scholarly journals The importance of alternative splicing in adaptive evolution

2021 ◽  
Author(s):  
Pooja Singh ◽  
Ehsan Pashay Ahi
Keyword(s):  
Gene Expression ◽  
Alternative Splicing ◽  
Adaptive Evolution ◽  
Adaptive Divergence ◽  
Mrna Isoforms ◽  
Evolutionary Transitions ◽  
Splice Variation ◽  
Gene Regulatory ◽  
Splice Forms

Although alternative splicing is a ubiquitous gene regulatory mechanism in plants and animals, its contribution to evolutionary transitions is understudied. Splicing enables different mRNA isoforms to be generated from the same gene, expanding transcriptomic and proteomic diversity. While the role of gene expression in adaptive evolution is widely accepted, biologists still debate the functional impact of alternative isoforms on phenotype. In light of recent empirical research linking splice variation to ecological adaptations, we propose that alternative splicing is an important substrate for adaptive evolution and speciation, particularly at short timescales. We synthesise what is known about the role of splicing in adaptive evolution. We discuss the contribution of standing splice variation to phenotypic plasticity and how hybridisation can produce novel splice forms. Going forwards, we propose that splicing be included as a standard analysis alongside gene expression analysis so we can better understand of how splicing contributes to adaptive divergence at the micro- and macroevolutionary levels.

scholarly journals Gene regulatory evolution in cold-adapted fly populations neutralizes plasticity and may undermine genetic canalization

2022 ◽  
Author(s):  
Yuheng Huang ◽  
Justin Lack ◽  
Grant Hoppel ◽  
John E Pool
Keyword(s):  
Gene Expression ◽  
Alternative Splicing ◽  
Adaptive Evolution ◽  
Empirical Studies ◽  
Natural Populations ◽  
Plastic Response ◽  
Cold Adapted ◽  
Thermal Environments ◽  
Gene Regulatory ◽  
Transcriptomic Level

The relationships between adaptive evolution, phenotypic plasticity, and canalization remain incompletely understood. Theoretical and empirical studies have made conflicting arguments on whether adaptive evolution may enhance or oppose the plastic response. Gene regulatory traits offer excellent potential to study the relationship between plasticity and adaptation, and they can now be studied at the transcriptomic level. Here we take advantage of three closely-related pairs of natural populations of Drosophila melanogaster from contrasting thermal environments that reflect three separate instances of cold tolerance evolution. We measure the transcriptome-wide plasticity in gene expression levels and alternative splicing (intron usage) between warm and cold laboratory environments. We find that suspected adaptive changes in both gene expression and alternative splicing tend to neutralize the ancestral plastic response. Further, we investigate the hypothesis that adaptive evolution can lead to decanalization of selected gene regulatory traits. We find strong evidence that suspected adaptive gene expression (but not splicing) changes in cold-adapted populations are more vulnerable to the genetic perturbation of inbreeding than putatively neutral changes. We find some evidence that these patterns may reflect a loss of genetic canalization accompanying adaptation, although other processes including hitchhiking recessive deleterious variants may contribute as well. Our findings augment our understanding of genetic and environmental effects on gene regulation in the context of adaptive evolution.

scholarly journals What else is in an evolved name? Exploring evolvable specificity with SignalGP

2018 ◽  
Author(s):  
Alexander Lalejini ◽  
Charles Ofria
Keyword(s):  
Adaptive Evolution ◽  
Gene Regulatory Networks ◽  
Regulatory Networks ◽  
De Novo ◽  
Direct Access ◽  
Evolutionary Transitions ◽  
Fine Grained ◽  
Flexible Mechanism ◽  
Gene Regulatory ◽  
Program Modules

Tags are evolvable labels that provide genetic programs a flexible mechanism for specification. Tags are used to label and refer to programmatic elements, such as functions or jump targets. However, tags differ from traditional, more rigid methods for handling labeling because they allow for inexact references; that is, a referring tag need not exactly match its referent. Here, we explore how adjusting the threshold for how what qualifies as a match affects adaptive evolution. Further, we propose broadened applications of tags in the context of a genetic programming (GP) technique called SignalGP. SignalGP gives evolution direct access to the event-driven paradigm. Program modules in SignalGP are tagged and can be triggered by signals (with matching tags) from the environment, from other agents, or due to internal regulation. Specifically, we propose to extend this tag based system to: (1) provide more fine-grained control over module execution and regulation (e.g., promotion and repression) akin to natural gene regulatory networks, (2) employ a mosaic of GP representations within a single program, and (3) facilitate major evolutionary transitions in individuality (i.e., allow hierarchical program organization to evolve de novo).

