Animal Gene最新文献

{"title":"Computational analysis of hypothetical proteins from Mycobacterium orygis identifies proteins with therapeutic and diagnostic potentials","authors":"Ayan Mukherjee ,&nbsp;Premanshu Dandapat ,&nbsp;Molla Zakirul Haque ,&nbsp;Sangeeta Mandal ,&nbsp;Partha Sarathi Jana ,&nbsp;Sukhen Samanta ,&nbsp;Santanu Pal ,&nbsp;Arun Kumar Das ,&nbsp;Pramod Kumar Nanda ,&nbsp;Samiran Bandyopadhyay ,&nbsp;Chanchal Guha","doi":"10.1016/j.angen.2023.200154","DOIUrl":"10.1016/j.angen.2023.200154","url":null,"abstract":"<div><p>The genome of <span><em>Mycobacterium</em><em> orygis</em></span> encodes 3767 proteins that includes 442 functionally uncharacterized proteins, known as hypothetical proteins (HPs). These functionally unknown proteins may play significant biological role in bacterium's survivability, virulence <em>etc.</em>, hence functional annotation of these HPs with bioinformatics techniques might shed light on these aspects. So, the present study aimed to assign functions to those HPs in <em>M. orygis</em> genome. With the help of an extensive <em>in silico</em><span><span> workflow involving several bioinformatic tools, physicochemical characteristics, protein-protein interaction, sub-cellular localization, functional classification, and antigenicity of the HPs were analyzed. Out of 4039 genes and 3767 encoded proteins, 422 were annotated as “hypothetical protein, unknown function” in NCBI database. Out of 422 HPs, the FASTA sequences of 400 proteins, available in the NCBI database, were extracted. Preliminarily 400 proteins were screened for presence of conserved domain by different bioinformatic tools and 32 shortlisted proteins were further analyzed. The analysis revealed that these proteins may be involved in enzymatic, toxin-antitoxin system, cellular and other processes. Virulence and antigenicity of the complete set of HPs were also predicted. Based on antigenicity scores and sub-cellular localization, four proteins were selected for secondary and </span>tertiary structure<span> modelling. Molecular docking and MD-simulation of four proteins with TLR1 showed stable binding. B-cell and T-cell epitopes were identified for two proteins (QOY47331.1 and QOY49361.1) with highest antigenicity scores. The result of the present study may facilitate better understanding of virulence, pathogenesis and therapeutic target. The information about the structures of the HPs with highest antigenicity score could aid in structure-based inhibitor design and devising novel diagnostic assays.</span></span></p></div>","PeriodicalId":7893,"journal":{"name":"Animal Gene","volume":"29 ","pages":"Article 200154"},"PeriodicalIF":0.0,"publicationDate":"2023-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42021660","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Investigating the effect of human apolipoprotein E isoforms on expression level of CLS and MINO genes involved in mitochondrial function in transgenic Drosophila model","authors":"Faraneh Aghaei,&nbsp;Samaneh Reiszadeh Jahromi","doi":"10.1016/j.angen.2023.200152","DOIUrl":"10.1016/j.angen.2023.200152","url":null,"abstract":"<div><p><span><span>Alzheimer's disease (AD) is a neurodegenerative disorder characterized by aberrant lipid metabolism and mitochondrial dysfunction, features related to mitochondria-associated </span>ER membranes (MAM). </span><em>ApoE</em> is recognized as the major AD risk factor. Human <em>ApoE</em><span> has three isoforms<span><span> including Apoε2, Apoε3 and Apoε4. It has revealed that ε4 allele carriers are at higher risk of developing AD than ε3 allele carriers. Given that Apoε4 is a major AD risk factor and that MAM dysfunction in lipid metabolism may affect mitochondrial function, we assessed the expression pattern of cardiolipin synthetase (CLS) and glycerol-3-phosphate </span>acyltransferase 2 (MINO) genes in </span></span><em>Drosophila</em> model of AD. To the best of our knowledge, this is the first study to investigate the effect of <em>ApoE</em> isoforms on mitochondrial function in <em>Drosophila</em><span> model of AD. RNA extraction<span> was performed using glazt2a.gal4.UAS.hapoe transgenic flies harboring </span></span><em>Apoε</em><span> isoforms. Following cDNA synthesis, mRNA expression levels<span> of target (CLS and MINO) and housekeeping (eEF1α) genes were measured by qRT-PCR. Our results did not show a significant decrease in CLS and MINO expression level in Apoɛ3 and Apoɛ4 groups as compared to the control. Although this reduction was not statistically significant, the decreasing trend indicates a kind of disruption in lipid biosynthesis and may directly affect mitochondrial function. Though the impact of Apoɛ4 on AD pathogenesis has been elucidated, the exact mechanism through which Apoɛ4 mediates AD progression is still unknown. Investigating the biology of </span></span><em>ApoE</em><span> isoforms using both human and AD animal models is recommended.