Human T-cell leukemia virus type 1 uses a specific tRNA < sup > Pro < /sup > isodecoder to prime reverse transcription
RNA. 2024 Apr 29:rna.080006.124. doi: 10.1261/rna.080006.124. Online ahead of print.ABSTRACTHuman T-cell leukemia virus type 1 (HTLV-1) is the only oncogenic human retrovirus discovered to date. All retroviruses are believed to use a host cell tRNA to prime reverse transcription (RT). In HTLV-1, the primer binding site (PBS) in the genomic RNA is complementary to the 3'-18 nucleotides (nt) of human tRNAPro The human genome encodes 20 cytoplasmic tRNAPro genes representing seven isodecoders, all of which share the same 3' 18-nt sequence but vary elsewhere. Whether all tRNAPro isodecoders are used to prime RT in cells is unk...
Source: RNA - April 29, 2024 Category: Genetics & Stem Cells Authors: Yu-Ci Syu Joshua Hatterschide Christina R Budding Yingke Tang Karin Musier-Forsyth Source Type: research
The modification landscape of P. aeruginosa tRNAs
RNA. 2024 Apr 29:rna.080004.124. doi: 10.1261/rna.080004.124. Online ahead of print.ABSTRACTRNA modifications have a substantial impact on tRNA function, with modifications in the anticodon loop contributing to translational fidelity and modifications in the tRNA core impacting structural stability. In bacteria, tRNA modifications are crucial for responding to stress and regulating the expression of virulence factors. Although tRNA modifications are well-characterized in a few model organisms, our knowledge of tRNA modifications in human pathogens, such as Pseudomonas aeruginosa, remains limited. Here we leveraged two orth...
Source: RNA - April 29, 2024 Category: Genetics & Stem Cells Authors: Mariana D Mandler Siddhardha S Maligireddy Wilfried M Guiblet Christina M Fitzsimmons Kayla S McDonald Delayna L Warrell Pedro J Batista Source Type: research
A new reagent for in vivo structure probing of RNA G and U residues that improves RNA structure prediction alone and combined with DMS
RNA. 2024 Apr 26:rna.079974.124. doi: 10.1261/rna.079974.124. Online ahead of print.ABSTRACTA key to understanding the roles of RNA in regulating gene expression is knowing their structures in vivo. One way to obtain this information is through probing structures of RNA with chemicals. To probe RNA structure directly in cells, membrane-permeable reagents that modify the Watson-Crick (WC) face of unpaired nucleotides can be used. While dimethyl sulfate (DMS) has led to substantial insight into RNA structure, it has limited nucleotide specificity in vivo, with WC face reactivity only at adenine (A) and cytosine (C) at neutra...
Source: RNA - April 26, 2024 Category: Genetics & Stem Cells Authors: Catherine A Douds Paul Babitzke Philip Bevilacqua Source Type: research
A new reagent for in vivo structure probing of RNA G and U residues that improves RNA structure prediction alone and combined with DMS
RNA. 2024 Apr 26:rna.079974.124. doi: 10.1261/rna.079974.124. Online ahead of print.ABSTRACTA key to understanding the roles of RNA in regulating gene expression is knowing their structures in vivo. One way to obtain this information is through probing structures of RNA with chemicals. To probe RNA structure directly in cells, membrane-permeable reagents that modify the Watson-Crick (WC) face of unpaired nucleotides can be used. While dimethyl sulfate (DMS) has led to substantial insight into RNA structure, it has limited nucleotide specificity in vivo, with WC face reactivity only at adenine (A) and cytosine (C) at neutra...
Source: RNA - April 26, 2024 Category: Genetics & Stem Cells Authors: Catherine A Douds Paul Babitzke Philip Bevilacqua Source Type: research
Mapping RNA-Protein Interactions with Subcellular Resolution Using Colocalization CLIP
RNA. 2024 Apr 24:rna.079890.123. doi: 10.1261/rna.079890.123. Online ahead of print.ABSTRACTRNA binding proteins (RBPs) are essential for RNA metabolism and profoundly impact health and disease. The subcellular organization of RBP interaction networks with target RNAs remains largely unexplored. Here, we develop colocalization CLIP, a method that combines CrossLinking and ImmunoPrecipitation (CLIP) with proximity labeling, to explore in-depth the subcellular RNA interactions of the RNA-binding protein HuR. Using this method, we uncover HuR's dynamic and location-specific interactions with RNA, revealing alterations in sequ...
