Dissertations / Theses on the topic 'RNA-binding motifs'
Create a spot-on reference in APA, MLA, Chicago, Harvard, and other styles
Consult the top 38 dissertations / theses for your research on the topic 'RNA-binding motifs.'
Next to every source in the list of references, there is an 'Add to bibliography' button. Press on it, and we will generate automatically the bibliographic reference to the chosen work in the citation style you need: APA, MLA, Harvard, Chicago, Vancouver, etc.
You can also download the full text of the academic publication as pdf and read online its abstract whenever available in the metadata.
Browse dissertations / theses on a wide variety of disciplines and organise your bibliography correctly.
Taylor, Adam. "Functional analysis of Kaposi's Sarcoma-Associated Herpesvirus ORF57 RNA binding motifs." Thesis, University of Leeds, 2011. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.540582.
Full textFu, Yang. "Identification and Characterization of Novel Ribosomal Protein-binding RNA motifs in Bacteria." Thesis, Boston College, 2014. http://hdl.handle.net/2345/3795.
Full textAs the factory responsible for producing proteins, ribosomes are of great importance. In bacteria, ribosomes are composed of three ribosomal RNAs (rRNA) of different sizes, and around 50 ribosomal proteins (r-protein). During ribosome biogenesis in bacteria, synthesis of rRNAs and r-proteins are both tightly regulated and coordinated to ensure robust growth. In particular, a group of cis-regulatory RNA elements located in the 5' untranslated regions or the intergenic regions in r-protein operons are responsible for the regulation of r-protein biosynthesis. Based on the fact that RNA-regulated r-protein biosynthesis is essential and universal in bacteria, such unique and varied regulatory RNAs could provide new targets for antibacterial purpose. In this thesis, we report and experimentally verify a novel r-protein L1 regulation model that contains dual L1-binding RNA motif, and for the first time, a S6:S18 dimer-binding RNA structure in the S6 operon. We also describe Escherichia coli-based and Schizosaccharomyces pombe-based reporter systems for in vivo characterization of RNA-protein interactions. So far, both in vivo systems failed to report RNA-protein interactions, and thus need further tuning. In addition, we performed phage-display to select for regulatory RNA-binding small peptides and examined their effects on bacteria viability. One selected peptide, N-TVNFKLY-C, caused defective growth when overexpressed in E. coli. Yet, further studies must be conducted to verify the possibility that bacteria were killed by direct RNA-peptide interaction that disrupted the native r-protein regulation
Thesis (MS) — Boston College, 2014
Submitted to: Boston College. Graduate School of Arts and Sciences
Discipline: Biology
Purcell, Jamie, and Jamie Purcell. "Investigating the RNA Binding Domains of MBNL1 and the Alternative Splicing Motifs They Recognize." Thesis, University of Oregon, 2012. http://hdl.handle.net/1794/12331.
Full textGuarnaccia, Corrado. "Interaction of RGG and HTH motifs with nucleic acids : a study with rationally designed synthetic and recombinant polypeptides." Thesis, Open University, 2001. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.368806.
Full textYin, Ziwei. "RNA-binding motifs of hnRNP K are critical for induction of antibody diversification by activation-induced cytidine deaminase." Kyoto University, 2020. http://hdl.handle.net/2433/254518.
Full textNareen, Misbah. "NMR structural studies of the binding of peptidyl transferase antibiotics to conserved secondary structural motifs of 23S ribosomal RNA." Thesis, University of Manchester, 2011. https://www.research.manchester.ac.uk/portal/en/theses/nmr-structural-studies-of-the-binding-of-peptidyl-transferase-antibiotics-to-conserved-secondary-structural-motifs-of-23s-ribosomal-rna(6666811e-1fe0-49ba-9da6-5999bc9ec93e).html.
Full textAnderson, Ross Calley. "Expression and characterisation of a novel poly(A)-binding protein, PABP5." Thesis, University of Edinburgh, 2010. http://hdl.handle.net/1842/5942.
Full textPrichard, Lisa. "The role of the IQ motif, a protein kinase C and calmodulin regulatory domain, in neuroplasticity, RNA processing, and RNA metabolism /." Thesis, Connect to this title online; UW restricted, 1998. http://hdl.handle.net/1773/6302.
Full textWilking, Julia Friederike Elisabeth [Verfasser], and Guido [Akademischer Betreuer] Sauter. "Untersuchung zum RNA-binding motif protein 3 (RBM3) imProstatakarzinom / Julia Friederike Elisabeth Wilking ; Betreuer: Guido Sauter." Hamburg : Staats- und Universitätsbibliothek Hamburg, 2017. http://d-nb.info/1143868846/34.