</span></p></div>","PeriodicalId":7893,"journal":{"name":"Animal Gene","volume":"29 ","pages":"Article 200152"},"PeriodicalIF":0.0,"publicationDate":"2023-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41720802","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Effects of probiotic (Saccharomyces cerevisiae) and ascorbic acid on oxidative gene damage biomarker, heat shock protein 70 and interleukin 10 in broiler chickens exposed to heat stress","authors":"Victory Osirimade Sumanu ,&nbsp;Charles Byaruhanga ,&nbsp;Anna-Mari Bosman ,&nbsp;Sunday Ochonu Ochai ,&nbsp;Vinny Naidoo ,&nbsp;Marinda Catharina Oosthuizen ,&nbsp;Joseph Panashe Chamunorwa","doi":"10.1016/j.angen.2023.200150","DOIUrl":"10.1016/j.angen.2023.200150","url":null,"abstract":"<div><p>Heat stress is a prominent factor responsible for losses economically in poultry meat industry due to adverse effects on the general performance of broiler chickens. In this study, we evaluated the effects of probiotic (<em>Saccharomyces cerevisiae</em>) and ascorbic acid on oxidative gene damage biomarker, heat shock protein 70 (<em>HSP70</em>) and interleukin 10 (<em>IL-10</em>) in broiler chickens exposed to heat stress under natural conditions. Fifty-six broiler chickens served as the subjects, they were divided into 4 groups of 14 as follows: group I (control), group II (probiotic <em>S. cerevisiae</em> at 1 g/kg of feed), group III (ascorbic acid at 200 mg/kg of feed) and group IV (probiotic + ascorbic acid at 1 g/kg and 200 mg/kg of feed, respectively). The treatments were administered via feed for 35 days (D1 to D35). Enzyme-linked immunosorbent assay (ELISA) and one step real time reverse transcription polymerase chain reaction (RT-PCR) was utilised to study the effects of heat stress on the expression levels of 8-hydroxy-2′-deoxyguanosine (<em>8-OHdG</em>), <em>HSP70</em> and <em>IL-10</em> respectively, in broiler chickens raised during the hot summer season. The level of <em>8-OHdG</em> gene was significantly lower in the probiotic administered group. The expression level of <em>HSP70</em> was lowest in the ascorbic acid group while, <em>IL-10</em> level of expression was highest in the probiotic + ascorbic acid group. The administered antioxidants were efficient in exhibiting anti-stress effects at the level of gene expression. We conclude that probiotic, ascorbic acid and probiotic + ascorbic acid reduced oxidative gene damage, affected the expression of <em>HSP70</em> and increased the level of <em>IL-10</em> gene respectively, in broiler chickens exposed to heat stress.</p></div>","PeriodicalId":7893,"journal":{"name":"Animal Gene","volume":"28 ","pages":"Article 200150"},"PeriodicalIF":0.0,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43419384","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Identification and in silico structural and functional analysis of a histone H2A-derived antimicrobial peptide from teleost fishes","authors":"K.L. Dhanya Lenin,&nbsp;Athira Raveendran,&nbsp;Swapna P. Antony","doi":"10.1016/j.angen.2023.200148","DOIUrl":"10.1016/j.angen.2023.200148","url":null,"abstract":"<div><h3>Background</h3><p><span>Antimicrobial peptides<span> (AMPs) are small peptides that form the first line of defence in all living organisms. In addition to conventional AMPs, there exist molecules that are often not regarded as part of the innate defences, but possess antimicrobial activity<span>. Histone H2A-derived peptides are a group of unconventional AMPs that represent very ancient defence factors, re-used in new ways during evolution. The present study attempts to compare histone H2A-derived AMPs from four commercially important teleost fishes inhabiting various habitats, </span></span></span><em>viz.</em> Asian sea bass (<span><em>Lates calcarifer</em></span>), tank goby (<span><em>Glossogobius</em><em> giuris</em></span><span>), grey mullet (</span><span><em>Mugil cephalus</em></span>), and Malabar trevally (<em>Carangoides malabaricus</em>).