Source: RNA - April 24, 2024 Category: Genetics & Stem Cells Authors: Soon Yi Shashi S Singh Kathryn Rozen-Gagnon Joseph M Luna Source Type: research
Mapping RNA-Protein Interactions with Subcellular Resolution Using Colocalization CLIP
RNA. 2024 Apr 24:rna.079890.123. doi: 10.1261/rna.079890.123. Online ahead of print.ABSTRACTRNA binding proteins (RBPs) are essential for RNA metabolism and profoundly impact health and disease. The subcellular organization of RBP interaction networks with target RNAs remains largely unexplored. Here, we develop colocalization CLIP, a method that combines CrossLinking and ImmunoPrecipitation (CLIP) with proximity labeling, to explore in-depth the subcellular RNA interactions of the RNA-binding protein HuR. Using this method, we uncover HuR's dynamic and location-specific interactions with RNA, revealing alterations in sequ...
Source: RNA - April 24, 2024 Category: Genetics & Stem Cells Authors: Soon Yi Shashi S Singh Kathryn Rozen-Gagnon Joseph M Luna Source Type: research
Mapping RNA-Protein Interactions with Subcellular Resolution Using Colocalization CLIP
RNA. 2024 Apr 24:rna.079890.123. doi: 10.1261/rna.079890.123. Online ahead of print.ABSTRACTRNA binding proteins (RBPs) are essential for RNA metabolism and profoundly impact health and disease. The subcellular organization of RBP interaction networks with target RNAs remains largely unexplored. Here, we develop colocalization CLIP, a method that combines CrossLinking and ImmunoPrecipitation (CLIP) with proximity labeling, to explore in-depth the subcellular RNA interactions of the RNA-binding protein HuR. Using this method, we uncover HuR's dynamic and location-specific interactions with RNA, revealing alterations in sequ...
Source: RNA - April 24, 2024 Category: Genetics & Stem Cells Authors: Soon Yi Shashi S Singh Kathryn Rozen-Gagnon Joseph M Luna Source Type: research
PACRAT: Pathogen detection with aptamer-detected cascaded recombinase polymerase amplification-in vitro transcription
RNA. 2024 Apr 18:rna.079891.123. doi: 10.1261/rna.079891.123. Online ahead of print.ABSTRACTThe SARS-CoV-2 pandemic underscored the need for early, rapid, and widespread pathogen detection tests that are readily accessible. Many existing rapid isothermal detection methods employ the recombinase polymerase amplification (RPA), which exhibits PCR-like sensitivity, specificity, and even higher speed. However, coupling RPA to other enzymatic reactions has proven difficult. For the first time, we demonstrate that with tuning of buffer conditions and optimization of reagent concentrations, RPA can be cascaded into an in vitro tr...
Source: RNA - April 18, 2024 Category: Genetics & Stem Cells Authors: Pavana Khan Lauren Aufdembrink Katarzyna P Adamala Aaron Engelhart Source Type: research
PACRAT: Pathogen detection with aptamer-detected cascaded recombinase polymerase amplification-in vitro transcription
RNA. 2024 Apr 18:rna.079891.123. doi: 10.1261/rna.079891.123. Online ahead of print.ABSTRACTThe SARS-CoV-2 pandemic underscored the need for early, rapid, and widespread pathogen detection tests that are readily accessible. Many existing rapid isothermal detection methods employ the recombinase polymerase amplification (RPA), which exhibits PCR-like sensitivity, specificity, and even higher speed. However, coupling RPA to other enzymatic reactions has proven difficult. For the first time, we demonstrate that with tuning of buffer conditions and optimization of reagent concentrations, RPA can be cascaded into an in vitro tr...
Source: RNA - April 18, 2024 Category: Genetics & Stem Cells Authors: Pavana Khan Lauren Aufdembrink Katarzyna P Adamala Aaron Engelhart Source Type: research
The Prp19C subunit Syf2 and the Prp19C-associated protein Cwc15 function in TREX occupancy and transcription elongation
RNA. 2024 Apr 16:rna.079944.124. doi: 10.1261/rna.079944.124. Online ahead of print.ABSTRACTThe Prp19 complex (Prp19C) also named NineTeen Complex (NTC) is conserved from yeast to human and functions in many different processes such as genome stability, splicing and transcription elongation. In the latter, Prp19C ensures TREX occupancy at transcribed genes. TREX in turn couples transcription to nuclear mRNA export by recruiting the mRNA exporter to transcribed genes and consequently to nascent mRNAs. Here, we assess the function of the nonessential Prp19C subunit Syf2 and the nonessential Prp19C-associated protein Cwc15 in...
Source: RNA - April 16, 2024 Category: Genetics & Stem Cells Authors: Laura Henke-Schulz Rashmi Minocha Nils Holger Maier Katja Str äβer Source Type: research
Regulation of the Drosophila transcriptome by Pumilio and the CCR4-NOT deadenylase complex
In this study, we utilize knockdown and knockout approaches coupled with RNA-Seq to measure the impact of Pumilio on the transcriptome of Drosophila cells in culture. We also use an improved RNA co-immunoprecipitation method to identify Pumilio-bound mRNAs in Drosophila embryos. Integration of these datasets with the locations of Pumilio binding motifs across the transcriptome reveal novel direct Pumilio target genes involved in neural, muscle, wing, and germ cell development, and cellular proliferation. These genes include components of Wnt, TGF-beta, MAPK/ERK, and Notch signaling pathways, DNA replication, and lipid meta...