Full textHoffmann, Patrick [Verfasser], and Friedrich [Akademischer Betreuer] Grässer. "RNA binding motif protein 4 (RBM4) a/b Proteinexpression in humanen Leberzellkarzinomen / Patrick Hoffmann. Betreuer: Friedrich Grässer." Saarbrücken : Saarländische Universitäts- und Landesbibliothek, 2015. http://d-nb.info/1065232578/34.
Full textShi, Zhongjie. "Biochemical properties and substrate reactivities of Aquifex Aeolicus Ribonuclease III." Diss., Temple University Libraries, 2012. http://cdm16002.contentdm.oclc.org/cdm/ref/collection/p245801coll10/id/213666.
Full textPh.D.
Ribonuclease III is a highly-conserved bacterial enzyme that cleaves double-stranded (ds) RNA structures, and participates in diverse RNA maturation and decay pathways. Essential insight on the RNase III mechanism of dsRNA cleavage has been provided by crystallographic studies of the enzyme from the hyperthermophilic bacterium, Aquifex aeolicus. However, those crystals involved complexes containing either cleaved RNA, or a mutant RNase III that is catalytically inactive. In addition, neither the biochemical properties of A. aeolicus (Aa)-RNase III, nor the reactivity epitopes of its cognate substrates are known. The goal of this project is to use Aa-RNase III, for which there is atomic-level structural information, to determine how RNase III recognizes its substrates and selects the target site. I first purified recombinant Aa-RNase III and defined the conditions that support its optimal in vitro catalytic activity. The catalytic activity of purified recombinant Aa-RNase III exhibits a temperature optimum of 70-85°C, a pH optimum of 8.0, and with either Mg2+ or Mn2+ supports efficient catalysis. Cognate substrates for Aa-RNase III were identified and their reactivity epitopes were characterized, including the specific bp sequence elements that determine processing reactivity and selectivity. Small RNA hairpins, based on the double-stranded structures associated with the Aquifex 16S and 23S rRNA precursors, are cleaved in vitro at sites that are consistent with production of the immediate precursors to the mature rRNAs. Third, the role of the dsRBD in scissile bond selection was examined by a mutational analysis of the conserved interactions of RNA binding motif 1 (RBM1) with the substrate proximal box (pb). The individual contributions towards substrate recognition were determined for conserved amino acid side chains in the RBM1. It also was shown that the dsRBD plays key dual roles in both binding energy and selectivity, through RBM1 responsiveness to proximal box bp sequence. The dsRBD is specifically responsive to an antideterminant (AD) bp in pb position 2. The relative structural rigidity of both dsRNA and dsRBD rationalizes the strong effect of an inhibitory bp at pb position 2: disruption of one RBM1 side chain interaction can effectively disrupt the other RBM1 side chain interactions. Finally, a cis-acting model was developed for subunit involvement in substrate recognition by RNase III. Structurally asymmetric mutant heterodimers of Escherichia coli (Ec)-RNase III were constructed, and asymmetric substrates were employed to reveal how RNase III can bind and deliver hairpin substrates to the active site cleft in a pathway that requires specific binding configurations of both enzyme and substrate.
Temple University--Theses
Boman, Karolina, Ulrika Segersten, Göran Ahlgren, Jakob Eberhard, Mathias Uhlén, Karin Jirström, and Per-Uno Malmström. "Decreased expression of RNA-binding motif protein 3 correlates with tumour progression and poor prognosis in urothelial bladder cancer." Uppsala universitet, Urologkirurgi, 2013. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-199938.
Full textGupta, Janhavi. "Nuclear speckle localization of RNA binding motif protein 5 an immediate early gene up-regulated by vascular endothelial growth factor /." College Park, Md. : University of Maryland, 2006. http://hdl.handle.net/1903/4083.
Full textThesis research directed by: Cell Biology & Molecular Genetics. Title from t.p. of PDF. Includes bibliographical references. Published by UMI Dissertation Services, Ann Arbor, Mich. Also available in paper.
Loiselle, Julie Jennifer. "Analysis of RBM5 and RBM10 expression throughout H9C2 skeletal and cardiac muscle cell differentiation." Thesis, Laurentian University of Sudbury, 2013. https://zone.biblio.laurentian.ca/dspace/handle/10219/2032.
Full textBuchholz, Frank, Anja Nitzsche, Maciej Paszkowski-Rogacz, Filomena Matarese, Eva M. Janssen-Megens, Nina C. Hubner, Herbert Schulz, et al. "RAD21 Cooperates with Pluripotency Transcription Factors in the Maintenance of Embryonic Stem Cell Identity." Saechsische Landesbibliothek- Staats- und Universitaetsbibliothek Dresden, 2016. http://nbn-resolving.de/urn:nbn:de:bsz:14-qucosa-191596.
