Panagiotis Boumpas (Universität Heidelberg)
Panagiotis Boumpas's Master thesis was awarded with the Prize for the Best Plant Science Master Thesis, which was carried out at Universität Heidelberg in the year 2023 with the title:
Investigating the RNA-binding ability of the homeodomain-containing transcription factor WUSCHEL in Arabidopsis thaliana
For the first time, Panagiotis Boumpas described a so-far-unknown and novel RNA-binding ability of the Arabidopsis thaliana stem cell regulator WUSCHEL and identified candidate RNA binding targets of the protein.
In the shoot apical meristem of Arabidopsis thaliana, the homeodomain-containing transcription factor WUSCHEL (WUS) is required to specify stem cell identity. So far, most studies aiming to decipher the molecular mechanism of WUS have focused on its known DNA-binding ability. However, various studies have already reported on the RNA-binding ability of known homeodomain-containing transcription factors in different organisms. Hence, we hypothesized that WUS might also be able to associate with RNA via its conserved homeodomain.
In order to identify transcripts bound by WUS, we took advantage of RNA immunoprecipitation (RIP) followed by high-throughput sequencing. The RIP protocol Boumpas established using Arabidopsis thaliana seedlings overexpressing WUS as starting material allowed for co-immunoprecipitating WUS along with its bound RNAs.
Bioinformatic analyses of RIP-Seq data demonstrated that WUS associates with mostly exonic regions of hundreds of protein-coding transcripts. Genes which the RNAs bound by WUS are transcribed from were enriched for various biological processes known to be regulated by WUS. Moreover, bound transcripts were enriched in mobile messenger RNAs, indicating a possible role of WUS in RNA trafficking. Finally, Boumpas highlighted that genes bound by WUS both at the chromatin and transcript level are enriched for similar biological processes, further suggesting a possible tight connection between the different molecular functions of WUS towards common biological outcomes.
In conclusion, Boumpas described a so-far-unknown and novel RNA-binding ability of WUS. In the future, the results obtained will constitute a solid basis to precisely decipher the biological function behind the RNA-binding ability of WUS in order to better understand plant stem cell regulation.
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Panagiotis Boumpas conducted this work at the institute Centre for Organismal Studies (COS) Heidelberg, Department of Stem Cell Biology in the working group of Prof. Dr. Jan Lohmann.
