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Housekeeping protein-coding genes interrogated with tissue and individual variations

SCIENTIFIC REPORTS 2024年第1期14卷 1-12页

作者： Tung, Kuo-Feng Pan, Chao-Yu Lin, Wen-chang Acad Sinica Inst Biomed Sci Taipei 115 Taiwan

Housekeeping protein-coding genes are stably expressed genes in cells and tissues that are thought to be engaged in fundamental cellular biological functions. They are often utilized as normalization references in molecular biology research and are especially important in integrated bioinformatic investigations. Prior studies have examined human housekeeping protein-coding genes by analyzing various gene expression datasets. The inclusion of different tissue types significantly impacted the discovery of housekeeping genes. In this report, we investigated particularly individual human subject expression differences in protein-coding genes across different tissue types. We used GTEx V8 gene expression datasets obtained from more than 16,000 human normal tissue samples. Furthermore, the Gini index is utilized to investigate the expression variations of protein-coding genes between tissue and individual donor subjects. Housekeeping protein-coding genes found using Gini index profiles may vary depending on the tissue subtypes investigated, particularly given the diverse sample size collections across the GTEx tissue subtypes. We subsequently selected major tissues and identified subsets of housekeeping genes with stable expression levels among human donors within those tissues. In this work, we provide alternative sets of housekeeping protein-coding genes that show more consistent expression patterns in human subjects across major solid organs. Weblink: https://***.

关键词： protein-coding gene Housekeeping genes GTEx project Next-generation sequencing Gini index

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Comprehensive analysis of candidate signatures of long non-coding RNA LINC01116 and related protein-coding genes in patients with hepatocellular carcinoma

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BMC GASTROENTEROLOGY 2023年第1期23卷 216-216页

作者： Wang, Xiang-Kun Zhang, Xu-Dong Luo, Kai Yu, Long Huang, Shuai Liu, Zhong-Yuan Li, Ren-Feng Zhengzhou Univ Dept Hepatobiliary & Pancreat Surg Affiliated Hosp 1 Zhengzhou 450052 Henan Peoples R China

BackgroundHepatocellular carcinoma (HCC) is a long-term malignancy that causes high morbidities and mortalities worldwide. Notably, long non-coding RNAs (LncRNAs) have been identified as candidate targets for malignancy *** LINC01116 and its Pearson-correlated genes (PCGs) were identified and analyzed in HCC patients. The diagnostic and prognostic value of the lncRNA was evaluated using data from The Cancer Genome Atlas (TCGA). Further, we explored the target drugs of LINC01116 for clinical application. Relationships between immune infiltration and PCGs, methylation and PCGs were explored. The diagnostic potentials were then validated by Oncomine ***01116 and the PCG OLFML2B are differentially and highly expressed in tumor tissues (both P <= 0.050). We found that LINC01116, TMSB15A, PLAU, OLFML2B, and MRC2 have diagnostic potentials (all AUC >= 0.700, all P <= 0.050) while LINC01116 and TMSB15A have prognostic significance (both adjusted P <= 0.050). LINC01116 was enriched in the vascular endothelial growth factor (VEGF) receptor signaling pathway, mesenchyme morphogenesis, etc. After that, candidate target drugs with potential clinical significance were identified: Thiamine, Cromolyn, Rilmenidine, Chlorhexidine, Sulindac_sulfone, Chloropyrazine, and Meprylcaine. Analysis of immune infiltration revealed that MRC2, OLFML2B, PLAU, and TMSB15A are negatively associated with the purity but positively associated with the specific cell types (all P < 0.050). Analysis of promoter methylation demonstrated that MRC2, OLFML2B, and PLAU have differential and high methylation levels in primary tumors (all P < 0.050). Validation results of the differential expressions and diagnostic potential of OLFML2B (Oncomine) were consistent with those obtained in the TCGA cohort (P < 0.050, AUC > 0.700).ConclusionsDifferentially expressed LINC01116 could be a candidate diagnostic and an independent prognostic signature in HCC. Besides, its target drugs

关键词： Long non-coding RNA LINC01116 protein-coding gene Signature Hepatocellular carcinoma

