Comparative genome-wide analysis and expression analysis of histone acetyltransferase (HAT) gene family in response to hormonal applications, metal and abiotic stresses in cotton

Authors: MUHAMMAD, I - Chinese Academy Of Sciences; SHAFIQ, S - Chinese Academy Of Sciences; FAROOQ, M - University Of Agriculture - Pakistan; NAEEM, M - Chinese Academy Of Sciences; Jensen, Kevin; Wang, Richard

Submitted to: International Journal of Molecular Sciences
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/24/2019
Publication Date: 10/25/2019
Citation: Muhammad, I., Shafiq, S., Farooq, M.A., Naeem, M.K., Jensen, K.B., Wang, R. 2019. Comparative genome-wide analysis and expression analysis of histone acetyltransferase (HAT) gene family in response to hormonal applications, metal and abiotic stresses in cotton. International Journal of Molecular Sciences. 20(21). https://doi.org/10.3390/ijms20215311.
DOI: https://doi.org/10.3390/ijms20215311

Interpretive Summary: Nucleosomes, the basic unit of chromatin, are composed of -147 bp of DNA wrapped around a histone octamer. Nucleosomes are dynamic in response to developmental and environmental signals, thus alter the DNA accessibility and DNA-template processes to regulate the various processes in plants, including flowering time, root growth, and response to environmental changes. The N-terminal tails of histone are subjected to various post-transcriptional modifications, including histone acetylation, and methylation. Histone acetylation is carried out by histone acetyltransferases (HATs) in eukaryotes and is associated with transcriptional activation. In plants, the genome-wide analysis of HATs has been performed in several species including Arabidopsis, rice, Vitis vinifera, and Citrus sinensis. HATs have been widely reported to play an important role in various aspects of plant development, including floral development, root growth, and gametophyte development. In addition to developmental functions, HATs are also involved in plant adaptation to various environmental fluctuations, such as salt stress, cold stress, heat stress, light signaling, abscisic acid (ABA) and other hormone signaling. Therefore, the understanding of the molecular mechanism of HATs in field crops may play an important role in sustainable agriculture and food security. We identified and analyzed HAT genes from the whole genome of G. hirsutum, G raimondii and G. arboretum. This study provides a fundamental understanding of HATs' roles in cotton growth and development. Furthermore, this study will be useful for functional genomic studies on the regulations of histone acetylation and will eventually lead to long-term improvement of stress tolerance in cotton.

Technical Abstract: Post-translational modifications are involved in regulating diverse developmental processes. Histone acetyltransferases (HATs) play vital roles in the regulation of chromation structure and activate the gene transcription implicated in various cellular processes. However, HATs in cotton remain unidentified as well as their regulation in response to developmental and environmental cues. In this study, 9 HATs were identified from Gossyipium raimondi and Gossypium arboretum, while 18 HATs were identified from Gossypium raimondi and Gossypium arboreturn, while 18 HATs were identified from Gossypium hirsutum. Based on their sequences, Gossypium HATs were divided into 3 groups: CPB, GNAT/MYST, and TAF11250. Almost all of the HATs within each subgroup share similar gene structure and conserved motifs. Gossypium HATs are unevenly distributed on the chromosomes, and duplication analysis suggests that Gossypium HATs are under strong purifying selection. Gene expression analysis showed that all the HATs have distinct expression profiles in different vegetative tissues, and at different stages of fiber development. Furthermore, all of the HATs were differentially regulated in response to various stresses (salt, drought, cold, heavy metal and DNA damage) and hormones (ABA and NAA). Finally, co-localization of HAT genes with reported QTLs of fiber development were reported. Altogether, these results highlight the functional diversification of HATs in cotton growth, fiber development as well as in response to different environmental cues. This study enhances our understanding of function of histone acetylation in cotton growth, fiber development, and stress adaptation, which will eventually lead to long-term improvement of stress tolerance and fiber quality in cotton.