Increased long-distance interactions related to heterotic expression in Arabidopsis hybrids (clf)
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA918355 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR22967606_1.fastq.gz | Fastqsanger.gz | |||
| SRR22967606_2.fastq.gz | Fastqsanger.gz | |||
| SRR22967607_1.fastq.gz | Fastqsanger.gz | |||
| SRR22967607_2.fastq.gz | Fastqsanger.gz | |||
| SRR22967608_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 24 |
Similar Datasets
Project description:In plants, the genomic structure of hybrids changed compared with their parents. However, the effects of genomic structure changes on heterotic expression in hybrids remain elusive. By comparing interspecific hybrids between Col×C24 and their backcross C24×Col in Arabidopsis with Hi-C analysis, we found that the three-dimensional (3D) chromatin organization had more long-distance interactions relative to parents. The compartment strength related to the increased A-B compartment interactions decreased in hybrids. In the boundaries of topologically associated domains (TADs) like regions in hybrids, the values of Interchromosomal Fraction of Interactions (ICF) and Distal-to-Local [log2] (DLR) were higher than or close to the highest value of their parents. While in the hybrids of CURLY LEAF (clf) mutants, which affects the long-distance interactions, the heterosis phenotype disappeared and the ICF and DLR in hybrids were lower than their parents. In addition, compared with the clf mutant, the differential expressed genes located in TAD boundaries and loop regions in the wild type changed more obviously. In the long-distance interaction and the loop region between WT and clf, there were obvious differences in the functional enrichment for DEGs. The genes with cell cycle and mitotic related process were specifically enriched in clf. By analyzing ChIP-seq data, we found that the enrichment of H3K27me3 were higher in the hybrids in WT, which may lead to more long-distance interactions. Our findings may therefore propose a new epigenetic explanation of the heterotic expression in Arabidopsis hybrids and provide new insights into crop breeding and yield increasing.
2024-03-24 | GSE222132 | GEO
Project description:In plants, the genomic structure of hybrids changed compared with their parents. However, the effects of genomic structure changes on heterotic expression in hybrids remain elusive. By comparing interspecific hybrids between Col×C24 and their backcross C24×Col in Arabidopsis with Hi-C analysis, we found that the three-dimensional (3D) chromatin organization had more long-distance interactions relative to parents. The compartment strength related to the increased A-B compartment interactions decreased in hybrids. In the boundaries of topologically associated domains (TADs) like regions in hybrids, the values of Interchromosomal Fraction of Interactions (ICF) and Distal-to-Local [log2] (DLR) were higher than or close to the highest value of their parents. While in the hybrids of CURLY LEAF (clf) mutants, which affects the long-distance interactions, the heterosis phenotype disappeared and the ICF and DLR in hybrids were lower than their parents. In addition, compared with the clf mutant, the differential expressed genes located in TAD boundaries and loop regions in the wild type changed more obviously. In the long-distance interaction and the loop region between WT and clf, there were obvious differences in the functional enrichment for DEGs. The genes with cell cycle and mitotic related process were specifically enriched in clf. By analyzing ChIP-seq data, we found that the enrichment of H3K27me3 were higher in the hybrids in WT, which may lead to more long-distance interactions. Our findings may therefore propose a new epigenetic explanation of the heterotic expression in Arabidopsis hybrids and provide new insights into crop breeding and yield increasing.
2024-03-24 | GSE221446 | GEO
Project description:Increased long-distance interactions related to heterotic expression in Arabidopsis hybrids
| PRJNA914316 | ENA
Project description:Arabidopsis thaliana shows hybrid vigour (heterosis) in progeny of crosses between Col and C24 accessions (1). Hybrid vigour was evident as early as the mature seeds and in the seedlings 3 days after sowing (DAS). At 3 DAS genes encoding chloroplast-located proteins were significantly overrepresented (187) among the 724 genes which have greater than mid parent values of expression in the hybrid. Many of these genes are involved in chlorophyll biosynthesis and photosynthesis. The rate of photosynthesis was constant per unit leaf area in parents and hybrids. Larger cell sizes in the hybrids were associated with more chloroplasts per cell, more total chlorophyll and more photosynthesis. The increased transcription of the chloroplast-targeted genes was restricted to the 3 to 7 DAS period. At 10 DAS only 118 genes had expression levels different from the expected mid parent value in the hybrid and only 12 of these genes were differentially expressed at 3 DAS. The early increase in activity of genes involved in photosynthesis and the associated phenomena of increase in cell size and number through development, leading to larger leaf areas of all leaves in the hybrid, suggest a central role for increased photosynthesis in the production of the heterotic biomass. In support of this correlation we found that an inhibitor of photosynthesis eliminated heterosis and higher light intensities enhanced both photosynthesis and heterosis. In hybrids with low level heterosis (Ler x Col) chloroplast-targeted genes were not upregulated and leaf areas were only marginally increased. Whole plants in Col, C24, and their F1 hybrids with two replications
2012-03-06 | E-GEOD-36273 | biostudies-arrayexpress
Project description:In this study, we grew three tetraploid alfalfa hybrids, two of which expressed heterosis for biomass yield in field experiments and a third that did not, and assessed global gene expression using Affymetrix Medicago GeneChip arrays. With these data, we tested the hypotheses that (i) more nonadditively expressed genes would be identified in heterotic than non-heterotic hybrids when hybrids were compared to their respective parents, (ii) more over- and under-dominant gene expression would be observed in heterotic than non-heterotic hybrids, and (iii) the two heterotic hybrids would have similar expression profiles.
2009-01-01 | E-MEXP-1579 | biostudies-arrayexpress
Project description:Arabidopsis thaliana shows hybrid vigour (heterosis) in progeny of crosses between Col and C24 accessions (1). Hybrid vigour was evident as early as the mature seeds and in the seedlings 3 days after sowing (DAS). At 3 DAS genes encoding chloroplast-located proteins were significantly overrepresented (187) among the 724 genes which have greater than mid parent values of expression in the hybrid. Many of these genes are involved in chlorophyll biosynthesis and photosynthesis. The rate of photosynthesis was constant per unit leaf area in parents and hybrids. Larger cell sizes in the hybrids were associated with more chloroplasts per cell, more total chlorophyll and more photosynthesis. The increased transcription of the chloroplast-targeted genes was restricted to the 3 to 7 DAS period. At 10 DAS only 118 genes had expression levels different from the expected mid parent value in the hybrid and only 12 of these genes were differentially expressed at 3 DAS. The early increase in activity of genes involved in photosynthesis and the associated phenomena of increase in cell size and number through development, leading to larger leaf areas of all leaves in the hybrid, suggest a central role for increased photosynthesis in the production of the heterotic biomass. In support of this correlation we found that an inhibitor of photosynthesis eliminated heterosis and higher light intensities enhanced both photosynthesis and heterosis. In hybrids with low level heterosis (Ler x Col) chloroplast-targeted genes were not upregulated and leaf areas were only marginally increased.
2012-03-06 | GSE36273 | GEO
Project description:By using ChIP-seq, we found that loss of BRM activity in developing seedlings leads to ectopic and increased H3K27me3 deposition at several hundred genes, indicating the critical role of BRM in preventing the inappropriate deposition of this histone mark. Removal of CLF in brm mutant could partcially suppress the increased H3K27me3. Examination of H3K27me3 in 14-day-old wt, brm, clf, and brm clf seedlings. Two biological replicates for each one.
2015-03-09 | E-GEOD-53620 | biostudies-arrayexpress
Project description:The behavior of transcriptomes and epigenomes in hybrids of heterotic parents is of fundamental interest. Here we report highly integrated maps of the epigenome, mRNA and small RNA transcriptomes of two rice subspecies and their reciprocal hybrids. We found that gene activity was correlated with DNA methylation and both active and repressive histone modifications in transcribed regions. Differential epigenetic modifications correlated with changes in transcript levels among hybrids and parental lines. Distinct patterns in gene expression and epigenetic modifications in reciprocal hybrids were observed. Through analyses of single nucleotide polymorphisms from our sequence data, we observed a high correlation of allelic bias of epigenetic modifications or gene expression in reciprocal hybrids with their differences in the parental lines. The abundance of distinct small RNA size classes differed between the parents and more small RNAs were down-regulated than up-regulated in the reciprocal hybrids. Together, our data reveals a comprehensive overview of transcriptional and epigenetic trends in heterotic rice crosses, and provides a very useful resource for the rice community.
2010-01-20 | GSE19602 | GEO
Project description:Wide-type, brm, clf, and brm clf mutant seedlings
| PRJNA232492 | ENA