scholarly journals The rapid evolution of alternative splicing in plants

2017 ◽  
Author(s):  
Zhihao Ling ◽  
Thomas Brockmöller ◽  
Ian T. Baldwin ◽  
Shuqing Xu
Keyword(s):  
Alternative Splicing ◽  
Related Species ◽  
Donor Site ◽  
Rapid Evolution ◽  
Acceptor Site ◽  
Mrna Levels ◽  
Evolutionary Patterns ◽  
Closely Related Species ◽  
Nonsense Mediated Decay ◽  
Splicing Regulators

AbstractAlternative pre-mRNA splicing (AS) is prevalent among all plants and is involved in many interactions with environmental stresses. However, the evolutionary patterns and underlying mechanisms of AS in plants remain unclear. By analyzing the transcriptomes of six plant species, we revealed that AS diverged rapidly among closely related species, largely due to the gains and losses of AS events among orthologous genes. Furthermore, AS that generates transcripts containing premature termination codons (PTC), although only representing a small fraction of the total AS, are more conserved than those that generate non-PTC containing transcripts, suggesting that AS coupled with nonsense-mediated decay (NMD) might play an important role in regulating mRNA levels post-transcriptionally. With a machine learning approach we analyzed the key determinants of AS to understand the mechanisms underlying its rapid divergence. Among the studied species, the presence/absence of alternative splicing site (SS) within the junction, the distance between the authentic SS and the nearest alternative SS, the size of exon-exon junctions were the major determinants for both alternative 5’ donor site and 3’acceptor site, suggesting a relatively conserved AS mechanism. Comparative analysis further demonstrated that variations of the identified AS determinants, mostly are located in introns, significantly contributed to the AS turnover among closely related species in both Solanaceae and Brassicaceae taxa. These new mechanistic insights into the evolution of AS in plants highlight the importance of post-transcriptional regulation in mediating plant-environment interactions.One sentence summaryChanges of intron located splicing regulators contributed to the rapid evolution of alternative splicing in plants.

scholarly journals Evolutionary Patterns in the Genus Homo

2021 ◽  
Vol 21 (01) ◽  
Author(s):  
Nisar A. Shar
Keyword(s):  
Related Species ◽  
Homo Sapiens ◽  
Demographic History ◽  
Human Intelligence ◽  
Evolutionary Patterns ◽  
Closely Related Species ◽  
Genus Homo ◽  
Wide Range ◽  
History Of

ABSTRACT The demographic history of Homo sapiens is complex; it involves a wide range of migrations and genetic adaptations. One of the closely related species to Homo sapiens is Neanderthals, which became extinct about 30,000 years ago. The aim of this research is to compare Homo sapiens with Neanderthals and chimpanzees to understand the patterns of inheritance and survival instincts of Homo sapiens. Results show that out of all selected groups of genes in this study, metabolism, and language genes are found to be the most evolving group of genes. This shows that these most evolving genes are contributing to the advancement of Homo sapiens. However, after comparing human intelligence genes with the primates, it is found that exonic regions are contributing more to the evolution of human intelligence hence, making Homo sapiens unique in terms of intelligence.

scholarly journals Selection constrains high rates of satellite DNA mutation in Daphnia pulex

2017 ◽  
Author(s):  
Jullien M. Flynn ◽  
Ian Caldas ◽  
Melania E. Cristescu ◽  
Andrew G. Clark
Keyword(s):  
Satellite Dna ◽  
Related Species ◽  
Rapid Evolution ◽  
Daphnia Pulex ◽  
Selective Constraint ◽  
Mutation Rates ◽  
Stabilizing Selection ◽  
Closely Related Species ◽  
Dna Mutation ◽  
Evolutionary Forces

