Homology-mediated inter-chromosomal interactions in hexaploid wheat lead to specific subgenome territories following polyploidization and introgression
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PROVIDER: PRJNA578098 | ENA |
REPOSITORIES: ENA
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Project description:Polyploidization and introgression are major events driving plant genome evolution and influencing crop breeding. However, the mechanisms underlying the higher-order chromatin organization of subgenomes and alien chromosomes are largely unknown. We probe the three-dimensional chromatin architecture of Aikang 58 (AK58), a widely-cultivated allohexaploid wheat variety carrying the 1RS/1BL translocation chromosome. The regions involved in inter-chromosomal interactions, both within and between subgenomes, have highly similar sequences. Subgenome-specific territories tend to be connected by subgenome-dominant homologous transposable elements (TEs). The alien 1RS chromosomal arm, which was introgressed from rye and differs from its wheat counterpart, has relatively few inter-chromosome interactions with wheat chromosomes. An analysis of local chromatin structures reveals topologically associating domain (TAD)-like regions covering 52% of the AK58 genome, the boundaries of which are enriched with active genes, zinc-finger factor-binding motifs, CHH methylation, and 24-nt small RNAs. The chromatin loops are mostly localized around TAD boundaries, and the number of gene loops is positively associated with gene activity. The present study reveals the impact of the genetic sequence context on the higher-order chromatin structure and subgenome stability in hexaploid wheat. Specifically, we characterized the sequence homology-mediated inter-chromosome interactions and the non-canonical role of subgenome-biased TEs. Our findings may have profound implications for future investigations of the interplay between genetic sequences and higher-order structures and their consequences on polyploid genome evolution and introgression-based breeding of crop plants.
2020-11-30 | GSE139020 | GEO
Project description: Not available
| S-EPMC7792079 | biostudies-literature
Project description:Polyploidization events are known to trigger extensive epigenetic and transcriptional alteration of the duplicated or merged genomes, accompanied by small- and large-scale conformational changes. The genome of modern hexaploid wheat (Triticum aestivum L.; 2n = 6x = 42) is the product of two rounds of interspecific hybridization between three closely related diploid species, resulting in the presence of distinct but highly syntenic sub-genomes (AA, BB and DD). We examined the large-scale chromatin architecture of the nucleus of wheat using Hi-C, a genome-wide chromatin conformation capture (3C) method and GISH, (genomic in situ hybridization). We found evidence that physical interactions occur with significantly higher frequency within sub genomes (A with A, B with B or D with D) than between sub genomes (A with B or D, etc. ...), defining sub-nuclear “genomic territories”. In addition, we observed a polarized distribution of facultative and constitutive heterochromatin that suggests a functional compartmentalization within the nucleus. On a local scale, we found that genes tend to interact mainly with other genes over long-distance “loops” that are especially established between genes presenting similar expression levels and bearing the same histone marks. Moreover, gene pairs in spatial proximity show similar changes in expression levels between shoots and roots. Consistently, we found that physical contact between genes is mediated by RNA polymerase II (RNAPII). Immunofluorescence assays with anti RNAP2 antibodies revealed the presence of “transcription factories” in which multiple interacting genes are co-transcribed. This indicates that local-scale topology is an important factor for transcriptional regulation as it determines the micro-compartimentalization of active genes within the nucleus.Our results provide a framework for understanding the physical organization of wheat genome and highlight the interplay between chromosome conformation and gene expression in wheat.
2020-03-02 | GSE133880 | GEO
Project description:Polyploidization events are known to trigger extensive epigenetic and transcriptional alteration of the duplicated or merged genomes, accompanied by small- and large-scale conformational changes. The genome of modern hexaploid wheat (Triticum aestivum L.; 2n = 6x = 42) is the product of two rounds of interspecific hybridization between three closely related diploid species, resulting in the presence of distinct but highly syntenic sub-genomes (AA, BB and DD). We examined the large-scale chromatin architecture of the nucleus of wheat using Hi-C, a genome-wide chromatin conformation capture (3C) method and GISH, (genomic in situ hybridization). We found evidence that physical interactions occur with significantly higher frequency within sub genomes (A with A, B with B or D with D) than between sub genomes (A with B or D, etc. ...), defining sub-nuclear “genomic territories”. In addition, we observed a polarized distribution of facultative and constitutive heterochromatin that suggests a functional compartmentalization within the nucleus. On a local scale, we found that genes tend to interact mainly with other genes over long-distance “loops” that are especially established between genes presenting similar expression levels and bearing the same histone marks. Moreover, gene pairs in spatial proximity show similar changes in expression levels between shoots and roots. Consistently, we found that physical contact between genes is mediated by RNA polymerase II (RNAPII). Immunofluorescence assays with anti RNAP2 antibodies revealed the presence of “transcription factories” in which multiple interacting genes are co-transcribed. This indicates that local-scale topology is an important factor for transcriptional regulation as it determines the micro-compartimentalization of active genes within the nucleus.Our results provide a framework for understanding the physical organization of wheat genome and highlight the interplay between chromosome conformation and gene expression in wheat.
