Upstream regulatory architecture of rice genes: summarizing the baseline towards genus-wide comparative analysis of regulatory networks and allele mining

Abstract

Dissecting the upstream regulatory architecture of rice genes and their cognate regulator proteins is at the core of network biology and its applications to comparative functional genomics. With the rapidly advancing comparative genomics resources in the genus Oryza, a reference genome annotation that defines the various cis-elements and trans-acting factors that interface each gene locus with various intrinsic and extrinsic signals for growth, development, reproduction and adaptation must be established to facilitate the understanding of phenotypic variation in the context of regulatory networks. Such information is also important to establish the foundation for mining non-coding sequence variation that defines novel alleles and epialleles across the enormous phenotypic diversity represented in rice germplasm. This review presents a synthesis of the state of knowledge and consensus trends regarding the various cis-acting and trans-acting components that define spatio-temporal regulation of rice genes based on representative examples from both foundational studies in other model and non-model plants, and more recent studies in rice. The goal is to summarize the baseline for systematic upstream sequence annotation of the rapidly advancing genome sequence resources in Oryza in preparation for genus-wide functional genomics. Perspectives on the potential applications of such information for gene discovery, network engineering and genomics-enabled rice breeding are also discussed.

Rice pyramided line IRBB67 (Xa4/Xa7) homeostasis under combined stress of high temperature and bacterial blight

“…Expression of SA related genes in both rice NILs appears to be a general response to pathogens, which is enhanced by high temperature in the resistant plant. Salicylic acid has numerously been reported to play an important role in resistance against pathogens [54][55][56][57][58][59][60] .…”

Potential of Oryza officinalis to augment the cold tolerance genetic mechanisms of Oryza sativa by network complementation

“…Earlier studies in Nipponbare showed that the mechanisms associated with early defenses to cold involve three sequentially expressing regulons 17 , 20 , 21 , 45 . First is the oxidative-mediated regulon involving bZIP -TGA-type transcription factors binding to the as1/ocs-like cis-elements.…”

“…Cis-element spatial maps were visualized using the Matlab version R2017a ( http://www.mathworks.com ). Baseline annotation of all putative cis-elements in PLACE database 58 was further elaborated with additional information from the literature 29 , 45 .…”

Transcriptoma, sítios de ligação para fatores de transcrição e região promotora de cana-de-açúcar

“…O processo de regulação gênica pode ser dividido em diferentes etapas que envolvem desde a acessibilidade do DNA genômico até o processamento pós transcricional do gene [Ladunga, 1.2 2010, Levo and Segal, 2014, Villar et al, 2014. Entre estes mecanismos podemos destacar os realizados pelos Fatores de Transcrição (Transcription Factor -TF), a remodelagem do Nucleossoma, a ação de microRNAs, as alterações químicas na estrutura das Histonas e por fim a região Promotora [de los Reyes et al, 2015, Holoch and Moazed, 2015, Keung et al, 2015, Watson et al, 2015.…”

“…Na ausência do complexo transcricional a RNA pol II não poderá transcrever o mRNA da sequência de DNA codificante que fica à jusante da região Promotora. Além disso, qualquer erro durante a montagem do complexo transcricional influenciará diretamente a transcrição do gene [de los Reyes et al, 2015, Rombauts et al, 2003]. Portanto, a região Promotora pode determinar de forma direta a quantidade, o tipo e o período de produção dos transcritos [Mejía-Guerra et al, 2015, Yamamoto et al, 2009.…”