AbstractA long-standing evolutionary puzzle is that all eukaryotic genomes contain large amounts of tandemly-repeated satellite DNA whose composition varies greatly among even closely related species. To elucidate the evolutionary forces governing satellite dynamics, quantification of the rates and patterns of mutations in satellite DNA copy number and tests of its selective neutrality are necessary. Here we used whole-genome sequences of 28 mutation accumulation (MA) lines of Daphnia pulex in addition to six isolates from a non-MA population originating from the same progenitor to both estimate mutation rates of abundances of satellite sequences and evaluate the selective regime acting upon them. We found that mutation rates of individual satellite sequence “kmers” were both high and highly variable, ranging from additions/deletions of 0.29 – 105 copies per generation (reflecting changes of 0.12 - 0.80 percent per generation). Our results also provide evidence that new kmer sequences are often formed from existing ones. The non-MA population isolates showed a signal of either purifying or stabilizing selection, with 33 % lower variation in kmer abundance on average than the MA lines, although the level of selective constraint was not evenly distributed across all kmers. The changes between many pairs of kmers were correlated, and the pattern of correlations was significantly different between the MA lines and the non-MA population. Our study demonstrates that kmer sequences can experience extremely rapid evolution in abundance, which can lead to high levels of divergence in genome-wide satellite DNA composition between closely related species.

scholarly journals Prognostic Signatures of Alternative Splicing Events in Esophageal Carcinoma Based on TCGA Splice-Seq Data

2021 ◽  
Vol 11 ◽  
Author(s):  
Ping Ye ◽  
Yan Yang ◽  
Liqiang Zhang ◽  
Guixi Zheng
Keyword(s):  
Alternative Splicing ◽  
Esophageal Carcinoma ◽  
Cox Regression ◽  
Donor Site ◽  
Area Under The Curve ◽  
Clinical Information ◽  
Roc Curves ◽  
The Cancer Genome Atlas ◽  
Acceptor Site ◽  
Cox Regression Analysis

An alternative splicing (AS) event is a highly complex process that plays an essential role in post-transcriptional gene expression. Several studies have suggested that abnormal AS events were the primary element in the pathological process of cancer. However, few works are dedicated to the study of AS events in esophageal carcinoma (EC). In the present study, clinical information and RNA-seq data of EC patients were downloaded from The Cancer Genome Atlas (TCGA) database. The percent spliced in (PSI) values of AS events were acquired from the TCGA Splice-seq. A total of 183 EC patients were enrolled in this study, and 2,212 AS events were found significantly associated with the overall survival of these patients by univariate Cox regression analysis. The prognostic signatures based on AS events were built by multivariate Cox analysis. Receiver operating characteristic (ROC) curves displayed that the area under the curve (AUC) of the following prognostic signatures, including exon skip (ES), alternate terminator (AT), alternate acceptor site (AA), alternate promoter (AP), alternate donor site (AD), retained intron (RI), and total events, was greater than 0.8, suggesting that these seven signatures had valuable prognosis prediction capacity. Finally, the risk score of prognostic signatures was indicated as an independent risk factor of survival. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were performed to explore the function of splicing factors (SFs) that were associated with AS events. Also, the interactive network between AS events and SFs identified several hub genes and AS events which need further study. This was a comprehensive study that explored prognosis-related AS events and established valuable prognosis signatures in EC patients. The network of interactions between AS events and SFs might offer novel insights into the fundamental mechanisms of tumorigenesis and progression of EC.

scholarly journals A Comprehensive Curation Shows the Dynamic Evolutionary Patterns of Prokaryotic CRISPRs

2016 ◽  
Vol 2016 ◽  
pp. 1-7 ◽  
Author(s):  
Guoqin Mai ◽  
Ruiquan Ge ◽  
Guoquan Sun ◽  
Qinghan Meng ◽  
Fengfeng Zhou
Keyword(s):  
Related Species ◽  
Evolutionary History ◽  
Genetic Element ◽  
Evolutionary Patterns ◽  
Closely Related Species ◽  
Prokaryotic Genomes ◽  
Active Regulation ◽  
Short Palindromic Repeat ◽  
Comprehensive Comparison ◽  
Cas Gene

Motivation.Clustered regularly interspaced short palindromic repeat (CRISPR) is a genetic element with active regulation roles for foreign invasive genes in the prokaryotic genomes and has been engineered to work with the CRISPR-associated sequence (Cas) gene Cas9 as one of the modern genome editing technologies. Due to inconsistent definitions, the existing CRISPR detection programs seem to have missed some weak CRISPR signals.Results.This study manually curates all the currently annotated CRISPR elements in the prokaryotic genomes and proposes 95 updates to the annotations. A new definition is proposed to cover all the CRISPRs. The comprehensive comparison of CRISPR numbers on the taxonomic levels of both domains and genus shows high variations for closely related species even in the same genus. The detailed investigation of how CRISPRs are evolutionarily manipulated in the 8 completely sequenced species in the genusThermoanaerobacterdemonstrates that transposons act as a frequent tool for splitting long CRISPRs into shorter ones along a long evolutionary history.