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The evolutionary characterization of Gamasida based on mitochondrial genes codon usage pattern

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PARASITOLOGY RESEARCH 2024年第1期123卷 1-11页

作者： Yuan, Bili He, Gangxian Dong, Wenge Dali Univ Inst Pathogens & Vectors Yunnan Prov Key Lab Zoonosis Control & Prevent Dali 671000 Yunnan Peoples R China

Mites belonging to the suborder Gamasida are species-rich and habitat-diverse, with a worldwide distribution. To adapt to the environment and obtain better living conditions, all species of the suborder Gamasida have been undergoing constant evolution. The complete mitochondrial genome (mitogenome) is an invaluable molecular marker for studying the origin of species, genetic differentiation between closely related species, and between intraspecific groups. In some species of the suborder Gamasida, mitochondrial tRNA genes are truncated and carried unstable genetic information. This study presents a comparative analysis of codon usage pattern and preference of 13 protein-coding genes of 24 species in 17 genera and 10 families of the suborder Gamasida. Results showed that have an obvious AT preference (0.664-0.829) for codon usage in the suborder Gamasida. Most of the optimal and high-frequency codons also end in A/T. The degree of natural selection varies between the same protein-coding genes of different gamasid mites or among different protein-coding genes within the same gamasid mites. Base and codon usage pattern and preference are very similar between the same species and genus, namely the closer species, the more similar their bases and codons usage patterns and preference are. T bases and C bases were the preference bases for codon usage of 24 species in the suborder Gamasida. Evolution of the suborder Gamasida was dominated by natural selection (64.1%). This study provides the first comprehensive analysis of codon usage in the suborder Gamasida, which will greatly improve our understanding of codon usage patterns and preference, genetics, and evolution of the suborder Gamasida. It will help to evaluate the degree of molecular adaptation in the suborder Gamasida and to further explore evolutionary features of the suborder Gamasida.

关键词： Gamasida protein-coding gene Mutation pressure Evolution Codon usage

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Distinctive physical properties of DNA shared by RNA polymerase II gene promoters and 5′-flanking regions of tRNA genes

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JOURNAL OF BIOCHEMISTRY 2024年第4期175卷 395-404页

作者： Uemura, Kohei Ohyama, Takashi Waseda Univ Grad Sch Sci & Engn Major Integrat Biosci & Biomed Engn 2-2Wakamatsu ChoShinjuku Tokyo 1628480 Japan Waseda Univ Fac Educ & Integrated Arts & Sci Dept Biol 2-2 Wakamatsu ChoShinjuku Tokyo 1628480 Japan

Numerous noncoding (nc)RNAs have been identified. Similar to the transcription of protein-coding (mRNA) genes, long noncoding (lnc)RNA genes and most of micro (mi)RNA genes are transcribed by RNA polymerase II (Pol II). In the transcription of mRNA genes, core promoters play an indispensable role;they support the assembly of the preinitiation complex (PIC). However, the structural and/or physical properties of the core promoters of lncRNA and miRNA genes remain largely unexplored, in contrast with those of mRNA genes. Using the core promoters of human genes, we analyzed the repertoire and population ratios of residing core promoter elements (CPEs) and calculated the following five DNA physical properties (DPPs): duplex DNA free energy, base stacking energy, protein-induced deformability, rigidity and stabilizing energy of Z-DNA. Here, we show that their CPE and DPP profiles are similar to those of mRNA gene promoters. Importantly, the core promoters of these three classes of genes have two highly distinctive sites in their DPP profiles around the TSS and position -27. Similar characteristics in DPPs are also found in the 5 '-flanking regions of tRNA genes, indicating their common essential roles in transcription initiation over the kingdom of RNA polymerases. Graphical Abstract

关键词： Core promoter lncRNA miRNA physical properties of DNA protein-coding gene tRNA

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Extant thrips diverged in the early tertiary period

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BMC GENOMIC DATA 2023年第1期24卷 46页

作者： Wu, Chunying Zhang, Hongrui Yunnan Agr Univ Plant Protect Coll Kunming 650201 Peoples R China Yunnan Agr Univ State Key Lab Conservat & Utilizat Bioresources Yu Kunming 650201 Peoples R China Chinese Acad Sci Kunming Inst Zool State Key Lab Genet Resources & Evolut Kunming 650201 Peoples R China

