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Conference on Frontiers in the Convergence of Bioscience and Information Technologies

作者： Jaiswal, Mohenish Prasanna, S. R. Mahadeva Rangan, Latha Department of Biotechnology IIT Guwahati Assam 781 039 India Department of Electronics and Communication IIT Guwahati Assam 781 039 India

ISBN: (纸本)9780769529998

In this study, the resonant recognition model (RRM), was developed to locate the so called 'lead-in regions' or residues that contribute to the creation of the environment that enables proteins to perform their complex functions. The RRM is a physical and mathematical model and provides a significant correlation between spectra of numerical presentation of amino acids and their biological activity. We developed a preliminary model for this purpose and applied it on two well characterized classes of enzymes viz., human proteases and kinases. The results obtained (positions of 'lead-in residues' in the primary structure of the proteins) were used in association with the 3D-structure data of the proteins for the purpose of predicting the catalytic residue of the enzyme.

关键词： catalytic site : lead-in-regions protein coding resonant recognition model (RRM)

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DSP technique for gene and exon prediction taking Complex indicator sequence

DSP technique for gene and exon prediction taking Complex in...

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IEEE Region 10 Conference (TENCON 2008)

作者： Hota, M. K. Srivastava, V. K. Motilal Nehru Natl Inst Technol Elect & Commun Engn Dept Allahabad 211004 Uttar Pradesh India

ISBN: (纸本)9781424424085

It has been observed by many researchers that the protein coding regions of DNA exhibit a period-3 behavior due to the codon structure. The period-3 property is not present outside coding regions, and can be exploited to locate coding regions. For eukaryotes (cells with nucleus) this periodicity has mostly been observed within the exons and not within the introns. Previously binary indicator sequence and electron-ion interaction pseudo potentials (EIIP) indicator sequence has been used for the identification of the coding regions. In this paper we observed that complex indicator sequence provides strong spectral component compared to EIIP indicator sequence. We also observed that windowed DFT taking complex indicator sequence provides better exon prediction compared to windowed DFT taking EIIP indicator sequence and digital filters methods. Computational overhead is reduced by 75% in complex indicator sequence compared to binary indicator sequence. There is maximum discrimination between coding and non-coding regions in complex indicator sequence.

关键词： DNA protein coding exons period-3 windowed DFT digital filters binary indicator sequence EIIP indicator sequence complex indicator sequence

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Prediction of Long Non-coding RNAs Using Support Vector Machine

Prediction of Long Non-coding RNAs Using Support Vector Mach...

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第六届全国生物信息学与系统生物学学术大会暨国际生物信息学前沿研讨会

作者：孙磊许驰胡学龙电子与通信工程专业部信息工程学院扬州大学扬州225127 电子与通信工程专业部信息工程学院扬州大学扬州225127 信息中心扬州大学扬州225009

Background: Thousands of newly discovered long non-coding RNAs (lncRNAs) have been bringing novel insight into biological ***, it is still not trivial to accurately distinguish the novel lncRNA transcripts from the pr... 详细信息

关键词： long non-coding RNA protein coding support vector machine prediction

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RNA coding Potential Prediction Using Alignment-Free Logistic Regression Model

RNA Coding Potential Prediction Using Alignment-Free Logisti...

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作者： Ying Li Liguo Wang

CPAT (coding-Potential Assessment Tool) is a logistic regression model–based classifier that can accurately and quickly distinguish protein-coding and noncoding RNAs using pure linguistic features calculated from the RNA sequences. CPAT takes as input the nucleotides sequences or genomic coordinates of RNAs and outputs the probabilities p (0 ≤ p ≤ 1), which measure the likelihood of protein coding. Users can run CPAT online (http://***/cpat/ ) or from the local computers after installation. CPAT provides prebuilt logistic models to recognize RNAs originated from human (Homo sapiens), mouse (Mus musculus), zebrafish (Danio rerio), and fly (Drosophila melanogaster) genomes. Instructions on how to train models for other genomes are described in CPAT website (http://***/ ) and this chapter. less

关键词： Cufflinks Prediction Noncoding RNA Logistic regression protein coding LncRNA LincRNA