</p></div><div><h3>Methods and results</h3><p><span><span><span>RT-PCR amplification of the mRNAs extracted from these fishes yielded H2A-derived AMP genes with slight differences in the nucleotide sequences, nevertheless with similar translated </span>amino acid sequences. The amino acid sequence was found to possess marked similarity at the N-terminal region and showed antimicrobial </span>motif sequence<span><span> characteristic of histone H2A-derived AMPs. Phylogenetic analysis showed an evolutionary relationship with invertebrate ones suggesting a common ancestral origin for the vertebrate and invertebrate histone H2A. The </span>secondary structure of histone H2A-derived AMP showed the presence of α-helices and intermittent coils having a </span></span>proline hinge connecting the N- and C-terminus. The peptide was also predicted to be a cell-penetrating one.</p></div><div><h3>Conclusion</h3><p><em>In silico</em><span> structural and functional characterization of histone H2A-derived AMP revealed its potential antibacterial property and point towards the possibility of being an efficient AMP with the potential of being made use of in therapeutics.</span></p></div>","PeriodicalId":7893,"journal":{"name":"Animal Gene","volume":"28 ","pages":"Article 200148"},"PeriodicalIF":0.0,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43976156","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A histone H2A amino terminal derived peptide Etroplusin from Pearl spot, Etroplus suratensis (Bloch, 1790): Phylogenetic and functional characterization","authors":"P.P. Athira,&nbsp;M.V. Anju,&nbsp;V.V. Anooja,&nbsp;K. Archana,&nbsp;Dhanya Kesavan,&nbsp;S. Neelima,&nbsp;Anjali S. Mohan,&nbsp;M.R. Revathy,&nbsp;Rosamma Philip","doi":"10.1016/j.angen.2023.200149","DOIUrl":"10.1016/j.angen.2023.200149","url":null,"abstract":"<div><p><span>Antimicrobial peptides<span> (AMPs) derived from histone precursors form a significant class of therapeutic molecules. The study explores the comprehensive molecular characterization of core histone H2A-derived antimicrobial peptide, Etroplusin from Pearl spot, </span></span><em>Etroplus suratensis.</em><span> Etroplusin exhibited characteristic features of AMP such as net +11 charge and amphipathic alpha-helical structure. Multiple sequence alignment<span> showed the homologous nature of etroplusin with previously reported H2A peptides. Phylogenetic analysis revealed that etroplusin is similar to </span></span><span><em>Carassius auratus</em></span><span> H2A-derived peptide and comes under the fish H2A peptide clade. Structure modelling with bioinformatics tools predicted alpha-helical structure and random coils with a proline hinge. The functional characterization of etroplusin revealed its antibacterial, antifungal, and anticancer activities. Significant upregulation of etroplusin was observed in the systemic tissues of </span><em>E. suratensis</em> on a challenge with the bacterial fish pathogen, <span><em>Streptococcus agalactiae</em><em>.</em></span> The present study will shed light on fish innate immune responses and the importance of etroplusin, the H2A-derived peptide as a defense molecule.</p></div>","PeriodicalId":7893,"journal":{"name":"Animal Gene","volume":"28 ","pages":"Article 200149"},"PeriodicalIF":0.0,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45259747","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The neuroprotective effect of betanin nanoparticles on brain ischemia–reperfusion injury","authors":"Yalda Saghari ,&nbsp;Monireh Movahedi ,&nbsp;Majid Tebianian ,&nbsp;Maliheh Entezari","doi":"10.1016/j.angen.2023.200145","DOIUrl":"10.1016/j.angen.2023.200145","url":null,"abstract":"<div><h3>Background</h3><p><span>Betanin is an antioxidant and anti-inflammatory compound that has attracted the attention of researchers in a variety of diseases in recent years. Therefore, In the present study the effect of </span>pretreatment<span> of betanin nanoparticles<span> (NB) in cerebral ischemia rats was investigated.</span></span></p></div><div><h3>Methods</h3><p><span><span><span>Oral administration of NB started five days before bilateral common carotid artery<span><span> occlusion (BCCAO) induction and continued for three days thereafter in rats. The neurological disorder scores (NDS), brain swelling and edema were evaluated. After preparing brain homogenate, the intensity of </span>oxidative stress<span>, the activities of antioxidant enzymes, GSH content, the activities of mitochondrial enzymes </span></span></span>SDH, </span>MDH and </span>LDH were studied. Also, the expressions of IL-1β, IL-6, TNF-α cytokines were measured. The expression levels of NF-ĸB and pSTAT3 genes and proteins and ERK and TFEB proteins were also studied.