scholarly journals The microRNA gene <i>bta-mir-2313</i> in cattle: an atlas of regulatory elements and an association analysis with growth and carcass traits in the Slovenian Simental cattle breed

2018 ◽  
Vol 61 (3) ◽  
pp. 271-278 ◽  
Author(s):  
Špela Malovrh ◽  
Tanja Kunej ◽  
Milena Kovač ◽  
Peter Dovč
Keyword(s):  
Expression Profiles ◽  
Carcass Traits ◽  
Mirna Gene ◽  
Cattle Breed ◽  
Regulatory Elements ◽  
Phenotypic Traits ◽  
Seed Region ◽  
Microrna Gene ◽  
Simmental Cattle ◽  
Mirna Seed

Abstract. MicroRNAs (miRNA) are a class of non-coding RNAs important in posttranscriptional regulation of target genes. Regulation requires complementarity between the target mRNA and the miRNA region responsible for their recognition and binding, also called the seed region. Previous studies have proven that expression profiles and genetic variations of miRNA genes (miR-SNP; SNP – single nucleotide polymorphism) and their target sites (miR-TS-SNPs) have an impact on phenotypic variation and disease susceptibility in human, animal models, and livestock. MicroRNA-associated polymorphisms therefore represent biomarker potential for phenotypic traits in livestock. Effects of miRNA gene polymorphisms on phenotypic traits have been studied in several animal species but much less in cattle. The aim of the present study was therefore to analyze the genetic variability in the bta-mir-2313 gene and test associations with growth and carcass traits of the Slovenian Simmental cattle breed. Additionally, validated and predicted genomic information related to the miRNA gene bta-mir-2313 has been obtained and presented as an atlas of miRNA regulatory elements. Sanger sequencing has been used for biomarker development and genotyping of 145 animals of Slovenian dual-purpose Simmental cattle. Out of nine known polymorphisms located within pre-miRNA regions, one mature miRNA seed SNP was polymorphic in the Slovenian Simmental cattle breed. An additional three polymorphisms were identified within the flanking pri-miRNA regions. There was no significant effect of polymorphisms on 18 tested fattening and carcass traits; however, validated polymorphisms could now be tested in association with other traits in other cattle populations. The microRNA gene bta-mir-2313 warrants further genetic and functional analyses since it overlaps with a large number of quantitative trait loci (QTL), has over 3100 predicted targets and highly polymorphic mature seed regions, and is located within protein-coding gene GRAMD1B, previously associated with production traits in cattle. Mature miRNA seed SNPs present important genomic loci for functional studies because they could affect the gain/loss of downstream targets and should be systematically studied in cattle.

scholarly journals Can miRNA Indicate Risk of Illness after Continuous Exposure to M. tuberculosis?

2021 ◽  
Vol 22 (7) ◽  
pp. 3674
Author(s):  
Cleonardo Augusto Silva ◽  
Arthur Ribeiro-dos-Santos ◽  
Wanderson Gonçalves Gonçalves ◽  
Pablo Pinto ◽  
Rafael Pompeu Pantoja ◽  
...  
Keyword(s):  
Infectious Diseases ◽  
Immune Modulation ◽  
Target Genes ◽  
Expression Profiles ◽  
Mirna Gene ◽  
Regulatory Elements ◽  
Continuous Exposure ◽  
Network Analyses ◽  
Small Ncrnas ◽  
Mirna Expression Profiles

The role of regulatory elements such as small ncRNAs and their mechanisms are poorly understood in infectious diseases. Tuberculosis is one of the oldest infectious diseases of humans and it is still a challenge to prevent and treat. Control of the infection, as well as its diagnosis, are still complex and current treatments used are linked to several side effects. This study aimed to identify possible biomarkers for tuberculosis by applying NGS techniques to obtain global miRNA expression profiles from 22 blood samples of infected patients with tuberculosis (n = 9), their respective healthy physicians (n = 6) and external healthy individuals as controls (n = 7). Samples were run through a pipeline consisting of differential expression, target genes, gene set enrichment and miRNA–gene network analyses. We observed 153 altered miRNAs, among which only three DEmiRNAs (hsa-let-7g-5p, hsa-miR-486-3p and hsa-miR-4732-5p) were found between the investigated patients and their respective physicians. These DEmiRNAs are suggested to play an important role in granuloma regulation and their immune physiopathology. Our results indicate that miRNAs may be involved in immune modulation by regulating gene expression in cells of the immune system. Our findings encourage the application of miRNAs as potential biomarkers for tuberculosis.

