scholarly journals A 100-kD complex of two RNA-binding proteins from mitochondria of Leishmania tarentolae catalyzes RNA annealing and interacts with several RNA editing components

RNA ◽  
2003 ◽  
Vol 9 (1) ◽  
pp. 62-76 ◽  
Author(s):  
R. APHASIZHEV
Keyword(s):  
Rna Editing ◽  
Binding Proteins ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Leishmania Tarentolae

scholarly journals TRIBE: Hijacking an RNA-Editing Enzyme to Identify Cell-Specific Targets of RNA-Binding Proteins

Cell ◽  
2016 ◽  
Vol 165 (3) ◽  
pp. 742-753 ◽  
Author(s):  
Aoife C. McMahon ◽  
Reazur Rahman ◽  
Hua Jin ◽  
James L. Shen ◽  
Allegra Fieldsend ◽  
...  
Keyword(s):  
Rna Editing ◽  
Binding Proteins ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Editing Enzyme

scholarly journals Differential Binding of Mitochondrial Transcripts by MRB8170 and MRB4160 Regulates Distinct Editing Fates of Mitochondrial mRNA in Trypanosomes

mBio ◽  
2017 ◽  
Vol 8 (1) ◽  
Author(s):  
Sameer Dixit ◽  
Michaela Müller-McNicoll ◽  
Vojtěch David ◽  
Kathi Zarnack ◽  
Jernej Ule ◽  
...  
Keyword(s):  
Trypanosoma Brucei ◽  
Rna Editing ◽  
Binding Proteins ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Affinity Purification ◽  
Mitochondrial Rna ◽  
Nucleotide Resolution ◽  
Additional Role

ABSTRACT A dozen mRNAs are edited by multiple insertions and/or deletions of uridine residues in the mitochondrion of Trypanosoma brucei . Several protein complexes have been implicated in performing this type of RNA editing, including the mitochondrial RNA-binding complex 1 (MRB1). Two paralogous novel RNA-binding proteins, MRB8170 and MRB4160, are loosely associated with the core MRB1 complex. Their roles in RNA editing and effects on target mRNAs are so far not well understood. In this study, individual-nucleotide-resolution UV-cross-linking and affinity purification (iCLAP) revealed a preferential binding of both proteins to mitochondrial mRNAs, which was positively correlated with their extent of editing. Integrating additional in vivo and in vitro data, we propose that binding of MRB8170 and/or MRB4160 onto pre-mRNA marks it for the initiation of editing and that initial binding of both proteins may facilitate the recruitment of other components of the RNA editing/processing machinery to ensure efficient editing. Surprisingly, MRB8170 also binds never-edited mRNAs, suggesting that at least this paralog has an additional role outside RNA editing to shape the mitochondrial transcriptome. IMPORTANCE Trypanosoma brucei mitochondrial mRNAs undergo maturation by RNA editing, a unique process involving decrypting open reading frames by the precise deletion and/or insertion of uridine (U) residues at specific positions on an mRNA. This process is catalyzed by multiprotein complexes, such as the RNA editing core complex, which provides the enzymatic activities needed for U insertion/deletion at a single editing site. Less well understood is how RNA editing occurs throughout an mRNA bearing multiple sites. To address this question, we mapped at single-nucleotide resolution the RNA interactions of two unique RNA-binding proteins (RBPs). These RBPs are part of the mitochondrial RNA-binding complex 1, hypothesized to mediate multiple rounds of RNA editing. Both RBPs were shown to mark mRNAs for the process in correlation with the number of editing sites on the transcript. Surprisingly, one also binds mRNAs that bypass RNA editing, indicating that it may have an additional role outside RNA editing.

scholarly journals RNA Interference Analyses Suggest a Transcript-specific Regulatory Role for Mitochondrial RNA-binding Proteins MRP1 and MRP2 in RNA Editing and Other RNA Processing inTrypanosoma brucei

