scholarly journals 3 Characterization of intergenic regions and gene definition

Nature ◽  
2019 ◽  
Keyword(s):  
Gene Definition ◽  
Intergenic Regions

scholarly journals Molecular characterization of Trypanosoma cruzi Mexican strains and their behavior in the mouse experimental model

2011 ◽  
Vol 44 (6) ◽  
pp. 684-690 ◽  
Author(s):  
César Gómez-Hernández ◽  
Karine Rezende-Oliveira ◽  
Gabriel Antônio Nogueira Nascentes ◽  
Lara Rocha Batista ◽  
Henrique Borges Kappel ◽  
...  
Keyword(s):  
Trypanosoma Cruzi ◽  
Chagas Disease ◽  
Random Amplified Polymorphic Dna ◽  
Geographic Origin ◽  
Pcr Amplification ◽  
Biological Characterization ◽  
Long Time ◽  
Intergenic Regions ◽  
Mexican Strains

INTRODUCTION: For a long time, the importance of Chagas disease in Mexico, where many regarded it as an exotic malady, was questioned. Considering the great genetic diversity among isolates of Trypanosoma cruzi, the importance of this biological characterization, and the paucity of information on the clinical and biological aspects of Chagas disease in Mexico, this study aimed to identify the molecular and biological characterization of Trypanosoma cruzi isolates from different endemic areas of this country, especially of the State of Jalisco. METHODS: Eight Mexican Trypanosoma cruzi strains were biologically and genetically characterized (PCR specific for Trypanosoma cruzi, multiplex-PCR, amplification of space no transcript of the genes of the mini-exon, amplification of polymorphic regions of the mini-exon, classification by amplification of intergenic regions of the spliced leader genes, RAPD - (random amplified polymorphic DNA). RESULTS: Two profiles of parasitaemia were observed, patent (peak parasitaemia of 4.6×10(6) to 10(7) parasites/mL) and subpatent. In addition, all isolates were able to infect 100% of the animals. The isolates mainly displayed tropism for striated (cardiac and skeletal) muscle. PCR amplification of the mini-exon gene classified the eight strains as TcI. The RAPD technique revealed intraspecies variation among isolates, distinguishing strains isolated from humans and triatomines and according to geographic origin. CONCLUSIONS: The Mexican T. cruzi strains are myotrophic and belong to group TcI.

Nuclear and cytoplasmic genome composition of Solanum bulbocastanum (+) S. tuberosum somatic hybrids

Genome ◽  
2007 ◽  
Vol 50 (5) ◽  
pp. 443-450 ◽  
Author(s):  
Marina Iovene ◽  
Salvatore Savarese ◽  
Teodoro Cardi ◽  
Luigi Frusciante ◽  
Nunzia Scotti ◽  
...  
Keyword(s):  
Parental Species ◽  
Somatic Hybrids ◽  
Solanum Bulbocastanum ◽  
Genome Composition ◽  
Specific Primers ◽  
Genetic Studies ◽  
Cytoplasmic Genome ◽  
Intergenic Regions

Somatic hybrids between the wild incongruent species Solanum bulbocastanum (2n = 2x = 24) and S. tuberosum haploids (2n = 2x = 24) have been characterized for their nuclear and cytoplasmic genome composition. Cytologic observations revealed the recovery of 8 (near-)tetraploid and 3 hexaploid somatic hybrids. Multicolor genomic in situ hybridization (GISH) analysis was carried out to study the genomic dosage of the parental species in 5 somatic hybrids with different ploidy. The GISH procedure used was effective in discriminating parental genomes in the hybrids; most chromosomes were unambiguously colored. Two (near-)tetraploid somatic hybrids showed the expected 2:2 cultivated-to-wild genomic dosage; 2 hexaploids revealed a 4:2 cultivated-to-wild genomic dosage, and 1 hexaploid had a 2:4 cultivated-to-wild genomic dosage. Characterization of hybrid cytoplasmic genomes was performed using gene-specific primers that detected polymorphisms between the fusion parents in the intergenic regions. The analysis showed that most of the somatic hybrids inherited the plastidial and mitochondrial DNA of the cultivated parent. A few hybrids, with a rearranged mitochondrial genome (showing fragments derived from both parents), were also identified. These results confirmed the potential of somatic hybridization in producing new variability for genetic studies and breeding.

