Gene: XPub Date : 2020-01-16eCollection Date: 2020-12-01DOI: 10.1016/j.gene.2020.100027
Gabriel L Galea, Christopher R Paradise, Lee B Meakin, Emily T Camilleri, Hanna Taipaleenmaki, Gary S Stein, Lance E Lanyon, Joanna S Price, Andre J van Wijnen, Amel Dudakovic
{"title":"Mechanical strain-mediated reduction in RANKL expression is associated with RUNX2 and BRD2.","authors":"Gabriel L Galea, Christopher R Paradise, Lee B Meakin, Emily T Camilleri, Hanna Taipaleenmaki, Gary S Stein, Lance E Lanyon, Joanna S Price, Andre J van Wijnen, Amel Dudakovic","doi":"10.1016/j.gene.2020.100027","DOIUrl":"https://doi.org/10.1016/j.gene.2020.100027","url":null,"abstract":"<p><p>Mechanical loading-related strains trigger bone formation by osteoblasts while suppressing resorption by osteoclasts, uncoupling the processes of formation and resorption. Osteocytes may orchestrate this process in part by secreting sclerostin (SOST), which inhibits osteoblasts, and expressing receptor activator of nuclear factor-κB ligand (RANKL/TNFSF11) which recruits osteoclasts. Both SOST and RANKL are targets of the master osteoblastic transcription factor RUNX2. Subjecting human osteoblastic Saos-2 cells to strain by four point bending down-regulates their expression of SOST and RANKL without altering RUNX2 expression. RUNX2 knockdown increases basal SOST expression, but does not alter SOST down-regulation following strain. Conversely, RUNX2 knockdown does not alter basal RANKL expression, but prevents its down-regulation by strain. Chromatin immunoprecipitation revealed RUNX2 occupies a region of the RANKL promoter containing a consensus RUNX2 binding site and its occupancy of this site decreases following strain. The expression of epigenetic acetyl and methyl writers and readers was quantified by RT-qPCR to investigate potential epigenetic bases for this change. Strain and RUNX2 knockdown both down-regulate expression of the bromodomain acetyl reader BRD2. BRD2 and RUNX2 co-immunoprecipitate, suggesting interaction within regulatory complexes, and BRD2 was confirmed to interact with the RUNX2 promoter. BRD2 also occupies the RANKL promoter and its occupancy was reduced following exposure to strain. Thus, RUNX2 may contribute to bone remodeling by suppressing basal SOST expression, while facilitating the acute strain-induced down-regulation of RANKL through a mechanosensitive epigenetic loop involving BRD2.</p>","PeriodicalId":37140,"journal":{"name":"Gene: X","volume":"5 ","pages":"100027"},"PeriodicalIF":0.0,"publicationDate":"2020-01-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7285908/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148991707","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Gene: XPub Date : 2020-01-13eCollection Date: 2020-12-01DOI: 10.1016/j.gene.2019.100026
Diane J Rowold, Shilpa Chennakrishnaiah, Tenzin Gayden, Javier Rodriguez Luis, Miguel A Alfonso-Sanchez, Areej Bukhari, Ralph Garcia-Bertrand, Rene J Herrera
{"title":"The Y-chromosome of the Soliga, an ancient forest-dwelling tribe of South India.","authors":"Diane J Rowold, Shilpa Chennakrishnaiah, Tenzin Gayden, Javier Rodriguez Luis, Miguel A Alfonso-Sanchez, Areej Bukhari, Ralph Garcia-Bertrand, Rene J Herrera","doi":"10.1016/j.gene.2019.100026","DOIUrl":"10.1016/j.gene.2019.100026","url":null,"abstract":"<p><p>A previous autosomal STR study provided evidence of a connection between the ancient Soliga tribe at the southern tip of the Indian subcontinent and Australian aboriginal populations, possibly reflecting an eastbound coastal migration circa (15 Kya). The Soliga are considered to be among India's earliest inhabitants. In this investigation, we focus on the Y chromosomal characteristics shared between the Soliga population and other Indian tribes as well as western Eurasia and Sub-Saharan Africa groups. Some noteworthy findings of this present analysis include the following: The three most frequent haplogroups detected in the Soliga population are F*, H1 and J2. F*, the oldest (43 to 63 Kya), has a significant frequency bias in favor of Indian tribes versus castes. This observation coupled with the fact that Y-STR haplotypes shared with sub-Saharan African populations are found only in F* males of the Soliga, Irula and Kurumba may indicate a unique genetic connection between these Indian tribes and sub-Saharan Africans. In addition, our study suggests that haplogroup H is confined mostly to South Asia and immediate neighbors and the H1 network may indicate minimal sharing of Y-STR haplotypes among South Asian collections, tribal and otherwise. Also, J2, brought into India by Neolithic farmers, is present at a significantly higher frequency in caste versus tribal communities. This last observation may reflect the marginalization of Indian tribes to isolated regions not ideal for agriculture.</p>","PeriodicalId":37140,"journal":{"name":"Gene: X","volume":"5 ","pages":"100026"},"PeriodicalIF":0.0,"publicationDate":"2020-01-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7286085/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147505124","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Gene: XPub Date : 2019-11-12eCollection Date: 2019-12-01DOI: 10.1016/j.gene.2019.100024
