Repertory of nucleic acid binding proteins in eukaryotes

Ph.D.For a better understanding of almost all biological processes, one must gain a deep understanding towards gene regulation. Nucleic acid binding proteins (NBPs), including DNA binding proteins (DBPs) and RNA-binding proteins (RBPs), are capable of regulating genes by interacting with DNA or RNA. They are highly cooperated with each other and perform in every stage of gene regulation as they are involved in activation and suppression of gene transcription, alternative splicing of transcripts, transcripts stability, and RNA degradation, etc. To enhance and facilitate our understanding of nucleic acid binding proteins mediated gene regulation, the DBP and RBP repertories of various organisms were constructed based on analyzing and scanning through their sequenced genomes. Despite the advances of technology and relative ease of sequencing a genome, there are still many groups of eukaryotes lacking a sequenced genome for analysis. Fortunately, many of these species possess sequenced transcriptomes as an alternative for analysis. Therefore, a huge nucleic acid binding protein repertory was constructed based on manual curation and a newly developed pipeline utilizing both sequenced transcriptomes and genomes in this study. The repertory has recorded 2.8 million of NBPs and their binding motifs from 662 NBP families and 2423 species. The wide species coverage includes evolutionarily important lineages which have never been recorded in the previous NBP databases before. Evolutionary analyses on NBP groups have also been conducted, lineage specific NBP family expansions including those in evolutionary important lineages were found. The conservation level of different NBP ortholog groups differ significantly, some are fast evolving, contributing to recent speciation events while some are highly conserved to maintain basal developmental processes. Functional analyses specifically on DNA and RNA binding proteins (DRBPs) which bind both DNAs and RNAs were also carried out. DNA to DRBP to RNA interacting triplets were screened from interactomes. To conclude, this study has three major significant contributions: 1) It largely expands our knowledge base of NBPs broadly in eukaryotes; 2) Understanding the different rates of evolution in varies NBP groups; 3) Protein-DNA-RNA interactions are identified with high potential of functional importance.為了更好地理解整個完整的生物過程，我們需要對基因調控有深入的了解。 核酸結合蛋白 (NBPs), 包括DNA結合蛋白(DBPs) 和RNA結合蛋白(RBPs), 通過與DNA或RNA相互作用來調節基因的表達。它們相互高度配合，在基因調控的各個階段都發揮著重要作用，如參與基因轉錄的激活和抑制、轉錄本的可變剪接、轉錄本的穩定性、RNA的降解等。為了加強和促進我們對核酸結合蛋白介導的基因調控的了解，我們通過分析和掃描各種生物體的基因序列組，構建了它們的DBP和RBP庫。 雖然隨著技術的進步使得基因組測序相對容易，但仍有許多真核生物缺乏基因組數據進行分析。幸運的是，這些物種中有許多有轉錄組數據可以用於分析。因此，通過人工收集與一個新的基于已測序轉錄組和基因組的分析流程，本研究構建了一個龐大的核酸結合蛋白數據庫。該數據庫記錄了來自662個NBP家族和2423個物種的280萬個NBPs及其結合序列模體。數據庫的物種覆蓋范圍非常廣，包括了一些在進化上非常重要，但在以前的NBP數據庫中從未記錄過的譜系。我們還對NBP家族群進行了進化分析，並發現了譜系特異性的NBP基因家族擴張，其中包括了一些在進化上具有重要意義的譜系。不同NBP同源基因組群的保守性水平存在顯著差異，有的同源基因組群進化較快，對近期的物種形成有推動作用，有的同源基因組群高度保守，以維持物種的基礎發育過程。本研究還對能同時結合DNA和RNA的DNA和RNA結合蛋白(DRBPs)進行了功能分析。並採用不同的相互作用組對DNA、DRBP和RNA相互作用的三聚體進行了篩選。 本研究有三个重要意义：1）它在很大程度上扩展了我们在真核生物中的NBP知识库。 2）了解不同NBP组的不同进化速度。 3）鉴定了具有高功能重要性的蛋白质-DNA-RNA相互作用。Leung, Wai Tak.Thesis Ph.D. Chinese University of Hong Kong 2019.Includes bibliographical references (leaves 130-145).Abstracts also in Chinese.Title from PDF title page (viewed on 28, January, 2021)