scholarly journals Characterization of fsr, a Regulator Controlling Expression of Gelatinase and Serine Protease inEnterococcus faecalis OG1RF

2001 ◽  
Vol 183 (11) ◽  
pp. 3372-3382 ◽  
Author(s):  
Xiang Qin ◽  
Kavindra V. Singh ◽  
George M. Weinstock ◽  
Barbara E. Murray
Keyword(s):  
Serine Protease ◽  
Parent Strain ◽  
Deletion Mutant ◽  
Regulatory Function ◽  
Direct Repeats ◽  
Promoter Regions ◽  
Intergenic Regions ◽  
Peritonitis Model ◽  
Transcriptional Fusions

ABSTRACT We have previously identified a locus, fsr, a homologue of staphylococcal agr loci, which positively regulates the expression of gelatinase and serine protease (encoded bygelE and sprE, respectively) inEnterococcus faecalis OG1RF. The expression of the three genes in the fsr locus, fsrA,fsrB, and fsrC, appears to be autoregulated, and we have shown that mutants with insertion disruptions in each of these three genes were significantly attenuated in a mouse peritonitis model compared to the parent strain. In the present study, we showed that fsrB andfsrC are highly expressed in the postexponential growth phase and that their expression is cell density dependent. Reverse transcriptase PCR using primers covering the intergenic regions in the fsr/gelE loci confirmed thatfsrB and fsrC, as well asgelE and sprE, are cotranscribed. We also showed, using a nonpolar fsrB deletion mutant, thatfsrB, the homologue of agrB of staphylococci with unknown function, is required for the regulatory function of fsr. Primer extension and analysis of transcriptional fusions indicated the presence of promoters immediately upstream of fsrA, of fsrB, and ofgelE and that the fsrB andgelE promoters are fsr dependent, while the fsrA promoter is an fsr-independent weak constitutive promoter. Two conserved 7-bp direct repeats were found immediately upstream of the fsrB andgelE promoters, similar to the repeats found upstream of P2 and P3 promoters of the agr locus; deletions and mutations in the repeated sequences completely abolished thefsrB and gelE promoter activities, suggesting that the repeats are important for the regulatory function in the fsrB and gelE promoter regions.

scholarly journals Evolutionary adaptability linked to length variation in short genic tandem repeats

2018 ◽  
Author(s):  
William B Reinar ◽  
Jonfinn B Knutsen ◽  
Sissel Jentoft ◽  
Ole K Tørresen ◽  
Melinka A Butenko ◽  
...  
Keyword(s):  
Protein Function ◽  
Tandem Repeats ◽  
Phenotypic Traits ◽  
Length Variation ◽  
Interaction Sites ◽  
Genome Wide ◽  
Mutational Hotspots ◽  
Intergenic Regions ◽  
Gene Expression Levels

AbstractThere is increasing evidence that short tandem repeats (STRs) – mutational hotspots present in genes and in intergenic regions throughout most genomes – may influence gene and protein function and consequently affect the phenotype of an organism. However, the overall importance of STRs and their standing genetic variation within a population, e.g. if and how they facilitate evolutionary change and local adaptation, is still debated. Through genome-wide characterization of STRs in over a thousand wild Arabidopsis thaliana accessions we demonstrate that STRs display significant variation in length across the species’ geographical distribution. We find that length variants are correlated with environmental conditions, key adaptive phenotypic traits as well as gene expression levels. Further, we show that coding STRs are overrepresented in putative protein interaction sites. Taken together, our results suggest that these hypervariable loci play a major role in facilitating adaptation in plants, and due to the ubiquitous presence of STRs throughout the tree of life, similar roles in other organisms are likely.

scholarly journals Identification and characterization of melon circular RNAs involved in powdery mildew responses through comparative transcriptome analysis