Manoswini Dash, Veena Pande, Abhinav Sinha
{"title":"Putative circumsporozoite protein (CSP) of <i>Plasmodium vivax</i> is considerably distinct from the well-known CSP and plays a role in the protein ubiquitination pathway.","authors":"Manoswini Dash, Veena Pande, Abhinav Sinha","doi":"10.1016/j.gene.2019.100024","DOIUrl":"10.1016/j.gene.2019.100024","url":null,"abstract":"<p><p>Amidst technical challenges which limit successful culture and genetic manipulation of <i>P. vivax</i> parasites, we used a computational approach to identify a critical target with evolutionary significance. The putative circumsporozoite protein on chromosome 13 of <i>P. vivax</i> (<i>Pv</i>puCSP)is distinct from the well-known vaccine candidate <i>Pf</i>CSP. The aim of this study was to understand the role of <i>Pv</i>puCSP and its relatedness to the well-known CSP. The study revealed <i>Pv</i>puCSP as a membrane bound E3 ubiquitin ligase involved in ubiquitination. It has a species-specific tetra-peptide unit which is differentially repeated in various <i>P. vivax</i> strains. The <i>Pv</i>puCSP is different from CSP in terms of stage-specific expression and function. Since E3 ubiquitin ligases are known antimalarial drug targets targeting the proteasome pathway, <i>Pv</i>puCSP, with evolutionary connotation and a key role in orchestrating protein degradation in <i>P. vivax</i>, can be explored as a potential drug target.</p>","PeriodicalId":37140,"journal":{"name":"Gene: X","volume":"4 ","pages":"100024"},"PeriodicalIF":0.0,"publicationDate":"2019-11-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7285988/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140308492","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Gene: XPub Date : 2019-11-06eCollection Date: 2020-12-01DOI: 10.1016/j.gene.2019.100023
Amelia Meecham, John F Marshall
{"title":"The ITGB6 gene: its role in experimental and clinical biology.","authors":"Amelia Meecham, John F Marshall","doi":"10.1016/j.gene.2019.100023","DOIUrl":"https://doi.org/10.1016/j.gene.2019.100023","url":null,"abstract":"<p><p>Integrin αvβ6 is a membrane-spanning heterodimeric glycoprotein involved in wound healing and the pathogenesis of diseases including fibrosis and cancer. Therefore, it is of great clinical interest for us to understand the molecular mechanisms of its biology. As the limiting binding partner in the heterodimer, the β6 subunit controls αvβ6 expression and availability. Here we describe our understanding of the <i>ITGB6</i> gene encoding the β6 subunit, including its structure, transcriptional and post-transcriptional regulation, the biological effects observed in <i>ITGB6</i> deficient mice and clinical cases of <i>ITGB6</i> mutations.</p>","PeriodicalId":37140,"journal":{"name":"Gene: X","volume":"5 ","pages":"100023"},"PeriodicalIF":0.0,"publicationDate":"2019-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7285966/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148991680","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Gene: XPub Date : 2019-06-01Epub Date: 2019-02-12DOI: 10.1016/j.gene.2019.100007
Safia Livingston, Carol Carlton, Madhulika Sharma, Donovan Kearns, Richard Baybutt, Gregory B Vanden Heuvel
{"title":"Cux1 regulation of the cyclin kinase inhibitor p27<sup>kip1</sup> in polycystic kidney disease is attenuated by HDAC inhibitors.","authors":"Safia Livingston, Carol Carlton, Madhulika Sharma, Donovan Kearns, Richard Baybutt, Gregory B Vanden Heuvel","doi":"10.1016/j.gene.2019.100007","DOIUrl":"https://doi.org/10.1016/j.gene.2019.100007","url":null,"abstract":"<p><p>Cux1 is a homeodomain protein involved in cell cycle regulation and kidney development. Cux1 represses the cyclin kinase inhibitor p27 during early kidney development, promoting cell proliferation in the nephrogenic zone. Promoter reporter analysis of p27 revealed that Cux1 represses p27 in a concentration dependent manner, and immunoprecipitation showed that Cux1 interacts with the co-repressor Grg4 and the histone deacetylases HDAC1 and HDAC3. Chromatin