 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Mar 02, 2020 |
| Title |
Chromatin architecture in hexaploid wheat is hierarchically organized around genome territories and transcription factories (Wheat_Hi-C) |
| Organism |
Triticum aestivum |
| Experiment type |
Other
|
| Summary |
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.
|
| |
|
| Overall design |
2 Hi-C-seq library were sequenced
|
| |
|
| Contributor(s) |
Concia L, Benhamed M, Latrasse D |
| Citation(s) |
32349780 |
| |
| Submission date |
Jul 05, 2019 |
| Last update date |
May 08, 2020 |
| Contact name |
Lorenzo Concia |
| E-mail(s) |
colore@gmail.com, concia@bio.ens.psl.eu
|
| Phone |
769929568
|
| Organization name |
École Normale Supérieure
|
| Department |
Institut de Biologie
|
| Lab |
Plant and Algal Genomics Lab
|
| Street address |
46 Rue d'Ulm
|
| City |
Paris |
| ZIP/Postal code |
75020 |
| Country |
France |
| |
|
| Platforms (1) |
| GPL23509 |
Illumina HiSeq 4000 (Triticum aestivum) |
|
| Samples (2) |
|
| This SubSeries is part of SuperSeries: |
| GSE133885 |
Chromatin architecture in hexaploid wheat is hierarchically organized around genome territories and transcription factories |
|
| Relations |
| BioProject |
PRJNA552874 |
| SRA |
SRP213169 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE133882_RAW.tar |
53.8 Gb |
(http)(custom) |
TAR (of BIGWIG, TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
