LARP4 Is an RNA-Binding Protein That Binds Nuclear-Encoded Mitochondrial mRNAs To Promote Mitochondrial Function
RNA. 2023 Dec 20:rna.079799.123. doi: 10.1261/rna.079799.123. Online ahead of print.ABSTRACTMitochondria-associated RNA-binding proteins (RBPs) have emerged as key contributors to mitochondrial biogenesis and homeostasis. With few examples known, we set out to identify RBPs that regulate nuclear-encoded mitochondrial mRNAs (NEMmRNAs). Our systematic analysis of RNA targets of 150 RBPs identified RBPs with a preference for binding NEMmRNAs, including LARP4, a La RBP family member. We show that LARP4's targets are particularly enriched in mRNAs that encode respiratory chain complex proteins (RCCPs) and mitochondrial ribosome...
Source: RNA - January 2, 2024 Category: Genetics & Stem Cells Authors: Benjamin M Lewis Chae Yun Cho Hsuan-Lin Her Orel Mizrahi Tony Hunter Gene W Yeo Source Type: research
RlmQ: A Newly Discovered rRNA Modification Enzyme Bridging RNA Modification and Virulence Traits in < em > Staphylococcus aureus < /em >
In this study, we identified a new methyltransferase, RlmQ, in Staphylococcus aureus responsible for the Gram-positive specific m7G2601, which is not modified in E. coli (G2574). We also demonstrate the absence of methylation on C1989, equivalent to E. coli C1962, which is methylated at position 5 by the Gram-negative specific RlmI methyltransferase, a paralogue of RlmQ. Both modifications (S. aureus m7G2601 and E. coli m5C1962) are situated within the same tRNA accommodation corridor, hinting at a potential shared function in translation. Inactivation of S. aureus rlmQ causes the loss of methylation at G2601 and significa...
Source: RNA - January 2, 2024 Category: Genetics & Stem Cells Authors: Roberto Bahena-Ceron Chloe Teixeira Jose R Jaramillo Ponce Philippe Wolff Florence Couzon Pauline Fran çois Bruno Klaholz Fran çois Vandenesch Pascale Romby Karen Moreau Stefano Marzi Source Type: research
Genome-wide kinetic profiling of pre-mRNA 3' end cleavage
RNA. 2023 Dec 29:rna.079783.123. doi: 10.1261/rna.079783.123. Online ahead of print.ABSTRACTCleavage and polyadenylation is necessary for the formation of mature mRNA molecules. The rate at which this process occurs can determine the temporal availability of mRNA for subsequent function throughout the cell and is likely tightly regulated. Despite advances in high-throughput approaches for global kinetic profiling of RNA maturation, genome-wide 3' end cleavage rates have never been measured. Here, we describe a novel approach to estimate the rates of cleavage, using metabolic labeling of nascent RNA, high-throughput sequenc...
Source: RNA - January 2, 2024 Category: Genetics & Stem Cells Authors: Leslie Torres-Ulloa Ezequiel Calvo-Roitberg Athma A Pai Source Type: research
Dissection of protein and RNA regions required for SPEN binding to XIST A-repeat RNA
RNA. 2023 Dec 26:rna.079713.123. doi: 10.1261/rna.079713.123. Online ahead of print.ABSTRACTXIST non-coding RNA promotes the initiation of X chromosome silencing by recruiting the protein SPEN to one X chromosome in female mammals. The SPEN protein is also called SHARP (SMRT and HDAC Associated Repressor Protein) and MINT (Msx-2 interacting nuclear target) in humans. SPEN recruits N-CoR2 and HDAC3 to initiate histone deacetylation on the X chromosome, leading to the formation of repressive chromatin marks and silencing gene expression. We dissected the contributions of different RNA and protein regions to the formation of ...
Source: RNA - January 2, 2024 Category: Genetics & Stem Cells Authors: Aileen C Button Simone D Hall Ethan L Ashley Colleen Adare McHugh Source Type: research
Examining the Capacity of Human U1 snRNA Variants to Facilitate Pre-mRNA Splicing
In this study, we found that placing the variants in the context of the regulatory elements of the RNU1-1 gene improves expression of many variants to levels comparable to the canonical U1 snRNA. Application of a previously established HeLa cell based minigene reporter assay to examine the capacity of the vU1 snRNAs to support pre-mRNA splicing revealed that even though the exogenously expressed variant snRNAs were enriched in the nucleus, only a few had a measurable effect on splicing.PMID:38164604 | DOI:10.1261/rna.079892.123 (Source: RNA)
Source: RNA - January 2, 2024 Category: Genetics & Stem Cells Authors: Jason Wong Ryan Yellamaty Christina Gallante Ethan Lawrence William Martelly Shalini Sharma Source Type: research
An easy tool to monitor the elemental steps of in vitro translation via gel electrophoresis of fluorescently labelled small peptides
RNA. 2023 Dec 26:rna.079766.123. doi: 10.1261/rna.079766.123. Online ahead of print.ABSTRACTSeveral methods are available to visualize and assess the kinetics and efficiency of elemental steps of protein biosynthesis. However, each of these methods has its own limitations. Here, we present a novel, simple and convenient tool for monitoring stepwise in vitro translation initiated by BODIPY-Met-tRNA. Synthesis and release of very short, 1 to 7 amino acids, BODIPY-labelled peptides, can be monitored using urea-polyacrylamide gel electrophoresis. Very short BODIPY-labelled oligopeptides might be resolved this way, in contrast ...
