scholarly journals Response toIL‐17A inhibitors secukinumab and ixekizumab cannot be explained by genetic variation in the protein‐coding and untranslated regions of theIL‐17A gene: results from a multicentre study of four European psoriasis cohorts

2019 ◽  
Vol 34 (1) ◽  
pp. 112-118 ◽  
Author(s):  
L.J. Vugt ◽  
J.M.P.A. Reek ◽  
E. Meulewaeter ◽  
M. Hakobjan ◽  
N. Heddes ◽  
...  
1991 ◽  
Vol 11 (3) ◽  
pp. 1770-1776
Author(s):  
R G Collum ◽  
D F Clayton ◽  
F W Alt

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.


2010 ◽  
Vol 1 (3) ◽  
pp. 97-112 ◽  
Author(s):  
Richipal Singh Bindra ◽  
Jason T. L. Wang ◽  
Paramjeet Singh Bagga

MicroRNAs (miRNAs) are short single-stranded RNA molecules with 21-22 nucleotides known to regulate post-transcriptional expression of protein-coding genes involved in most of the cellular processes. Prediction of miRNA targets is a challenging bioinformatics problem. AU-rich elements (AREs) are regulatory RNA motifs found in the 3’ untranslated regions (UTRs) of mRNAs, and they play dominant roles in the regulated decay of short-lived human mRNAs via specific interactions with proteins. In this paper, the authors review several miRNA target prediction tools and data sources, as well as computational methods used for the prediction of AREs. The authors discuss the connection between miRNA and ARE-mediated post-transcriptional gene regulation. Finally, a data mining method for identifying the co-occurrences of miRNA target sites in ARE containing genes is presented.


2020 ◽  
Vol 60 (2) ◽  
pp. 318-331
Author(s):  
April D Garrett ◽  
Reid S Brennan ◽  
Anya L Steinhart ◽  
Aubrey M Pelletier ◽  
Melissa H Pespeni

Synopsis Environmental variation experienced by a species across space and time can promote the maintenance of genetic diversity that may be adaptive in future global change conditions. Selection experiments have shown that purple sea urchin, Strongylocentrotus purpuratus, populations have adaptive genetic variation for surviving pH conditions at the “edge” (pH 7.5) of conditions experienced in nature. However, little is known about whether populations have genetic variation for surviving low-pH events beyond those currently experienced in nature or how variation in pH conditions affects organismal and genetic responses. Here, we quantified survival, growth, and allele frequency shifts in experimentally selected developing purple sea urchin larvae in static and variable conditions at three pH levels: pH 8.1 (control), pH 7.5 (edge-of-range), and pH 7.0 (extreme). Variable treatments recovered body size relative to static treatments, but resulted in higher mortality, suggesting a potential tradeoff between survival and growth under pH stress. However, within each pH level, allele frequency changes were overlapping between static and variable conditions, suggesting a shared genetic basis underlying survival to mean pH regardless of variability. In contrast, genetic responses to pH 7.5 (edge) versus pH 7.0 (extreme) conditions were distinct, indicating a unique genetic basis of survival. In addition, loci under selection were more likely to be in exonic regions than regulatory, indicating that selection targeted protein-coding variation. Loci under selection in variable pH 7.5 conditions, more similar to conditions periodically experienced in nature, performed functions related to lipid biosynthesis and metabolism, while loci under selection in static pH 7.0 conditions performed functions related to transmembrane and mitochondrial processes. While these results are promising in that purple sea urchin populations possess genetic variation for surviving extreme pH conditions not currently experienced in nature, they caution that increased acidification does not result in a linear response but elicits unique physiological stresses and survival mechanisms.


2015 ◽  
Vol 11 (5) ◽  
pp. 1378-1388 ◽  
Author(s):  
Ting Liu ◽  
Kui Lin

The relationships among the types of transcripts, the classes of coding SNPs and the population frequencies in the human genome.


PLoS ONE ◽  
2013 ◽  
Vol 8 (3) ◽  
pp. e57615 ◽  
Author(s):  
Ricardo Ramirez-Gonzalez ◽  
Douglas W. Yu ◽  
Catharine Bruce ◽  
Darren Heavens ◽  
Mario Caccamo ◽  
...  