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The novel ß-TrCP protein isoform hidden in circular RNA confers trastuzumab resistance in HER2-positive breast cancer

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REDOX BIOLOGY 2023年 67卷 102896页

作者： Wang, Shengting Wang, Yufang Li, Qian Li, Xiaoming Feng, Xinghua Zeng, Kaixuan Xian Peihua Univ Clin Med Ctr Xian 710125 Shaanxi Peoples R China Xi An Jiao Tong Univ Affiliated Hosp 2 Precis Med Res Inst 28 Xianning West Rd Xian 710000 Shaanxi Peoples R China

Trastuzumab notably improves the outcome of human epidermal growth factor receptor 2 (HER2)-positive breast cancer patients, however, resistance to trastuzumab remains a major hurdle to clinical treatment. In the present study, we identify a circular RNA intimately linked to trastuzumab resistance. circ-beta-TrCP, derived from the back-splicing of beta-TrCP exon 7 and 13, confers trastuzumab resistance by regulating NRF2-mediated antioxidant pathway in a KEAP1-independent manner. Concretely, circ-beta-TrCP encodes a novel truncated 343-amino acid peptide located in the nucleus, referred as ss-TrCP-343aa, which competitively binds to NRF2, blocks SCFss-TrCP- mediated NRF2 proteasomal degradation, and this protective effect of ss-TrCP-343aa on NRF2 protein requires GSK3 activity. Subsequently, the elevated NRF2 transcriptionally upregulates a cohort of antioxidant genes, giving rise to trastuzumab resistance. Moreover, the translation ability of circ-beta-TrCP is inhibited by eIF3j under both basal and oxidative stress conditions, and eIF3j is transcriptionally repressed by NRF2, thus forming a positive feedback circuit between ss-TrCP-343aa and NRF2, expediting trastuzumab resistance. Collectively, our data demonstrate that circ-beta-TrCP-encoded ss-TrCP protein isoform drives HER2-targeted therapy resistance in a NRF2-dependent manner, which provides potential therapeutic targets for overcoming trastuzumab resistance.

关键词： Circular RNA protein coding Trastuzumab resistance NRF2 protein degradation

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Multiple RNAs from the mouse carboxypeptidase M locus: functional RNAs or transcription noise?

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BMC MOLECULAR BIOLOGY 2009年第1期10卷 7-7页

作者： Guimaraes, Alessander O. Motta, Fabiana L. Alves, Viviane S. Castilho, Beatriz A. Pesquero, Joao B. Univ Fed Sao Paulo Dept Biofis Sao Paulo Brazil Univ Fed Sao Paulo Dept Microbiol & Imunol Sao Paulo Brazil

Background: A major effort of the scientific community has been to obtain complete pictures of the genomes of many organisms. This has been accomplished mainly by annotation of structural and functional elements in the genome sequence, a process that has been centred in the gene concept and, as a consequence, biased toward protein coding sequences. Recently, the explosion of transcriptome data generated and the discovery of many functional non-protein coding RNAs have painted a more detailed and complex scenario for the genome. Here we analyzed the mouse carboxypeptidase M locus in this broader perspective in order to define the mouse CPM gene structure and evaluate the existence of other transcripts from the same genomic region. Results: Bioinformatic analysis of nucleotide sequences that map to the mouse CPM locus suggests that, in addition to the mouse CPM mRNA, it expresses at least 33 different transcripts, many of which seem to be non-coding RNAs. We randomly chose to evaluate experimentally four of these extra transcripts. They are expressed in a tissue specific manner, indicating that they are not artefacts or transcriptional noise. Furthermore, one of these four extra transcripts shows expression patterns that differed considerably from the other ones and from the mouse CPM gene, suggesting that there may be more than one transcriptional unit in this locus. In addition, we have confirmed the mouse CPM gene RefSeq sequence by rapid amplification of cDNA ends (RACE) and directional cloning. Conclusion: This study supports the recent view that the majority of the genome is transcribed and that many of the resulting transcripts seem to be non-coding RNAs from introns of genes or from independent transcriptional units. Although some of the information on the transcriptome of many organisms may actually be artefacts or transcriptional noise, we argue that it can be experimentally evaluated and used to find and define biological functional elements on the genome.

关键词： .RNAs define functional elements protein coding carboxypeptidase obtain BMC Molecular Biology Genomic Region transcription noise mouse CPM

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A novel protein encoded by a circular RNA circPPP1R12A promotes tumor pathogenesis and metastasis of colon cancer via Hippo-YAP signaling

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MOLECULAR CANCER 2019年第1期18卷 47-47页

作者： Zheng, Xiao Chen, Lujun Zhou, You Wang, Qi Zheng, Zhuojun Xu, Bin Wu, Chen Zhou, Qi Hu, Wenwei Wu, Changping Jiang, Jingting Soochow Univ Affiliated Hosp 3 Dept Tumor Biol Treatment Changzhou 213003 Peoples R China Jiangsu Engn Res Ctr Tumor Immunotherapy Changzhou 213003 Peoples R China Soochow Univ Inst Cell Therapy Changzhou 213003 Peoples R China Soochow Univ Affiliated Hosp 3 Dept Hematol Changzhou 213003 Peoples R China Soochow Univ Affiliated Hosp 3 Dept Oncol Changzhou 213003 Peoples R China

BackgroundIt has been well established that circular RNAs (circRNAs) play an important regulatory role during tumor progression. Recent studies have indicated that even though circRNAs generally regulate gene expression through miRNA sponges, they may encode small peptides in tumor pathogenesis. However, it remains largely unexplored whether circRNAs are involved in the tumorigenesis of colon cancer (CC).MethodsThe expression profiles of circRNAs in CC tissues were assessed by circRNA microarray. Quantitative real-time PCR, RNase R digestion assay and tissue microarray were used to confirm the existence and expression pattern of circPPP1R12A. The subcellular distribution of circPPP1R12A was analyzed by nuclear mass separation assay and fluorescence in situ hybridization (FISH). SDS-PAGE and LC/MS were employed to evaluate the protein-coding ability of circPPP1R12A. CC cells were stably transfected with lentivirus approach, and cell proliferation, migration and invasion, as well as tumorigenesis and metastasis in nude mice were assessed to clarify the functional roles of circPPP1R12A and its encoded protein circPPP1R12A-73aa. RNA-sequencing and Western blotting analysis were furthered employed to identify the critical signaling pathway regulated by *** firstly screened the expression profiles of human circRNAs in CC tissues and found that the expression of hsa_circ_0000423 (termed as circPPP1R12A) was significantly increased in CC tissues. We also found that circPPP1R12A was mostly localized in the cytoplasm of CC cells. Kaplan-Meier analysis showed that patients with higher levels of circPPP1R12A had a significantly shorter overall survival. By gain- and loss-of-function approaches, the results suggested that circPPP1R12A played a critical role in proliferation, migration and invasion of CC cells. Furthermore, we showed that circPPP1R12A carried an open reading frame (ORF), which encoded a functional protein (termed as circPPP1R12A-73aa). Nex

关键词： Colon cancer Circular RNA (circRNA) protein coding Proliferation Metastasis

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Transcriptomics reveals that NAD(P)H affects the development of the Zig-zag eel (Mastacembelus armatus ♀) x Spiny eel (Sinobdella sinensis ♂) hybrid offspring leading to low hatching rates

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ANIMAL REPRODUCTION SCIENCE 2024年 268卷 107561页

作者： Sun, Di Wang, Shaodan Wang, Chong Zou, Jixing South China Agr Univ Coll Marine Sci 483 Wushan RdWushan St Guangzhou 510642 Guangdong Peoples R China Fujian Agr & Forestry Univ Coll Marine Sci Fuzhou 350002 Peoples R China