Thysanoptera, commonly known as thrips, are diverse tiny insects whose earliest fossil record dates back to the Triassic period. Since there are few studies on the divergence time of taxa under Thysanoptera, this study used 13 mitochondrial coding protein genes to reconstruct the phylogenetic tree with divergence time of 26 species of this order and show a reliable phylogenetic relationship of thrips species. The time tree of this study shows that most extant thrips diverged in the early Tertiary period, while the fossil records also support that most extinct thrips appeared in this period. This study expands our understanding of the evolution of thrips and provides a feasible way of using multiple mitochondrial genes to establish robust phylogenetic relationships and explore divergence time between species.

关键词： Thysanoptera Thrips protein-coding gene Phylogeny Divergence time

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Screening and Identification of Differentially Expressed and Adipose Growth-Related protein-coding genes During the Deposition of Perirenal Adipose Tissue in Rabbits

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DIABETES METABOLIC SYNDROME AND OBESITY 2020年 13卷 4669-4680页

作者： Wang, Guoze Du, Kun Xie, Zhenjian Tang, Renyong Jia, Xianbo Chen, Shiyi Lai, Songjia Sichuan Agr Univ Farm Anim Genet Resources Explorat & Innovat Key Chengdu 611130 Peoples R China Guizhou Med Univ Coll Food Sci Guiyang 550025 Peoples R China Chengdu Univ Coll Pharm & Biol Engn Chengdu 610106 Peoples R China

Background: Rabbit is a good model for genetic and medical studies in other livestock species. The rabbit shows low adipose tissue deposition, and the phenomena indicates that there is some specificity of adipose deposition during the rabbit growth. However, little is known about genes that regulate the growth of adipose tissue in rabbits. Materials and Methods: Deep RNA-seq and comprehensive bioinformatics analyses were used to characterize the genes of rabbit visceral adipose tissue (VAT) at 35, 85 and 120 days after birth. Differentially expressed genes (DEGs) were identified at the three growth stages by DESeq. To explore the function of the candidate genes, gene Ontology (GO) enrichment and Kyoto Encyclopedia of genes and Genomes (KEGG) pathway analyses were performed. Six DEGs were randomly selected, and their expression profiles were validated by q-PCR. Results: A total of 20,303 known transcripts and 99,199 new transcripts from 8 RNA sequencing libraries were identified, and 34 differentially expressed genes (DEGs) were screened. GO enrichment and KEGG pathway analyses revealed that the DEGs were mainly involved in lipid metabolism regulation including acylglycerol metabolic process and mobilization, and decomposition of lipids to generate ATP in adipocytes and fatty acid metabolism, included LOC100342322 and LOC100342572. In addition, 133 protein-coding genes that play a role in adipose growth and development were screened, including acyl-CoA synthetase long chain family member 5 (ACSL5) and fatty acid-binding protein 2 (FABP2). The validation results of six DEGs by q-PCR showed similar trends with the results of RNA-seq. Conclusion: In summary, this study provides the first report of the coding genes profiles of rabbit adipose tissue during different growth stages. These data allow for the identification of candidate genes for subsequent studies on rabbit genetics and regulation of adipose cells, and provide an animal model for studying obesity in humans.

关键词： rabbit RNA-seq adipose tissue growth protein-coding gene fat deposition

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Identification of Long Non-coding RNAs and Their Target genes from Mycelium and Primordium in Model Mushroom Schizophyllum commune

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MYCOBIOLOGY 2022年第5期50卷 357-365页

作者： Wu, Tuheng Chen, Jian Jiao, Chunwei Hu, Huiping Wu, Qingping Xie, Yizhen Guangdong Yuewei Edible Fungi Technol Co Guangzhou Peoples R China South China Univ Technol Sch Biosci & Bioengn Guangzhou Peoples R China Guangdong Acad Sci Inst Microbiol Guangdong Prov Key Lab Microbial Safety & Hlth State Key Lab Appl Microbiol Southern China Guangzhou Peoples R China

