Relationship between 5′ UTR length and gene expression pattern in chicken

Rao, You Sheng; Wang, Zhang F; Chai, Xue Wen; Nie, Qing; Zhang, Xi Q

doi:10.1007/s10709-013-9730-9

Cited by 16 publications

(17 citation statements)

References 37 publications

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“…S6 and S7), which show that both 3′-and 5′-UTR lengths fall off rapidly with K A at small values of K A but level off at very high values. There has been a debate concerning the extent to which UTR sequences and the lengths of UTR are under the control of selection (37)(38)(39)(40)(41). The patterns we have just described, and the fact that our results and previous Drosophila studies (14,21,42) have revealed both positive and negative selection on UTR sequences, argue against nonadaptive hypotheses for their evolution, such as that of refs.…”

Section: Discussionsupporting

confidence: 41%

Estimating the parameters of background selection and selective sweeps in Drosophila in the presence of gene conversion

Campos

Zhao

Charlesworth

2017

Proc. Natl. Acad. Sci. U.S.A.

118

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We used whole-genome resequencing data from a population of Drosophila melanogaster to investigate the causes of the negative correlation between the within-population synonymous nucleotide site diversity (π S ) of a gene and its degree of divergence from related species at nonsynonymous nucleotide sites (K A ). By using the estimated distributions of mutational effects on fitness at nonsynonymous and UTR sites, we predicted the effects of background selection at sites within a gene on π S and found that these could account for only part of the observed correlation between π S and K A . We developed a model of the effects of selective sweeps that included gene conversion as well as crossing over. We used this model to estimate the average strength of selection on positively selected mutations in coding sequences and in UTRs, as well as the proportions of new mutations that are selectively advantageous. Genes with high levels of selective constraint on nonsynonymous sites were found to have lower strengths of positive selection and lower proportions of advantageous mutations than genes with low levels of constraint. Overall, background selection and selective sweeps within a typical gene reduce its synonymous diversity to ∼75% of its value in the absence of selection, with larger reductions for genes with high K A . Gene conversion has a major effect on the estimates of the parameters of positive selection, such that the estimated strength of selection on favorable mutations is greatly reduced if it is ignored. background selection | selective sweeps | sequence diversity | gene conversion | Drosophila melanogaster

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Section: Discussionsupporting

confidence: 41%

Estimating the parameters of background selection and selective sweeps in Drosophila in the presence of gene conversion

Campos

Zhao

Charlesworth

2017

Proc. Natl. Acad. Sci. U.S.A.

118

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“…Also changing amino acid might not have been exposed to the outer surface, which could have damaging effect on the protein 53 . The UTR regions on either side of the gene play an important role in expression, modulation and transport of mRNA from the nucleus along with efficient translation of mRNA 54,55 . Nine variants were detected in the UTR genes involved in fatty acid metabolism (see Supplementary Information; Table S5 online), like fatty acid binding proteins (FABP), acyl-CoA synthetases (ACSL), ATP-binding cassette, sub-family G (ABCG) 56,57 .…”

Section: Discussionmentioning

confidence: 99%

Identification of Single Nucleotide Polymorphism from Indian <i>Bubalus bubalis</i> through Targeted Sequence Capture

Patel¹,

Subramanian²,

Padh³

et al. 2017

Current Science

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Bubalus bubalis (water buffalo) is an agro-economically important livestock species due to its multipurpose use in India and other Asian countries. The aim of this study was to identify single nucleotide polymorphisms (SNPs) from buffalo genome. Genomic DNA was isolated from 24 blood samples of three Indian buffalo breeds and subjected to targeted pyrosequencing, followed by variant calling and annotation. Target probes for enrichment were designed from exome and 5 and 3 untranslated regions of cattle genome. By targeted pyro-sequencing and variant calling from 3.92 Gb data, 923,964 high-quality SNPs were identified. Many SNPs were identified in regulatory regions, leading to conformational changes in factor-binding sites, which play a role in gene expression as in the case of LPL gene from low-milkproducing samples. Gene ontology (GO) enrichment and clustering, resulted in the enrichment of GO terms involved in milk production and transport, and fertility-related categories. Around 75% of SNPs were located on cattle quantitative trait loci, supporting trait-wise sample collection approach. Further, PCA analysis from the identified SNPs also supported sample selection strategy based on contrasting trait performance.

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“…However, generalized stimulation of cap-dependent translational activity by GNRH does not explain gene-specific regulation. Although evidence of differential utilization of mRNA based on 5’UTR structure has been presented (Ding et al, 2012; Rao et al, 2013) and this may contribute to sensitivity to cap-dependent initiation, targeting of specific mRNA's may require additional regulatory schemes that affect other aspects of the length and structure of the 5’UTR and mRNA exposure to the translational machinery (Wegrzyn et al, 2008). …”

Section: Control Of Mrna Translationmentioning

confidence: 99%

Translational control of gene expression in the gonadotrope

Kim

Minh‐Ha

Lawson

2014

Molecular and Cellular Endocrinology

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The study of gene expression in gonadotropes has largely focused on the variety of mechanisms regulating transcription of the gonadotropin genes and ancillary factors that contribute to the overall phenotype and function of these cells in reproduction. However, there are aspects of the response to GNRH signaling that are not readily explained by changes at the level of transcription. As our understanding of regulation at the level of mRNA translation has increased, it has become evident that GNRH receptor signaling engages multiple aspects of translational regulation. This includes activation of cap-dependent translation initiation, translational pausing caused by the unfolded protein response and RNA binding protein interaction. Gonadotropin mRNAs and the mRNAs of other factors that control the transcriptional and signaling responses to GNRH have been identified as targets of regulation at the level of translation. In this review we examine the impact of translational control of the expression of gonadotropin genes and other genes relevant to GNRH-mediated control of gonadotrope function.

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Relationship between 5′ UTR length and gene expression pattern in chicken

Cited by 16 publications

References 37 publications

Estimating the parameters of background selection and selective sweeps in Drosophila in the presence of gene conversion

Estimating the parameters of background selection and selective sweeps in Drosophila in the presence of gene conversion

Identification of Single Nucleotide Polymorphism from Indian <i>Bubalus bubalis</i> through Targeted Sequence Capture

Translational control of gene expression in the gonadotrope

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