Gene Conversion Between Direct Noncoding Repeats Promotes Genetic and Phenotypic Diversity at a Regulatory Locus of <i>Zea mays</i> (L.)

Zhang, Feng; Peterson, T.

doi:10.1534/genetics.105.053942

Cited by 6 publications

(20 citation statements)

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“…Therefore, one way to molecularly explain the phenotypic diversity may be in terms of gene regulation. Not just the presence or absence of a gene but also when, how, and where certain genes are expressed are also important in the evolution of phenotypic diversity observed among and within orders ( Zhang and Peterson 2006 ; Takahashi and Saitou 2012 ; Wittkopp and Kalay 2012 ). A genetic theory of morphological evolution states that form evolves largely by mutations in cis - regulatory sequences that alter the expression of functionally conserved proteins ( Carroll 2008 ).…”

Section: Discussionmentioning

confidence: 99%

Heterogeneous Tempo and Mode of Conserved Noncoding Sequence Evolution among Four Mammalian Orders

Babarinde

Saitou

2013

Genome Biology and Evolution

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Conserved noncoding sequences (CNSs) of vertebrates are considered to be closely linked with protein-coding gene regulatory functions. We examined the abundance and genomic distribution of CNSs in four mammalian orders: primates, rodents, carnivores, and cetartiodactyls. We defined the two thresholds for CNS using conservation level of coding genes; using all the three coding positions and using only first and second codon positions. The abundance of CNSs varied among lineages, with primates and rodents having highest and lowest number of CNSs, respectively, whereas carnivores and cetartiodactyls had intermediate values. These CNSs cover 1.3–5.5% of the mammalian genomes and have signatures of selective constraints that are stronger in more ancestral than the recent ones. Evolution of new CNSs as well as retention of ancestral CNSs contribute to the differences in abundance. The genomic distribution of CNSs is dynamic with higher proportions of rodent and primate CNSs located in the introns compared with carnivores and cetartiodactyls. In fact, 19% of orthologous single-copy CNSs between human and dog are located in different genomic regions. If CNSs can be considered as candidates of gene expression regulatory sequences, heterogeneity of CNSs among the four mammalian orders may have played an important role in creating the order-specific phenotypes. Fewer CNSs in rodents suggest that rodent diversity is related to lower regulatory conservation. With CNSs shown to cluster around genes involved in nervous systems and the higher number of primate CNSs, our result suggests that CNSs may be involved in the higher complexity of the primate nervous system.

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Section: Discussionmentioning

confidence: 99%

Heterogeneous Tempo and Mode of Conserved Noncoding Sequence Evolution among Four Mammalian Orders

Babarinde

Saitou

2013

Genome Biology and Evolution

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“…P1-rr4B2 contains two large repeats flanking the coding sequence, which are about 5.2 kb in size [6,12,17]. Interestingly, the sequence upstream of the 5' large repeat contains fragments of Opie and Eninu retroelements inserted in the same position as in p1-ww[4Co63] and p1/p2[B73] as described above (Figures 2 and 3).…”

Section: Resultsmentioning

confidence: 99%

“…Gene conversion events then could have transferred the altered region that originated at the 3' large repeat to the 5' large repeat where the distal enhancer sequence functions [17]. Alternatively, P1-rw1077 arose from P1-wr repeats upstream of the retrotransposon cluster.…”

Section: Discussionmentioning

confidence: 99%

“…Subsequently, gene conversion events could have placed part of the modified enhancer sequence of the downstream copy to the upstream large repeat [17]. Alternatively, if this P1-rr module arose on the P1-wr[B73] side of the retroelement cluster as we also discussed for P1-rw1077 , then a recombination event between p1-ww[4Co63] and the P1-rr ancestor could have transferred the P1-rr end to a position downstream of the retrotransposon cluster (Additional file 6: Supplemental Figure S4B).…”

Section: Discussionmentioning

confidence: 99%

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Divergence of gene regulation through chromosomal rearrangements