scholarly journals Transcriptome architecture and regulation at environmental transitions in flavobacteria: the case of an important fish pathogen

2021 ◽  
Vol 1 (1) ◽  
Author(s):  
Cyprien Guérin ◽  
Bo-Hyung Lee ◽  
Benjamin Fradet ◽  
Erwin van Dijk ◽  
Bogdan Mirauta ◽  
...  
Keyword(s):  
Expression Profiles ◽  
Expression Patterns ◽  
Gene Expression Profiles ◽  
Regulatory Elements ◽  
Freshwater Ecosystems ◽  
Phylogenetic Position ◽  
Future Research ◽  
Phenotypic Traits ◽  
Transcription Start Sites ◽  
Environmental Transitions

AbstractThe family Flavobacteriaceae (phylum Bacteroidetes) is a major component of soil, marine and freshwater ecosystems. In this understudied family, Flavobacterium psychrophilum is a freshwater pathogen that infects salmonid fish worldwide, with critical environmental and economic impact. Here, we report an extensive transcriptome analysis that established the genome map of transcription start sites and transcribed regions, predicted alternative sigma factor regulons and regulatory RNAs, and documented gene expression profiles across 32 biological conditions mimicking the pathogen life cycle. The results link genes to environmental conditions and phenotypic traits and provide insights into gene regulation, highlighting similarities with better known bacteria and original characteristics linked to the phylogenetic position and the ecological niche of the bacterium. In particular, osmolarity appears as a signal for transition between free-living and within-host programs and expression patterns of secreted proteins shed light on probable virulence factors. Further investigations showed that a newly discovered sRNA widely conserved in the genus, Rfp18, is required for precise expression of proteases. By pointing proteins and regulatory elements probably involved in host–pathogen interactions, metabolic pathways, and molecular machineries, the results suggest many directions for future research; a website is made available to facilitate their use to fill knowledge gaps on flavobacteria.

EFFICIENCY AND COMPARISON OF THE TEST-DAY MODEL AND BLUP METHOD MODIFICATIONS FOR ASSESSING BULLS BREEDING VALUE IN SIMMENTAL CATTLE BREED

2020 ◽  
Author(s):  
А.И. МАМОНТОВА ◽  
С.А. НИКИТИН ◽  
Е.Е. МЕЛЬНИКОВА ◽  
А.А. СЕРМЯГИН
Keyword(s):  
Animal Model ◽  
Milk Yield ◽  
Cattle Breed ◽  
Breeding Value ◽  
Am1 Method ◽  
Production Traits ◽  
Genetic Trend ◽  
Sire Model ◽  
The Russian Federation ◽  
Simmental Cattle

Целью проведенных исследований являлась отработка и адаптация применения методик BLUP AM (Animal Model — модель животного) и TDM (Test-Day Model — модель тестового дня) для прогнозирования племенной ценности быков-производителей и оценки селекционно-генетических параметров на популяции скота симментальской породы четырех регионов РФ. Проведен сравнительный анализ указанных методов с более ранним методом BLUP SM (Sire Model — модель отца). Рассчитана племенная ценность быков и коров симментальской породы по признакам молочной продуктивности: удой за 305 дней, выход молочного жира, выход молочного белка. Анализ полученных средних значений достоверности оценок быков-производителей, рассчитанных на основе сопоставляемых методов, свидетельствует, что достоверность для признака «удой за 305 дней» при переходе от метода SM1 к AM1 увеличивается на 2,4%, а при переходе от SM1 к TDM1 — на 7,8%. Даны варианты генетического тренда по удою с использованием различных уравнений моделей расчета племенной ценности. На основании полученных данных можно сделать вывод о том, что модель тестового дня позволяет не только повысить точность оценок быков, но и более рельефно выявить их ранги, а также несколько уменьшить срок получения достоверных оценок производителей по качеству потомства по продуктивным признакам. The purpose of this research was to develop and adapt the application of BLUP AM (Animal Model) and TDM (Test-Day Model) methods for predicting the sires breeding value and evaluating genetic parameters for Simmental cattle population in four regions of the Russian Federation. A comparative analysis of these methods with the earlier BLUP SM (Sire Model) method is performed. The breeding value for sires and cows of Simmental breed was calculated by milk production traits: milk yield for 305 days; milk fatyield; milk proteinyield. The sires reliability of average breeding value calculated by different methods reveal that milk yield for 305 days when switching from the SM1 to AM1 method increases by 2.4%, and when switching from SM1 to TDM1 — by 7.8%.The variants of the genetic trend for milk yield are given using various equations of BLUP and TDM. Based on the obtained data, it can be concluded that the Test-Day model allows increasing the accuracy of bull’s evaluation and also more clearly identifying their ranks, as well as slightly reducing the time for obtaining reliable estimates of bulls by offspring for production traits.

