scholarly journals On the origins and evolution of trans-splicing of bursicon in mosquitos

2016 ◽  
Author(s):  
Scott William Roy
Keyword(s):  
Last Common Ancestor ◽  
Protein Coding ◽  
Rna Transcripts ◽  
Coding Regions ◽  
Transcriptomic Sequencing ◽  
Trans Splicing ◽  
Internal Exon ◽  
History Of ◽  
Rna Transcript ◽  
Distinct Locus

Broad transcriptomic sequencing of eukaryotes has revealed the ubiquity of splicing of nuclear genes. While the vast majority of splicing events join segments of the same RNA transcript, various studies have found a few intriguing cases of trans-splicing of introns, in which splicing events within protein coding regions join segments of different RNA transcripts. The most structurally intricate case known involves the bursicon gene in mosquitos, in which an internal exon is encoded at a distinct locus, requiring multiple trans-splicing events form the mature mRNA. This arrangement is known to be ancestral to mosquitos, however the exact timing of the origin of trans-splicing and the history of the bursicon gene within mosquitos is unknown. Taking advantage of the recent availability of genomes from various Anopheles mosquitos and from relatives of mosquitos, I determined trans versus cis encoding of bursicon across Culicomorpha. I conclude that trans-splicing emerged in the last common ancestor of mosquitos, and that trans-splicing has been retained in all 19 studied Anopheles species. The retention of trans-splicing could indicate functional importance of this arrangement, or could alternatively reflect the rarity of mutations giving rise to viable allelic alternatives.

scholarly journals The role of deleterious substitutions in crop genomes

2015 ◽  
Author(s):  
Thomas J. Y. Kono ◽  
Fengli Fu ◽  
Mohsen Mohammadi ◽  
Paul J. Hoffman ◽  
Chaochih Liu ◽  
...  
Keyword(s):  
Demographic History ◽  
Crop Improvement ◽  
Crop Productivity ◽  
Ratio Test ◽  
Protein Coding ◽  
Coding Regions ◽  
Fitness Effects ◽  
Genome Wide ◽  
History Of ◽  
New Mutations

AbstractPopulations continually incur new mutations with fitness effects ranging from lethal to adaptive. While the distribution of fitness effects (DFE) of new mutations is not directly observable, many mutations likely have either no effect on organismal fitness or are deleterious. Historically, it has been hypothesized that a population may carry many mildly deleterious variants as segregating variation, which reduces the mean absolute fitness of the population. Recent advances in sequencing technology and sequence conservation-based metrics for inferring the functional effect of a variant permit examination of the persistence of deleterious variants in populations. The issue of segregating deleterious variation is particularly important for crop improvement, because the demographic history of domestication and breeding allows deleterious variants to persist and reach moderate frequency, potentially reducing crop productivity. In this study, we use exome resequencing of fifteen barley accessions and genome resequencing of eight soybean accessions to investigate the prevalence of deleterious SNPs in the protein-coding regions of the genomes of two crops. We conclude that individual cultivars carry hundreds of deleterious SNPs on average, and that nonsense variants make up a minority of deleterious SNPs. Our approach annotates known phenotype-altering variants as deleterious more frequently than the genome-wide average, suggesting that putatively deleterious variants are likely to affect phenotypic variation. We also report the implementation of a SNP annotation tool (BAD_Mutations) that makes use of a likelihood ratio test based on alignment of all currently publicly available Angiosperm genomes.

scholarly journals Identification of protein coding regions in RNA transcripts

2015 ◽  
Vol 43 (12) ◽  
pp. e78-e78 ◽  
Author(s):  
Shiyuyun Tang ◽  
Alexandre Lomsadze ◽  
Mark Borodovsky
Keyword(s):  
Protein Coding ◽  
Rna Transcripts ◽  
Coding Regions

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 Characterization of the nuclear and cytosolic transcriptomes in human brain tissue reveals new insights into the subcellular distribution of RNA transcripts

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Ammar Zaghlool ◽  
Adnan Niazi ◽  
Åsa K. Björklund ◽  
Jakub Orzechowski Westholm ◽  
Adam Ameur ◽  
...  
Keyword(s):  
Human Brain ◽  
Expression Analysis ◽  
Differential Expression Analysis ◽  
Adult Brain ◽  
Sequencing Data ◽  
Human Brain Tissue ◽  
Protein Coding ◽  
Rna Transcripts ◽  
Nuclear Rna ◽  
The Impact

AbstractTranscriptome analysis has mainly relied on analyzing RNA sequencing data from whole cells, overlooking the impact of subcellular RNA localization and its influence on our understanding of gene function, and interpretation of gene expression signatures in cells. Here, we separated cytosolic and nuclear RNA from human fetal and adult brain samples and performed a comprehensive analysis of cytosolic and nuclear transcriptomes. There are significant differences in RNA expression for protein-coding and lncRNA genes between cytosol and nucleus. We show that transcripts encoding the nuclear-encoded mitochondrial proteins are significantly enriched in the cytosol compared to the rest of protein-coding genes. Differential expression analysis between fetal and adult frontal cortex show that results obtained from the cytosolic RNA differ from results using nuclear RNA both at the level of transcript types and the number of differentially expressed genes. Our data provide a resource for the subcellular localization of thousands of RNA transcripts in the human brain and highlight differences in using the cytosolic or the nuclear transcriptomes for expression analysis.

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.

scholarly journals Sequence and phylogenetic analysis of the non-structural 3A and 3B protein-coding regions of foot-and-mouth disease virus subtype A Iran 05

2010 ◽  
Vol 11 (3) ◽  
pp. 243
Author(s):  
Saber Jelokhani-Niaraki ◽  
Majid Esmaelizad ◽  
Morteza Daliri ◽  
Rasoul Vaez-Torshizi ◽  
Morteza Kamalzadeh ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Disease Virus ◽  
Foot And Mouth Disease ◽  
Mouth Disease ◽  
Protein Coding ◽  
Coding Regions ◽  
Mouth Disease Virus ◽  
Foot And Mouth ◽  
Subtype A ◽  
Virus Subtype
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