Lineage-Specific Conserved Noncoding Sequences of Plant Genomes: Their Possible Role in Nucleosome Positioning

Hettiarachchi, Nilmini; Kryukov, Kirill; Sumiyama, Kenta; Saitou, Naruya

doi:10.1093/gbe/evu188

Cited by 16 publications

(13 citation statements)

References 74 publications

(110 reference statements)

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“…In stickleback, loss of a CNS containing a transcriptional enhancer regulating the pleiotropic Pitx1 gene led to major phenotypic change (loss of pelvic spines) ( Chan et al 2010 ). In several studies in animals ( Hiller et al 2012 ; Takahashi and Saitou 2012 ; Babarinde and Saitou 2013 ) and plants ( Hettiarachchi et al 2014 ), CNSs are also proposed to be involved in lineage-specific phenotypes.…”

Section: Introductionmentioning

confidence: 99%

Emergence and Evolution of Hominidae-Specific Coding and Noncoding Genomic Sequences

et al. 2016

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Family Hominidae, which includes humans and great apes, is recognized for unique complex social behavior and intellectual abilities. Despite the increasing genome data, however, the genomic origin of its phenotypic uniqueness has remained elusive. Clade-specific genes and highly conserved noncoding sequences (HCNSs) are among the high-potential evolutionary candidates involved in driving clade-specific characters and phenotypes. On this premise, we analyzed whole genome sequences along with gene orthology data retrieved from major DNA databases to find Hominidae-specific (HS) genes and HCNSs. We discovered that Down syndrome critical region 4 (DSCR4) is the only experimentally verified gene uniquely present in Hominidae. DSCR4 has no structural homology to any known protein and was inferred to have emerged in several steps through LTR/ERV1, LTR/ERVL retrotransposition, and transversion. Using the genomic distance as neutral evolution threshold, we identified 1,658 HS HCNSs. Polymorphism coverage and derived allele frequency analysis of HS HCNSs showed that these HCNSs are under purifying selection, indicating that they may harbor important functions. They are overrepresented in promoters/untranslated regions, in close proximity of genes involved in sensory perception of sound and developmental process, and also showed a significantly lower nucleosome occupancy probability. Interestingly, many ancestral sequences of the HS HCNSs showed very high evolutionary rates. This suggests that new functions emerged through some kind of positive selection, and then purifying selection started to operate to keep these functions.

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Section: Introductionmentioning

confidence: 99%

Emergence and Evolution of Hominidae-Specific Coding and Noncoding Genomic Sequences

et al. 2016

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“…As alternative approach, many studies of evolution of noncoding sequences have used whole genome comparative analysis in order to identify regions with unusually slow or rapid evolutionary rates. Mainly in these studies, the sequences with significantly low nucleotide substitution rate are considered as regions under purifying selection whereas the sequences with dramatically high substitution rate in the noncoding region are considered to be under positive selection ( Bejerano et al 2004 ; Pollard et al 2006 ; Prabhakar et al 2006 ; Hettiarachchi et al 2014 ; Babarinde and Saitou 2016 ).…”

Section: Introductionmentioning

confidence: 99%

Silencing Effect of Hominoid Highly Conserved Noncoding Sequences on Embryonic Brain Development

Saber

Saitou

2017

Genome Biology and Evolution

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Superfamily Hominoidea, which consists of Hominidae (humans and great apes) and Hylobatidae (gibbons), is well-known for sharing human-like characteristics, however, the genomic origins of these shared unique phenotypes have mainly remained elusive. To decipher the underlying genomic basis of Hominoidea-restricted phenotypes, we identified and characterized Hominoidea-restricted highly conserved noncoding sequences (HCNSs) that are a class of potential regulatory elements which may be involved in evolution of lineage-specific phenotypes. We discovered 679 such HCNSs from human, chimpanzee, gorilla, orangutan and gibbon genomes. These HCNSs were demonstrated to be under purifying selection but with lineage-restricted characteristics different from old CNSs. A significant proportion of their ancestral sequences had accelerated rates of nucleotide substitutions, insertions and deletions during the evolution of common ancestor of Hominoidea, suggesting the intervention of positive Darwinian selection for creating those HCNSs. In contrary to enhancer elements and similar to silencer sequences, these Hominoidea-restricted HCNSs are located in close proximity of transcription start sites. Their target genes are enriched in the nervous system, development and transcription, and they tend to be remotely located from the nearest coding gene. Chip-seq signals and gene expression patterns suggest that Hominoidea-restricted HCNSs are likely to be functional regulatory elements by imposing silencing effects on their target genes in a tissue-restricted manner during fetal brain development. These HCNSs, emerged through adaptive evolution and conserved through purifying selection, represent a set of promising targets for future functional studies of the evolution of Hominoidea-restricted phenotypes.

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“…Such CNSs are located in introns, intergenic regions proximal or distal to genes, and the 5′ and 3′ untranslated regions (UTRs) of genes. Comparative genomic studies have identified thousands of CNSs in the genomes of humans and model organisms such as mouse and A. thaliana [ 36 – 41 ]. In plants, CNSs have been hypothesized to affect the transcription levels of neighboring genes [ 33 , 42 ] and several studies have shown that CNSs are enriched for transcription factor binding sites [ 36 , 40 , 43 – 45 ].…”

Section: Introductionmentioning

confidence: 99%

Purifying selection acts on coding and non-coding sequences of paralogous genes in Arabidopsis thaliana

Hoffmann

Palmgren

2016

BMC Genomics

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BackgroundWhole-genome duplications in the ancestors of many diverse species provided the genetic material for evolutionary novelty. Several models explain the retention of paralogous genes. However, how these models are reflected in the evolution of coding and non-coding sequences of paralogous genes is unknown.ResultsHere, we analyzed the coding and non-coding sequences of paralogous genes in Arabidopsis thaliana and compared these sequences with those of orthologous genes in Arabidopsis lyrata. Paralogs with lower expression than their duplicate had more nonsynonymous substitutions, were more likely to fractionate, and exhibited less similar expression patterns with their orthologs in the other species. Also, lower-expressed genes had greater tissue specificity. Orthologous conserved non-coding sequences in the promoters, introns, and 3′ untranslated regions were less abundant at lower-expressed genes compared to their higher-expressed paralogs. A gene ontology (GO) term enrichment analysis showed that paralogs with similar expression levels were enriched in GO terms related to ribosomes, whereas paralogs with different expression levels were enriched in terms associated with stress responses.ConclusionsLoss of conserved non-coding sequences in one gene of a paralogous gene pair correlates with reduced expression levels that are more tissue specific. Together with increased mutation rates in the coding sequences, this suggests that similar forces of purifying selection act on coding and non-coding sequences. We propose that coding and non-coding sequences evolve concurrently following gene duplication.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2803-2) contains supplementary material, which is available to authorized users.

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Lineage-Specific Conserved Noncoding Sequences of Plant Genomes: Their Possible Role in Nucleosome Positioning

Cited by 16 publications

References 74 publications

Emergence and Evolution of Hominidae-Specific Coding and Noncoding Genomic Sequences

Emergence and Evolution of Hominidae-Specific Coding and Noncoding Genomic Sequences

Silencing Effect of Hominoid Highly Conserved Noncoding Sequences on Embryonic Brain Development

Purifying selection acts on coding and non-coding sequences of paralogous genes in Arabidopsis thaliana

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