 and G6PC promoter regions revealed 75% sensitivity for our method of discovery. Additionally, we intersected our predictions with known cattle SNP variants in dbSNP and on the lllumina BovineHD 770k and Bos 1 SNP chips, finding 7534, 444 and 346 overlaps, respectively. Due to our stringent filtering criteria, these results represent high quality predictions of putative TFBSs within the cattle genome. All binding site predictions are freely available at http：//bfgl. ***/BovineTFBS/or http：//199.***.54.77/BovineTFBS.

关键词： Cattle Transcription factor bindingsites In silico prediction

Unintended Changes in Genetically Modified Rice Expressing the Lysine-Rich Fusion Protein Gene Revealed by a proteomics Approach

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Journal of Integrative Agriculture 2013年第11期12卷 2013-2021页

作者： ZHAO Xiang-xiang TANG Tang LIU Fu-xia LU Chang-li HU Xiao-lan JI Li-lian LIU Qiao-quan Jiangsu Key laboratory for Eco-Agricultural Biotechnology Around Hongze Lake Huaiyin Normal University Key Laboratories of Crop Genetics and Physiology of the Jiangsu Province and Plant functional genomics Ministry of Education/Yangzhou University

Development of new technologies for evaluating genetically modiifed （GM） crops has revealed that there are unintended insertions and expression changes in GM crops. Proifling techniques are non-targeted approaches and are capable of detecting more unintended changes in GM crops. Here, we report the application of a comparative proteomic approach to investigate the protein proifle differences between a GM rice line, which has a lysine-rich protein gene, and its non-transgenic parental line. Proteome analysis by two-dimensional gel electrophoresis （2-DE） and mass spectrum analysis of the seeds identiifed 22 differentially expressed protein spots. Apart from a number of glutelins that were detected as targeted proteins in the GM line, the majority of the other changed proteins were involved in carbohydrate metabolism, protein synthesis and stress responses. These results indicated that the altered proteins were not associated with plant allergens or toxicity.

关键词： transgenic rice proteome profiling techniques unintended changes two-dimensional gel electrophoresis

Chasing Sequencing Perfection:Marching Toward Higher Accuracy and Lower Costs

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genomics, proteomics & Bioinformatics 2024年第2期22卷 1-12页

作者： Hangxing Jia Shengjun Tan Yong E.Zhang CAS Key laboratory of Zoological Systematics and Evolution&State Key laboratory of Integrated Management of Pest Insects and Rodents Institute of ZoologyChinese Academy of SciencesBeijing 100101China University of Chinese Academy of Sciences Beijing 100049China CAS Center for Excellence in Animal Evolution and Genetics Chinese Academy of SciencesKunming 650223China

Next-generation sequencing(NGS),represented by Illumina platforms,has been an essential cornerstone of basic and applied ***,the sequencing error rate of 1 per 1000 bp(10^(−3))represents a serious hurdle for research areas focusing on rare mutations,such as somatic mosaicism or microbe *** examining the high-fidelity sequencing methods developed in the past decade,we summarized three major factors underlying errors and the corresponding 12 strategies mitigating these *** then proposed a novel framework to classify 11 preexisting representative methods according to the corresponding combinatory strategies and identified three trends that emerged during methodological *** further extended this analysis to eight long-read sequencing methods,emphasizing error reduction ***,we suggest two promising future directions that could achieve comparable or even higher accuracy with lower costs in both NGS and long-read sequencing.

关键词： Sequencing error High-fidelity sequencing Consensus sequencing Single-molecule sequencing Rare mutation

Molecular Evolution of Protein Sequences and Codon Usage in Monkeypox Viruses

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genomics, proteomics & Bioinformatics 2024年第1期22卷 89-97页

作者： Ke-Jia Shan Changcheng Wu Xiaolu Tang Roujian Lu Yaling Hu Wenjie Tan Jian Lu State Key laboratory of Protein and Plant Gene Research Center for BioinformaticsSchool of Life SciencesPeking UniversityBeijing 100871China Sinovac Biotech Ltd. Beijing 100085China NHC Key laboratory of Biosafety National Institute for Viral Disease Control and PreventionChinese Center for Disease Control and PreventionBeijing 100052China