2019 ◽  
Author(s):  
HS Steber ◽  
C Gallante ◽  
S O’Brien ◽  
P.-L Chiu ◽  
M Mangone

ABSTRACT3’-Untranslated Regions (3’-UTRs) of mRNAs emerged as central regulators of cellular function as they contain important but poorly-characterized cis-regulatory elements targeted by a multitude of regulatory factors. The model nematode C. elegans is ideal to study these interactions since it possesses a well-defined 3’-UTRome. In order to improve its annotation, we have used a genomics approach to download raw transcriptome data for 1,088 transcriptome datasets corresponding to the entire collection of C. elegans trancriptomes from 2015 to 2018 from the Sequence Read Archive at the NCBI. We then extracted and mapped high-quality 3’-UTR data at ultra-deep coverage. Here we describe and release to the community the updated version of the worm 3’-UTRome, which we named 3’-UTRome v2. This resource contains high-quality 3’-UTR data mapped at single base ultra-resolution for 23,084 3’-UTR isoform variants corresponding to 14,788 protein-coding genes and is updated to the latest release of WormBase. We used this dataset to study and probe principles of mRNA cleavage and polyadenylation in C. elegans. The worm 3’-UTRome v2 represents the most comprehensive and high-resolution 3’-UTR dataset available in C. elegans and provides a novel resource to investigate the mRNA cleavage and polyadenylation reaction, 3’-UTR biology and miRNA targeting in a living organism.


2019 ◽  
Author(s):  
Xujun Wang ◽  
Jingru Tian ◽  
Peng Cui ◽  
Stephen Mastriano ◽  
Dingyao Zhang ◽  
...  

AbstractMicroRNAs (miRNAs) regulate protein-coding gene expression primarily through cognitive binding sites in the 3’ untranslated regions (3′ UTRs). Seed sites are sequences in messenger RNAs (mRNAs) that form perfect Watson-Crick base-paring with a miRNA’s seed region, which can effectively reduce mRNA abundance and/or repress protein translation. Some seedless sites, which do no form perfect seed-pairing with a miRNA, can also lead to target repression, often with lower efficacy. Here we report the surprising finding that when seedless sites and seed sites are co-present in the same 3’UTR, seedless sites attenuate strong-seed-site-mediated target suppression, independent of 3′ UTR length. This attenuation effect is detectable in >70% of transcriptomic datasets examined, in which specific miRNAs are experimentally increased or decreased. The attenuation effect is confirmed by 3’UTR reporter assays and mediated through base-pairing between miRNA and seedless sites. Furthermore, this seedless-site-based attenuation effect could affect seed sites of the same miRNA or another miRNA, thus partially explaining the variability in target suppression and miRNA-mediated gene upregulation. Our findings reveal an unexpected principle of miRNA-mediated gene regulation, and could impact the understanding of many miRNA-regulated biological processes.


Author(s):  
Andrea Burton ◽  
Sarah Gravem ◽  
Felipe Barreto

The keystone species, Pisaster ochraceus, suffered mass mortalities along the northeast Pacific Ocean from Sea Star Wasting Syndrome (SSWS) outbreaks in 2013-2016. Causation of SSWS is still debated, leading to concerns as to whether outbreaks will continue to impact this species. Considering the apparent link between ocean temperature and SSWS, the future of this species and intertidal communities remains uncertain. We surveyed populations of sea stars along the Oregon coast in 2016, two years after the epidemic began. Cohabitation of asymptomatic and symptomatic individuals allowed us to ask whether lower susceptibility in asymptomatic individuals differed genetically. We performed restriction site-associated DNA sequencing (2bRAD-seq) to genotype thousands of single nucleotide polymorphism (SNP) loci. By comparing allele frequencies between symptomatic and asymptomatic individuals, we detected three loci that may be under selection. A multivariate analysis showed a clear separation between groups based on disease status in two of the three geographic regions, along with several regions across the genome having small statistical contributions to this separation. A draft annotation of protein-coding regions allowed us to identify 120 predicted genes that are linked to these markers and are putatively associated with lower susceptibility. Our results suggest that some variation in disease severity can be attributed to genetic variation. However, differences in phenotype have a highly polygenic nature with no single or few genomic regions having strong predictive effects. The genes associated with these regions may form the basis for functional studies aiming to understand disease progression in infected individuals.


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