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11216
Author(s):  
Jianlei Sun ◽  
Yumei Dong ◽  
Chongqi Wang ◽  
Shouhua Xiao ◽  
Zigao Jiao ◽  
...  
Keyword(s):  
Powdery Mildew ◽  
Regulation Of Gene Expression ◽  
Circular Rnas ◽  
Abiotic And Biotic Stresses ◽  
Biotic Stresses ◽  
Oxidation Reduction ◽  
Whole Transcriptome Sequencing ◽  
Intergenic Regions ◽  
Whole Transcriptome

Circular RNAs (circRNAs) are a class of newly discovered non-coding RNAs that are typically derived from a genome’s exonic, intronic, and intergenic regions. Recent studies of circRNAs in animals and plants have shown that circRNAs are vital in response to various abiotic and biotic stresses. Powdery mildew disease (PM) is a serious fungal disease threatening the melon industry. We performed whole transcriptome sequencing using the leaves of a PM-resistant (M1) and a PM-susceptible (B29) melon to identify circRNAs and determine their molecular functions. A total of 303 circRNAs were identified and >50% circRNAs were derived from exonic regions. Expression levels were significantly altered in 17 and 23 circRNAs after PM infections in B29 and M1, respectively. Melon circRNAs may participate in the response to biotic stimuli, oxidation reduction, metabolic processes, and the regulation of gene expression based on the functional annotation of circRNA parental genes. Furthermore, 27 circRNAs were predicted to be potential targets or ‘sponges’ for 18 microRNAs (miRNAs). Our results are the first to identify and characterize circRNA functions in melon and may contribute to a better understanding of the role and regulatory mechanisms of circRNAs in resisting PM.

scholarly journals An integrative atlas of chicken long non-coding genes and their annotations across 25 tissues

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Frédéric Jehl ◽  
Kévin Muret ◽  
Maria Bernard ◽  
Morgane Boutin ◽  
Laetitia Lagoutte ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Biological Processes ◽  
Rna Seq ◽  
Protein Coding ◽  
Tissue Specific ◽  
Protein Coding Genes ◽  
Intergenic Regions ◽  
Immune Tissues ◽  
Non Coding Rnas

AbstractLong non-coding RNAs (LNC) regulate numerous biological processes. In contrast to human, the identification of LNC in farm species, like chicken, is still lacunar. We propose a catalogue of 52,075 chicken genes enriched in LNC (http://www.fragencode.org/), built from the Ensembl reference extended using novel LNC modelled here from 364 RNA-seq and LNC from four public databases. The Ensembl reference grew from 4,643 to 30,084 LNC, of which 59% and 41% with expression ≥ 0.5 and ≥ 1 TPM respectively. Characterization of these LNC relatively to the closest protein coding genes (PCG) revealed that 79% of LNC are in intergenic regions, as in other species. Expression analysis across 25 tissues revealed an enrichment of co-expressed LNC:PCG pairs, suggesting co-regulation and/or co-function. As expected LNC were more tissue-specific than PCG (25% vs. 10%). Similarly to human, 16% of chicken LNC hosted one or more miRNA. We highlighted a new chicken LNC, hosting miR155, conserved in human, highly expressed in immune tissues like miR155, and correlated with immunity-related PCG in both species. Among LNC:PCG pairs tissue-specific in the same tissue, we revealed an enrichment of divergent pairs with the PCG coding transcription factors, as for example LHX5, HXD3 and TBX4, in both human and chicken.

scholarly journals MeRIP-seq and RNA-seq data of mycelium and spore of Ascosphaera apis, a widespread bee fungal pathogen

2020 ◽  
Author(s):  
Yu Du ◽  
Haibin Jiang ◽  
Zhiwei Zhu ◽  
Jie Wang ◽  
Huazhi Chen ◽  
...  
Keyword(s):  
Fungal Pathogen ◽  
Rna Isolation ◽  
Transcript Level ◽  
Current Data ◽  
List Type ◽  
Rna Seq ◽  
Ascosphaera Apis ◽  
Bee Health ◽  
Intergenic Regions