2020-03-02 | GSE133879 | GEO
Project description:Polyploidization events are known to trigger extensive epigenetic and transcriptional alteration of the duplicated or merged genomes, accompanied by small- and large-scale conformational changes. The genome of modern hexaploid wheat (Triticum aestivum L.; 2n = 6x = 42) is the product of two rounds of interspecific hybridization between three closely related diploid species, resulting in the presence of distinct but highly syntenic sub-genomes (AA, BB and DD). We examined the large-scale chromatin architecture of the nucleus of wheat using Hi-C, a genome-wide chromatin conformation capture (3C) method and GISH, (genomic in situ hybridization). We found evidence that physical interactions occur with significantly higher frequency within sub genomes (A with A, B with B or D with D) than between sub genomes (A with B or D, etc. ...), defining sub-nuclear “genomic territories”. In addition, we observed a polarized distribution of facultative and constitutive heterochromatin that suggests a functional compartmentalization within the nucleus. On a local scale, we found that genes tend to interact mainly with other genes over long-distance “loops” that are especially established between genes presenting similar expression levels and bearing the same histone marks. Moreover, gene pairs in spatial proximity show similar changes in expression levels between shoots and roots. Consistently, we found that physical contact between genes is mediated by RNA polymerase II (RNAPII). Immunofluorescence assays with anti RNAP2 antibodies revealed the presence of “transcription factories” in which multiple interacting genes are co-transcribed. This indicates that local-scale topology is an important factor for transcriptional regulation as it determines the micro-compartimentalization of active genes within the nucleus.Our results provide a framework for understanding the physical organization of wheat genome and highlight the interplay between chromosome conformation and gene expression in wheat.
2020-03-02 | GSE133884 | GEO
Project description:Polyploidization events are known to trigger extensive epigenetic and transcriptional alteration of the duplicated or merged genomes, accompanied by small- and large-scale conformational changes. The genome of modern hexaploid wheat (Triticum aestivum L.; 2n = 6x = 42) is the product of two rounds of interspecific hybridization between three closely related diploid species, resulting in the presence of distinct but highly syntenic sub-genomes (AA, BB and DD). We examined the large-scale chromatin architecture of the nucleus of wheat using Hi-C, a genome-wide chromatin conformation capture (3C) method and GISH, (genomic in situ hybridization). We found evidence that physical interactions occur with significantly higher frequency within sub genomes (A with A, B with B or D with D) than between sub genomes (A with B or D, etc. ...), defining sub-nuclear “genomic territories”. In addition, we observed a polarized distribution of facultative and constitutive heterochromatin that suggests a functional compartmentalization within the nucleus. On a local scale, we found that genes tend to interact mainly with other genes over long-distance “loops” that are especially established between genes presenting similar expression levels and bearing the same histone marks. Moreover, gene pairs in spatial proximity show similar changes in expression levels between shoots and roots. Consistently, we found that physical contact between genes is mediated by RNA polymerase II (RNAPII). Immunofluorescence assays with anti RNAP2 antibodies revealed the presence of “transcription factories” in which multiple interacting genes are co-transcribed. This indicates that local-scale topology is an important factor for transcriptional regulation as it determines the micro-compartimentalization of active genes within the nucleus.Our results provide a framework for understanding the physical organization of wheat genome and highlight the interplay between chromosome conformation and gene expression in wheat.