Source: RNA - April 16, 2024 Category: Genetics & Stem Cells Authors: Rebecca J Haugen Catherine Barnier Nathan D Elrod Hua Luo Madeline K Jensen Ping Ji Craig A Smibert Howard D Lipshitz Eric J Wagner P Lydia Freddolino Aaron C Goldstrohm Source Type: research
The Prp19C subunit Syf2 and the Prp19C-associated protein Cwc15 function in TREX occupancy and transcription elongation
RNA. 2024 Apr 16:rna.079944.124. doi: 10.1261/rna.079944.124. Online ahead of print.ABSTRACTThe Prp19 complex (Prp19C) also named NineTeen Complex (NTC) is conserved from yeast to human and functions in many different processes such as genome stability, splicing and transcription elongation. In the latter, Prp19C ensures TREX occupancy at transcribed genes. TREX in turn couples transcription to nuclear mRNA export by recruiting the mRNA exporter to transcribed genes and consequently to nascent mRNAs. Here, we assess the function of the nonessential Prp19C subunit Syf2 and the nonessential Prp19C-associated protein Cwc15 in...
Source: RNA - April 16, 2024 Category: Genetics & Stem Cells Authors: Laura Henke-Schulz Rashmi Minocha Nils Holger Maier Katja Str äβer Source Type: research
Regulation of the Drosophila transcriptome by Pumilio and the CCR4-NOT deadenylase complex
In this study, we utilize knockdown and knockout approaches coupled with RNA-Seq to measure the impact of Pumilio on the transcriptome of Drosophila cells in culture. We also use an improved RNA co-immunoprecipitation method to identify Pumilio-bound mRNAs in Drosophila embryos. Integration of these datasets with the locations of Pumilio binding motifs across the transcriptome reveal novel direct Pumilio target genes involved in neural, muscle, wing, and germ cell development, and cellular proliferation. These genes include components of Wnt, TGF-beta, MAPK/ERK, and Notch signaling pathways, DNA replication, and lipid meta...
Source: RNA - April 16, 2024 Category: Genetics & Stem Cells Authors: Rebecca J Haugen Catherine Barnier Nathan D Elrod Hua Luo Madeline K Jensen Ping Ji Craig A Smibert Howard D Lipshitz Eric J Wagner P Lydia Freddolino Aaron C Goldstrohm Source Type: research
The Prp19C subunit Syf2 and the Prp19C-associated protein Cwc15 function in TREX occupancy and transcription elongation
RNA. 2024 Apr 16:rna.079944.124. doi: 10.1261/rna.079944.124. Online ahead of print.ABSTRACTThe Prp19 complex (Prp19C) also named NineTeen Complex (NTC) is conserved from yeast to human and functions in many different processes such as genome stability, splicing and transcription elongation. In the latter, Prp19C ensures TREX occupancy at transcribed genes. TREX in turn couples transcription to nuclear mRNA export by recruiting the mRNA exporter to transcribed genes and consequently to nascent mRNAs. Here, we assess the function of the nonessential Prp19C subunit Syf2 and the nonessential Prp19C-associated protein Cwc15 in...
Source: RNA - April 16, 2024 Category: Genetics & Stem Cells Authors: Laura Henke-Schulz Rashmi Minocha Nils Holger Maier Katja Str äβer Source Type: research
Regulation of the Drosophila transcriptome by Pumilio and the CCR4-NOT deadenylase complex
In this study, we utilize knockdown and knockout approaches coupled with RNA-Seq to measure the impact of Pumilio on the transcriptome of Drosophila cells in culture. We also use an improved RNA co-immunoprecipitation method to identify Pumilio-bound mRNAs in Drosophila embryos. Integration of these datasets with the locations of Pumilio binding motifs across the transcriptome reveal novel direct Pumilio target genes involved in neural, muscle, wing, and germ cell development, and cellular proliferation. These genes include components of Wnt, TGF-beta, MAPK/ERK, and Notch signaling pathways, DNA replication, and lipid meta...
Source: RNA - April 16, 2024 Category: Genetics & Stem Cells Authors: Rebecca J Haugen Catherine Barnier Nathan D Elrod Hua Luo Madeline K Jensen Ping Ji Craig A Smibert Howard D Lipshitz Eric J Wagner P Lydia Freddolino Aaron C Goldstrohm Source Type: research