immunoprecipitation (ChIP) identified the interaction of Cux1, Grg4, HDAC1, and HDAC3 at two different sites in the p27 promoter. To determine whether there was an interaction between these two loci in the developing kidney, we performed chromatin conformation capture (3C) assay. Analysis of newborn kidney tissue with 3C and ChIP-loop showed that the p27 promoter forms a loop intersecting at these two loci and that Cux1 bridges these two sites. To determine whether HDACs are required for Cux1 repression of p27 we analyzed p27 promoter activity in the presence of the HDAC inhibitor trichostatin A (TSA). TSA treatment completely relieved the repression of p27 by Cux1 and Grg4, demonstrating that Cux1 represses p27 in an HDAC dependent manner. To begin to test whether HDAC inhibitors could be used to target Cux1 repression of p27 for the treatment of PKD, we treated Pkd1 targeted pregnant mice with TSA or vehicle beginning at embryonic day 10.5 until embryonic day 18.5. Newborn Pkd1 mutant mice that received vehicle exhibited extensive collecting duct cysts, while newborn Pkd1 mutant mice that received TSA showed a significant reduction in cysts. Moreover, p27 expression was upregulated in TSA treated Pkd1 mice. Taken together, these results suggest that HDACs are required for cyst growth, and further support studies indicating that HDAC inhibitors may be an effective treatment for PKD.</p>","PeriodicalId":37140,"journal":{"name":"Gene: X","volume":"2 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2019-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6687066/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148991811","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Gene: XPub Date : 2019-06-01Epub Date: 2019-02-17DOI: 10.1016/j.gene.2019.100010
Heather M Fallquist, Jin Tao, Xiaoya Cheng, Sebastian Aguilar Pierlé, Shira L Broschat, Kelly A Brayton
{"title":"Dynamics of repeat-associated plasticity in the <i>aaap</i> gene family in <i>Anaplasma marginale</i>.","authors":"Heather M Fallquist, Jin Tao, Xiaoya Cheng, Sebastian Aguilar Pierlé, Shira L Broschat, Kelly A Brayton","doi":"10.1016/j.gene.2019.100010","DOIUrl":"https://doi.org/10.1016/j.gene.2019.100010","url":null,"abstract":"<p><p>Anaplasmosis, the most prevalent tick-transmitted disease of cattle, is caused by the rickettsial intracellular parasite <i>Anaplasma marginale</i>. The pathogen replicates within a parasitophorous vacuole formed from the invagination of the erythrocyte membrane. Several strains of <i>A. marginale</i> form \"tails\" or \"appendages\" which are attached to, and extend out from, the cytoplasmic side of the parasitophorous vacuole. Genomic analysis of the parasite antigen distributed along the appendage led to the discovery of the <i>aaap</i> (<i>Anaplasma</i> appendage associated protein) gene family located within a highly plastic region in the genome. The <i>aaap</i> gene family consists of <i>aaap</i> and several <i>alps</i> (for aaap-like proteins), depending on the strain. These genes/proteins are characterized by repeat sequences. To investigate locus plasticity, different versions of the locus were cloned from the same strain as well as from different strains, sequenced and aligned to identify changes. Our findings show that repeat sequences both within and between genes facilitated rearrangement events within the locus. Structural variation of the locus in the St. Maries strain was further investigated during infection of different cellular environments, i.e., bovine erythrocytes and tick cells, with a reduction in subpopulations of the <i>aaap</i> locus within the tick as compared to erythrocytes. Interestingly, subpopulations bearing alternative locus structures began to arise again when the pathogen was transferred from the tick environment into a naïve calf. Additionally, the Aaap protein expression profile between blood and tick samples showed a regulatory shift, indicating a host-specific response. Alignment of the protein sequences from different species of <i>Anaplasma</i> reveals six similar repeating motifs that appear to be unique to a few species of <i>Anaplasma</i>. The role the <i>aaap</i> locus may play in the pathogenesis of the bovine host or in tick infection/transmission remains unknown; however, the changes in <i>aaap</i> locus subpopulations, locus structure, and protein expression indicate that these genes have a role in strain diversification.</p>","PeriodicalId":37140,"journal":{"name":"Gene: X","volume":"2 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2019-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7041399/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148991566","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Gene: XPub Date : 2019-06-01DOI: 10.1016/j.gene.2019.100011