</p></div><div><h3>Results</h3><p>NB showed strong anti-inflammatory and antioxidant effects in cerebral I/R rats and improved mitochondrial and antioxidant enzymes activities. Decreases in NDS, swelling and edema of the brain were also observed in the cerebral I/R rats receiving NB. Also, administration of NB decreased the expressions of inflammatory cytokines and upregulated the expressions of NF-KB and pSTAT3 genes and proteins and overexpressed ERK and TEFB proteins.</p></div><div><h3>Conclusion</h3><p>NB has neuroprotective effects in cerebral I/R condition due to its antioxidant and anti-inflammation properties, which can be considered as a suitable treatment option in stroke conditions.</p></div>","PeriodicalId":7893,"journal":{"name":"Animal Gene","volume":"27 ","pages":"Article 200145"},"PeriodicalIF":0.0,"publicationDate":"2023-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45669085","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Biosafety assessment of lactic acid probiotic isolates obtained from the gastrointestinal tract of livestock, poultry and bees native to Iran","authors":"Ramin Seighalani ,&nbsp;Maryam Royan ,&nbsp;Morteza Fardi","doi":"10.1016/j.angen.2022.200140","DOIUrl":"10.1016/j.angen.2022.200140","url":null,"abstract":"<div><p><span><span><span>Probiotics are suitable substitutes to reduce the use of growth-promoting antibiotics and antibiotics used to treat </span>livestock infections due to new international laws and consumers' expectations of livestock products. Although </span>lactic acid bacteria, especially </span><span><em>Lactobacillus</em></span>, are safe strains (GRAS<span>¹</span><span><span>), a safety study of new probiotic strains is needed to evaluate their safety and pathogenicity<span> parameters. Such investigations can reduce concerns about antibiotic resistance genes transfer and observe rare cases of infection caused by probiotic usage. In the previous project of Iran Animal Biotechnology Research Institute, several lactic acid species were isolated and identified from the </span></span>gastrointestinal tract<span> of different farm animals via phenotypic characteristics and 16S rRNA sequencing. These bacteria had probiotic properties and were assessed for acid resistance, antibiotic resistance, bile salts, and antimicrobial activity. In this study, the presence or absence of several genes, such as pathogenic genes, amine-producing genes, and genes associated with antibiotic resistance, were examined by PCR.</span></span><span>²</span> Furthermore, genes that lead to the emergence of antibiotic resistance through other mechanisms such as efflux pumps were also studied in the same way. These studies have led to the achievement of safe strains for the introduction to the large market of livestock, poultry, and aquatic probiotics.</p></div>","PeriodicalId":7893,"journal":{"name":"Animal Gene","volume":"27 ","pages":"Article 200140"},"PeriodicalIF":0.0,"publicationDate":"2023-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48220561","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Characterization of the complete mitochondrial genome of the Indian crested porcupine (Hystrix indica)","authors":"Asylulan Amirgazin ,&nbsp;Vladislav Shevtsov ,&nbsp;Dilnur Tussipkan ,&nbsp;Victoriya Lutsay ,&nbsp;Yerlan Ramankulov ,&nbsp;Alexandr Shevtsov ,&nbsp;Shuga Manabayeva","doi":"10.1016/j.angen.2022.200144","DOIUrl":"10.1016/j.angen.2022.200144","url":null,"abstract":"<div><p>The Indian crested porcupine (<em>Hystrix indica</em><span><span>) is a hystricomorph rodent species and has been suggested to be native to southern Asia and the Middle East. Complete mitochondrial genomes are available that can be used to identify and clarify the evolutionary history and </span>phylogenetic relationships, but until now the mitochondrial genome of the crested porcupine was not available. The present study is the first report of the complete mitochondrial genome sequence of the </span><em>H. indica</em><span>, with a length of 16,811 bp (GenBank accession number: ON408241). The mitochondrial genome sequence encompassed 13 protein-coding genes, 22 transfer RNA genes<span>, two ribosomal RNA genes, and one non-coding region (D-loop) in this study. The overall AT and GC contents of the mitochondrial genome of </span></span><em>H. indica</em><span><span> were 62.18% and 37.81% respectively. Ten protein-coding genes used ATG as the start codon except for ND-2 (ATC), ND3, and ND5 (ATA). Diverse patterns of </span>stop codons were observed, such as TAG, TAA, AGA, and TA. Based on the phylogenic analysis, the 15 species included in the analysis were assembled into three main groups and were largely congruent with families of rodents, including </span><em>Sciuridae</em> species in the first group, <em>Hystricidae</em> species in the second group, and species of <span><span><em>Castoridae, Dipodidae, </em><em>Spalacidae</em><em>, </em></span><em>Cricetidae</em><em>,</em></span> and <span><em>Muridae</em></span> families in the third group. The complete mitochondrial genome of <em>H. indica</em> provides fundamental information for future research studies.