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
Cytosolic RNA binding of the mitochondrial TCA cycle enzyme malate dehydrogenase (MDH2)
RNA. 2024 Apr 12:rna.079925.123. doi: 10.1261/rna.079925.123. Online ahead of print.ABSTRACTSeveral enzymes of intermediary metabolism have been identified to bind RNA in 2 cells, with potential consequences for the bound RNAs and/or the enzyme. In this 3 study, we investigate the RNA-binding activity of the mitochondrial enzyme malate 4 dehydrogenase 2 (MDH2), which functions in the tricarboxylic acid (TCA) cycle and 5 the malate-aspartate shuttle. We confirmed in cellulo RNA-binding of MDH2 using 6 orthogonal biochemical assays and performed enhanced crosslinking and 7 immunoprecipitation (eCLIP) to identify the cellular...
Source: RNA - April 12, 2024 Category: Genetics & Stem Cells Authors: Michelle Noble Aindrila Chatterjee Thileepan Sekaran Thomas Schwarzl Matthias W Hentze Source Type: research
Cytosolic RNA binding of the mitochondrial TCA cycle enzyme malate dehydrogenase (MDH2)
RNA. 2024 Apr 12:rna.079925.123. doi: 10.1261/rna.079925.123. Online ahead of print.ABSTRACTSeveral enzymes of intermediary metabolism have been identified to bind RNA in 2 cells, with potential consequences for the bound RNAs and/or the enzyme. In this 3 study, we investigate the RNA-binding activity of the mitochondrial enzyme malate 4 dehydrogenase 2 (MDH2), which functions in the tricarboxylic acid (TCA) cycle and 5 the malate-aspartate shuttle. We confirmed in cellulo RNA-binding of MDH2 using 6 orthogonal biochemical assays and performed enhanced crosslinking and 7 immunoprecipitation (eCLIP) to identify the cellular...
Source: RNA - April 12, 2024 Category: Genetics & Stem Cells Authors: Michelle Noble Aindrila Chatterjee Thileepan Sekaran Thomas Schwarzl Matthias W Hentze Source Type: research
Cytosolic RNA binding of the mitochondrial TCA cycle enzyme malate dehydrogenase (MDH2)
RNA. 2024 Apr 12:rna.079925.123. doi: 10.1261/rna.079925.123. Online ahead of print.ABSTRACTSeveral enzymes of intermediary metabolism have been identified to bind RNA in 2 cells, with potential consequences for the bound RNAs and/or the enzyme. In this 3 study, we investigate the RNA-binding activity of the mitochondrial enzyme malate 4 dehydrogenase 2 (MDH2), which functions in the tricarboxylic acid (TCA) cycle and 5 the malate-aspartate shuttle. We confirmed in cellulo RNA-binding of MDH2 using 6 orthogonal biochemical assays and performed enhanced crosslinking and 7 immunoprecipitation (eCLIP) to identify the cellular...
Source: RNA - April 12, 2024 Category: Genetics & Stem Cells Authors: Michelle Noble Aindrila Chatterjee Thileepan Sekaran Thomas Schwarzl Matthias W Hentze Source Type: research
The novel pre-rRNA detection workflow "Riboprobing" allows simple identification of undescribed RNA species
RNA. 2024 Apr 5:rna.079912.123. doi: 10.1261/rna.079912.123. Online ahead of print.ABSTRACTRibosomes translate mRNA into proteins and are essential for every living organism. In eukaryotes both ribosomal subunits are rapidly assembled in a strict hierarchical order, starting in the nucleolus with transcription of a common precursor ribosomal RNA (pre-rRNA). This pre-rRNA encodes three of the four mature rRNAs which are formed by several, consecutive endonucleolytic and exonucleolytic processing steps. Historically, Northern Blots are used to analyze the variety of different pre-rRNA species, only allowing rough length esti...
Source: RNA - April 5, 2024 Category: Genetics & Stem Cells Authors: Magdalena Gerhalter Lisa Kofler Gertrude Zisser Juliane Merl-Pham Stefanie M Hauck Helmut Bergler Source Type: research
The novel pre-rRNA detection workflow "Riboprobing" allows simple identification of undescribed RNA species
RNA. 2024 Apr 5:rna.079912.123. doi: 10.1261/rna.079912.123. Online ahead of print.ABSTRACTRibosomes translate mRNA into proteins and are essential for every living organism. In eukaryotes both ribosomal subunits are rapidly assembled in a strict hierarchical order, starting in the nucleolus with transcription of a common precursor ribosomal RNA (pre-rRNA). This pre-rRNA encodes three of the four mature rRNAs which are formed by several, consecutive endonucleolytic and exonucleolytic processing steps. Historically, Northern Blots are used to analyze the variety of different pre-rRNA species, only allowing rough length esti...
Source: RNA - April 5, 2024 Category: Genetics & Stem Cells Authors: Magdalena Gerhalter Lisa Kofler Gertrude Zisser Juliane Merl-Pham Stefanie M Hauck Helmut Bergler Source Type: research
The novel pre-rRNA detection workflow "Riboprobing" allows simple identification of undescribed RNA species
RNA. 2024 Apr 5:rna.079912.123. doi: 10.1261/rna.079912.123. Online ahead of print.ABSTRACTRibosomes translate mRNA into proteins and are essential for every living organism. In eukaryotes both ribosomal subunits are rapidly assembled in a strict hierarchical order, starting in the nucleolus with transcription of a common precursor ribosomal RNA (pre-rRNA). This pre-rRNA encodes three of the four mature rRNAs which are formed by several, consecutive endonucleolytic and exonucleolytic processing steps. Historically, Northern Blots are used to analyze the variety of different pre-rRNA species, only allowing rough length esti...
Source: RNA - April 5, 2024 Category: Genetics & Stem Cells Authors: Magdalena Gerhalter Lisa Kofler Gertrude Zisser Juliane Merl-Pham Stefanie M Hauck Helmut Bergler Source Type: research