Valeria Nittoli, Antonio Emidio Fortunato, Giulia Fasano, Ugo Coppola, Alessandra Gentile, Sylvie Maiella, Fernanda Langellotto, Immacolata Porreca, Raffaella De Paolo, Rita Marino, Marcella Fiengo, Aldo Donizetti, Francesco Aniello, Takashi Kondo, Filomena Ristoratore, Lorella M T Canzoniero, Denis Duboule, Stephen W Wilson, Paolo Sordino
{"title":"Characterization of paralogous <i>uncx</i> transcription factor encoding genes in zebrafish.","authors":"Valeria Nittoli, Antonio Emidio Fortunato, Giulia Fasano, Ugo Coppola, Alessandra Gentile, Sylvie Maiella, Fernanda Langellotto, Immacolata Porreca, Raffaella De Paolo, Rita Marino, Marcella Fiengo, Aldo Donizetti, Francesco Aniello, Takashi Kondo, Filomena Ristoratore, Lorella M T Canzoniero, Denis Duboule, Stephen W Wilson, Paolo Sordino","doi":"10.1016/j.gene.2019.100011","DOIUrl":"10.1016/j.gene.2019.100011","url":null,"abstract":"<p><p>The paired-type homeodomain transcription factor Uncx is involved in multiple processes of embryogenesis in vertebrates. Reasoning that zebrafish genes <i>uncx4.1</i> and <i>uncx</i> are orthologs of mouse <i>Uncx</i>, we studied their genomic environment and developmental expression. Evolutionary analyses indicate the zebrafish <i>uncx</i> genes as being paralogs deriving from teleost-specific whole-genome duplication. Whole-mount <i>in situ</i> mRNA hybridization of <i>uncx</i> transcripts in zebrafish embryos reveals novel expression domains, confirms those previously known, and suggests sub-functionalization of paralogs. Using genetic mutants and pharmacological inhibitors, we investigate the role of signaling pathways on the expression of zebrafish <i>uncx</i> genes in developing somites. In identifying putative functional role(s) of zebrafish <i>uncx</i> genes, we hypothesized that they encode transcription factors that coordinate growth and innervation of somitic muscles.</p>","PeriodicalId":37140,"journal":{"name":"Gene: X","volume":"2 ","pages":"100011"},"PeriodicalIF":0.0,"publicationDate":"2019-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6543554/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144182557","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Gene: XPub Date : 2019-05-18eCollection Date: 2019-09-01DOI: 10.1016/j.gene.2019.100019
Stefan G J A Camps, Sanne P M Verhoef, Freek G Bouwman, Edwin C M Mariman, Klaas R Westerterp
{"title":"Association of <i>FTO</i> and <i>ADRB2</i> gene variation with energy restriction induced adaptations in resting energy expenditure and physical activity.","authors":"Stefan G J A Camps, Sanne P M Verhoef, Freek G Bouwman, Edwin C M Mariman, Klaas R Westerterp","doi":"10.1016/j.gene.2019.100019","DOIUrl":"https://doi.org/10.1016/j.gene.2019.100019","url":null,"abstract":"<p><strong>Background: </strong>Energy restriction induces adaptations in resting energy expenditure (REE) and physical activity; inter-individual variability could be ascribed to genetic predisposition.The aim was to examine if changes in REE and physical activity as a result of weight loss were affected by candidate single nucleotide polymorphisms (SNPs).</p><p><strong>Methods: </strong>148 subjects (39 men, 109 women), mean ± SD age: 41 ± 9 year; body mass index (BMI): 31.9 ± 3.0 kg/m<sup>2</sup>, followed a very low energy diet for 8 weeks. SNPs were selected from six candidate genes: <i>ADRB2</i>, <i>FTO</i>, <i>MC4R</i>, <i>PPARG2</i>, <i>PPARD</i> and <i>PPARGC1A</i>. REE (ventilated hood) and physical activity (tri-axial accelerometer) were assessed before and after the diet. General linear modelling included gender, age and additional relevant covariates for all parameters.</p><p><strong>Results: </strong>The heterozygotic genotype of <i>FTO</i> was associated with a higher amount of physical activity (1.71 Mcounts/d; CI 1.62-1.81) compared to the homozygotic major genotype (1.50 Mcounts/d; CI 1.40-1.59) (P < 0.001) while the homozygotic risk allele genotype was not different (1.56 Mcounts/d; CI 1.39-1.74) at baseline; moreover, a similar pattern was observed after energy restriction. Carrying the homozygotic minor genotype of <i>ADRB2</i> was associated with a larger decrease in REE (P < 0.05) and greater adaptive thermogenesis (P < 0.05) after weight loss.