Source: RNA - January 2, 2024 Category: Genetics & Stem Cells Authors: Valeriya I Marina Medina Bidzhieva Andrey G Tereshchenkov Dmitry Orekhov Vladislava E Sagitova Nataliya V Sumbatyan Vadim N Tashlitsky Artem S Ferberg Tinashe P Maviza Pavel Kasatsky Olga Tolicheva Alena Paleskava Vladimir I Polshakov Ilya A Osterman Olga Source Type: research
Diversity and modularity of tyrosine-accepting tRNA-like structures
RNA. 2023 Dec 27:rna.079768.123. doi: 10.1261/rna.079768.123. Online ahead of print.ABSTRACTCertain positive-sense single-stranded RNA viruses contain elements at their 3' termini that structurally mimic tRNAs. These tRNA-like structures (TLSs) are classified based on which amino acid is covalently added to the 3' end by host aminoacyl-tRNA synthetase. Recently, a cryoEM reconstruction of a representative tyrosine-accepting tRNA-like structure (TLSTyr) from brome mosaic virus (BMV) revealed a unique mode of recognition of the viral anticodon-mimicking domain by tyrosyl-tRNA synthetase. Some viruses in the hordeivirus genus...
Source: RNA - January 2, 2024 Category: Genetics & Stem Cells Authors: Madeline E Sherlock Conner J Langeberg Jeffrey S Kieft Source Type: research
AptaDB: A Comprehensive Database Integrating Aptamer-Target Interactions
RNA. 2023 Dec 19:rna.079784.123. doi: 10.1261/rna.079784.123. Online ahead of print.ABSTRACTAptamers have emerged as research hotspots of the next generation due to excellent performance benefits and application potentials in pharmacology, medicine and analytical chemistry. Despite the numerous aptamer investigations, the lack of comprehensive data integration hindered the development of computational methods for aptamers and the reuse of aptamers. A public access database named AptaDB, derived from experimentally validated data manually collected from the literature, was hence developed, integrating comprehensive aptamer-...
Source: RNA - January 2, 2024 Category: Genetics & Stem Cells Authors: Long Chen Zhuohang Yu Zengrui Wu Moran Zhou Yimeng Wang Xinxin Yu Weihua Li Guixia Liu Yun Tang Source Type: research
LARP4 Is an RNA-Binding Protein That Binds Nuclear-Encoded Mitochondrial mRNAs To Promote Mitochondrial Function
RNA. 2023 Dec 20:rna.079799.123. doi: 10.1261/rna.079799.123. Online ahead of print.ABSTRACTMitochondria-associated RNA-binding proteins (RBPs) have emerged as key contributors to mitochondrial biogenesis and homeostasis. With few examples known, we set out to identify RBPs that regulate nuclear-encoded mitochondrial mRNAs (NEMmRNAs). Our systematic analysis of RNA targets of 150 RBPs identified RBPs with a preference for binding NEMmRNAs, including LARP4, a La RBP family member. We show that LARP4's targets are particularly enriched in mRNAs that encode respiratory chain complex proteins (RCCPs) and mitochondrial ribosome...
Source: RNA - January 2, 2024 Category: Genetics & Stem Cells Authors: Benjamin M Lewis Chae Yun Cho Hsuan-Lin Her Orel Mizrahi Tony Hunter Gene W Yeo Source Type: research
RlmQ: A Newly Discovered rRNA Modification Enzyme Bridging RNA Modification and Virulence Traits in < em > Staphylococcus aureus < /em >
In this study, we identified a new methyltransferase, RlmQ, in Staphylococcus aureus responsible for the Gram-positive specific m7G2601, which is not modified in E. coli (G2574). We also demonstrate the absence of methylation on C1989, equivalent to E. coli C1962, which is methylated at position 5 by the Gram-negative specific RlmI methyltransferase, a paralogue of RlmQ. Both modifications (S. aureus m7G2601 and E. coli m5C1962) are situated within the same tRNA accommodation corridor, hinting at a potential shared function in translation. Inactivation of S. aureus rlmQ causes the loss of methylation at G2601 and significa...