Characterization of Nucleotide Binding ­Site-Encoding Genes in Sweetpotato, Ipomoea batatas(L.) Lam., and Their Response to Biotic and Abiotic Stresses

2021 ◽  
pp. 1-15
Author(s):  
Zengzhi Si ◽  
Yake Qiao ◽  
Kai Zhang ◽  
Zhixin Ji ◽  
Jinling Han
Keyword(s):  
Binding Site ◽  
Abiotic Stresses ◽  
Ipomoea Batatas ◽  
Expression Profiles ◽  
Nucleotide Binding ◽  
Regulatory Elements ◽  
Nucleotide Binding Site ◽  
Biotic And Abiotic Stresses ◽  
Encoding Genes

Sweetpotato, <i>Ipomoea batatas</i> (L.) Lam., is an important and widely grown crop, yet its production is affected severely by biotic and abiotic stresses. The nucleotide binding site (NBS)-encoding genes have been shown to improve stress tolerance in several plant species. However, the characterization of NBS-encoding genes in sweetpotato is not well-documented to date. In this study, a comprehensive analysis of NBS-encoding genes has been conducted on this species by using bioinformatics and molecular biology methods. A total of 315 NBS-encoding genes were identified, and 260 of them contained all essential conserved domains while 55 genes were truncated. Based on domain architectures, the 260 NBS-encoding genes were grouped into 6 distinct categories. Phylogenetic analysis grouped these genes into 3 classes: TIR, CC (I), and CC (II). Chromosome location analysis revealed that the distribution of NBS-encoding genes in chromosomes was uneven, with a number ranging from 1 to 34. Multiple stress-related regulatory elements were detected in the promoters, and the NBS-encoding genes’ expression profiles under biotic and abiotic stresses were obtained. According to the bioinformatics analysis, 9 genes were selected for RT-qPCR analysis. The results revealed that <i>IbNBS75</i>, <i>IbNBS219</i>, and <i>IbNBS256</i> respond to stem nematode infection; <i>Ib­NBS240</i>, <i>IbNBS90</i>, and <i>IbNBS80</i> respond to cold stress, while <i>IbNBS208</i>, <i>IbNBS71</i>, and <i>IbNBS159</i> respond to 30% PEG treatment. We hope these results will provide new insights into the evolution of NBS-encoding genes in the sweetpotato genome and contribute to the molecular breeding of sweetpotato in the future.

scholarly journals Non-Coding RNAs as Biomarkers of Tumor Progression and Metastatic Spread in Epithelial Ovarian Cancer

Cancers ◽  
2021 ◽  
Vol 13 (8) ◽  
pp. 1839
Author(s):  
Karolina Seborova ◽  
Radka Vaclavikova ◽  
Lukas Rob ◽  
Pavel Soucek ◽  
Pavel Vodicka
Keyword(s):  
Ovarian Cancer ◽  
Tumor Progression ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Distant Metastases ◽  
Regulatory Elements ◽  
Metastatic Spread ◽  
Response To Treatment ◽  
Primary Tumors ◽  
Non Coding Rnas

