MaizeCODE reveals bi-directionally expressed enhancers that harbor molecular signatures of maize domestication

Cahn, Jonathan, Regulski, Michael, Lynn, Jason, Ernst, Evan, Alves, Cristiane de Santis, Ramakrishnan, Srividya, Chougule, Kapeel, Wei, Sharon, Lu, Zhenyuan, Xu, Xiaosa, Drenkow, Jorg, Kramer, Melissa, Seetharam, Arun, Hufford, Matthew, McCombie, Richard, Ware, Doreen, Jackson, David, Schatz, Michael, Gingeras, Thomas, Martienssen, Robert (February 2024) MaizeCODE reveals bi-directionally expressed enhancers that harbor molecular signatures of maize domestication. bioRxiv. (Submitted)

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Abstract

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 non- coding 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 breakage- fusion-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.

Item Type: Paper
Subjects: organism description > plant > maize
organism description > plant
CSHL Authors:
Communities: CSHL labs > Gingeras lab
CSHL labs > Jackson lab
CSHL labs > Martienssen lab
CSHL labs > McCombie lab
CSHL labs > Schatz lab
CSHL labs > Ware lab
SWORD Depositor: CSHL Elements
Depositing User: CSHL Elements
Date: 23 February 2024
Date Deposited: 13 May 2025 15:14
Last Modified: 13 May 2025 15:14
Related URLs:
URI: https://repository.cshl.edu/id/eprint/41869

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