Full textHsiao, Chiaolong. "Computational bioinformatics on three-dimensional structures of ribosomes using multiresolutional analysis." Diss., Atlanta, Ga. : Georgia Institute of Technology, 2008. http://hdl.handle.net/1853/26634.
Full textCommittee Chair: Williams, Loren; Committee Member: Doyle, Donald; Committee Member: Harvey, Stephen; Committee Member: Hud, Nicholas; Committee Member: Wartell, Roger. Part of the SMARTech Electronic Thesis and Dissertation Collection.
Buchholz, Frank, Anja Nitzsche, Maciej Paszkowski-Rogacz, Filomena Matarese, Eva M. Janssen-Megens, Nina C. Hubner, Herbert Schulz, et al. "RAD21 Cooperates with Pluripotency Transcription Factors in the Maintenance of Embryonic Stem Cell Identity." Public Library of Science, 2011. https://tud.qucosa.de/id/qucosa%3A29134.
Full textZhang, Da Jiang. "Involvement of the Polypyrimidine Tract-Binding Protein-Associated Splicing Factor (PSF) in the Hepatitis Delta Virus (HDV) RNA-Templated Transcription." Thèse, Université d'Ottawa / University of Ottawa, 2014. http://hdl.handle.net/10393/31095.
Full textKondo, Hiroshi. "Mis3 with a conserved RNA Binding Motif Is Essential for Ribosome Biogenesis and Implicated in the Start of Cell Growth and S Phase Checkpoint"に関する研究." Kyoto University, 2000. http://hdl.handle.net/2433/151426.
Full textKhisamutdinov, Emil. "Part I Nucleic Acid Site-Selective Binding Studies of Isomers of Dihydrodioxin-Masked Ortho-Quinones as Potential Antitumor Drugs Part II The Role of Non-Watson-Crick Base Pairs in Stabilizing Recurrent RNA Motif." Bowling Green State University / OhioLINK, 2012. http://rave.ohiolink.edu/etdc/view?acc_num=bgsu1339432575.
Full textYang, Tianyu. "Two novel mechanisms of MHC class I down-regulation in human cancer accelerated degradation of TAP-1 mRNA and disruption of TAP-1 protein function /." Connect to this title online, 2004. http://rave.ohiolink.edu/etdc/view?acc%5Fnum=osu1078192113.
Full textTitle from first page of PDF file. Document formatted into pages; contains x, 117 p.; also includes graphics (some col.) Includes bibliographical references (p. 99-117). Available online via OhioLINK's ETD Center
Beka, Sylvia Enobong. "The genomics of Type 1 Diabetes susceptibility regions and effect of regulatory SNPs." Thesis, University of Hertfordshire, 2016. http://hdl.handle.net/2299/17200.
Full textReveal, Bradley Steven. "Bruno regulates mRNA translation by binding to multiple sequence motifs." Thesis, 2010. http://hdl.handle.net/2152/ETD-UT-2010-08-1853.
Full texttext
Friedersdorf, Matthew Burk. "RNA Recognition and Regulation of the AU-rich RNA Binding Proteins: HuR, TTP and BRF1." Diss., 2011. http://hdl.handle.net/10161/5717.
Full textPosttranscriptional gene expression is controlled and coordinated by RNA binding proteins (RBPs), many of which recognize specific RNAs through cis-regulatory RNA elements. One of the most highly studied classes of cis-regulatory RNA elements is the AU-rich elements (AREs). AREs are bound by a class of RBPs called ARE binding proteins (ARE-BPs), of which there are over a dozen in humans including HuR, tristetraprolin (TTP) and butyrate response factors 1 and 2 (BRF1 and BRF2). TTP, BRF1 and BRF2 belong to a family of tandem C3H zinc finger proteins that destabilize ARE-containing mRNAs. HuR acts to enhance the stability and translation of ARE-containing mRNAs, a function that is rare among ARE-BPs. While each of these ARE-BPs regulates the expression of ARE-containing mRNAs, some ARE-BPs themselves are also encoded by ARE-containing mRNAs, raising the possibility that each of these ARE-BPs may regulate one another's expression. In order to determine how these ARE-BPs influence each others expression and how this affects the regulation of global gene expression programs we have focused on three different aspects of these ARE-BP networks: control, response to stimuli, and global effects.
To address of network control of ARE-BPs we have focused on how HuR regulates a network of mRNAs including TTP, BRF1 and HuR's own mRNA. We demonstrate that HuR can bind to TTP's, BRF1's and its own mRNA. Furthermore, by employing overexpression and siRNA knockdown approaches we demonstrate that these mRNAs and their corresponding 3'UTR luciferase reporters are resilient to fluctuations in HuR levels and that the degree of this resiliency is cell type and condition specific.