Source: RNA - January 2, 2024 Category: Genetics & Stem Cells Authors: Roberto Bahena-Ceron Chloe Teixeira Jose R Jaramillo Ponce Philippe Wolff Florence Couzon Pauline Fran çois Bruno Klaholz Fran çois Vandenesch Pascale Romby Karen Moreau Stefano Marzi Source Type: research
Genome-wide kinetic profiling of pre-mRNA 3' end cleavage
RNA. 2023 Dec 29:rna.079783.123. doi: 10.1261/rna.079783.123. Online ahead of print.ABSTRACTCleavage and polyadenylation is necessary for the formation of mature mRNA molecules. The rate at which this process occurs can determine the temporal availability of mRNA for subsequent function throughout the cell and is likely tightly regulated. Despite advances in high-throughput approaches for global kinetic profiling of RNA maturation, genome-wide 3' end cleavage rates have never been measured. Here, we describe a novel approach to estimate the rates of cleavage, using metabolic labeling of nascent RNA, high-throughput sequenc...
Source: RNA - January 2, 2024 Category: Genetics & Stem Cells Authors: Leslie Torres-Ulloa Ezequiel Calvo-Roitberg Athma A Pai Source Type: research
Dissection of protein and RNA regions required for SPEN binding to XIST A-repeat RNA
RNA. 2023 Dec 26:rna.079713.123. doi: 10.1261/rna.079713.123. Online ahead of print.ABSTRACTXIST non-coding RNA promotes the initiation of X chromosome silencing by recruiting the protein SPEN to one X chromosome in female mammals. The SPEN protein is also called SHARP (SMRT and HDAC Associated Repressor Protein) and MINT (Msx-2 interacting nuclear target) in humans. SPEN recruits N-CoR2 and HDAC3 to initiate histone deacetylation on the X chromosome, leading to the formation of repressive chromatin marks and silencing gene expression. We dissected the contributions of different RNA and protein regions to the formation of ...
Source: RNA - January 2, 2024 Category: Genetics & Stem Cells Authors: Aileen C Button Simone D Hall Ethan L Ashley Colleen Adare McHugh Source Type: research
Examining the Capacity of Human U1 snRNA Variants to Facilitate Pre-mRNA Splicing
In this study, we found that placing the variants in the context of the regulatory elements of the RNU1-1 gene improves expression of many variants to levels comparable to the canonical U1 snRNA. Application of a previously established HeLa cell based minigene reporter assay to examine the capacity of the vU1 snRNAs to support pre-mRNA splicing revealed that even though the exogenously expressed variant snRNAs were enriched in the nucleus, only a few had a measurable effect on splicing.PMID:38164604 | DOI:10.1261/rna.079892.123 (Source: RNA)
Source: RNA - January 2, 2024 Category: Genetics & Stem Cells Authors: Jason Wong Ryan Yellamaty Christina Gallante Ethan Lawrence William Martelly Shalini Sharma Source Type: research
An easy tool to monitor the elemental steps of in vitro translation via gel electrophoresis of fluorescently labelled small peptides
RNA. 2023 Dec 26:rna.079766.123. doi: 10.1261/rna.079766.123. Online ahead of print.ABSTRACTSeveral methods are available to visualize and assess the kinetics and efficiency of elemental steps of protein biosynthesis. However, each of these methods has its own limitations. Here, we present a novel, simple and convenient tool for monitoring stepwise in vitro translation initiated by BODIPY-Met-tRNA. Synthesis and release of very short, 1 to 7 amino acids, BODIPY-labelled peptides, can be monitored using urea-polyacrylamide gel electrophoresis. Very short BODIPY-labelled oligopeptides might be resolved this way, in contrast ...
Source: RNA - January 2, 2024 Category: Genetics & Stem Cells Authors: Valeriya I Marina Medina Bidzhieva Andrey G Tereshchenkov Dmitry Orekhov Vladislava E Sagitova Nataliya V Sumbatyan Vadim N Tashlitsky Artem S Ferberg Tinashe P Maviza Pavel Kasatsky Olga Tolicheva Alena Paleskava Vladimir I Polshakov Ilya A Osterman Olga Source Type: research
Diversity and modularity of tyrosine-accepting tRNA-like structures
RNA. 2023 Dec 27:rna.079768.123. doi: 10.1261/rna.079768.123. Online ahead of print.ABSTRACTCertain positive-sense single-stranded RNA viruses contain elements at their 3' termini that structurally mimic tRNAs. These tRNA-like structures (TLSs) are classified based on which amino acid is covalently added to the 3' end by host aminoacyl-tRNA synthetase. Recently, a cryoEM reconstruction of a representative tyrosine-accepting tRNA-like structure (TLSTyr) from brome mosaic virus (BMV) revealed a unique mode of recognition of the viral anticodon-mimicking domain by tyrosyl-tRNA synthetase. Some viruses in the hordeivirus genus...
Source: RNA - January 2, 2024 Category: Genetics & Stem Cells Authors: Madeline E Sherlock Conner J Langeberg Jeffrey S Kieft Source Type: research