Schizophyllum commune has emerged as the most promising model mushroom to study developmental stages (mycelium, primordium), which are two primary processes of fruit body development. Long non-coding RNA (lncRNA) has been proved to participate in fruit development and sex differentiation in fungi. However, potential lncRNAs have not been identified in S. commune from mycelium to primordium developmental stages. In this study, lncRNA-seq was performed in S. commune and 61.56 Gb clean data were generated from mycelium and primordium developmental stages. Furthermore, 191 lncRNAs had been obtained and a total of 49 lncRNAs were classified as differently expressed lncRNAs. Additionally, 26 up-regulated differently expressed lncRNAs and 23 down-regulated between mycelium and primordia libraries were detected. Further, Kyoto Encyclopedia of genes and Genomes (KEGG) analysis showed that differentially expressed lncRNAs target genes from the MAPK pathway, phosphatidylinositol signal, ubiquitin-mediated proteolysis, autophagy, and cell cycle. This study provides a new resource for further research on the relationship between lncRNA and two developmental stages (mycelium, primordium) in S. commune.

关键词： Schizophyllum commune mycelium and primordium long non-coding RNA protein-coding gene post-transcriptional modification

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Proposal of a new nomenclature for introns in protein-coding genes in fungal mitogenomes

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IMA FUNGUS 2019年第1期10卷 1-8页

作者： Zhang, Shu Zhang, Yong-Jie Shanxi Univ Inst Appl Chem Taiyuan 030006 Shanxi Peoples R China Shanxi Univ Sch Life Sci Taiyuan 030006 Shanxi Peoples R China

Fungal mitochondrial genes are often invaded by group I or II introns, which represent an ideal marker for understanding fungal evolution. A standard nomenclature of mitochondrial introns is needed to avoid confusion when comparing different fungal mitogenomes. Currently, there has been a standard nomenclature for introns present in rRNA genes, but there is a lack of a standard nomenclature for introns present in protein-coding genes. In this study, we propose a new nomenclature system for introns in fungal mitochondrial protein-coding genes based on (1) three-letter abbreviation of host scientific name, (2) host gene name, (3), one capital letter P (for group I introns), S (for group II introns), or U (for introns with unknown types), and (4) intron insertion site in the host gene according to the cyclosporin-producing fungus Tolypodadium inflatum. The suggested nomenclature was proved feasible by naming introns present in mitogenomes of 16 fungi of different phyla, including both basal and higher fungal lineages although minor adjustment of the nomenclature is needed to fit certain special conditions. The nomenclature also had the potential to name plant/protist/animal mitochondrial introns. We hope future studies follow the proposed nomenclature to ensure direct comparison across different studies.

关键词： Nomenclature Fungi Mitogenome Intron protein-coding gene

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protein-coding genes combined with long noncoding RNA as a novel transcriptome molecular staging model to predict the survival of patients with esophageal squamous cell carcinoma

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Cancer Communications 2018年第1期38卷 50-62页

作者： Jin-Cheng Guo Yang Wu Yang Chen Feng Pan Zhi-Yong Wu Jia-Sheng Zhang Jian-Yi Wu Xiu-E Xu Jian-Mei Zhao En-Min Li Yi Zhao Li-Yan Xu Key Laboratory of Molecular Biology in High Cancer Incidence Coastal Chaoshan Area of Guangdong Higher Education Institutes Shantou University Medical CollegeShantouGuangdong 515041P.R.China Department of Biochemistry and Molecular Biology Shantou University Medical CollegeShantouGuangdong 515041P.R.China Departments of Oncology Surgery Shantou Central HospitalAffiliated Shantou Hospital of Sun Yat-Sen UniversityShantouGuangdong 515041P.R.China Institute of Oncologic Pathology Shantou University Medical CollegeShantouGuangdong 515041P.R.China Key Laboratory of Intelligent Information Processing Advanced Computer Research CenterState Key Laboratory of Computer ArchitectureInstitute of Computing TechnologyChinese Academy of SciencesBeijing 100190P.R.China

