Dataset Information

ChIP-Seq reveals that QsMYB1 directly targets genes involved in lignin and suberin biosynthesis pathways in cork oak (Quercus suber).

ABSTRACT:

Background

Gene activity is largely controlled by transcriptional regulation through the action of transcription factors and other regulators. QsMYB1 is a member of the R2R3-MYB transcription factor family related to secondary growth, and in particular, with the cork development process. In order to identify the putative gene targets of QsMYB1 across the cork oak genome we developed a ChIP-Seq strategy.

Results

Results provide direct evidence that QsMY1B targets genes encoding for enzymes involved in the lignin and suberin pathways as well as gene encoding for ABCG transporters and LTPs implicated in the transport of monomeric suberin units across the cellular membrane. These results highlight the role of QsMYB1 as a regulator of lignin and suberin biosynthesis, transport and assembly.

Conclusion

To our knowledge, this work constitutes the first ChIP-Seq experiment performed in cork oak, a non-model plant species with a long-life cycle, and these results will contribute to deepen the knowledge about the molecular mechanisms of cork formation and differentiation.

SUBMITTER: Capote T

PROVIDER: S-EPMC6142680 | biostudies-literature | 2018 Sep

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

ChIP-Seq reveals that QsMYB1 directly targets genes involved in lignin and suberin biosynthesis pathways in cork oak (Quercus suber).

Capote Tiago T Barbosa Pedro P Usié Ana A Ramos António Marcos AM Inácio Vera V Ordás Ricardo R Gonçalves Sónia S Gonçalves Sónia S Morais-Cecílio Leonor L

BMC plant biology 20180917 1

<h4>Background</h4>Gene activity is largely controlled by transcriptional regulation through the action of transcription factors and other regulators. QsMYB1 is a member of the R2R3-MYB transcription factor family related to secondary growth, and in particular, with the cork development process. In order to identify the putative gene targets of QsMYB1 across the cork oak genome we developed a ChIP-Seq strategy.<h4>Results</h4>Results provide direct evidence that QsMY1B targets genes encoding for ...[more]

PMID: 30223777

Similar Datasets

Project description:BACKGROUND: Cork oak (Quercus suber) is one of the rare trees with the ability to produce cork, a material widely used to make wine bottle stoppers, flooring and insulation materials, among many other uses. The molecular mechanisms of cork formation are still poorly understood, in great part due to the difficulty in studying a species with a long life-cycle and for which there is scarce molecular/genomic information. Cork oak forests are of great ecological importance and represent a major economic and social resource in Southern Europe and Northern Africa. However, global warming is threatening the cork oak forests by imposing thermal, hydric and many types of novel biotic stresses. Despite the economic and social value of the Q. suber species, few genomic resources have been developed, useful for biotechnological applications and improved forest management. RESULTS: We generated in excess of 7 million sequence reads, by pyrosequencing 21 normalized cDNA libraries derived from multiple Q. suber tissues and organs, developmental stages and physiological conditions. We deployed a stringent sequence processing and assembly pipeline that resulted in the identification of ~159,000 unigenes. These were annotated according to their similarity to known plant genes, to known Interpro domains, GO classes and E.C. numbers. The phylogenetic extent of this ESTs set was investigated, and we found that cork oak revealed a significant new gene space that is not covered by other model species or EST sequencing projects. The raw data, as well as the full annotated assembly, are now available to the community in a dedicated web portal at http://www.corkoakdb.org. CONCLUSIONS: This genomic resource represents the first trancriptome study in a cork producing species. It can be explored to develop new tools and approaches to understand stress responses and developmental processes in forest trees, as well as the molecular cascades underlying cork differentiation and disease response.

Project description:Purpose:Acetylcholinesterase (AChE) inhibitors are used to treat Alzheimer's patients because they enhance cholinergic neurotransmission. It is urgent to find new and efficient inhibitors from natural sources, highly bioavailable with low or no toxicity. The plant kingdom is extremely rich in a variety of compounds that are potent AChE inhibitors: flavonoids and other phenolic compounds have been recognized as promising Alzheimer's treatment agents. In this study, in vitro acetylcholinesterase inhibition, antioxidant activities, and total flavonoid and phenolic contents of ethanol-water extracts from Quercus suber cork and corkback were evaluated. Methods:The acetylcholinesterase activity was determined by a colorimetric assay based on Ellman's methodology. The Folin-Ciocalteu colorimetric method was used for total phenolic content determination and the aluminium chloride method for the determination of total flavonoid content. Antioxidant activity assays were performed using the DPPH and FRAP assays. Results:The acetylcholinesterase inhibitory activity from Q. suber cork and corkback ethanol-water extracts was as follows: 62% inhibition with corkback extracts over 0.5?mg/mL and around 49% inhibition in cork extracts over 1.0?mg/mL extracts' concentration. Regarding the DPPH radical scavenging activity, the concentrations of cork and corkback ethanol-water extracts required for 50% DPPH inhibition (IC50) were 3.2??g/mL and 4.0-5.2??g/mL. Corkback extracts are less effective than Trolox standard (3.2??g/mL) but cork extracts showed the same free radical scavenging activity compared to Trolox. Cork and corkback extracts have antioxidant power of 750.9-775.4?mg TEAC/g extract and 1051.2-2052.4?mg TEAC/g extract, respectively, which are significantly higher than the ones obtained with Trolox: 19.6-21.0?mg TEAC/g extract (cork assays) and 57.4-66.3?mg TEAC/g extract (corkback assays). The amounts of total phenolic (TPC) and flavonoid (TFC) compounds were 8.7-32.3?mg GAE/g and 4.8-10.7?mg CE/g dry mass for cork and 5.4-5.7?mg GAE/g and 42.5?mg CE/g dry mass for corkback extracts, respectively, using catechin (CE) and GAE (gallic acid) as standards. Conclusion:These findings demonstrate the remarkable potential of these extracts as valuable source of antioxidants with interesting acetylcholinesterase inhibitory activity.

Dataset Information

ChIP-Seq reveals that QsMYB1 directly targets genes involved in lignin and suberin biosynthesis pathways in cork oak (Quercus suber).

Background

Results

Conclusion

Publications

ChIP-Seq reveals that QsMYB1 directly targets genes involved in lignin and suberin biosynthesis pathways in cork oak (Quercus suber).

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets