Author: Chunzi SongPublisher:
ISBN:
Category :
Languages : en
Pages : 62
Book Description
Functions of the Double-stranded RNA Binding Domains of Adenosine Deaminase Acting on RNA 1
Author: Chunzi SongAdenosine Deaminases Acting on RNA (ADARs) and A-to-I Editing
Author: Charles E. SamuelPublisher: Springer Science & Business Media
ISBN: 3642228011
Category : Science
Languages : en
Pages : 244
Book Description
“The objective of this CTMI volume is to provide readers with a foundation for understanding what ADARs are and how they act to affect gene expression and function. It is becoming increasingly apparent that ADARs may possess roles not only as enzymes that deaminate adenosine to produce inosine in RNA substrates with double-stranded character, but also as proteins independent of their catalytic property. Because A-to-I editing may affect base-pairing and RNA structure, processes including translation, splicing, RNA replication, and miR and siRNA silencing may be affected. Future studies of ADARs no doubt will provide us with additional surprises and new insights into the modulation of biological processes by the ADAR family of proteins.”
RNA Recognition by Adenosine Deaminases Acting on RNA
Author: Yuru WangPublisher:
ISBN: 9780355461879
Category :
Languages : en
Pages :
Book Description
Adenosine deaminases acting on RNA (ADAR) catalyze adenosine to inosine changes in double stranded RNAs, a type of post-transcriptional modification that can change the codon meaning and contribute to protein diversity in higher organisms. This modification is also known to regulate the fate of the RNA, including its expression, turnover, involvement in RNA interference and so forth. Three types of ADARs have been found in mammals, with ADAR1 and ADAR2 being catalytically active whereas ADAR3 being considered catalytically inactive. Malfunctions of ADARs have been correlated with various human diseases, including cancer. The Beal lab over the years has devoted extensive efforts in elucidating how ADARs recognize RNA substrates, and understanding the mechanism behind the RNA recognition difference between ADAR1 and ADAR2. These efforts not only advance our understanding of how these enzymes function, but also pave the way for future development of ADAR specific inhibitors of therapeutic significance. This thesis is a continuation of these efforts contributing to our understanding of how these fascinating enzymes function and providing new tools for future studies of them. Chapter 1 is an introduction of background knowledge about A-to-I RNA editing and ADAR. Chapter 2 introduced a new phenotypic reporter system that utilizes an RNA substrate efficiently processed by both ADAR1 and ADAR2 catalytic domains (ADAR-D) and a study utilizing this reporter to probe the RNA recognition by the base flipping residue in ADAR1. On the basis of this reporter system, in Chapter 3, a fluorescent reporter assay was developed to achieve high-throughput and quantitative evaluation of ADAR editing activity never achieved by other assays before, and a method called Sat-FACS-seq was introduced which provides information-rich landscape of sequence requirement across any region in ADARs. Applying this method to the 5’ binding loop of ADAR2, a novel insight into how this loop recognizes RNA was obtained. Chapter 4 detailed a study on the RNA secondary structural features that could distinguish ADAR1-D editing from ADAR2-D editing. Experimental evidence was shown, for the first time, to prove that the 5’ binding loops contribute to the site selectivity difference between ADAR1 and ADAR2, probably through differential recognition of RNA structure in the region 5’ from the editing site. Lastly, in Chapter 5, an effort to evolve the inactive ADAR3 into an active deaminase was described. Our success in turning ADAR3 into an active deaminase not only provides structural explanation of why wild-type ADAR3 is catalytically inactive, but also advances our knowledge of important residues required for proper ADAR function other than the ones traditionally appreciated. Moreover, the active ADAR3 mutant obtained was introduced with a minimal number of mutations (five), none of which was located in the RNA binding domains or on the primary RNA recognition surfaces. Thus, the mutant would be of great value for identifying the cellular binding targets of ADAR3 in vivo, which is important for understanding its biological function.
Modulators of Nuclear Localization of the Human Enzyme ADAR1
Author: Alexander StrehblowPublisher: Sudwestdeutscher Verlag Fur
ISBN: 9783838103617
Category : Science
Languages : de
Pages : 104
Book Description
The RNA editing enzyme hsADAR1 (human adenosine deaminase that acts on RNA 1) converts adenosines to inosines in double-stranded RNA and is a transcription-dependent shuttling protein. To enter the nucleus ADAR1 contains an atypical nuclear localization signal (NLS) overlapping the third double-stranded RNA binding domain (dsRBD) in the center of the enzyme. This study is concentrating on the characterization of the roles of dsRBD1 and 3 in the shuttling behavior of the enzyme. On the one hand our results indicate that NLS comprising residues are spread throughout the entire dsRBD. Additionally, several karyopherins were tested whether they can interact with dsRBD3 and mediate nuclear import of hsADAR1. Recent data revealed Transportin-1 as the most probable candidate. On the other hand to elucidate the mechanism that interferes with nuclear accumulation of hsADAR1, experiments were focused on Exportin-5, a karyopherin exporting dsRBDs and micro RNAs. Although the export factor binds ADAR1's dsRBDs in a RNA- and RanGTP dependent manner in vitro, cell based assays fail to confirm an involvement of Exportin-5 in the export of ADAR1.
Functional and Mechanistic Studies of Adenosine Deaminases Acting on RNA
Author: Rena Aviva MizrahiPublisher:
ISBN: 9781303792342
Category :
Languages : en
Pages :
Book Description
ADARs (adenosine deaminases acting on RNA) are enzymes that catalyze the post-transcriptional deamination of adenosine to inosine in double-stranded RNA, a type of RNA editing. Inosine is recognized by the translation machinery as guanosine, so RNA editing can result in incorporation of different amino acids than those encoded in the genome. While some structural information is available for one enzyme in this family, ADAR2, there is a distinct lack of structural information regarding ADAR1. In addition, many questions exist regarding the biological function of these enzymes. In recent years new substrates for these enzymes have been identified, but their role is unknown. This dissertation describes experiments in which we work towards better understanding the mechanism and specificity of these enzymes, in the hopes of developing new tools to study A-to-I RNA editing. In the past our lab has extensively studied ADAR2, one member of this enzyme family. We have incorporated nucleoside analogues at the editing site to probe the active site, both before any structural information was available and afterwards to complement it. None of this was possible for ADAR1 until our recent characterization of a new ADAR1 substrate RNA, described in Chapter 2. Discovery and characterization of this editing site allowed us to develop an assay to probe the ADAR1 active site using nucleoside analogues. Chapter 3 details the development and use of this assay to uncover similarities and differences in how ADAR1 and ADAR2 recognize their substrate. These differences may pave the way for development of ADAR-specific inhibitors, and further use of this assay may allow us to uncover additional intriguing differences within this family of enzymes. With the abundance of new editing sites coming to light due to recent deep sequencing studies, more tools are needed to elucidate the biological consequences of these editing events. We developed substrate-specific inhibitors of editing by targeting RNA structure and sequence, described in Chapter 4. Importantly, we found that antisense oligonucleotides can bind to ADAR substrate RNAs, disrupt the native secondary structure and inhibit editing. We tested three different analogues and found that locked nucleic acid/2'-O-methyl mixmer oligonucleotides work most efficiently to inhibit editing. This will be an important new tool for the field, as labs can now use antisense oligonucleotides to inhibit editing of their RNA of choice. Finally, we developed several new assays for ADAR2 editing, for the most part based on the serotonin 2C receptor (5HT(2C)R) pre-mRNA. This work is described in Chapter 5. Similar assays have been used in the past with the GluR-B R/G site RNA, but adapting them to use the 5HT(2C)R RNA means that new sequence and secondary structure questions can now be addressed. In addition, we have used these assays to investigate how the part of ADAR2 linking the second double-stranded RNA binding domain and the catalytic domain may influence specificity and activity.
Role of Double-stranded RNA Binding Proteins, TRBP, ADAR1 and PACT, on PKR Activation and HIV-1 Production
Author: Jean-François GélinasHepatitis Delta Virus
Author: John L. CaseyPublisher: Springer Science & Business Media
ISBN: 3540298029
Category : Medical
Languages : en
Pages : 231
Book Description
Hepatitis delta virus (HDV), which causes severe acute and chronic liver disease, was discovered nearly 30 years ago following the detection of a novel antigen-antibody system in hepatitis B virus carriers. HDV has continued to surprise and fascinate medical science ever since. This volume reviews recent developments in HDV research, from molecular virology to genetics to experimental investigation of new therapeutic and vaccine candidates.
RNA-protein Interactions
Author: Kiyoshi NagaiPublisher: Oxford University Press, USA
ISBN:
Category : Medical
Languages : en
Pages : 302
Book Description
The study of RNA-protein interactions is crucial to understanding the mechanisms and control of gene expression and protein synthesis. The realization that RNAs are often far more biologically active than was previously appreciated has stimulated a great deal of new research in this field. Uniquely, in this book, the world's leading researchers have collaborated to produce a comprehensive and current review of RNA-protein interactions for all scientists working in this area. Timely, comprehensive, and authoritative, this new Frontiers title will be invaluable for all researchers in molecular biology, biochemistry and structural biology.
Genome Plasticity in Health and Disease
Author: Publisher: Academic Press
ISBN: 0128178205
Category : Medical
Languages : en
Pages : 290
Book Description
Genome Plasticity in Health and Disease provides a fully up-to-date overview on genome plasticity and its role in human physiology and disease. Following an introduction to the field, a diverse range of chapters cover genomic and epigenomic analysis and the use of model organisms and genomic databases in studies. Specific molecular and biochemical mechanisms of genome plasticity are examined, including somatic variants, De Novo variants, founder variations, isolated populations dynamics, copy-number variations, mobile elements, DNA methylation, histone modifications, transcription factors, non-coding RNAs, telomere dynamics and RNA editing. Later chapters explore disease relevance for cancer, as well as cardiovascular, neuropsychiatric, inflammatory, and endocrine disease, and associated pathways for drug discovery. - Examines the role of genome plasticity across a range of disease types, from cardiovascular disease, to cancer and neuropsychiatric disorders - Adopts an interdisciplinary approach, with expert contributions across the spectrum of basic science and disease relevance to drug discovery
Adenosine Deaminases Acting on RNA (ADARs) and A-to-I Editing
Author: Charles E. SamuelPublisher: Springer
ISBN: 9783642228025
Category : Science
Languages : en
Pages : 238
Book Description
“The objective of this CTMI volume is to provide readers with a foundation for understanding what ADARs are and how they act to affect gene expression and function. It is becoming increasingly apparent that ADARs may possess roles not only as enzymes that deaminate adenosine to produce inosine in RNA substrates with double-stranded character, but also as proteins independent of their catalytic property. Because A-to-I editing may affect base-pairing and RNA structure, processes including translation, splicing, RNA replication, and miR and siRNA silencing may be affected. Future studies of ADARs no doubt will provide us with additional surprises and new insights into the modulation of biological processes by the ADAR family of proteins.”