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
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
Computational analysis of super-resolved in situ sequencing data reveals genes modified by immune-tumor contact events
RNA. 2024 Apr 4:rna.079801.123. doi: 10.1261/rna.079801.123. Online ahead of print.ABSTRACTCancer cells can manipulate immune cells and escape from the immune system response. Quantifying the molecular changes that occur when an immune cell is touching a tumor cell can increase our understanding of the underlying mechanisms. Recently, it became possible to perform such measurements in situ, for example using expansion sequencing, which enabled in situ sequencing of genes with super-resolution. We systematically examined whether individual immune cells from specific cell types express genes differently when in physical prox...
Source: RNA - April 4, 2024 Category: Genetics & Stem Cells Authors: Michal Danino-Levi Tal Goldberg Maya Keter Nikol Akselrod Noa Shprach-Buaron Modi Safra Gonen Singer Shahar Alon Source Type: research
Inefficient recruitment of DDX39B impedes pre-spliceosome assembly on FOXP3 introns
RNA. 2024 Apr 4:rna.079933.123. doi: 10.1261/rna.079933.123. Online ahead of print.ABSTRACTForkhead box P3 (FOXP3) is the master fate-determining transcription factor in regulatory T (Treg) cells and is essential for their development, function and homeostasis. Mutations in FOXP3 cause immunodysregulation polyendocrinopathy enteropathy X-linked (IPEX) syndrome, and aberrant expression of FOXP3 has been implicated in other diseases such as multiple sclerosis and cancer. We previously demonstrated that pre-mRNA splicing of FOXP3 RNAs is highly sen-sitive to levels of DExD-box polypeptide 39B (DDX39B) and here we investigate ...
Source: RNA - April 4, 2024 Category: Genetics & Stem Cells Authors: Chloe K Nagasawa Aaron O Bailey William Russell Mariano A Garcia-Blanco Source Type: research