2020-03-02 | GSE133881 | GEO
Project description:Polyploidization events are known to trigger extensive epigenetic and transcriptional alteration of the duplicated or merged genomes, accompanied by small- and large-scale conformational changes. The genome of modern hexaploid wheat (Triticum aestivum L.; 2n = 6x = 42) is the product of two rounds of interspecific hybridization between three closely related diploid species, resulting in the presence of distinct but highly syntenic sub-genomes (AA, BB and DD). We examined the large-scale chromatin architecture of the nucleus of wheat using Hi-C, a genome-wide chromatin conformation capture (3C) method and GISH, (genomic in situ hybridization). We found evidence that physical interactions occur with significantly higher frequency within sub genomes (A with A, B with B or D with D) than between sub genomes (A with B or D, etc. ...), defining sub-nuclear “genomic territories”. In addition, we observed a polarized distribution of facultative and constitutive heterochromatin that suggests a functional compartmentalization within the nucleus. On a local scale, we found that genes tend to interact mainly with other genes over long-distance “loops” that are especially established between genes presenting similar expression levels and bearing the same histone marks. Moreover, gene pairs in spatial proximity show similar changes in expression levels between shoots and roots. Consistently, we found that physical contact between genes is mediated by RNA polymerase II (RNAPII). Immunofluorescence assays with anti RNAP2 antibodies revealed the presence of “transcription factories” in which multiple interacting genes are co-transcribed. This indicates that local-scale topology is an important factor for transcriptional regulation as it determines the micro-compartimentalization of active genes within the nucleus.Our results provide a framework for understanding the physical organization of wheat genome and highlight the interplay between chromosome conformation and gene expression in wheat.
2020-03-02 | GSE133882 | GEO
Project description:Polyploidization events are known to trigger extensive epigenetic and transcriptional alteration of the duplicated or merged genomes, accompanied by small- and large-scale conformational changes. The genome of modern hexaploid wheat (Triticum aestivum L.; 2n = 6x = 42) is the product of two rounds of interspecific hybridization between three closely related diploid species, resulting in the presence of distinct but highly syntenic sub-genomes (AA, BB and DD). We examined the large-scale chromatin architecture of the nucleus of wheat using Hi-C, a genome-wide chromatin conformation capture (3C) method and GISH, (genomic in situ hybridization). We found evidence that physical interactions occur with significantly higher frequency within sub genomes (A with A, B with B or D with D) than between sub genomes (A with B or D, etc. ...), defining sub-nuclear “genomic territories”. In addition, we observed a polarized distribution of facultative and constitutive heterochromatin that suggests a functional compartmentalization within the nucleus. On a local scale, we found that genes tend to interact mainly with other genes over long-distance “loops” that are especially established between genes presenting similar expression levels and bearing the same histone marks. Moreover, gene pairs in spatial proximity show similar changes in expression levels between shoots and roots. Consistently, we found that physical contact between genes is mediated by RNA polymerase II (RNAPII). Immunofluorescence assays with anti RNAP2 antibodies revealed the presence of “transcription factories” in which multiple interacting genes are co-transcribed. This indicates that local-scale topology is an important factor for transcriptional regulation as it determines the micro-compartimentalization of active genes within the nucleus.Our results provide a framework for understanding the physical organization of wheat genome and highlight the interplay between chromosome conformation and gene expression in wheat.
2020-03-02 | GSE133883 | GEO
Project description:Chromatin architecture in hexaploid wheat is hierarchically organized around genome territories and transcription factories
| PRJNA552868 | ENA
Project description:affy_hexaploid_wheat - hexa - Changes upon polyploidization in hexaploid wheat - transcriptomic changes in synthetic hexaploid derived from a cross between tetraploid and natural diploid. Study aims to understand regulation of gene expression in synthetic and natural wheat allohexaploids (Triticum aestivum), that combines the AB genome of T. turgidum and the D genome of Aegilops tauschii; and which we have recently characterized as genetically stable. We conducted a comprehensive genome-wide analysis of gene expression that allowed us to compare the effect of variability of the D genome progenitor, the trans-generation stability as well as comparison to natural wheat allohexaploid. We used the Affymetrix GeneChip® Wheat Genome Array, on which 55,049 transcripts are represented. Additive expression was shown to represent majority of expression regulation in the synthetic allohexaploids, where expression for more than 93% of transcripts was equal to the one evaluated from equal mixture of parental RNA. This leaves ~2000 (~7%) transcripts, which expression was non-additive. No global gene expression bias or dominance towards any of the progenitor genomes was observed whereas high trans-generational stability and low effect of the D genome progenitor variability were revealed. Our study suggests that gene expression regulation in wheat allohexaploids is early established upon allohexaploidization and highly conserved over generations, as demonstrated by the high similarity of expression with natural wheat allohexaploids. Keywords: genotype and ecotype comparison
2010-02-18 | GSE20169 | GEO