The monkeypox virus(mpox virus,MPXV)epidemic in 2022 has posed a significant public health ***,the evolutionary principles of MPXV remain largely ***,we examined the evolutionary patterns of protein sequences and codon usage in *** first demonstrated the signal of positive selection in OPG027,specifically in the CladeⅠlineage of ***,we discovered accelerated protein sequence evolution over time in the variants responsible for the 2022 ***,we showed strong epistasis between amino acid substitutions located in different *** codon adaptation index(CAI)analysis revealed that MPXV genes tended to use more non-preferred codons compared to human genes,and the CAI decreased over time and diverged between clades,with CladeⅠ>Ⅱa andⅡb-A>Ⅱ*** the decrease in fatality rate among the three groups aligned with the CAI pattern,it remains unclear whether this correlation was coincidental or if the deoptimization of codon usage in MPXV led to a reduction in fatality *** study sheds new light on the mechanisms that govern the evolution of MPXV in human populations.

关键词： Mpox virus Positive selection OPG027 Accelerated evolution Codon usage bias

Global Marine Cold Seep Metagenomes Reveal Diversity of Taxonomy,Metabolic Function,and Natural Products

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genomics, proteomics & Bioinformatics 2024年第2期22卷 121-134页

作者： Tao Yu Yingfeng Luo Xinyu Tan Dahe Zhao Xiaochun Bi Chenji Li Yanning Zheng Hua Xiang Songnian Hu State Key laboratory of Microbial Resources Institute of MicrobiologyChinese Academy of SciencesBeijing 100101China University of Chinese Academy of Sciences Beijing 100049China

Cold seeps in the deep sea are closely linked to energy exploration as well as global climate *** alkane-dominated chemical energy-driven model makes cold seeps an oasis of deep-sea life,showcasing an unparalleled reservoir of microbial genetic ***,by analyzing 113 metagenomes collected from 14 global sites across 5 cold seep types,we present a comprehensive Cold Seep Microbiomic Database(CSMD)to archive the genomic and functional diversity of cold seep *** CSMD includes over 49 million non-redundant genes and 3175 metagenome-assembled genomes,which represent 1895 species spanning 105 *** addition,beta diversity analysis indicates that both the sampling site and cold seep type have a substantial impact on the prokaryotic microbiome community *** and anaerobic metabolisms are prevalent in microbial communities,accompanied by considerable mixotrophs and facultative anaerobes,highlighting the versatile metabolic potential in cold ***,secondary metabolic gene cluster analysis indicates that at least 98.81%of the sequences potentially encode novel natural products,with ribosomally synthesized and post-translationally modified peptides being the predominant type widely distributed in archaea and ***,the CSMD represents a valuable resource that would enhance the understanding and utilization of global cold seep microbiomes.

关键词： Global marine cold seep Metagenome Prokaryotic microbiome Metabolic function Natural product

On the Observable Transition to Living Matter

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genomics, proteomics & Bioinformatics 2011年第1期9卷 7-14页

作者： Samanta Pino Edward N. Trifonov Ernesto Di Mauro Charles Darwin Department of Biology and Biotechnology Sapienza University of Roma Roma 00185 Italy Genome Diversity Center Institute of Evolution University of Haifa Haifa 31905 Israel Division of functional genomics and proteomics Faculty of Science Masaryk University Brno 61137 Czech Republic

In recent developments in chemistry and genetic engineering, the humble researcher dealing with the origin of life finds her（him）self in a grey area of tackling something that even does not yet have a clear definition agreed upon. A series of chemical steps is described to be considered as the life-nonlife transition, if one adheres to the minimalistic definition： life is self-reproduction with variations. The fully artificial RNA system chosen for the exploration corresponds sequence-wise to the reconstructed initial triplet repeats, presumably corresponding to the earliest protein-coding molecules. The demonstrated occurrence of the mismatches （variations） in otherwise complementary syntheses （＂self-reproduction＂）, in this RNA system, opens an experimental and conceptual perspective to explore the origin of life （and its definition）, on the apparent edge of the origin.