Background:Esophageal squamous cell carcinoma(ESCC)is the predominant subtype of esophageal carcinoma in *** study was to develop a staging model to predict outcomes of patients with ***:Using Cox regression analysis,principal component analysis(PCA),partitioning clustering,Kaplan-Meier analysis,receiver operating characteristic(ROC)curve analysis,and classification and regression tree(CART)analysis,we mined the gene Expression Omnibus database to determine the expression profiles of genes in 179 patients with ESCC from GSE63624 and GSE63622 ***:Univariate cox regression analysis of the GSE63624 dataset revealed that 2404 protein-coding genes(PCGs)and 635 long non-coding RNAs(lncRNAs)were associated with the survival of patients with *** categorized these PCGs and lncRNAs into three principal components(PCs),which were used to cluster the patients into three *** analysis demonstrated that the predictive ability of PCG-lncRNA PCs when applied to new patients was better than that of the tumor-node-metastasis staging(area under ROC curve[AUC]:0.69 vs.0.65,P<0.05).Accord-ingly,we constructed a molecular disaggregated model comprising one lncRNA and two PCGs,which we desig-nated as the LSB staging model using CART analysis in the GSE63624 *** LSB staging model classified the GSE63622 dataset of patients into three different groups,and its effectiveness was validated by analysis of another cohort of 105 ***:The LSB staging model has clinical significance for the prognosis prediction of patients with ESCC and may serve as a three-gene staging microarray.

关键词： Long non-coding RNA protein-coding gene Esophageal squamous cell carcinoma Overall survival Staging model Transcriptome

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Metatranscriptomic analysis reveals co-expression pattern of mitochondrial oxidative phosphorylation (OXPHOS) genes among different species of bony fishes in muscle tissue

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JOURNAL OF KING SAUD UNIVERSITY SCIENCE 2020年第7期32卷 3084-3090页

作者： Lin, Geng-Ming Audira, Gilbert Juniardi, Stevhen Hsiao, Chung-Der Minist Nat Resources Lab Marine Biol & Ecol Inst Oceanog 3 Xiamen 361005 Peoples R China Chung Yuan Christian Univ Dept Chem Chungli 32023 Taiwan Chung Yuan Christian Univ Dept Biosci Technol Chungli 32023 Taiwan Chung Yuan Christian Univ Ctr Biomed Technol Chungli 32023 Taiwan Chung Yuan Christian Univ Ctr Nanotechnol Chungli 32023 Taiwan

Mitochondrion is an organelle responding to providing cell energy by oxidative phosphorylation (OXPHOS) reaction. In the mitochondrial genome of animals, 13 important protein-coding genes (ND1, ND2, ND3, ND4, ND4L, ND5, ND6, CTYB, COX1, COX2, COX3 ATP6, ATP8) play important roles on mediating the OXPHOS reaction. The study is to compare the expressional level of 13 mitochondrial PCGs among muscle of diverse fish species to ask whether the 13 PCGs expressional level is correlated to fish living habitat or phylogenetic position. We used a metatranscriptomic approach to explore the expression level of 13 PCGs among diverse fish species (24 bony fish and one cartilaginous fish) by downloading the raw next-generation data from the NCBI SRA database and using two commercial software of geneious and CLCBio to perform gene mapping and gene expression profiling. Principal component analysis (PCA) and hierarchy clustering were utilized to study the gene or species relationship based on 13 PCGs' expression pattern. Based on the results, we discovered the expression pattern of PCG genes derived from the same OXPHOS complex is closer to each other showing co-expression or coregulation relationship. The 13 PCGs expression profile was not co-related to fish living habitats but instead, well correlated to their phylogenetic position. The clustering results for 13 PCGs' expressional patterns showed bony fish and cartilaginous fish were grouped into two distinct clades. For bony fish clades, all COX genes displayed high expression patterns while for the cartilaginous Glade, the CYTB gene was highly expressed with the low expression level of COX3. In conclusion, by using the metatranscriptomic approach, we were able to explore and compare the gene expression profiles of 13 PCGs from diverse fish species for the first time. The co-expression pattern of 13 PCGs discovered in fish was well consistent with previous observations done in plants or mammals. However, one has to keep in mind t

关键词： Metagenomics Muscle Transcriptome protein-coding gene Mitogenome

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