To address the temporal responses within an ARE-BP network we focused on how each of the members of the TTP family of ARE-BPs reacts following the induction of the other family members by using epidermal growth factor (EGF) stimulation. Here we show that induction of TTP family member mRNAs during EGF stimulation is partially attributable to changes in mRNA stability. Furthermore, we also show that TTP and BRF1 are able to bind each of the TTP family member mRNAs and subsequently affect their expression by altering their mRNA degradation rates. In addition, we demonstrate that the unique temporal induction patterns of the TTP family member RBPs is correlated with the EGF stimulated induction of TTP-bound mRNAs, suggesting that a network comprised of TTP family members is able to influence the timing of complex gene expression patterns.
Finally, to address the influence of these networks on regulation of global gene expression programs we have focused on how HuR recognizes AREs and whether it can globally recognize multiple classes of ARE-containing mRNAs, including the canonical class of AREs recognized by the TTP family members. To investigate how the three RNA recognition motifs (RRMs) of HuR contribute to ARE recognition we generated a series of RRM point mutants and test their ability to disrupt RNA recognition of each of the RRMs. To identify different classes of ARE-containing mRNAs we examined these mutants with a global RNA binding site detection method called photoactivatable ribonucleoside crosslinking immunoprecipitation (PAR-CLIP). Together these techniques suggest that the RRMs of HuR cooperate to recognize mRNA targets and that HuR's ability to bind RNA is coupled to the cellular distribution of HuR, and thus, are important in its role for regulating expression of bound mRNAs.
Together these studies indicate that ARE-BP posttranscriptional networks are highly interconnected and display complex regulatory interactions depending on cell type and stimuli. Furthermore, these networks can create complex behaviors such as timing of expression events or resiliency to fluctuations in protein levels. Finally, the components of these ARE-BP networks target partially overlapping sets of mRNAs to impact global gene expression patterns that ultimately coordinate the cellular responses to external stimuli.
Dissertation
Ho, Yuan-Ta, and 何沅達. "ATP-Independent dsDNA Helicases Could be Evolved from Potent RNA-Recognition Motifs Leveraging a Guanine-Binding Specificity." Thesis, 2017. http://ndltd.ncl.edu.tw/handle/dujy6j.
Full textChen, Chih-Chien, and 陳志堅. "WildPiRa: improve the prediction of RNA-binding residues of protein sequence using support-vector machine and co-conserved motifs." Thesis, 2011. http://ndltd.ncl.edu.tw/handle/98003144745351997799.
Full text元智大學
生物與醫學資訊碩士學位學程
99
The identification of RNA-binding residues (RBRs) in proteins is important in molecular recognition. In the absence of structures for RNA-protein complexes, it is strongly desirable to predict RBRs by protein sequences alone. In this thesis, we proposed a novel hybrid prediction method WildPiRa to tackle this problem, which combines co-conserved motifs discovered by WildSpan with the results predicted by a best SVM-based classifier PiRaNhA as we have known so far for identifying RBRs in protein sequences. The WildSpan and PiRaNhA are invoked to discover concurrently conserved patterns composed of multiple motifs spanning large wildcard regions in homologous sequences and to predict RBRs through trained classifier from protein sequence, respectively. Finally, both results are cooperatively used to identify RBRs in protein sequences by using several different combined methods that we proposed. We compare WildSpan, PiRaNhA, and WildPiRa on a dataset of 117 RNA-binding proteins in average; the predicting power of WildSpan using all of discovered co-conserved motifs achieves an F-measure of 0.402, which is better than an F-measure of 0.298 predicted by the structure-based trained classifier PiRaNhA. The performance of WildPiRa further improved the F-measure to 0.509 when both results are cooperatively integrated to identify RBRs in protein sequences. Conclusively, the efficiency of sequence-based WildPiRa is not only favorable in predicting complex-structure-unknow protein but also largely desired in large-scale proteomics.
Wu, Chia-Wei, and 吳家維. "Physical association between EBV protein EBNA-1 and P32/TAP/hyaluronectin-interaction through "RGG" RNA binding motifs of EBNA-1." Thesis, 1998. http://ndltd.ncl.edu.tw/handle/94931810097654324186.