scholarly journals CELF RNA binding proteins promote axon regeneration in C. elegans and mammals through alternative splicing of Syntaxins

eLife ◽  
2016 ◽  
Vol 5 ◽  
Author(s):  
Lizhen Chen ◽  
Zhijie Liu ◽  
Bing Zhou ◽  
Chaoliang Wei ◽  
Yu Zhou ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcriptional Regulation ◽  
Alternative Splicing ◽  
Binding Proteins ◽  
Rna Binding ◽  
Axon Regeneration ◽  
Rna Binding Proteins ◽  
Mrna Isoforms ◽  
C Elegans ◽  
Mrna Targets

Axon injury triggers dramatic changes in gene expression. While transcriptional regulation of injury-induced gene expression is widely studied, less is known about the roles of RNA binding proteins (RBPs) in post-transcriptional regulation during axon regeneration. In C. elegans the CELF (CUGBP and Etr-3 Like Factor) family RBP UNC-75 is required for axon regeneration. Using crosslinking immunoprecipitation coupled with deep sequencing (CLIP-seq) we identify a set of genes involved in synaptic transmission as mRNA targets of UNC-75. In particular, we show that UNC-75 regulates alternative splicing of two mRNA isoforms of the SNARE Syntaxin/unc-64. In C. elegans mutants lacking unc-75 or its targets, regenerating axons form growth cones, yet are deficient in extension. Extending these findings to mammalian axon regeneration, we show that mouse Celf2 expression is upregulated after peripheral nerve injury and that Celf2 mutant mice are defective in axon regeneration. Further, mRNAs for several Syntaxins show CELF2 dependent regulation. Our data delineate a post-transcriptional regulatory pathway with a conserved role in regenerative axon extension.

scholarly journals Solitary ecology as a phenomenon extending beyond insular systems: exaptive evolution in Anolis lizards

2019 ◽  
Vol 15 (5) ◽  
pp. 20190056 ◽  
Author(s):  
Julián A. Velasco ◽  
Steven Poe ◽  
Constantino González-Salazar ◽  
Oscar Flores-Villela
Keyword(s):  
Body Size ◽  
Adaptive Evolution ◽  
Environmental Filtering ◽  
Phenotypic Evolution ◽  
Phenotypic Differentiation ◽  
Evolutionary Transitions ◽  
Ecological Release ◽  
Selective Pressures ◽  
Island Species

The mechanisms driving phenotypic evolution have been of interest to biologists since Darwin. Ecological release—wherein adaptive evolution occurs following relaxation of constraining selective pressures—and environmental filtering—wherein exaptive traits allow colonization of a new area—have been studied in several insular cases. Anolis lizards, which may exist in solitude or sympatry with multiple congeners, are an excellent system for evaluating whether ecological release and environmental filtering are associated with phenotypic shifts across phylogenetic and geographical scales. Insular solitary Anolis exhibit phenotypic differentiation in body size and sexual size dimorphism—SSD—through exaptive and adaptive evolution, respectively. But, the generality of these effects has not yet been addressed. Here, we analyse the evolution of body size and SSD relative to sympatry in mainland Anolis . We found that mainland species co-occurring with few congeners exhibit uniform body size and greater SSD relative to other random mainland assemblages, consistent with the insular solitary pattern. The locations of evolutionary shifts for both traits do not coincide with evolutionary transitions to decreased levels of sympatry. These results are consistent with exaptive environmental filtering but not adaptive ecological release. Future studies should be conducted at local scales to evaluate the role of these factors in the evolution of solitary existence in mainland and island species.

scholarly journals Alternative Splicing of the Drosophila Dscam Pre-mRNA Is Both Temporally and Spatially Regulated

Genetics ◽  
2001 ◽  
Vol 159 (2) ◽  
pp. 599-608
Author(s):  
Alicia M Celotto ◽  
Brenton R Graveley
Keyword(s):  
Alternative Splicing ◽  
Axon Guidance ◽  
Neural Development ◽  
Cell Adhesion Molecule ◽  
Developmental Regulation ◽  
Mrna Isoforms ◽  
Developmentally Regulated ◽  
Early Embryos ◽  
Exon 4