Mechanisms That Link Promoter Choice with Downstream Alternative Splicing in the Erythroid Protein 4.1R Gene.

Blood ◽  
2006 ◽  
Vol 108 (11) ◽  
pp. 1562-1562
Author(s):  
Marilyn Parra ◽  
Jeff Tan ◽  
Narla Mohandas ◽  
John G. Conboy
Keyword(s):  
Alternative Splicing ◽  
Splice Site ◽  
Rna Processing ◽  
Regulatory Element ◽  
Donor Site ◽  
Splice Acceptor Site ◽  
Acceptor Site ◽  
Splice Acceptor ◽  
Exon 2 ◽  
Protein 4.1R

Abstract The protein 4.1R gene is a large transcription unit (240kb) that utilizes complex RNA processing pathways to encode distinct protein isoforms, both during erythropoiesis and also in nonerythroid cells. Proper regulation of these pathways is essential for stage-specific synthesis of the 80-kDa isoforms of 4.1R protein during terminal erythroid differentiation. The 5′ region of the gene contains multiple alternative first exons that map far upstream of the coding exons, and we have shown previously that promoter choice is coupled to alternative splicing decisions 100kb downstream in exon 2′/2. Transcripts that initiate at exon 1A predominate in late stages of erythropoiesis and splice only to a weak internal 3′ splice acceptor site in exon 2, skipping translation start site AUG1 and ensuring proper translation initiation at AUG2 in exon 4 for synthesis of the 80-kDa isoforms. In contrast, 4.1 transcripts initiated at exons 1B or 1C exclusively splice to the strong first 3′ splice acceptor site at exon 2′ to include AUG1 and encode a higher molecular weight 135-kDa isoform known to interact with different affinity to major erythroid membrane proteins in earlier stages of erythropoiesis. Our studies show that this linkage between transcription and splicing is (a) cell type independent; (b) conserved in the 4.1R gene from fish to man; and (c) conserved in the paralogous 4.1B gene. Our recent functional studies suggest that a novel re-splicing mechanism, reminiscent of recursive splicing of large introns previously described in the Drosophila ubx gene, may couple promoter choice with downstream splicing in the 4.1R gene. Using minigenes that reproduce the differential splicing patterns in transfected mammalian cells, we have shown that accurate splicing of exon 1A requires a unique downstream regulatory element. This element maps several kilobases downstream of exon 1A and is conserved among mammals. Analysis of wild type and mutated minigenes suggests a two step splicing model in which this element behaves as a temporary “intra-exon” that is present in a splicing intermediate but eliminated from the mature mRNA. According to this model, the regulatory element behaves as an exon in the first step as its consensus 5′ donor site splices to the strong 3′ splice site of exon 2′, removing this splice site pair and joining the intra-exon directly to exon 2′. In the second step, the juxtaposed region of the intra-exon then behaves as an intron, contributing to the activation of the weak internal splice acceptor at exon 2. This second splicing event joins exon 1A to exon 2, thus deleting the intra-exon, the 2′ region (and AUG1) and generating a mature 5′ end capable of encoding 80-kDa 4.1R. Importantly, pre-mRNA constructs that lack the intra-exon, or have a mutated intra-exon 5′ splice donor site, are uncoupled and exhibit inappropriate splicing of exon 1A to the first acceptor site at exon 2′. In support of the generality of this model, we have identified a candidate intra-exon with similar sequence properties in the long 5′ region of the human 4.1B gene, and have demonstrated that this element successfully rescues proper splicing of 4.1R exon 1A in our minigenes. Detailed molecular analysis is under way to identify the specific cis and trans elements required to effect this unusual, long-distance coupling between RNA processing events which have implications for detailed mechanistic understanding of membrane assembly during erythropoiesis.