Full text國立臺灣大學
微生物學研究所
86
EBNA-1在EB病毒潛伏感染的細胞內，以雙分子形式結合在特定的DNA序列上，促使潛伏期 EB病毒DNA的複製、調控潛伏期基因的表現，並維持EB病毒以質體形式穩定存在於細胞內 。EBNA-1同時是唯一在各種EB病毒相關腫瘤中都會表現的潛伏蛋白質。我們已經在EBNA-1 轉染的293細胞中利用免疫沉澱法找到一個細胞內蛋白質P32與EBNA-1共同免疫沉澱下來， 本論文更定位出EBNA-1是以胺基酸1-102, 325-498的區域與P32蛋白質結合。同時我們也 發現P32蛋白質會被一個辨識TAP (HIV Tat-associated protein)的抗血清所辨認。此外P 32/TAP也被證實會與其它RNA結合蛋白如HIV Rev及細胞內剪接因子SF2結合，暗示P32/TAP 參與RNA剪接或細胞核內到外運送等機制的可能性。除此之外P32/TAP還被證實是聚玻璃糖 酸(hyaluronic acid, HA)及補體C1q globular ''''head''''的接受器，因此P32/TAP/hyaluron ectin也可能參與HA所引起細胞增殖的訊息傳遞。另一方面由EBNA-1 dominant-negative mutant的研究發現EBNA-1胺基酸1-90及325-450的區域可能帶有重要的功能，而目前已知 此區域包括了"RGG" motifs及DNA linking區域。因此我們設計一系列的"RGG" motifs刪 除株並以RNA homopolymer binding assay分析，發現"RGG" motifs對於EBNA-1的RNA結合 功能確實是重要的，在不同濃度下測試EBNA-1對poly(G)的結合能力，發現EBNA-1在0.75 M NaCl下仍可與poly(G)結合，對poly(U)的結合能力較弱。同時，刪除了"RGG" motifs的 EBNA-1在細胞中無法共同免疫沉澱出P32/TAP/hyaluronectin，因此我們判斷EBNA-1是藉 由"RGG" RNA結合區域與細胞內P32/TAP/hyaluronectin產生交互作用。 Epstein-Barr virus (EBV) nuclear antigen-1 (EBNA-1) plays a key role at gene regulation and replication of EBV genome in latently infected cells by binding to specific DNA sequence as a dimer. It also helps the maintenance of viral episomal DNA within proliferating cells. EBNA-1 is the only viral protein con sistently expressed in EBV-associated malignancies, and believed to be importa nt for EBV transformation. A cellular 32 kD protein was co-immunoprecipitated with EBNA-1 by using a monoclonal antibody EBNA.OT1x in EBNA-1 transfected 29 3 cells. In this study, the P32 protein interacting region of EBNA-1 was mapp ed to EBNA-1 residues 1-102 and 325-498. P32 could be detected by a polyclona l antiserum against TAP (HIV Tat-associated protein) in Western blot. P32/TAP was reported to interact with some other RNA-binding proteins including HIV R ev and human splicing factor SF2, implying the possibility that P32/TAP may be involved in RNA processing. In addition, this protein was proved to be the H A (hyaluronic acid) receptor and the compliment C1q globular ''''head'''' receptor, and was proposed to mediate the proliferating signal induced by HA. On the ot her hand, study of dominant-negative mutants of EBNA-1 indicated that some imp ortant functions of EBNA-1 may be carried out within amino acids 1-90 and 325- 450, which contain "RGG" motifs and DNA linking region. Therefore, the import ance of "RGG" motifs on RNA binding activities was analyzed by RNA homopolymer binding assays. We found that "RGG" motifs play an important role for RNA bi nding of EBNA-1. EBNA-1 binds poly(G)-sepharose strongly in the presence of 0 .75 M NaCl and binds moderately to poly(U). Furthermore, "RGG" motifs deleted EBNA-1 expressed in 293 cell failed to co-immunoprecipitate P32/TAP/ hyaluron ectin. Thus, we concluded that EBNA-1 interacts with P32/TAP/hyaluronectin th rough "RGG" RNA binding motifs of EBNA-1. The possibility of whether P32 can modulate the RNA binding affinity of EBNA-1 and contribute to the regulation o f the complex splicing pattern of EBV genes during latency should be further i nvestigated in the future.
Wu, Jia-Wei, and 吳家維. "Physical association between EBV protein EBNA-1 and P32/TAP/hyaluronectin-interaction through ""RGG""RNA binding motifs of EBNA-1." Thesis, 1998. http://ndltd.ncl.edu.tw/handle/90467165535787976375.
Full textBenoit, Bouvrette Louis Philip. "Caractérisation systématique des motifs de régulation en cis à l’échelle transcriptomique et liens avec la localisation des ARN." Thesis, 2020. http://hdl.handle.net/1866/24578.