Goettel

Messing

2010

BMC Genomics

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BackgroundThe molecular mechanisms that modify genome structures to give birth and death to alleles are still not well understood. To investigate the causative chromosomal rearrangements, we took advantage of the allelic diversity of the duplicated p1 and p2 genes in maize. Both genes encode a transcription factor involved in maysin synthesis, which confers resistance to corn earworm. However, p1 also controls accumulation of reddish pigments in floral tissues and has therefore acquired a new function after gene duplication. p1 alleles vary in their tissue-specific expression, which is indicated in their allele designation: the first suffix refers to red or white pericarp pigmentation and the second to red or white glume pigmentation.ResultsComparing chromosomal regions comprising p1-ww[4Co63], P1-rw1077 and P1-rr4B2 alleles with that of the reference genome, P1-wr[B73], enabled us to reconstruct additive events of transposition, chromosome breaks and repairs, and recombination that resulted in phenotypic variation and chimeric regulatory signals. The p1-ww[4Co63] null allele is probably derived from P1-wr[B73] by unequal crossover between large flanking sequences. A transposon insertion in a P1-wr-like allele and NHEJ (non-homologous end-joining) could have resulted in the formation of the P1-rw1077 allele. A second NHEJ event, followed by unequal crossover, probably led to the duplication of an enhancer region, creating the P1-rr4B2 allele. Moreover, a rather dynamic picture emerged in the use of polyadenylation signals by different p1 alleles. Interestingly, p1 alleles can be placed on both sides of a large retrotransposon cluster through recombination, while functional p2 alleles have only been found proximal to the cluster.ConclusionsAllelic diversity of the p locus exemplifies how gene duplications promote phenotypic variability through composite regulatory signals. Transposition events increase the level of genomic complexity based not only on insertions but also on excisions that cause DNA double-strand breaks and trigger illegitimate recombination.

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“…In one case, the transposition of Ac into a distal enhancer of P1-rr resulted in the complete loss of cob pigmentation [17] . Accordingly, the lack of cob pigmentation in the endogenous P1-rw allele has been attributed to the absence of this enhancer [18] .…”

Section: Introductionmentioning

confidence: 99%

Gene Structure Induced Epigenetic Modifications of pericarp color1 Alleles of Maize Result in Tissue-Specific Mosaicism

et al. 2009

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BackgroundThe pericarp color1 (p1) gene encodes for a myb-homologous protein that regulates the biosynthesis of brick-red flavonoid pigments called phlobahpenes. The pattern of pigmentation on the pericarp and cob glumes depends upon the allelic constitution at the p1 locus. p1 alleles have unique gene structure and copy number which have been proposed to influence the epigenetic regulation of tissue-specific gene expression. For example, the presence of tandem-repeats has been correlated with the suppression of pericarp pigmentation though a mechanism associated with increased DNA methylation.Methodology/Principal FindingsHerein, we extensively characterize a p1 allele called P1-mosaic (P1-mm) that has mosaic pericarp and light pink or colorless cob glumes pigmentation. Relative to the P1-wr (white pericarp and red cob glumes), we show that the tandem repeats of P1-mm have a modified gene structure containing a reduced number of repeats. The P1-mm has reduced DNA methylation at a distal enhancer and elevated DNA methylation downstream of the transcription start site.Conclusions/SignificanceMosaic gene expression occurs in many eukaryotes. Herein we use maize p1 gene as model system to provide further insight about the mechanisms that govern expression mosaicism. We suggest that the gene structure of P1-mm is modified in some of its tandem gene repeats. It is known that repeated genes are susceptible to chromatin-mediated regulation of gene expression. We discuss how the modification to the tandem repeats of P1-mm may have disrupted the epigenetic mechanisms that stably confer tissue-specific expression.

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Gene Conversion Between Direct Noncoding Repeats Promotes Genetic and Phenotypic Diversity at a Regulatory Locus of Zea mays (L.)

Cited by 6 publications

References 46 publications

Heterogeneous Tempo and Mode of Conserved Noncoding Sequence Evolution among Four Mammalian Orders

Heterogeneous Tempo and Mode of Conserved Noncoding Sequence Evolution among Four Mammalian Orders

Divergence of gene regulation through chromosomal rearrangements

Gene Structure Induced Epigenetic Modifications of pericarp color1 Alleles of Maize Result in Tissue-Specific Mosaicism

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