ABSTRACTAscosphaera apis is widespread fungal pathogen of honeybee larvae, causing chalkbrood, a chronic disease that weakens bee health and colony productivity. In this article, mecylia and spores of A. apis were respectively purified followed by RNA isolation, cDNA library construction, MeRIP-seq and RNA-seq. A total of 62,551,172, 41,773,158, 49,535,092 and 61,569,610 raw reads were produced from Aam_IP, Aas_IP, Aam_input and Aas_input groups, respectively. After quality control, 58,484,368, 37,381,432, 44,655,434 and 58,739,742 clean reads were obtained. Furthermore, 47,706,205, 31,356,690, 35,259,810 and 44,319,061 clean reads were mapped to the reference genome of A. apis, including 39,337,036, 26,731,957, 31,987,396 and 40,017,855 unique mapped reads, and 8,369,169, 4,624,733, 3,272,414 and 4,301,206 multiple mapped reads. Among them, 96.31%, 96.51%, 96.82% and 97.11% of clean reads were mapped to exons; 2.09%, 2.31%,1.83% and 1.81% to introns; 1.60%, 1.18%, 1.35% and 1.08% to intergenic regions.Value of the dataThe data can be used to investigate the relationship between the m6A modification extent and the transcript level in the A. apis transcriptome.This dataset contributes to transcriptome-wide characterization of the m6A distributing patterns in mRNAs and non-coding RNAs in A. apis mycelium and spore.Current data benefits new functions of m6A modification in the transcripts extensively modified by m6A in A. apis mycelium and spore.Our data could be used to characterize differential patterns of the m6A methylation between mycelium and spore of A. apis.

scholarly journals Molecular Characterization of Vancomycin-Resistant Enterococci from Hospitalized Patients and Poultry Products in The Netherlands

1998 ◽  
Vol 36 (7) ◽  
pp. 1927-1932 ◽  
Author(s):  
Nicole van den Braak ◽  
Alex van Belkum ◽  
Marrit van Keulen ◽  
John Vliegenthart ◽  
Henri A. Verbrugh ◽  
...  
Keyword(s):  
Intergenic Region ◽  
Bacterial Flora ◽  
Structure Mapping ◽  
Poultry Products ◽  
Vancomycin Resistant Enterococci ◽  
Genetic Overlap ◽  
Intergenic Regions ◽  
Vancomycin Resistant ◽  
High Level

Vancomycin-resistant enterococci (VRE) pose an emerging health risk, but little is known about the precise epidemiology of the genes coding for vancomycin resistance. To determine whether the bacterial flora of consumer poultry serves as a gene reservoir, the level of contamination of poultry products with VRE was determined. VRE were genotyped by pulsed-field gel electrophoresis (PFGE), and transposon structure mapping was done by PCR. ThevanX-vanY intergenic regions of several strains were further analyzed by sequencing. A total of 242 of 305 (79%) poultry products were found to be contaminated with VRE. Of these VRE, 142 (59%) were high-level-vancomycin-resistant Enterococcus faecium strains (VREF). PFGE revealed extensive VREF heterogeneity. Two genotypes were found nationwide on multiple occasions: type A (22 of 142 VREF [15%]) and type B (14 of 142 VREF [10%]). No PFGE-deduced genetic overlap was found when VREF from humans were compared with VREF from poultry. TwovanA transposon types were identified among poultry strains. In 59 of 142 (42%) of the poultry VREF, the size of the intergenic region between vanX and vanY was ∼1,300 bp. This transposon type was not found in human VREF. In contrast, all human strains and 83 of 142 (58%) of the poultry VREF contained an intergenic region 543 bp in size. Sequencing of this 543-bp intergenic vanX-vanY region demonstrated full sequence conservation. Though preliminary, these data suggest that dissemination of the resistance genes carried on transposable elements may be of greater importance than clonal dissemination of resistant strains. This observation is important for developing strategies to control the spread of glycopeptide resistance.

Sign in / Sign up

Export Citation Format

Share Document