Full textThe subcellular localization of RNA allows a rapid and spatially restricted deployment of protein and noncoding RNA activities. The trafficking of RNA is directed by sequence elements (primary subsequences, secondary structures), also called regulatory motifs, present in cis within the RNA molecule. These motifs are recognized by RNA-binding proteins that mediate the transport of transcripts to specific sites in the cell. Recent studies in the Drosophila embryo indicate that the majority of RNAs display an asymmetric subcellular localization, suggesting the existence of a complex "localization code". However, this may represent an exceptional example and the question remained, until now, whether a comparable prevalence of RNA localization is observable in standard cells grown in culture. In addition, readily available information about the topological distribution of pattern instances across full transcriptomes has been hitherto lacking. In order to have a broad overview of the extent and properties involved in RNA localization, we subjected Drosophila (D17) and human (HepG2) cells to biochemical fractionation to isolate the nuclear, cytosolic, membrane and insoluble fractions. We then performed deep sequencing on the extracted RNA and analyzed through mass spectrometry the proteins extracted from these fractions. We named this method CeFra-Seq. Through bioinformatics analyses, I then profiled the enrichment of various RNA biotypes (e.g. messenger RNA, long noncoding RNA, circular RNA) and proteins within the subcellular fractions. This revealed the high prevalence of asymmetric distribution of both coding and noncoding RNA species. An analysis of orthologous genes between fly and human has also shown strong similarities, suggesting that the localization process is evolutionarily conserved. In addition, I have observed distinct attributes (e.g. transcript size) among fraction-specific messenger RNA populations. Finally, I observed specific correlations and anti-correlations between defined groups of messenger RNAs and the proteins they encode. To study motifs topology and their conservation, I created oRNAment, a database of putative RNA-binding protein binding sites instances in coding and noncoding RNAs. Using data from protein binding motifs assessed by RNAcompete and by RNA Bind-n-Seq experiments, I have developed an algorithm allowing their rapid identification in a complete transcriptome. I was able to catalog the instances of 453 motifs from 223 RNA-binding proteins for 525,718 transcripts in five species. The results obtained were validated by comparing them with public data from eCLIP. I then used oRNAment to further analyze the topological aspects of these motifs’ instances and their relative evolutionary conservation. This showed that most motifs are distributed in a similar fashion between species. In addition, I have detected commonalities between the subgroups of proteins linking preferentially distinct biotypes or specific RNA regions. The presence or absence of such pattern between species is likely a reflection of the importance of their functions. Moreover, a more precise analysis of the position of a motif among comparable transcriptomic regions in vertebrates suggests a syntenic conservation, to varying degrees, in all RNA biotypes. The regional topology of certain motifs as repeated instances also appears to be evolutionarily conserved and may be important in order to allow adequate binding of the protein. Finally, the results compiled with oRNAment allowed to postulate on a potential new role for the long noncoding RNA HELLPAR as an RNA-binding protein sponge. The systematic characterization of RNA localization and cis regulatory motifs presented in this thesis demonstrates how the integration of information at a transcriptomic scale enables the assessment of the prevalence of asymmetry, the distinct characteristics and the evolutionary conservation of RNA clusters.
Hsu, Wen-Yuan, and 許文苑. "Characterization for the Function of RNA Recognition Motif 3 Mutant of RNA Binding Protein Rbp1p." Thesis, 2017. http://ndltd.ncl.edu.tw/handle/gfjva2.
Full text國立臺灣大學
分子醫學研究所
106
Rbp1p, as a RNA binding protein, was first identified as a negative growth regulator in Saccharomyces cerevisiae. Protein composition of Rbp1p contains three RNA recognition motifs (RRMs), two glutamine-rich regions, and one asparagine-methionine-proline-rich (NMP) region in the C terminus. Our previous studies have shown that deletion of RBP1 resulting in a hyper ager-invasive growth in ∑1278b strain. Recently, we had found that over-expressing Rbp1p-RRM mutants, especially Rbp1p-rrm3, into yeast induced a hyper-invasion growth phenotype. This hyper-invasion growth phenotype had not only been found in ∑1278b strain but also in BY4741 strain, which had no invasive ability because of its flo8-mutation. We had previously predicted eight putative phosphorylation sites of Rbp1p, which mainly are located at C-terminus. According to the mass-spectrometry-based results, phosphorylation at threonine 637 (T637) would change in response to glucose deprivation. We generated an antibody specifically recognizing T637 phosphorylation, and observed a high phosphorylation level at T637 when over-expressing Rbp1p-rrm3 into yeast. However, the invasion phenotype of Rbp1p was unchanged regardless of T637 phosphorylation state. It indicated that T637 phosphorylation is not sufficient to regulate the Rbp1p-dependant invasive ability. Here we showed that eight putative phosphorylation sites of Rbp1p partially participated in regulating the Rbp1p-dependant invasive ability. Furthermore, the deletion of SNF1 and BCY1 decreased the Rbp1p-rrm3-induced hyper-invasion. According to previous microarray results, we found that the mRNA levels of FLO genes family increased when over-expressing Rbp1p-rrm3 as compared to Rbp1p. The increased FLO genes were FLO1, FLO9, FLO10 and FLO11. These FLO genes were involved in filamentous growth in Saccharomyces cerevisiae, such as flocculation, adhesion and invasion. Here we showed that most increasing mRNA levels of these FLO genes were consistent to the filamentous growth relative phenotypes; however, transcription was not sufficient to reflect these phenotypes. The translation of these FLO genes are needed to be further investigated.