Abstract The Drosophila melanogaster Down syndrome cell adhesion molecule (Dscam) gene encodes an axon guidance receptor that can express 38,016 different mRNAs by virtue of alternative splicing. The Dscam gene contains 95 alternative exons that are organized into four clusters of 12, 48, 33, and 2 exons each. Although numerous Dscam mRNA isoforms can be synthesized, it remains to be determined whether different Dscam isoforms are synthesized at different times in development or in different tissues. We have investigated the alternative splicing of the Dscam exon 4 cluster, which contains 12 mutually exclusive alternative exons, and found that Dscam exon 4 alternative splicing is developmentally regulated. The most highly regulated exon, 4.2, is infrequently used in early embryos but is the predominant exon 4 variant used in adults. Moreover, the developmental regulation of exon 4.2 alternative splicing is conserved in D. yakuba. In addition, different adult tissues express distinct collections of Dscam mRNA isoforms. Given the role of Dscam in neural development, these results suggest that the regulation of alternative splicing plays an important role in determining the specificity of neuronal wiring. In addition, this work provides a framework to determine the mechanisms by which complex alternative splicing events are regulated.

scholarly journals Evolution of Gene Expression and Splicing in Parallel Cold-Adapted Fly Populations

2019 ◽  
Author(s):  
Yuheng Huang ◽  
Justin B. Lack ◽  
Grant T. Hoppel ◽  
John E. Pool
Keyword(s):  
Gene Expression ◽  
Adaptive Evolution ◽  
Parallel Evolution ◽  
Population Variation ◽  
Regulatory Evolution ◽  
Cold Adapted ◽  
Mitochondrial Functions ◽  
Expression Evolution ◽  
Gene Regulatory ◽  
Trans Regulation

AbstractChanges in gene regulation at multiple levels may comprise an important share of the molecular changes underlying adaptive evolution in nature. However, few studies have assayed within- and between-population variation in gene regulatory traits at a transcriptomic scale, and therefore inferences about the characteristics of adaptive regulatory changes have been elusive. Here, we assess quantitative trait differentiation in gene expression levels and alternative splicing (intron usage) between three closely-related pairs of natural populations of Drosophila melanogaster from contrasting thermal environments that reflect three separate instances of cold tolerance evolution. The cold-adapted populations were known to show population genetic evidence for parallel evolution at the SNP level, and here we find significant although somewhat limited evidence for parallel expression evolution between them, and less evidence for parallel splicing evolution. We find that genes with mitochondrial functions are particularly enriched among candidates for adaptive expression evolution. We also develop a method to estimate cis-versus trans-encoded contributions to expression or splicing differences that does not rely on the presence of fixed differences between parental strains. Applying this method, we infer important roles of both cis-and trans-regulation among our putatively adaptive expression and splicing differences. The apparent contributions of cis-versus trans-regulation to adaptive evolution vary substantially among population pairs, with an Ethiopian pair showing pervasive trans-effects, suggesting that basic characteristics of regulatory evolution may depend on biological context. These findings expand our knowledge of adaptive gene regulatory evolution and our ability to make inferences about this important and widespread process.

scholarly journals Deleterious mutation accumulation and the long-term fate of chromosomal inversions

PLoS Genetics ◽  
2021 ◽  
Vol 17 (3) ◽  
pp. e1009411
Author(s):  
Emma L. Berdan ◽  
Alexandre Blanckaert ◽  
Roger K. Butlin ◽  
Claudia Bank
Keyword(s):  
Adaptive Evolution ◽  
Simulation Study ◽  
Feedback Loop ◽  
Deleterious Mutation ◽  
Adaptive Divergence ◽  
Deleterious Mutations ◽  
Dynamic Features ◽  
Chromosomal Inversions

Chromosomal inversions contribute widely to adaptation and speciation, yet they present a unique evolutionary puzzle as both their allelic content and frequency evolve in a feedback loop. In this simulation study, we quantified the role of the allelic content in determining the long-term fate of the inversion. Recessive deleterious mutations accumulated on both arrangements with most of them being private to a given arrangement. This led to increasing overdominance, allowing for the maintenance of the inversion polymorphism and generating strong non-adaptive divergence between arrangements. The accumulation of mutations was mitigated by gene conversion but nevertheless led to the fitness decline of at least one homokaryotype under all considered conditions. Surprisingly, this fitness degradation could be permanently halted by the branching of an arrangement into multiple highly divergent haplotypes. Our results highlight the dynamic features of inversions by showing how the non-adaptive evolution of allelic content can play a major role in the fate of the inversion.

