|
| Status |
Public on Feb 23, 2024 |
| Title |
MaizeCODE reveals bi-directionally expressed enhancers that harbor molecular signatures of maize domestication |
| Organism |
Zea mays |
| Experiment type |
Expression profiling by high throughput sequencing
Non-coding RNA profiling by high throughput sequencing
|
| Summary |
Modern maize was domesticated from Teosinte parviglumis, with subsequent introgressions from Teosinte mexicana, yielding increased kernel row number, loss of the hard fruit case and dissociation from the cob upon maturity, as well as fewer tillers. Molecular approaches have identified several transcription factors involved in the development of these traits, yet revealed that a complex regulatory network is at play. MaizeCODE deploys ENCODE strategies to catalog regulatory regions in the maize genome, generating histone modification and transcription factor ChIP-seq in parallel with transcriptomics datasets in 5 tissues of 3 inbred lines which span the phenotypic diversity of maize, as well as the teosinte inbred TIL11. Integrated analysis of these datasets resulted in the identification of a comprehensive set of regulatory regions in each inbred, and notably of distal enhancers which were differentiated from gene bodies by their lack of H3K4me1. Many of these distal enhancers expressed noncoding enhancer RNAs bi-directionally, reminiscent of “super enhancers” in animal genomes. We show that pollen grains are the most differentiated tissue at the transcriptomic level, and share features with endosperm that may be related to McClintock’s chromosome breakagefusion-bridge cycle. Conversely, ears have the least conservation between maize and teosinte, both in gene expression and within regulatory regions, reflecting conspicuous morphological differences selected during domestication. The identification of molecular signatures of domestication in transcriptional regulatory regions provides a framework for directed breeding strategies in maize.
|
| |
|
| Overall design |
Whole transcriptome sequencing (RNA-seq) was performed on multiple tissues and multiple inbred lines of zea mays
|
| |
|
| Contributor(s) |
Cahn J, Kramer M, Denkow J, Xiaosa X, Regulski M, Martienssen R, Gingeras T |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| BioProject |
PRJNA431779 |
| Submission date |
Jan 29, 2024 |
| Last update date |
Feb 24, 2024 |
| Contact name |
Jonathan Cahn |
| E-mail(s) |
cahnjonathan@gmail.com
|
| Organization name |
CSHL
|
| Street address |
1 Bungtown Rd
|
| City |
Cold Spring Harbor |
| State/province |
NY |
| ZIP/Postal code |
11724 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL20156 |
Illumina NextSeq 500 (Zea mays) |
|
| Samples (30)
|
|
| This SubSeries is part of SuperSeries: |
| GSE254496 |
MaizeCODE reveals bi-directionally expressed enhancers that harbor molecular signatures of maize domestication |
|
Less...
More...