scholarly journals Compensatory sequence variation between trans-species small RNAs and their target sites

2019 ◽  
Author(s):  
Nathan R. Johnson ◽  
Claude W. dePamphilis ◽  
Michael J. Axtell
Keyword(s):  
Sequence Variation ◽  
Parasitic Plant ◽  
Synonymous Site ◽  
Protein Coding ◽  
Coding Regions ◽  
Mrna Targets ◽  
Target Sites ◽  
Site Variation ◽  
Small Regulatory Rnas ◽  
Multiple Species

AbstractTrans-species small regulatory RNAs (sRNAs) are delivered to host plants from diverse pathogens and parasites and can target host mRNAs. How trans-species sRNAs can be effective on diverse hosts has been unclear. Multiple species of the parasitic plant Cuscuta produce trans-species sRNAs that collectively target many host mRNAs. Confirmed target sites are nearly always in highly conserved, protein-coding regions of host mRNAs. Cuscuta trans-species sRNAs can be grouped into superfamilies that have variation in a three-nucleotide period. These variants compensate for synonymous-site variation in host mRNAs. By targeting host mRNAs at highly conserved protein-coding sites, and simultaneously expressing multiple variants to cover synonymous-site variation, Cuscuta trans-species sRNAs may be able to successfully target homologous mRNAs from diverse hosts.One Sentence SummaryThe parasitic plant Cuscuta produces a diverse set of sRNAs that compensate for sequence variation in mRNA targets in diverse hosts.

scholarly journals Compensatory sequence variation between trans-species small RNAs and their target sites

eLife ◽  
2019 ◽  
Vol 8 ◽  
Author(s):  
Nathan R Johnson ◽  
Claude W dePamphilis ◽  
Michael J Axtell
Keyword(s):  
Small Rnas ◽  
Synonymous Site ◽  
Protein Coding ◽  
Coding Regions ◽  
Target Sites ◽  
Site Variation ◽  
Small Regulatory Rnas ◽  
Regulatory Rnas ◽  
Multiple Species ◽  
Multiple Variants

Trans-species small regulatory RNAs (sRNAs) are delivered to host plants from diverse pathogens and parasites and can target host mRNAs. How trans-species sRNAs can be effective on diverse hosts has been unclear. Multiple species of the parasitic plant Cuscuta produce trans-species sRNAs that collectively target many host mRNAs. Confirmed target sites are nearly always in highly conserved, protein-coding regions of host mRNAs. Cuscuta trans-species sRNAs can be grouped into superfamilies that have variation in a three-nucleotide period. These variants compensate for synonymous-site variation in host mRNAs. By targeting host mRNAs at highly conserved protein-coding sites, and simultaneously expressing multiple variants to cover synonymous-site variation, Cuscuta trans-species sRNAs may be able to successfully target multiple homologous mRNAs from diverse hosts.

scholarly journals No Relationship between Sequence Variation in Protein Coding Regions of the Tas1r3 Gene and Saccharin Preference in Rats

2005 ◽  
Vol 30 (3) ◽  
pp. 231-240 ◽  
Author(s):  
K. Lu ◽  
A. H. McDaniel ◽  
M. G. Tordoff ◽  
X. Li ◽  
G. K. Beauchamp ◽  
...  
Keyword(s):  
Sequence Variation ◽  
Saccharin Preference ◽  
Protein Coding ◽  
Coding Regions

scholarly journals Extensive sequence divergence of non-coding regions between Aspergillus fumigatus, a major fungal pathogen of humans, and its relatives

2021 ◽  
Author(s):  
Alec Brown ◽  
Matthew E Mead ◽  
Jacob L. Steenwyk ◽  
Gustavo Goldman ◽  
Antonis Rokas
Keyword(s):  
Aspergillus Fumigatus ◽  
Sequence Variation ◽  
Sequence Divergence ◽  
Single Copy ◽  
Orthologous Genes ◽  
Sequence Alignments ◽  
Protein Coding ◽  
Extensive Sequence ◽  
Coding Regions ◽  
Close Relatives