scholarly journals Transcriptome Analysis of Alternative Splicing Events Induced by Arbuscular Mycorrhizal Fungi (Rhizophagus irregularis) in Pea (Pisum sativum L.) Roots

Plants ◽  
2020 ◽  
Vol 9 (12) ◽  
pp. 1700
Author(s):  
Evgeny A. Zorin ◽  
Alexey M. Afonin ◽  
Olga A. Kulaeva ◽  
Emma S. Gribchenko ◽  
Oksana Y. Shtark ◽  
...  
Keyword(s):  
Gene Expression ◽  
Alternative Splicing ◽  
Pisum Sativum ◽  
Mycorrhizal Fungi ◽  
Intron Retention ◽  
Protein A ◽  
Fine Tuning ◽  
Mrna Isoforms ◽  
Pisum Sativum L ◽  
Mycorrhizal Roots

Alternative splicing (AS), a process that enables formation of different mRNA isoforms due to alternative ways of pre-mRNA processing, is one of the mechanisms for fine-tuning gene expression. Currently, the role of AS in symbioses formed by plants with soil microorganisms is not fully understood. In this work, a comprehensive analysis of the transcriptome of garden pea (Pisum sativum L.) roots in symbiosis with arbuscular mycorrhiza was performed using RNAseq and following bioinformatic analysis. AS profiles of mycorrhizal and control roots were highly similar, intron retention accounting for a large proportion of the observed AS types (67%). Using three different tools (SUPPA2, DRIMSeq and IsoformSwitchAnalyzeR), eight genes with AS events specific for mycorrhizal roots of pea were identified, among which four were annotated as encoding an apoptosis inhibitor protein, a serine/threonine-protein kinase, a dehydrodolichyl diphosphate synthase, and a pre-mRNA-splicing factor ATP-dependent RNA helicase DEAH1. In pea mycorrhizal roots, the isoforms of these four genes with preliminary stop codons leading to a truncated ORFs were up-regulated. Interestingly, two of these four genes demonstrating mycorrhiza-specific AS are related to the process of splicing, thus forming parts of the feedback loops involved in fine-tuning of gene expression during mycorrhization.

scholarly journals Perspective in Alternative Splicing Coupled to Nonsense-Mediated mRNA Decay

2020 ◽  
Vol 21 (24) ◽  
pp. 9424
Author(s):  
Juan F. García-Moreno ◽  
Luísa Romão
Keyword(s):  
Gene Expression ◽  
Alternative Splicing ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Translation Termination ◽  
Mrna Isoforms ◽  
Isoform Diversity ◽  
Nonsense Mediated Mrna Decay ◽  
Protein Isoform ◽  
Nonsense Mediated Rna Decay

Alternative splicing (AS) of precursor mRNA (pre-mRNA) is a cellular post-transcriptional process that generates protein isoform diversity. Nonsense-mediated RNA decay (NMD) is an mRNA surveillance pathway that recognizes and selectively degrades transcripts containing premature translation-termination codons (PTCs), thereby preventing the production of truncated proteins. Nevertheless, NMD also fine-tunes the gene expression of physiological mRNAs encoding full-length proteins. Interestingly, around one third of all AS events results in PTC-containing transcripts that undergo NMD. Numerous studies have reported a coordinated action between AS and NMD, in order to regulate the expression of several genes, especially those coding for RNA-binding proteins (RBPs). This coupling of AS to NMD (AS-NMD) is considered a gene expression tool that controls the ratio of productive to unproductive mRNA isoforms, ultimately degrading PTC-containing non-functional mRNAs. In this review, we focus on the mechanisms underlying AS-NMD, and how this regulatory process is able to control the homeostatic expression of numerous RBPs, including splicing factors, through auto- and cross-regulatory feedback loops. Furthermore, we discuss the importance of AS-NMD in the regulation of biological processes, such as cell differentiation. Finally, we analyze interesting recent data on the relevance of AS-NMD to human health, covering its potential roles in cancer and other disorders.

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