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Allele-specific expression between Arabidopsis genus

ABSTRACT: We analyzed allele-specific expression (ASE) in leaf and floral tissues of F1 interspecific hybrids generated between the two closely related species of Arabidopsis thaliana and Arabidopsis lyrata with a whole-genome SNP tiling array (AtSNPtile1).

ORGANISM(S): Arabidopsis thaliana x Arabidopsis lyrata Arabidopsis thaliana Arabidopsis lyrata

PROVIDER: GSE29037 | GEO | 2011/07/27

SECONDARY ACCESSION(S): PRJNA140331

REPOSITORIES: GEO

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Allele-specific expression between Arabidopsis genus

Project description:We analyzed allele-specific expression (ASE) in leaf and floral tissues of F1 interspecific hybrids generated between the two closely related species of Arabidopsis thaliana and Arabidopsis lyrata with a whole-genome SNP tiling array (AtSNPtile1). 24 sampes, 12 DNA samples from parents and hybrids, 12 RNA sample from leaf and flowers of hybrids

2011-07-26 | E-GEOD-29037 | biostudies-arrayexpress

Expression array from mature leaves in the genus Arabidopsis

Project description:We compared the expression between inter-specific hybrids (A. thaliana-A. lyrata, A. thaliana-A. halleri) and mid parent values of their parental lines. Mature leaves in A. thaliana (Col), A. lyrata ssp. lyrata, A. halleri ssp. gemmifera and interspecific hybrid between A. thaliana and A. lyrata and between A. thaliana and A. halleri

2013-09-29 | E-GEOD-23318 | biostudies-arrayexpress

mRNA samples in Allele Specific Expression study

Project description:Col-0 and Van-0 total RNA were mixed at 1:1. Total RNA also extracted from F1 hybrid samples from Col x Van and Van x Col. PolyA RNA were purified and double-strand cDNA were synthesized, followed by bioprime random labeling. A total of 16ug labelled products were hybridized to AtSNPtile1. cis regulatory effect was identified as allele specific expression in F1 hybrids. Composite trans regulatory effect was detected as deviation between parental expression and F1 hybrids expression. Each sample type has four replicates. Single chanel. Three sample types (Col and Van RNA 1:1 mixture, Col x Van F1 hybrids, Van x Col F1 hybrids). Total 12 samples.

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Allele-specific expression in A. thaliana hybrids grown under control and drought stress conditions

Project description:We estimate Allele-specific expression in F1 hybrids between Col-0 and Cvi-0 accessions grown under well watered and drought stress conditions. We found that ~90% of the genes showed similar ASE under both stresses. Trans-effects were less robust across environments, however its effect was milder compared to cis-variation. Assessment of ASE in different environments

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Allele-specific expression in A. thaliana hybrids grown under control and drought stress conditions

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The footprint of polygenic adaptation on stress-responsive cis-regulatory divergence in the Arabidopsis genus

Project description:We generated F1 hybrids of each of the sister species A. halleri and A. lyrata with their outgroup relative of A. thaliana and monitored allele-specific levels of expression in standard growth conditions, in response to dehydration or cold exposure. This data allowed us to map the genome-wide distribution of cis-regulatory mutations active in three distinct environments reflecting divergent adaptations of the two species. Because the sister species were both crossed to an outgroup species, it was possible to assign a phylogenetic origin to cis-acting mutations. Cis-acting mutations observed in only one of the two hybrids were likely to be derived, whereas those observed in both hybrids either predate predated the split between the two species or arose along the A. thaliana lineage. By contrasting the distribution of cis-regulatory mutations derived in the A. halleri to those derived on the A. lyrata lineage, we could establish relative rates of cis-acting evolution across polygenic molecular functions and detect lineage-specific polygenic adaptation to environmental challenges. A.thalianaxA.lyrata under cold, dehydration and standard conditions, 3 biological replicates; A.thalianaxA.halleri under cold, dehydration and standard conditions, 3 biological replicates; toal 18 RNA-seq samples

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The footprint of polygenic adaptation on stress-responsive cis-regulatory divergence in the Arabidopsis genus

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Expression array from mature leaves in the genus Arabidopsis

Project description:We compared the expression between inter-specific hybrids (A. thaliana-A. lyrata, A. thaliana-A. halleri) and mid parent values of their parental lines.

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Global Epigenomic Analysis Indicates that Epialleles Contribute to Allele-specific Expression via Allele-specific Histone Modifications in Hybrid Rice

Project description:We used chromatin immunoprecipitation followed by next-generation sequencing (ChIP-seq) to investigate the global ASHM profiles of trimethylation on histone H3 lysine 27 (H3K27me3) and histone H3 lysine 36 (H3K36me3) in two rice F1 hybrids. A total of 522 to 550 allele-specific H3K27me3 genes and 428 to 494 allele-specific H3K36me3 genes were detected in GL×93-11 and GL×TQ, accounting for 11.09% and 26.13% of the total analyzed genes, respectively. The epialleles between parents were highly related to ASHMs. Further analysis indicated that 52.48% to 70.40% of the epialleles were faithfully inherited by the F1 hybrid and contributed to 33.18% to 46.55% of the ASHM genes. Importantly, 66.67% to 82.69% of monoallelic expression genes contained the H3K36me3 modification. Further studies demonstrated a significant positive correlation of ASE with allele-specific H3K36me3 but not with H3K27me3, indicating that ASHM-H3K36me3 primarily regulates ASE in this study.

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