2004 ◽  
Vol 280 (4) ◽  
pp. 2429-2438 ◽  
Author(s):  
Eva Vondrušková ◽  
Janny van den Burg ◽  
Alena Zíková ◽  
Nancy Lewis Ernst ◽  
Kenneth Stuart ◽  
...  
Keyword(s):  
Rna Interference ◽  
Rna Editing ◽  
Rna Processing ◽  
Binding Proteins ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Regulatory Role ◽  
Mitochondrial Rna

scholarly journals Investigation of RNA Editing Sites within Bound Regions of RNA-Binding Proteins

2019 ◽  
Vol 8 (4) ◽  
pp. 19 ◽  
Author(s):  
Tyler Weirick ◽  
Giuseppe Militello ◽  
Mohammed Rabiul Hosen ◽  
David John ◽  
Joseph B. Moore ◽  
...  
Keyword(s):  
Rna Editing ◽  
Binding Proteins ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Rna Seq ◽  
Rna Modifications ◽  
Adenosine Deaminases ◽  
Sequencing Errors ◽  
Additional Mode ◽  
Editing Enzyme

Studies in epitranscriptomics indicate that RNA is modified by a variety of enzymes. Among these RNA modifications, adenosine to inosine (A-to-I) RNA editing occurs frequently in the mammalian transcriptome. These RNA editing sites can be detected directly from RNA sequencing (RNA-seq) data by examining nucleotide changes from adenosine (A) to guanine (G), which substitutes for inosine (I). However, a careful investigation of such nucleotide changes must be conducted to distinguish sequencing errors and genomic mutations from the genuine editing sites. Building upon our recent introduction of an easy-to-use bioinformatics tool, RNA Editor, to detect RNA editing events from RNA-seq data, we examined the extent by which RNA editing events affect the binding of RNA-binding proteins (RBP). Through employing bioinformatic techniques, we uncovered that RNA editing sites occur frequently in RBP-bound regions. Moreover, the presence of RNA editing sites are more frequent when RNA editing islands were examined, which are regions in which RNA editing sites are present in clusters. When the binding of one RBP, human antigen R [HuR; encoded by ELAV-like protein 1 (ELAV1)], was quantified experimentally, its binding was reduced upon silencing of the RNA editing enzyme adenosine deaminases acting on RNA (ADAR) compared to the control—suggesting that the presence of RNA editing islands influence HuR binding to its target regions. These data indicate RNA editing as an important mediator of RBP–RNA interactions—a mechanism which likely constitutes an additional mode of post-transcription gene regulation in biological systems.

scholarly journals Regulation of RNA editing by RNA-binding proteins in human cells

2019 ◽  
Vol 2 (1) ◽  
Author(s):  
Giovanni Quinones-Valdez ◽  
Stephen S. Tran ◽  
Hyun-Ik Jun ◽  
Jae Hoon Bahn ◽  
Ei-Wen Yang ◽  
...  
Keyword(s):  
Rna Editing ◽  
Binding Proteins ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Human Cells

scholarly journals Unbiased identification of trans regulators of ADAR and A-to-I RNA editing

2019 ◽  
Author(s):  
Emily C. Freund ◽  
Anne L. Sapiro ◽  
Qin Li ◽  
Sandra Linder ◽  
James J. Moresco ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Rna Editing ◽  
Binding Proteins ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Neuroblastoma Cells ◽  
Negative Regulator ◽  
Interacting Proteins ◽  
The Novel ◽  
Site Specific

AbstractAdenosine-to-Inosine RNA editing is catalyzed by ADAR enzymes that deaminate adenosine to inosine. While many RNA editing sites are known, few trans regulators have been identified. We perform BioID followed by mass-spectrometry to identify trans regulators of ADAR1 and ADAR2 in HeLa and M17 neuroblastoma cells. We identify known and novel ADAR-interacting proteins. Using ENCODE data we validate and characterize a subset of the novel interactors as global or site-specific RNA editing regulators. Our set of novel trans regulators includes all four members of the DZF-domain-containing family of proteins: ILF3, ILF2, STRBP, and ZFR. We show that these proteins interact with each ADAR and modulate RNA editing levels. We find ILF3 is a global negative regulator of editing. This work demonstrates the broad roles RNA binding proteins play in regulating editing levels and establishes DZF-domain containing proteins as a group of highly influential RNA editing regulators.

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