Chapter 3 Evolution of Cis‐Regulatory Sequences in Drosophila

Simpson, Patricia; Ayyar, Savita

doi:10.1016/s0065-2660(07)00003-x

Cited by 11 publications

(9 citation statements)

References 141 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Microsatellite repeats, especially (CT)n motifs, exist in abundance in the 5′-UTRs of several eukaryotic genes (Bhattacharyya et al, 2004;Mohammadparast et al, 2014;Zhao et al, 2014). The microsatellites are present in the vicinity of TSSs, indicating that they are likely involved in regulating target gene transcription (Castillo-Davis, 2005;Simpson and Ayyar, 2008). Our first goal was to investigate the highly polymorphic CT repeat located in the core promoter of the LvIRF-5'-UTR.…”

Section: Discussionmentioning

confidence: 99%

A Polymorphic (CT)n-SSR Influences the Activity of the Litopenaeus vannamei IRF Gene Implicated in Viral Resistance

et al. 2019

View full text Add to dashboard Cite

Simple sequence repeats (SSRs) of short nucleotide motifs occur very frequently in the 5′ untranslated coding region (5′-UTR) of genes and have been implicated in the regulation of gene expression. In this study, we identified an SSR with a variable number of CT repeats in the 5′-UTR of the Litopenaeus vannamei IRF (LvIRF) gene that has been shown to mediate antiviral responses by inducing the expression of Vago, a functional homolog of mammalian IFN. We then explored the effects of varying the number of (CT)n repeats on the expression of LvIRF using both dual-luciferase reporter assays and Western blots. Our results demonstrate that the length of the (CT)n-SSR in this gene can influence the expressional level of LvIRF, in that a shorter (CT)n repeat had a stronger ability to induce the expression of LvIRF. Moreover, we found that the (CT)n repeat in LvIRF was associated with viral resistance in shrimp. Individual shrimps with shorter (CT)n repeats in the 5′-UTR of LvIRF exhibited high tolerance to white spot syndrome virus (WSSV), and this trait was inherited in offspring. Taken together, these results indicated that this (CT)n-SSR could be used as a molecular marker for shrimp breeding for WSSV resistance.

show abstract

Section: Discussionmentioning

confidence: 99%

A Polymorphic (CT)n-SSR Influences the Activity of the Litopenaeus vannamei IRF Gene Implicated in Viral Resistance

et al. 2019

View full text Add to dashboard Cite

show abstract

“…Enhancers that pattern the early Drosophila embryo have been one of the best models for studying the evolution of cis-regulatory sequences because they have well-defined functions under specific conditions (Simpson and Ayyar 2008). However, there is some uncertainty as to whether the results from these early-acting developmental enhancers can be generalized to other cis-regulatory sequences and other species.…”

Section: Discussionmentioning

confidence: 99%

Is Transcription Factor Binding Site Turnover a Sufficient Explanation for Cis-Regulatory Sequence Divergence?

Venkataram

Fay

2010

Genome Biology and Evolution

View full text Add to dashboard Cite

The molecular evolution of cis-regulatory sequences is not well understood. Comparisons of closely related species show that cis-regulatory sequences contain a large number of sites constrained by purifying selection. In contrast, there are a number of examples from distantly related species where cis-regulatory sequences retain little to no sequence similarity but drive similar patterns of gene expression. Binding site turnover, whereby the gain of a redundant binding site enables loss of a previously functional site, is one model by which cis-regulatory sequences can diverge without a concurrent change in function. To determine whether cis-regulatory sequence divergence is consistent with binding site turnover, we examined binding site evolution within orthologous intergenic sequences from 14 yeast species defined by their syntenic relationships with adjacent coding sequences. Both local and global alignments show that nearly all distantly related orthologous cis-regulatory sequences have no significant level of sequence similarity but are enriched for experimentally identified binding sites. Yet, a significant proportion of experimentally identified binding sites that are conserved in closely related species are absent in distantly related species and so cannot be explained by binding site turnover. Depletion of binding sites depends on the transcription factor but is detectable for a quarter of all transcription factors examined. Our results imply that binding site turnover is not a sufficient explanation for cis-regulatory sequence evolution.

show abstract

“…This paper considers functional diversity, but this will be only one of several factors associated with animal complexity. Amongst others, an increasing diversity in cis-acting regulatory elements (CAREs) across a phylogeny will play a role 4 5 28 and there may also be a contribution to complexity from changes to the complement of regulatory non-coding RNAs, including the miRNAs 29 30 and lncRNAs that have been shown to modulate gene expression 31 .…”

Section: Discussionmentioning

confidence: 99%

Variation in protein coding genes identifies information flow as a contributor to animal complexity

Dean

Sharpe

2019

Preprint

View full text Add to dashboard Cite

Across the metazoans there is a trend towards greater organismal complexity. How complexity is generated, however, is uncertain. Since C.elegans and humans have approximately the same number of genes, the explanation will depend on how genes are used, rather than their absolute number. Functional diversity is a measure that quantifies the isoforms, domains and paralogues of a gene. In this paper we determine functional diversity for each protein-coding gene in the human genome and its orthologues across eight commonly used model organisms. From this we derive the Compx list of genes that correlate positively with their increase in cell-type number. We then select genes common to the Compx list and the ExAC list, whose genes show minimal variation across many human genomes, and identify genes with common functions, notably in chromatin structure, RNA splicing, vesicular transport and ubiquitin-mediated protein degradation. Together these functions reveal that information flow within the cell relates to cell-type number, used as a measure of organismal complexity.

show abstract

Chapter 3 Evolution of Cis‐Regulatory Sequences in Drosophila

Cited by 11 publications

References 141 publications

A Polymorphic (CT)n-SSR Influences the Activity of the Litopenaeus vannamei IRF Gene Implicated in Viral Resistance

A Polymorphic (CT)n-SSR Influences the Activity of the Litopenaeus vannamei IRF Gene Implicated in Viral Resistance

Is Transcription Factor Binding Site Turnover a Sufficient Explanation for Cis-Regulatory Sequence Divergence?

Variation in protein coding genes identifies information flow as a contributor to animal complexity

Contact Info

Product

Resources

About