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sRNA-EMB Report Summary

Project ID: 637888
Funded under: H2020-EU.1.1.

Periodic Reporting for period 1 - sRNA-EMB (Small RNA regulation of the body plan and epigenome in Arabidopsis embryos)

Reporting period: 2015-07-01 to 2016-12-31

Summary of the context and overall objectives of the project

After fertilization, the basic body plans of both plants and animals are established during early embryo development. However, despite the fundamental importance of this formative phase of the plant’s life to society's understanding of developmental biology and agricultural practices, the molecular mechanisms that generate the most basic cell-types in plants remain largely uncharacterized. Small RNAs are short non-coding RNAs that regulate gene expression in plants and animals. Although small RNAs are essential for proper gene regulation and cellular differentiation, little is known regarding their embryonic functions, especially in plants. Arabidopsis thaliana is a highly suitable model system to study the regulatory roles of small RNAs because of the abundance of genetic resources and available (genome-wide) data. Moreover, Arabidopsis embryos undergo invariant division patterns and individual cells rapidly differentiate from each other to generate the most basic plant cell-types arranged in correct positions. Early Arabidopsis embryos are therefore morphologically simple structures composed of diverse cell types making them ideal for determining the influence of small RNAs on fundamental cellular differentiation and reprogramming events. The objectives of the proposed research are designed to assess the regulatory roles of small RNAs in establishing both the basic body plan of plant embryos. We will utilize modified next-generation sequencing technologies to identify small RNAs present in developing embryos. Because we will generate these RNA profiles from a mixture of cell-types, we will also use a fluorescent protein-based approach to quantify specific small RNA gene regulatory activities in individual cell-types. To determine the functions of individual small RNA/target interactions during embryogenesis, we will identify specific small RNAs required for embryo development and use both genetic and genome-wide approaches to investigate their embryonic activities in greater detail. Altogether, the experiments being funded by this action are expected to yield novel insights into how small RNAs help establish the basic body plan of early embryos, and thus clarify some of the most outstanding questions in small RNA and reproductive biology fields. Moreover, our research should open up new avenues for exploring the regulatory roles of these fascinating molecules during the earliest stages of life.

Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far

Overall, our ERC-funded project is well on-track to accomplish the originally proposed objectives. We currently have several manuscripts describing our progress during the first reporting period that are either under review or being prepared for submission. Because our research results are unpublished, only a very general overview is provided below to protect the confidential nature of our work. During the first 18 months of the project, we have developed a few biotechnology applications/tools that increase our ability to study genome-wide molecular biology phenomena from extremely low amounts of material. Through the development of such tools we have been able to examine RNA populations at unprecedented resolution from which we formed several hypotheses that we are currently testing in order to achieve our stated aims. For instance, we have identified several individual small RNAs that are required for distinct events required to generate the basic plant body plan. In addition to identifying additional small RNAs required for body plan formation, we are also studying select small RNAs, and their respective targets, to understand the molecular basis of such formative developmental mechanisms.

Progress beyond the state of the art and expected potential impact (including the socio-economic impact and the wider societal implications of the project so far)

Molecular biology approaches are increasingly being applied to specific cell-types and even individual cells in order to more precisely understand complex gene regulatory mechanisms at the cellular level. The applications and tools that we are developing are therefore not only instrumental to our ability to accomplish our project's stated aims, but are expected to be generally helpful to research groups studying cell-type specific processes. Moreover, we have developed a method that can be used to improve the interpretation of small RNA-related data that are routinely generated and used in both basic and applied research. Therefore, our work may also have a broad impact extending from fundamental molecular biology research to clinical assessment of molecular markers related to disease-afflicted cell-types.
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