</p><p><strong>Conclusion: </strong>Carrying the minor <i>ADRB2</i> allele homozygous was associated with a larger diet induced metabolic adaptation in energy expenditure and suggest a central role for reduced lipid mobilization. Carrying the risk allele of <i>FTO</i> homozygous was not associated with lower physical activity at baseline or after weight loss. Heterozygous carriers of one <i>FTO</i> risk allele showed greater physical activity before and after weight loss which might protect them in part from the higher obesity risk associated with <i>FTO</i>.</p>","PeriodicalId":37140,"journal":{"name":"Gene: X","volume":"3 ","pages":"100019"},"PeriodicalIF":0.0,"publicationDate":"2019-05-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7285957/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148991600","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Gene: XPub Date : 2019-03-25eCollection Date: 2019-06-01DOI: 10.1016/j.gene.2019.100014
Lingyun Xu, Hong Zhu, Fei Gao, Yinghua Tang, Yajun Zhu, Zhiqiang Sun, Jian Wang
{"title":"Upregulation of the long non-coding RNA CBR3-AS1 predicts tumor prognosis and contributes to breast cancer progression.","authors":"Lingyun Xu, Hong Zhu, Fei Gao, Yinghua Tang, Yajun Zhu, Zhiqiang Sun, Jian Wang","doi":"10.1016/j.gene.2019.100014","DOIUrl":"10.1016/j.gene.2019.100014","url":null,"abstract":"<p><p>Breast cancer is the most common female malignancy and the major cause of cancer-related death in women. Long non-coding RNAs (lncRNAs), as oncogenic or tumor suppressor factor, involved in the development and progression of various cancers. In this study, we sought to investigate the function of lncRNA CBR3-AS1 in breast cancer. We evaluated the expression pattern of CBR3-AS1 in breast cancer tissues and cell lines, explored the correlation between CBR3-AS1 expression and the survival time of breast cancer patients, and probed the effect of CBR3-AS1 on tumor progression of breast cancer through loss-of-function and gain-of-function strategies. Our results showed that CBR3-AS1 was overexpressed in breast cancer tissues and cell lines and predicted the prognosis of breast cancer patients. And CBR3-AS1 exerted biological function as an oncogenic lncRNA, involved in the regulation of cell proliferation, colony formation, apoptosis and tumor growth in breast cancer. Taken together, CBR3-AS1 was up-regulated in breast cancer and promoted the risk of breast cancer. It may be a novel therapeutic target and potential prognostic marker for breast cancer.</p>","PeriodicalId":37140,"journal":{"name":"Gene: X","volume":"2 ","pages":"100014"},"PeriodicalIF":0.0,"publicationDate":"2019-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7285981/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141793684","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Gene: XPub Date : 2019-03-06eCollection Date: 2019-06-01DOI: 10.1016/j.gene.2019.100012
Satyabrata Sahoo, Shib Sankar Das, Ria Rakshit
{"title":"Codon usage pattern and predicted gene expression in <i>Arabidopsis thaliana</i>.","authors":"Satyabrata Sahoo, Shib Sankar Das, Ria Rakshit","doi":"10.1016/j.gene.2019.100012","DOIUrl":"https://doi.org/10.1016/j.gene.2019.100012","url":null,"abstract":"<p><p>The extensive research for predicting highly expressed genes in plant genome sequences has been going on for decades. The codon usage pattern of genes in <i>Arabidopsis thaliana</i> genome is a classical topic for plant biologists for its significance in the understanding of molecular plant biology. Here we have used a gene expression profiling methodology based on the score of modified relative codon bias (MRCBS) to elucidate expression pattern of genes in <i>Arabidopsis thaliana</i>. MRCBS relies exclusively on sequence features for identifying the highly expressed genes. In this study, a critical analysis of predicted highly expressed (PHE) genes in <i>Arabidopsis thaliana</i> has been performed using MRCBS as a numerical estimator of gene expression level. Consistent with previous other results, our study indicates that codon composition plays an important role in the regulation of gene expression. We found a systematic strong correlation between MRCBS and CAI (codon adaptation index) or other expression-measures. Additionally, MRCBS correlates well with experimental gene expression data. Our study highlights the relationship between gene expression and compositional signature in relation to codon usage bias and sets the ground for the further investigation of the evolution of the protein-coding genes in the plant genome.</p>","PeriodicalId":37140,"journal":{"name":"Gene: X","volume":"2 ","pages":"100012"},"PeriodicalIF":0.0,"publicationDate":"2019-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7286098/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148991834","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}