Invasive aspergillosis is a deadly fungal disease; more than 400,000 patients are infected worldwide each year and the mortality rate can be as high as 50-95%. Of the ~450 species in the genus Aspergillus only a few are known to be clinically relevant, with the major pathogen Aspergillus fumigatus being responsible for ~50% of all invasive mold infections. Genomic comparisons of A. fumigatu to other Aspergillus species have historically focused on protein-coding regions. However, most A. fumigatus genes, including those that modulate its virulence, are also present in non-pathogenic close relatives of A. fumigatus. Our hypothesis is that differential gene regulation - mediated through the non-coding regions upstream of genes' transcription start sites - contributes to A. fumigatus pathogenicity. To begin testing this, we compared non-coding regions up to 500 base pairs upstream of the first codon of single-copy orthologous genes from the two A. fumigatus reference strains Af293 and A1163 and eight closely related Aspergillus section Fumigati species. We found that non-coding regions showed extensive sequence variation and lack of homology across species. By examining the evolutionary rates of both protein-coding and non-coding regions in a subset of orthologous genes with highly conserved non-coding regions across the phylogeny, we identified 418 genes, including 25 genes known to modulate A. fumigatus virulence, whose non-coding regions exhibit a different rate of evolution in A. fumigatus. Examination of sequence alignments of these non-coding regions revealed numerous instances of insertions, deletions, and other types of mutations of at least a few nucleotides in A. fumigatus compared to its close relatives. These results show that closely related Aspergillus species that vary greatly in their pathogenicity exhibit extensive non-coding sequence variation and identify numerous changes in non-coding regions of A. fumigatus genes known to contribute to virulence.

scholarly journals The open targets post-GWAS analysis pipeline

2020 ◽  
Vol 36 (9) ◽  
pp. 2936-2937 ◽  
Author(s):  
Gareth Peat ◽  
William Jones ◽  
Michael Nuhn ◽  
José Carlos Marugán ◽  
William Newell ◽  
...  
Keyword(s):  
Drug Targets ◽  
Gene Expression Regulation ◽  
Association Studies ◽  
Genome Wide Association Studies ◽  
Protein Coding ◽  
Data Resource ◽  
Coding Regions ◽  
Genome Wide ◽  
Causal Genes ◽  
Interactive Data

Abstract Motivation Genome-wide association studies (GWAS) are a powerful method to detect even weak associations between variants and phenotypes; however, many of the identified associated variants are in non-coding regions, and presumably influence gene expression regulation. Identifying potential drug targets, i.e. causal protein-coding genes, therefore, requires crossing the genetics results with functional data. Results We present a novel data integration pipeline that analyses GWAS results in the light of experimental epigenetic and cis-regulatory datasets, such as ChIP-Seq, Promoter-Capture Hi-C or eQTL, and presents them in a single report, which can be used for inferring likely causal genes. This pipeline was then fed into an interactive data resource. Availability and implementation The analysis code is available at www.github.com/Ensembl/postgap and the interactive data browser at postgwas.opentargets.io.

scholarly journals Sequence Variation in Two Protein-Coding Genes Correlates with Mycelial Compatibility Groupings in Sclerotium rolfsii

2013 ◽  
Vol 103 (5) ◽  
pp. 479-487 ◽  
Author(s):  
Efrén Remesal ◽  
Blanca B. Landa ◽  
María del Mar Jiménez-Gasco ◽  
Juan A. Navas-Cortés
Keyword(s):  
Rna Polymerase Ii ◽  
Sequence Variation ◽  
Geographic Origin ◽  
Sclerotium Rolfsii ◽  
Nuclear Ribosomal Dna ◽  
Causal Organism ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Wide Range ◽  
Mycelial Compatibility

Populations of Sclerotium rolfsii, the causal organism of Sclerotium root-rot on a wide range of hosts, can be placed into mycelial compatibility groups (MCGs). In this study, we evaluated three different molecular approaches to unequivocally identify each of 12 previously identified MCGs. These included restriction fragment length polymorphism (RFLP) patterns of the internal transcribed spacer (ITS) region of nuclear ribosomal DNA (rDNA) and sequence analysis of two protein-coding genes: translation elongation factor 1α (EF1α) and RNA polymerase II subunit two (RPB2). A collection of 238 single-sclerotial isolates representing 12 MCGs of S. rolfsii were obtained from diseased sugar beet plants from Chile, Italy, Portugal, and Spain. ITS-RFLP analysis using four restriction enzymes (AluI, HpaII, RsaI, and MboI) displayed a low degree of variability among MCGs. Only three different restriction profiles were identified among S. rolfsii isolates, with no correlation to MCG or to geographic origin. Based on nucleotide polymorphisms, the RPB2 gene was more variable among MCGs compared with the EF1α gene. Thus, 10 of 12 MCGs could be characterized utilizing the RPB2 region only, while the EF1α region resolved 7 MCGs. However, the analysis of combined partial sequences of EF1α and RPB2 genes allowed discrimination among each of the 12 MCGs. All isolates belonging to the same MCG showed identical nucleotide sequences that differed by at least in one nucleotide from a different MCG. The consistency of our results to identify the MCG of a given S. rolfsii isolate using the combined sequences of EF1α and RPB2 genes was confirmed using blind trials. Our study demonstrates that sequence variation in the protein-coding genes EF1α and RPB2 may be exploited as a diagnostic tool for MCG typing in S. rolfsii as well as to identify previously undescribed MCGs.