The Evolutionary Analysis of “Orphans” From the Drosophila Genome Identifies Rapidly Diverging and Incorrectly Annotated Genes

Genetics ◽  
2001 ◽  
Vol 159 (2) ◽  
pp. 589-598 ◽  
Author(s):  
Karl J Schmid ◽  
Charles F Aquadro
Keyword(s):  
Related Species ◽  
Rapid Evolution ◽  
Model Organisms ◽  
Drosophila Genome ◽  
Evolutionary Analysis ◽  
Orphan Genes ◽  
Closely Related Species ◽  
Reading Frame ◽  
Nearly Neutral Mutations ◽  
Neutral Mutations

Abstract In genome projects of eukaryotic model organisms, a large number of novel genes of unknown function and evolutionary history (“orphans”) are being identified. Since many orphans have no known homologs in distant species, it is unclear whether they are restricted to certain taxa or evolve rapidly, either because of a lack of constraints or positive Darwinian selection. Here we use three criteria for the selection of putatively rapidly evolving genes from a single sequence of Drosophila melanogaster. Thirteen candidate genes were chosen from the Adh region on the second chromosome and 1 from the tip of the X chromosome. We succeeded in obtaining sequence from 6 of these in the closely related species D. simulans and D. yakuba. Only 1 of the 6 genes showed a large number of amino acid replacements and in-frame insertions/deletions. A population survey of this gene suggests that its rapid evolution is due to the fixation of many neutral or nearly neutral mutations. Two other genes showed “normal” levels of divergence between species. Four genes had insertions/deletions that destroy the putative reading frame within exons, suggesting that these exons have been incorrectly annotated. The evolutionary analysis of orphan genes in closely related species is useful for the identification of both rapidly evolving and incorrectly annotated genes.

scholarly journals A broad analysis of splicing regulation in yeast using a large library of synthetic introns

PLoS Genetics ◽  
2021 ◽  
Vol 17 (9) ◽  
pp. e1009805
Author(s):  
Dvir Schirman ◽  
Zohar Yakhini ◽  
Yitzhak Pilpel ◽  
Orna Dahan
Keyword(s):  
Gene Expression ◽  
Alternative Splicing ◽  
Splice Site ◽  
Donor Site ◽  
Regulation Of Gene Expression ◽  
Combinatorial Design ◽  
Acceptor Site ◽  
Functional Sites ◽  
Splicing Efficiency ◽  
Splicing Machinery

RNA splicing is a key process in eukaryotic gene expression, in which an intron is spliced out of a pre-mRNA molecule to eventually produce a mature mRNA. Most intron-containing genes are constitutively spliced, hence efficient splicing of an intron is crucial for efficient regulation of gene expression. Here we use a large synthetic oligo library of ~20,000 variants to explore how different intronic sequence features affect splicing efficiency and mRNA expression levels in S. cerevisiae. Introns are defined by three functional sites, the 5’ donor site, the branch site, and the 3’ acceptor site. Using a combinatorial design of synthetic introns, we demonstrate how non-consensus splice site sequences in each of these sites affect splicing efficiency. We then show that S. cerevisiae splicing machinery tends to select alternative 3’ splice sites downstream of the original site, and we suggest that this tendency created a selective pressure, leading to the avoidance of cryptic splice site motifs near introns’ 3’ ends. We further use natural intronic sequences from other yeast species, whose splicing machineries have diverged to various extents, to show how intron architectures in the various species have been adapted to the organism’s splicing machinery. We suggest that the observed tendency for cryptic splicing is a result of a loss of a specific splicing factor, U2AF1. Lastly, we show that synthetic sequences containing two introns give rise to alternative RNA isoforms in S. cerevisiae, demonstrating that merely a synthetic fusion of two introns might be suffice to facilitate alternative splicing in yeast. Our study reveals novel mechanisms by which introns are shaped in evolution to allow cells to regulate their transcriptome. In addition, it provides a valuable resource to study the regulation of constitutive and alternative splicing in a model organism.

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