Ovarian cancer is one of the most common causes of death among gynecological malignancies. Molecular changes occurring in the primary tumor lead to metastatic spread into the peritoneum and the formation of distant metastases. Identification of these changes helps to reveal the nature of metastases development and decipher early biomarkers of prognosis and disease progression. Comparing differences in gene expression profiles between primary tumors and metastases, together with disclosing their epigenetic regulation, provides interesting associations with progression and metastasizing. Regulatory elements from the non-coding RNA families such as microRNAs and long non-coding RNAs seem to participate in these processes and represent potential molecular biomarkers of patient prognosis. Progress in therapy individualization and its proper targeting also rely upon a better understanding of interactions among the above-listed factors. This review aims to summarize currently available findings of microRNAs and long non-coding RNAs linked with tumor progression and metastatic process in ovarian cancer. These biomolecules provide promising tools for monitoring the patient’s response to treatment, and further they serve as potential therapeutic targets of this deadly disease.

scholarly journals Genome-Wide Analysis and Characterization of the Aux/IAA Family Genes Related to Floral Scent Formation in Hedychium coronarium

2019 ◽  
Vol 20 (13) ◽  
pp. 3235 ◽  
Author(s):  
Yanguo Ke ◽  
Farhat Abbas ◽  
Yiwei Zhou ◽  
Rangcai Yu ◽  
Yuechong Yue ◽  
...  
Keyword(s):  
Gene Family ◽  
Developmental Stages ◽  
Floral Scent ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Regulatory Elements ◽  
Virus Induced Gene Silencing ◽  
Cut Flowers ◽  
Flower Opening ◽  
Hedychium Coronarium

Auxin plays a key role in different plant growth and development processes, including flower opening and development. The perception and signaling of auxin depend on the cooperative action of various components, among which auxin/indole-3-acetic acid (Aux/IAA) proteins play an imperative role. In a recent study, the entire Aux/IAA gene family was identified and comprehensively analyzed in Hedychium coronarium, a scented species used as an ornamental plant for cut flowers. Phylogenetic analysis showed that the Aux/IAA gene family in H. coronarium is slightly contracted compared to Arabidopsis, with low levels of non-canonical proteins. Sequence analysis of promoters showed numerous cis-regulatory elements related to various phytohormones. HcIAA genes showed distinct expression patterns in different tissues and flower developmental stages, and some HcIAA genes showed significant responses to auxin and ethylene, indicating that Aux/IAAs may play an important role in linking hormone signaling pathways. Based on the expression profiles, HcIAA2, HcIAA4, HcIAA6 and HcIAA12, were selected as candidate genes and HcIAA2 and HcIAA4 were screened for further characterization. Downregulation of HcIAA2 and HcIAA4 by virus-induced gene silencing in H. coronarium flowers modified the total volatile compound content, suggesting that HcIAA2 and HcIAA4 play important roles in H. coronarium floral scent formation. The results presented here will provide insights into the putative roles of HcIAA genes and will assist the elucidation of their precise roles during floral scent formation.

scholarly journals Genome-wide characterization of MATE gene family and expression profiles in response to abiotic stresses in rice (Oryza sativa)

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Zhixuan Du ◽  
Qitao Su ◽  
Zheng Wu ◽  
Zhou Huang ◽  
Jianzhong Bao ◽  
...  
Keyword(s):  
Oryza Sativa ◽  
Gene Family ◽  
Tandem Repeats ◽  
Expression Profiles ◽  
Functional Divergence ◽  
Expression Patterns ◽  
Regulatory Elements ◽  
Genome Wide ◽  
Comprehensive Information ◽  
Family Gene

AbstractMultidrug and toxic compound extrusion (MATE) proteins are involved in many physiological functions of plant growth and development. Although an increasing number of MATE proteins have been identified, the understanding of MATE proteins is still very limited in rice. In this study, 46 MATE proteins were identified from the rice (Oryza sativa) genome by homology searches and domain prediction. The rice MATE family was divided into four subfamilies based on the phylogenetic tree. Tandem repeats and fragment replication contribute to the expansion of the rice MATE gene family. Gene structure and cis-regulatory elements reveal the potential functions of MATE genes. Analysis of gene expression showed that most of MATE genes were constitutively expressed and the expression patterns of genes in different tissues were analyzed using RNA-seq. Furthermore, qRT-PCR-based analysis showed differential expression patterns in response to salt and drought stress. The analysis results of this study provide comprehensive information on the MATE gene family in rice and will aid in understanding the functional divergence of MATE genes.

