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Studying the dynamics of gene expression and the role of NAC complex in male gametophyte development
Klodová, Božena ; Fíla, Jan (advisor) ; Fajkus, Jiří (referee) ; Hudzieczek, Vojtěch (referee)
This Ph.D. thesis presents a comprehensive study of gene expression regulation within the male gametophyte development focusing on transcriptional, translational, and post- translational levels. The research introduces an online tool, GOLEM, designed for the visualization and analysis of motif distribution within the DNA of various plant species. Utilizing RNA-seq data, GOLEM enables the study of gene expression across different tissues and developmental stages, as well as a comparative analysis across the evolution of plant lineages. Through an integrated multi-omics approach, combining transcriptomic and proteomic data, the thesis enriches the understanding of gene expression dynamics in male gametophyte development, identifying significant trends and categorizing gene families based on their expression patterns. This multifaceted dataset provides a valuable resource for future functional genomics studies. Additionally, prospects and challenges of studying gene expression regulation in male gametophyte are discussed. Furthermore, the thesis explores the regulatory potential of the nascent polypetide- associated complex (NAC) protein family in male gametophyte development, particularly their role in translation during pollen tube growth. Experiment results indicate that NACβ subunit knock-down...
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The role of alternative splicing in plants
Földi, Marek ; Klodová, Božena (advisor) ; Fischer, Lukáš (referee)
Alternative splicing is a mechanism of gene expression regulation that maintains, regulates, and creates genomic diversity and tissue specificity in plants. It involves the differential joining of exons in precursor mRNAs, leading to multiple mRNA isoforms from a single gene. The formation of these isoform variants and their subsequent translation leads to subfunctionalization of proteins, generating diversity in structure and function. Therefore, alternative splicing is often important in various biological processes in plants, such as development, stress response, immunity, and reproduction. Key types of alternative splicing events include intron retention, exon skipping, alternative 5'/3' splice sites, and mutually exclusive exons. Regulation of alternative splicing involves cis-regulatory elements and trans- acting protein factors such as serine/arginine-rich (SR) proteins and heterogeneous nuclear ribonucleoproteins (hnRNPs). This thesis aims to summarise the mechanisms and consequences of alternative splicing in plant development, including maturation of male and female gametophytes, meiosis, stress, and cell differentiation. It also describes methodological approaches that allow for a genome-wide study of alternative splicing, including microarrays, RNA-seq, and PCR. A better understanding of...
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Studying dimer formation and effectors of Arabidopsis thaliana nascent polypeptide-associated complex
Klodová, Božena ; Fíla, Jan (advisor) ; Robert Boisivon, Helene (referee)
The development of plant flowers represents a complex process controlled by numerous mechanisms. The creation of double homozygous mutant of both β subunits (sometimes also referred to as basic transcription factor 3) of nascent polypeptide associated complex in Arabidopsis thaliana (further referred to as nacβ1 nacβ2) caused quite a strong defective phenotype including abnormal number of flower organs, shorter siliques with a reduced seed set, and inferior pollen germination rate together with a lower ovule targeting efficiency. Previously, NAC complex was described to be formed as a heterodimer composed of an α- and β-subunit, which binds ribosome and acts as a chaperone in Saccharomyces cerevisiae. In plants, NACβ is connected to stress tolerance and to plant development as a transcription regulator. However, little is known of NAC heterodimer function in plants. In this thesis, yeast two hybrid system (Y2H) and bimolecular fluorescence complementation (BiFC) assays were used to verify the NAC heterodimer formation in A. thaliana and to establish any potential interaction preferences between both NACβ paralogues and five NACα paralogues. To deepen the understanding about molecular mechanisms behind the nacβ1 nacβ2 phenotype, flower bud transcriptome of the nacβ1 nacβ2 double homozygous mutants...
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Role of long non-coding RNAs in plants
Klodová, Božena ; Honys, David (advisor) ; Novotný, Marian (referee)
Long non-coding RNAs (lncRNAs) represent a group of transcripts with length greater than 200 nucleotides having low coding potential. It is a group of regulatory ribonucleic acid (RNA) still not fully understood but with significant potential in many biological processes across different species. For animals, many important lncRNA regulators and their roles in a range of events including their involvement in carcinogenic diseases have been reported. However, particular mechanisms of functions are often yet to be discovered. Considering plants, economically important species such as rice, maize or soybean are of particular interest. There are still only several fully annotated transcripts. However, with the constant improvement of sequencing and bioinformatic methods, the importance of lncRNA (for example in pathogen resistance or plant reproduction) becomes clear. This bachelor thesis reviews up-to-date knowledge about lncRNAs and their roles in plants. It also describes the difficulties of lncRNA research and discusses their future potential.
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