Icha, Jaroslav. "Role acetylace RNA vazebného motivu proteinu SRSF5." Master's thesis, 2012. http://www.nusl.cz/ntk/nusl-305774.
Full textLee, Shin-Jye, and 李欣潔. "The study on specificity of double strand RNA binding motif in protein-protein interaction." Thesis, 2006. http://ndltd.ncl.edu.tw/handle/21034699720264233131.
Full text中興大學
生物化學研究所
94
The dsRNA binding motifs (dsRBMs) contain 70 amino acid and share a common evolutionarily conserved αβββα motif specifically facilitating interaction with dsRNA. Although dsRBM is defined to interact with dsRNA, some experiments report dsRBM would interact with protein, Hstaufen interact with NS1 of influenza virus and HsRHA interact with CH3 of CBP. To study the specificity recognition of dsRBMs and NS1 and CH3 in protein-protein interaction. We selected eight dsRBMs that two dsRBMs of HsRHA , two dsRBMs of HsPKR , three dsRBMs of HsStaufen , one dsRBM of HYL1.Here we report dsRBM1 and 2 of HsRHA interact with CBP and dsRBM1of HsRHA , dsRBM2 and3 of HsStaufen , dsRBM1 of HsPKR interact with CBP. To find the dsRBM-binding region of NS1 we design four fragment of NS1 that 1-114 , 106-230 , 1-73 , 74-230 by Biacore experiment. HsRHA is a bridge factor that accociated with CBP and pol Ⅱ (Nakajima .T.,1997).The presented data suggest that the protein –protein interaction of RHA and NS1 and CBP in the cell.
Chang, Chia-Wei, and 張家維. "Functional Study of RNA-Binding Motif Protein 24 in Human Pluripotent Stem Cell-Derived Cardiomyocytes." Thesis, 2018. http://ndltd.ncl.edu.tw/handle/zmr2u8.
Full text國立臺灣大學
生命科學系
107
The abnormal expression of cardiac sarcomere genes usually results in cardiomyopathy. However, current treatments for heart failure do not address the root problem involving cardiac muscle deficiencies. RNA-binding motif protein 24 (RBM24) is a key regulator of the alternative splicing of mRNA during cardiomyogenesis and sarcomerogenesis. The functional region of RBM24 that mediates cardiac development in humans remains to be elucidated. In this thesis project, I used human embryonic stem cells (hESCs) as a model system and eliminated two RBM24 regions using the CRISPR/Cas9 system to functionally characterize the RBM24 RRM domain. Although cardiomyocytes (CMs) derived from two types of mutant lines were still able to induce a normal heartbeat, CMs derived from the ∆RRM-/- mutants exhibited a disorganized sarcomeric structure and abnormal mitochondrial morphology. In contrast, the ∆Exon2-/- mutants produced a well-organized sarcomeric structure, with a normal CM size and mitochondrial structure. Considered together, the data presented herein reveal that the RBM24 RRM domain is essential for ensuring a normal sarcomeric structure in hESC-derived CMs. These findings not only represent some evidence of the importance of the RBM24 RRM domain, they also suggest that RBM24 may regulate mitochondrial functions in human CMs. Future experiments will involve the application of RNA sequencing to further characterize the molecular mechanism underlying the effects of the RRM domain on sarcomerogenesis.
Lyon, Angeline Marie. "Biophysical studies of an expanded RNA recognition motif from the Bruno protein." Thesis, 2009. http://hdl.handle.net/2152/ETD-UT-2009-08-229.
Full texttext
Kao, Pei-chi, and 高佩琪. "The role of RNA binding motif on Y Chromosome (RBMY) expression in the outcome of human hepatocellular carcinoma." Thesis, 2014. http://ndltd.ncl.edu.tw/handle/01576191145641555690.