scholarly journals Novel exon 1 protein‐coding regions N‐terminally extend human KCNE3 and KCNE4

2016 ◽  
Vol 30 (8) ◽  
pp. 2959-2969 ◽  
Author(s):  
Geoffrey W. Abbott
Keyword(s):  
Protein Coding ◽  
Coding Regions ◽  
Exon 1 ◽  
Novel Exon

scholarly journals Crystal structure and RNA-binding properties of an Hfq homolog from the deep-branching Aquificae: conservation of the lateral RNA-binding mode

2017 ◽  
Vol 73 (4) ◽  
pp. 294-315 ◽  
Author(s):  
Kimberly A. Stanek ◽  
Jennifer Patterson-West ◽  
Peter S. Randolph ◽  
Cameron Mura
Keyword(s):  
Rna Binding ◽  
Binding Pocket ◽  
Binding Mode ◽  
Evolutionary Conservation ◽  
Aquifex Aeolicus ◽  
Binding Properties ◽  
Bacterial Phyla ◽  
Mrna Targets ◽  
Small Regulatory Rnas ◽  
And Function

The host factor Hfq, as the bacterial branch of the Sm family, is an RNA-binding protein involved in the post-transcriptional regulation of mRNA expression and turnover. Hfq facilitates pairing between small regulatory RNAs (sRNAs) and their corresponding mRNA targets by binding both RNAs and bringing them into close proximity. Hfq homologs self-assemble into homo-hexameric rings with at least two distinct surfaces that bind RNA. Recently, another binding site, dubbed the `lateral rim', has been implicated in sRNA·mRNA annealing; the RNA-binding properties of this site appear to be rather subtle, and its degree of evolutionary conservation is unknown. An Hfq homolog has been identified in the phylogenetically deep-branching thermophileAquifex aeolicus(Aae), but little is known about the structure and function of Hfq from basal bacterial lineages such as the Aquificae. Therefore,AaeHfq was cloned, overexpressed, purified, crystallized and biochemically characterized. Structures ofAaeHfq were determined in space groupsP1 andP6, both to 1.5 Å resolution, and nanomolar-scale binding affinities for uridine- and adenosine-rich RNAs were discovered. Co-crystallization with U6RNA reveals that the outer rim of theAaeHfq hexamer features a well defined binding pocket that is selective for uracil. ThisAaeHfq structure, combined with biochemical and biophysical characterization of the homolog, reveals deep evolutionary conservation of the lateral RNA-binding mode, and lays a foundation for further studies of Hfq-associated RNA biology in ancient bacterial phyla.

scholarly journals Protein-coding structured RNAs: A computational survey of conserved RNA secondary structures overlapping coding regions in drosophilids

Biochimie ◽  
2011 ◽  
Vol 93 (11) ◽  
pp. 2019-2023 ◽  
Author(s):  
Sven Findeiß ◽  
Jan Engelhardt ◽  
Sonja J. Prohaska ◽  
Peter F. Stadler
Keyword(s):  
Secondary Structures ◽  
Protein Coding ◽  
Rna Secondary Structures ◽  
Coding Regions

Structure and expression of canary myc family genes

1991 ◽  
Vol 11 (3) ◽  
pp. 1770-1776
Author(s):  
R G Collum ◽  
D F Clayton ◽  
F W Alt
Keyword(s):  
Untranslated Region ◽  
Untranslated Regions ◽  
Coding Region ◽  
Protein Coding ◽  
Coding Regions ◽  
Neuronal Precursors ◽  
Myc Gene ◽  
Mature Neurons

We found that the canary N-myc gene is highly related to mammalian N-myc genes in both the protein-coding region and the long 3' untranslated region. Examined coding regions of the canary c-myc gene were also highly related to their mammalian counterparts, but in contrast to N-myc, the canary and mammalian c-myc genes were quite divergent in their 3' untranslated regions. We readily detected N-myc and c-myc expression in the adult canary brain and found N-myc expression both at sites of proliferating neuronal precursors and in mature neurons.

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