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Evolution of heterochromatin and heterochromatin genes in the Oryza genomes reveals a new heterochromatin-euchromatin boundary

ABSTRACT: Evolution of heterochromatin and heterochromatin genes in the Oryza genomes reveals a new heterochromatin-euchromatin boundary

PROVIDER: PRJNA521948 | ENA |

REPOSITORIES: ENA

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Evolution of heterochromatin and heterochromatin genes in the Oryza genomes reveals a new heterochromatin-euchromatin boundary [ncRNA-Seq]

Project description:How heterochromatin genes evolve as ‘gene islands’ to fit into the repressive chromatin environment in plants are poorly understood. To address this question, we performed a comprehensive epigenetic profiling in the genus Oryza with high quality BAC-assembled regional sequences and near gap-free genomes. Comparative analyses of a heterochromatin knob demonstrated the dynamics of chromatin states (heterochromatin versus euchromatin) among the Oryza species in a phylogenetic context. LTR (long-terminal repeat) retrotransposons are the main contributor (~99%) to heterochromatin diversity. Heterochromatin genes are distributed as ‘gene islands’ in heterochromatin, but heterochromatin hardly projects expression disturbance to them. Heterochromatin genes are almost free of H3K9me2 histone modifications in exons, and have similar gene structure and transposon invasion rate in introns to its orthologous euchromatin counterparts. Analyses of the rice HiC data verified the topological existence of ‘gene islands’ and demonstrated that ‘gene islands’ are less spatially co-localized with heterochromatin. By examining evolutionarily recent inserted genes in the Oryza species, we found that the active promoters of six inserted genes can elevate CHH (H=A, C, T) methylation at the insertion sites. Our results reveals that heterochromatin genes evolve as heterochromatin-insulated ‘gene islands’ to escape the repressive influence of heterochromatin, contrasting to the ‘integration’ model in Drosophila. We suggest that active gene promoters may contribute to this insulation by acting as an important heterochromatin-euchromatin boundary in plants.

2020-12-02 | GSE127665 | GEO

Evolution of heterochromatin and heterochromatin genes in the Oryza genomes reveals a new heterochromatin-euchromatin boundary [ChIP-Seq]

2020-12-02 | GSE126436 | GEO

Evolution of heterochromatin and heterochromatin genes in the Oryza genomes reveals a new heterochromatin-euchromatin boundary [bisulfite-Seq]

2020-12-02 | GSE126432 | GEO

Evolution of heterochromatin and heterochromatin genes in the Oryza genomes reveals a new heterochromatin-euchromatin boundary [RNA-Seq]

2020-12-02 | GSE126431 | GEO

Evolution of heterochromatin and heterochromatin genes in the Oryza genomes reveals a new heterochromatin-euchromatin boundary [ncRNA-Seq]

Project description:Evolution of heterochromatin and heterochromatin genes in the Oryza genomes reveals a new heterochromatin-euchromatin boundary [ncRNA-Seq]

| PRJNA525004 | ENA

Evolution of heterochromatin and heterochromatin genes in the Oryza genomes reveals a new heterochromatin-euchromatin boundary [RNA-Seq]

Project description:Evolution of heterochromatin and heterochromatin genes in the Oryza genomes reveals a new heterochromatin-euchromatin boundary [RNA-Seq]

| PRJNA521881 | ENA

Evolution of heterochromatin and heterochromatin genes in the Oryza genomes reveals a new heterochromatin-euchromatin boundary [ChIP-Seq]

Project description:Evolution of heterochromatin and heterochromatin genes in the Oryza genomes reveals a new heterochromatin-euchromatin boundary [ChIP-Seq]

| PRJNA521886 | ENA

Evolution of heterochromatin and heterochromatin genes in the Oryza genomes reveals a new heterochromatin-euchromatin boundary [bisulfite-Seq]

Project description:Evolution of heterochromatin and heterochromatin genes in the Oryza genomes reveals a new heterochromatin-euchromatin boundary [bisulfite-Seq]

| PRJNA521891 | ENA

Array CGH of Drosophila translocations on heterochromatin custom array-eu_het boundary.

Project description:CGH analysis of translocations with breakpoints at the euchromatin/heterochromatin boundary. Three translocations with breakpoint at the euchromatin/heterochromatin boundary of 2L, 3L and X, respectively, were analyzed by CGH to distinguish heterochromatic sequences from euchromatic sequences. X: 101042(T(1;Y)B91); 2L: 130186 (T(Y;2)R146); and 3L: 102004(T(2;3)H31). To obtain embryos lacking the euchromatin portion of the chromosome arms, translocation males bearing breakpoint at the euchromatin/heterochromatin boundary of 2L, 3L and X were crossed to C(2)EN, C(3)EN or attached X females, respectively. All embryos were collected at room temperature.

2012-03-06 | E-GEOD-36261 | biostudies-arrayexpress

Array CGH of Drosophila translocations on heterochromatin custom array-eu_het boundary.

Project description:CGH analysis of translocations with breakpoints at the euchromatin/heterochromatin boundary.

2012-03-06 | GSE36261 | GEO