</p></div>","PeriodicalId":7893,"journal":{"name":"Animal Gene","volume":"27 ","pages":"Article 200144"},"PeriodicalIF":0.0,"publicationDate":"2023-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48878360","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The relationship between egg production, reproductive hormones, and the GDF9 gene in three different chicken strains","authors":"W.S. Habashy ,&nbsp;K. Adomako","doi":"10.1016/j.angen.2023.200147","DOIUrl":"10.1016/j.angen.2023.200147","url":null,"abstract":"<div><p>Egg production is the most important commercial attribute of layer hens since it has a direct impact on the efficiency of the poultry industry. This research aimed to study the age at first egg (AFE), egg number (EN), egg quality, and some plasma hormones<span> within the period from the start of laying eggs until day 90 of production in three strains of laying hens<span> (Lohman Brown (LB), Golden Sabahia (GS)) and White Leghorn<span> (WL) as the reference breed for egg production. In addition, a time series expression profile of growth differentiation factor<span> 9 (GDF9) gene was investigated to get a better understanding of the genetic basis of egg production. The LB laying hens recorded the highest improved estimates of egg production and egg quality traits. Further, GDF9 was highly expressed in LB tissues (magnum and isthmus) compared to WL except in the uterus. These results suggest that there is a direct relationship between number of eggs produced, quality of eggs and the expression level of the GDF9 gene in the LB strains. Besides, the LB strain is superior with candidate productive traits, therefore they can be used as proven ancestors to improve laying hens.</span></span></span></span></p></div>","PeriodicalId":7893,"journal":{"name":"Animal Gene","volume":"27 ","pages":"Article 200147"},"PeriodicalIF":0.0,"publicationDate":"2023-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44216905","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Cis-regulatory modules prediction in spliced genes associated with carcass and meat traits of Nelore cattle","authors":"Thaís Cristina Ferreira Dos Santos ,&nbsp;Evandro Neves Silva ,&nbsp;Larissa Fernanda Simielli Fonseca ,&nbsp;Lucia Galvão De Albuquerque ,&nbsp;Danielly Beraldo Dos Santos Silva","doi":"10.1016/j.angen.2022.200142","DOIUrl":"10.1016/j.angen.2022.200142","url":null,"abstract":"<div><p><span><span>The cis-regulatory modules are non-coding DNA regions responsible for controlling gene transcription and being involved in the anatomical and </span>embryonic development<span><span> of animal species. This study aimed to perform a prediction analysis of cis-regulatory modules in spliced genes associated, commonly, with ribeye area (REA) and intramuscular fat (IF) of </span>Nelore cattle. For this, JuncBASE v.0.9 (Junction-Based Analysis of Splicing Events) software was used to identify and classify exon-centered alternative splicing events in the group of animals selected for REA and IF. The prediction of transcription factors and cis-regulatory modules was performed for the genes found using iRegulon v.1.3. The prediction analysis exhibited 45 cis-regulatory modules, of which module 11 had the highest number (</span></span><em>N</em> = 9) of binding sites shared commonly by 11 spliced genes and five transcription factors from the <em>MEF2</em><span><span> family. These modules could potentially regulate spliced exons and, thus, contribute to the production of isoforms, which may be involved in essential pathways and </span>biological processes<span> involved in the evaluated animals muscular development and lipid metabolism.</span></span></p></div>","PeriodicalId":7893,"journal":{"name":"Animal Gene","volume":"27 ","pages":"Article 200142"},"PeriodicalIF":0.0,"publicationDate":"2023-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46229261","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}