关键词： triplet code origin of life definition of life life-nonlife transition

Collagen1α1 promoter drives the expression of Cre recombinase in osteoblasts of transgenic mice

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Journal of Genetics and genomics 2008年第9期35卷 525-530页

作者： Lagabaiyila Zha Ning Hou Jian Wang Guan Yang Yuanrong Gao Lin Chen Xiao Yang State Key laboratory of proteomics Genetic Laboratory of Development and Diseases Institute ofBiotechnology Beijing 100071 China laboratory of Trauma Center Daping Hospital The Third Military Medical University Chongqing 400042 China

Osteoblasts participate in bone formation, bone mineralization, osteoclast differentiation and many pathological processes. To study the function of genes in osteoblasts using Cre-LoxP system, we generated a mouse line expressing the Cre recombinase under the control of the rat Collagenlcd （Collα1） promoter （Collα1-Cre）. Two founders were identified by genomic PCR from 16 offsprings, and the integration efficiency is 12.5%. In order to determine the tissue distribution and the activity of Cre recombinase in the transgenic mice, the Coll αl-Cre transgenic mice were bred with the ROSA26 reporter strain and a mouse strain that carries Smad4 conditional alleles （Smad4^Co/Co）. Multiple tissue PCR of Collα1-Cre;Smad4^Co/＋ mice revealed the restricted Cre activity in bone tissues containing osteoblasts and tendon. LacZ staining in the Collα1-Cre;ROSA26 double transgenic mice revealed that the Cre recombinase began to express in the osteoblasts of calvaria at E14.5. Cre activity was observed in the osteoblasts and osteocytes of P10 double transgenic mice. All these data indicated that the Collα1-Cre transgenic mice could serve as a valuable tool for osteoblast lineage analysis and conditional gene knockout in osteoblasts.

关键词： Collagenl osteoblast Cre recombinase transgenic mouse

MakeHub:Fully Automated Generation of UCSC Genome Browser Assembly Hubs

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genomics, proteomics & Bioinformatics 2019年第5期17卷 546-549页

作者： Katharina Jasmin Hoff University of Greifswald Institute for Mathematics and Computer Science17489 GreifswaldGermany University of Greifswald Center for Functional Genomics of Microbes17489 GreifswaldGermany

Novel genomes are today often annotated by small consortia or individuals whose background is not from *** audience requires tools that are easy to *** need has been addressed by several genome annotation tools and *** resulting annotation is a crucial step of quality *** UCSC Genome Browser is a powerful and popular genome visualization *** Hubs,which can be hosted on any publicly available web server,allow browsing genomes via UCSC Genome Browser *** steps for creating custom Assembly Hubs are well documented and the required tools are publicly ***,the number of steps for creating a novel Assembly Hub is *** some cases,the format of input files needs to be adapted,which is a difficult task for scientists without programming ***,we describe Make Hub,a novel command line tool that generates Assembly Hubs for the UCSC Genome Browser in a fully automated *** pipeline also allows extending previously created Hubs by additional *** Hub is freely available for downloading at https://***/Gaius-Augustus/Make Hub.

关键词： Genome annotation Annotation visualization RNA-seq Genome browser

RNase P:Beyond Precursor tRNA Processing

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genomics, proteomics & Bioinformatics 2024年第1期22卷 19-28页

作者： Peipei Wang Juntao Lin Xiangyang Zheng Xingzhi Xu Guangdong Key laboratory for Genome Stability&Disease Prevention and Marshall laboratory of Biomedical Engineering Shenzhen University Medical SchoolShenzhen UniversityShenzhen 518060China Department of Urology The First Affiliated HospitalZhejiang University School of MedicineHangzhou 310000China Shenzhen University General Hospital-Dehua Hospital Joint Research Center on Precision Medicine Dehua HospitalDehua 362500China

Ribonuclease P(RNase P)was first described in the 1970’s as an endoribonuclease acting in the maturation of precursor transfer RNAs(tRNAs).More recent studies,however,have uncovered non-canonical roles for RNase P and its ***,we review the recent progress of its involvement in chromatin assembly,DNA damage response,and maintenance of genome stability with implications in *** possibility of RNase P as a therapeutic target in cancer is also discussed.

关键词： RNase P Chromatin assembly DNA damage response Genome stability Tumorigenesis