Full text國立臺灣大學
臨床醫學研究所
102
Background and aim: Liver cancer remains one of the commonest cancers worldwide. Hepatocellular carcinoma (HCC) and hepatoblastoma (HB) are two major types of human liver cancer. Chronic infection with hepatitis B virus (HBV) has been closely associated with the development of HCC, which was found in around 80% of adult HCC and nearly 100% of childhood HCC. HB accounted for 90% of primary malignant liver tumor in children less than 5 years of age in Taiwan. Male predominance had been observed in both adult and childhood HCC, especially HBV-related HCC, with man to woman sex ratio ranging from 2:1 to 7:1. HB occurs in males significantly more frequently than it does in females and the reason remains obscure. The RNA-binding motif gene on Y chromosome ( RBMY gene), encoding a male germ cell-specific RNA binding protein associated with spermatogenesis, was found integrated by HBV DNA in a childhood HCC tissue. The RBMY transcripts, expressed exclusively in the testis of normal people, were detected by reverse transcription – polymerase chain reaction in 32 (36%) out of 90 male HCCs and in 4 (67%) of 6 male HB in a previous study. Nontumor liver counter parts were all negative for RBMY transcripts. Besides, previous study also revealed liver-specific RBMY transgenic mice developed hepatic pre-cancerous lesions, adenoma, and HCC. This study was aimed to evaluate the expression of RBMY in HCC patients to determine if a correlation between RBMY expression and the survival outcome existed. Methods: We enrolled total 197 male patients of hepatocellular carcinoma, from National Taiwan University Hospital as the baseline-study group. The HCC liver tissues were collected from the surgery and they were dealt with frozen embedded. To elaborate our model further, an additional cohort of 75 male patients of hepatocellular carcinoma, from the same hospital was enrolled as the validation group. Their liver tissues were collected from the surgery and dealt with paraffin embedded. Clinical data and pathologic findings were obtained from the medical records, including clinical presentation, American joint committee on cancer (AJCC) pathologic staging system, tumor grading, and survival condition. We checked the RBMY protein expression status by immunohistochemistry assessment. We evaluated the correlation between the clinical presentation and survival condition with RBMY protein expression. Results: RBMY protein was expressed in 143 (72.6%) of baseline-study group, including two patterns of RBMY protein distribution within HCC hepatocytes, including nucleus and cytoplasm. RBMY protein expression correlated with high grade AJCC staging (p= 0.034) and also contributed to poor prognosis trend, especially those with RBMY protein expression within the cytoplasm of hepatocytes (p= 0.0027). We confirmed the similar results in the validation group. Conclusions: RBMY protein expression correlated with higher AJCC tumor stage and was a significant prognostic factor for human hepatocellular carcinoma.
Chang, Ya-Hui, and 張雅惠. "Characterization of Rbms3(RNA binding motif, single strand interacting protein 3), a novel protein that is preferentially expressed in early developing pancreas." Thesis, 2006. http://ndltd.ncl.edu.tw/handle/38620360649348191757.
Full text國立中正大學
分子生物研究所
94
Southwestern screening of human fibroblast cDNAs library has to the identification of a novel gene product, RBMS3(RNA binding motif, single strand interacting protein 3). RBMS3 gene encodes a protein of 414 amino acid which contains two pairs of RNA binding motifs . It is closely related to MSSPs( c-myc gene single-strand binding proteins) . MSSPs are believed to regulate DNA replication, transcription, apoptosis and cell cycle progression by interacting with the C-MYC protein. Proteins with RNA –binding motifs involve in a variety of cellular processes that are critical to the survival of the organism. Previously, expression of RBMS3 has been detected specifically in mouse embryonic pancreas with the use of microarray assay. To understand the effect of Rbms3 during pancreatic development, in situ hybridization and immunofluorecsence staining were applied to confirm the presence of RBMS3 in the embryonic pancreas. And western blot assay was also detected Rbms3 signal in mouse embryos but the adult mouse pancreas protein lysate was not made sure to detect Rbms3 signal. Because this was no Rbms3 RNA signal in adult mouse pancreas total RNA. In addition, in order to explore the functions of RBMS3, a yeast two-hybrid screening was performed in order to identified proteins which associated with RBMS3. The one of candidates gene-SPIN3(Spindlin family, member 3) which was relate to development was researched. To confirm the interaction, co-immunoprecipitation and pull down assay were used. The co- immunoprecipitation still was not observed the interaction of Rbsm3 and SPIN3, but pull down assay will be used to direct interaction of Rbms3 and SPIN3. Make use of understanding the roles and functions of Rbms3 during pancreas development, we hope to provide some contributes in pancreatic diseases.
Stieber, Johanna [Verfasser]. "Biochemische Charakterisierung des humanen RNA binding motif protein 4 und Untersuchung einer möglichen Interaktion des Proteins mit dem Epstein-Barr-Virus kodierten nukleären Antigen 2 / vorgelegt von Johanna Stieber." 2009. http://d-nb.info/1005225419/34.
Full textMa, Xiaojing 1982. "Studies on HIV-1 nucleocapsid chaperone role in protein/nucleic acid interactions by single molecule spectroscopy approaches." Thesis, 2009. http://hdl.handle.net/2152/ETD-UT-2009-12-557.
Full texttext