Dataset Information

Genetic and epigenetic changes in a genomic region containing MIR172 in Arabidopsis allopolyploids and their progenitors.

ABSTRACT: Combination of divergent genomes in allopolyploids creates genome-wide gene expression changes including many miRNA targets in Arabidopsis allotetraploids relative to the parents Arabidopsis thaliana and Arabidopsis arenosa. Here we report expression and epigenetic changes in a chromosomal region containing the MIR172b locus in the allotetraploids. Although mature miRNA sequences are conserved, A. thaliana and A. arenosa miRNA loci diverge rapidly in sequence and expression. Among four MIR172 loci in Arabidopsis, the level of nucleotide sequence divergence between A. thaliana and A. arenosa MIR172 loci is 15-25%, which is higher than that of protein-coding genes (?5%). MIR172b locus and its flanking genes in A. arenosa were expressed at low levels relative to that in A. thaliana, which is associated with hypermethylation of this region in the allotetraploids. Consistently with this notion, pri-miR172 transcripts in the allotetraploids were primarily derived from the A. thaliana MIR172b locus. Expression of homoeologous alleles in miR172 target loci is associated with allelic loss, allelic changes in outcrossing A. arenosa or repression of A. thaliana alleles. These data suggest that gene expression changes in this homoeologous region are associated with genetic diversity and epigenetic variation of miRNA genes and their targets in allopolyploids.

SUBMITTER: Tian L

PROVIDER: S-EPMC3907107 | biostudies-literature | 2014 Feb

REPOSITORIES: biostudies-literature

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Genetic and epigenetic changes in a genomic region containing MIR172 in Arabidopsis allopolyploids and their progenitors.

Tian L L Li X X Ha M M Zhang C C Chen Z J ZJ

Heredity 20130925 2

Combination of divergent genomes in allopolyploids creates genome-wide gene expression changes including many miRNA targets in Arabidopsis allotetraploids relative to the parents Arabidopsis thaliana and Arabidopsis arenosa. Here we report expression and epigenetic changes in a chromosomal region containing the MIR172b locus in the allotetraploids. Although mature miRNA sequences are conserved, A. thaliana and A. arenosa miRNA loci diverge rapidly in sequence and expression. Among four MIR172 lo ...[more]

PMID: 24065179

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Project description:MicroRNAs (miRNAs) and small interfering RNAs (siRNAs) are produced in diverse species and control gene expression and epigenetic regulation. Although physiological and developmental roles of miRNAs and siRNAs have been extensively studied in plants and animals, expression diversity and evolution of miRNAs and siRNAs in closely related species are poorly understood. Here we report comprehensive analyses of miRNA expression and siRNA distribution in two closely related species (Arabidopsis thaliana and A. arenosa), a natural allotetraploid (A. suecica), and two resynthesized allotetraploid lines (F1 and F7) derived from A. thaliana and A. arenosa. The siRNA populations present in A. thaliana were maintained in resynthesized allotetraploids and A. suecica. Although miRNA sequences were highly conserved, their expression patterns were highly variable between the allotetraploids and their progenitors. Significantly, many miRNAs were nonadditively expressed in the allotetraploids relative to the parents and preferentially degraded A. thaliana or A. arenosa targets. Stable inheritance of parental siRNAs in allopolyploids helps maintain genome stability in response to M-bM-^@M-^\genomic shockM-bM-^@M-^], whereas expression diversity of miRNAs and their target preference lead to interspecies variation in gene expression, growth, and development. NOTE: sff files unavailable for Samples AaL and F1L. 10 samples examined: Arabidopsis thaliana leaf, flower, Arabidopsis arenosa leaf and flower, F1 synthetic allopolyploid leaf and flower, F7 synthetic allopolyploid leaf and flower, Arabidopsis suecica leaf and flower. To determine small RNA profiles in Arabidopsis allotetraploids and their progenitors, we made 10 small RNA libraries from rosette leaves (L) and flower buds (F) in five lines, A. thaliana, A. arenosa, Allo(F1), Allo733(F7), and A. suecica. To examine expression of small RNAs among related species and their hybrids, we employed miRNA microarrays and compared small RNA levels.

Dataset Information

Genetic and epigenetic changes in a genomic region containing MIR172 in Arabidopsis allopolyploids and their progenitors.

Publications

Genetic and epigenetic changes in a genomic region containing MIR172 in Arabidopsis allopolyploids and their progenitors.

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