Zig-zag eel (Mastacembelus armatus (2 n = 48)) and Spiny eel (Sinobdella sinensis (2 n = 48)) are two species of the Mastacembelidae family commonly found in southern China. Hybridization between the two has a very high deformity rate and a very low hatching rate. In order to investigate the reasons for this, the first hybridization between M. armatus and S. sinensis was carried out using artificial insemination, and the embryonic development of the hybrid offspring was examined using microphotography, and the malformations of the hybrid offspring were investigated by transcriptomics. The experiments showed that the average egg production was 4265.7 +/- 322.94 (Mean +/- SD), the average fertilization rate of hybrid offspring was 98.67 +/- 0.58 % (Mean +/- SD), the hatching rate was 12.06 +/- 3.44 % (Mean +/- SD), the deformity rate was 98.15 +/- 3.21 % (Mean +/- SD), and the embryonic development successively went through the five main stages of fertilized egg, egg cleavage, embryo formation, organogenesis, and exertion of membranes. Transcriptomics showed that the expression of NAD(P)H-related enzyme activity DEGs was increased, and many DEGs related to cell signaling molecule transmission and metabolic regulation are enriched in KEGG pathways, such as IL-17 signaling pathway, Osteoclast differentiation, TNF signaling pathway and MAPK signaling pathway. etc. The major types of DEGs corresponded to those coding for proteins. This study suggests that the high malformation rate in hybrid offspring may be caused by impaired synthesis of proteins during embryonic development.

关键词： Post-fertilization isolation protein coding Hybrid deformity Embryonic development Distant hybrid

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Hsa_circ_0008833 promotes COPD progression via inducing pyroptosis in bronchial epithelial cells

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EXPERIMENTAL LUNG RESEARCH 2024年第1期50卷 1-14页

作者： Xie, Tian Yang, Zehua Xian, Shaojing Lin, Qi Huang, Linhui Ding, Yipeng Hainan Med Univ Hainan Gen Hosp Dept Pulm & Crit Care Med Hainan Affiliated Hosp Haikou Hainan Peoples R China Hainan Med Univ Hainan Gen Hosp Dept Gen Practice Hainan Affiliated Hosp Haikou Hainan Peoples R China Hainan Med Univ Hainan Gen Hosp Dept Pulm & Crit Care Med Hainan Affiliated Hosp 19 Xiuhua Rd Haikou 570311 Hainan Peoples R China

Purpose: Chronic obstructive pulmonary disease (COPD) is a common respiratory disorder. Pyroptosis represents a distinctive form of inflammatory cell death that is mediated through the activation of Caspase-1 and inflammasomes. CircRNAs have emerged as a novel class of biomolecules with implications in various human diseases. This study aims to investigate the circRNAs profile of in COPD progression and identify pivotal circRNAs associated with the development of this disease. Methods: he expression profiles of circRNAs in peripheral blood mononuclear cells of COPD patients were assessed by circRNA microarray. Furthermore, flag-labeled vectors were constructed to assess the potential protein-coding capacity of has-circ-0008833. 16HBE cells were stably transfected with lentivirus approach, and cell proliferation and death were assessed to clarify the functional roles of has-circ-0008833 and its encoded protein circ-0008833aa. Additionally, western blot analysis was furthered performed to determine the level of Caspase-1, IL-18, IL-1 beta, NLRP3, ASC, and cleaved GSDMD regulated by has-circ-0008833 and circ-0008833-57aa. Results: Initially, we screened the expression profiles of human circRNAs in peripheral blood mononuclear cells of COPD patients, and found that has-circ-0008833 exhibited a significant increase in COPD mononuclear cells. Subsequently, we demonstrated that has-circ-0008833 carried an open reading frame (ORF), which encoded a functional protein, referred to as circ-0008833-57aa. By employing gain-of-function approaches, our results suggested that both circ-0008833 and circ-0008833-57aa inhibited proliferation, but accelerated the rate of 16HBE cell death. Finally, we discovered that circ-0008833 and circ-0008833-57aa promoted the expression of Caspase-1, IL-18, IL-1 beta, NLRP3, ASC, and cleaved GSDMD in 16HBE cells. Conclusions: Upregulation of circ-0008833 might promote COPD progression by inducing pyroptosis of bronchial epithelial cells through the

关键词： Chronic obstructive pulmonary disease (COPD) human bronchial epithelial cell line (16HBE) pyroptosis has-circ-0008833 protein coding

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