PSIV-6 Differential gene expression of fibro/adipogenic progenitors between Wagyu and Brahman cattle: A possible contribution to their different meat quality

2021 ◽  
Vol 99 (Supplement_3) ◽  
pp. 301-301
Author(s):  
Chaoyang Li ◽  
Qianglin Liu ◽  
Matt Welborn ◽  
Leshan Wang ◽  
Yuxia Li ◽  
...  
Keyword(s):  
Gene Expression ◽  
Skeletal Muscle ◽  
Meat Quality ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Cattle Breed ◽  
Intramuscular Fat ◽  
Brahman Cattle ◽  
Differential Gene ◽  
The Difference

Abstract The amount of intramuscular fat directly influences the meat quality. However, significant differences in the ability to accumulate intramuscular fat are present among different beef cattle breeds. While Wagyu, a cattle breed that originated from Japan, is renowned for abundant intramuscular fat, Brahman cattle generally have very little intramuscular fat accumulation and produce tougher meat. We identified that bovine intramuscular fat is derived from a group of bipotent progenitor cells named fibro/adipogenic progenitors (FAPs) which also give rise to fibroblasts. Thus, the variation in intramuscular fat development between Wagyu and Brahman is likely attributed to the difference in FAPs between these two breeds. In order to understand the gene expression difference between FAPs of the two breeds, single-cell RNA-seq was performed using total single-nucleated cells isolated from the longissimus muscle of young purebred Wagyu, purebred Brahman, and Wagyu-Brahman cross cattle. FAPs constitute the largest single-nucleated cell population in both Wagyu and Brahman skeletal muscle. Multiple subpopulations of FAPs with different gene expression profiles were identified, suggesting that FAP is a heterogeneous population. A unique FAP cluster expressing lower levels of fibrillar collagen and extracellular remodeling enzyme genes but higher levels of select proadipogenic genes was identified exclusively in Wagyu skeletal muscle, which likely contributes to the robust intramuscular adipogenic efficiency of Wagyu FAPs. In conclusion, the difference in the cellular composition and gene expression of FAPs between Wagyu and Brahman cattle likely contribute to their distinct meat quality.

scholarly journals Using 3D epigenomic maps of primary olfactory neuronal cells from living individuals to understand gene regulation

2018 ◽  
Vol 4 (12) ◽  
pp. eaav8550 ◽  
Author(s):  
Suhn K. Rhie ◽  
Shannon Schreiner ◽  
Heather Witt ◽  
Chris Armoskus ◽  
Fides D. Lay ◽  
...  
Keyword(s):  
Cell Model ◽  
Expression Profiles ◽  
Neuronal Cells ◽  
Three Dimensional ◽  
Gene Expression Profiles ◽  
Regulatory Elements ◽  
A Genome ◽  
Wide Scale ◽  
Cell Model System ◽  
Distal Regulatory Elements

As part of PsychENCODE, we developed a three-dimensional (3D) epigenomic map of primary cultured neuronal cells derived from olfactory neuroepithelium (CNON). We mapped topologically associating domains and high-resolution chromatin interactions using Hi-C and identified regulatory elements using chromatin immunoprecipitation and nucleosome positioning assays. Using epigenomic datasets from biopsies of 63 living individuals, we found that epigenetic marks at distal regulatory elements are more variable than marks at proximal regulatory elements. By integrating genotype and metadata, we identified enhancers that have different levels corresponding to differences in genetic variation, gender, smoking, and schizophrenia. Motif searches revealed that many CNON enhancers are bound by neuronal-related transcription factors. Last, we combined 3D epigenomic maps and gene expression profiles to predict enhancer-target gene interactions on a genome-wide scale. This study not only provides a framework for understanding individual epigenetic variation using a primary cell model system but also contributes valuable data resources for epigenomic studies of neuronal epithelium.

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