Pervasive translation of Xrn1-sensitive unstable long non-coding RNAs in yeast
RNA. 2024 Mar 5:rna.079903.123. doi: 10.1261/rna.079903.123. Online ahead of print.ABSTRACTDespite being predicted to lack coding potential, cytoplasmic long non-coding (lnc)RNAs can associate with ribosomes. However, the landscape and biological relevance of lncRNAs translation remains poorly studied. In yeast, cytoplasmic Xrn1-sensitive lncRNAs (XUTs) are targeted by the Nonsense-Mediated mRNA Decay (NMD), suggesting a translation-dependent degradation process. Here, we report that XUTs are pervasively translated, which impacts their decay. We show that XUTs globally accumulate upon translation elongation inhibition, but...
Source: RNA - March 5, 2024 Category: Genetics & Stem Cells Authors: Sara Andjus Ugo Szachnowski Nicolas Vogt Stamatia Gioftsidi Isabelle Hatin David Cornu Chris Papadopoulos Anne Lopes Olivier Namy Maxime Wery Antonin Morillon Source Type: research
A Role for SNU66 in Maintaining 5' Splice Site Identity During Spliceosome Assembly
RNA. 2024 Mar 5:rna.079971.124. doi: 10.1261/rna.079971.124. Online ahead of print.ABSTRACTIn spliceosome assembly, the 5' splice site is initially recognized by U1snRNA. U1 leaves the spliceosome during the assembly process, therefore other factors contribute to maintenance of 5' splice site identity as it is loaded into the catalytic site. Recent structural data suggest that human tri-snRNP 27K (SNRP27) M141 and SNU66 H734 interact to stabilize the U4/U6 quasi-pseudo knot at the base of the U6 snRNA ACAGAGA box in pre-B complex. Previously, we found that mutations in C. elegans at SNRP-27 M141 promote changes in alternat...
Source: RNA - March 5, 2024 Category: Genetics & Stem Cells Authors: Kenna Sarka Sol Katzman Alan M Zahler Source Type: research
Pervasive translation of Xrn1-sensitive unstable long non-coding RNAs in yeast
RNA. 2024 Mar 5:rna.079903.123. doi: 10.1261/rna.079903.123. Online ahead of print.ABSTRACTDespite being predicted to lack coding potential, cytoplasmic long non-coding (lnc)RNAs can associate with ribosomes. However, the landscape and biological relevance of lncRNAs translation remains poorly studied. In yeast, cytoplasmic Xrn1-sensitive lncRNAs (XUTs) are targeted by the Nonsense-Mediated mRNA Decay (NMD), suggesting a translation-dependent degradation process. Here, we report that XUTs are pervasively translated, which impacts their decay. We show that XUTs globally accumulate upon translation elongation inhibition, but...
Source: RNA - March 5, 2024 Category: Genetics & Stem Cells Authors: Sara Andjus Ugo Szachnowski Nicolas Vogt Stamatia Gioftsidi Isabelle Hatin David Cornu Chris Papadopoulos Anne Lopes Olivier Namy Maxime Wery Antonin Morillon Source Type: research
Novel RNA molecular bioengineering technology efficiently produces functional miRNA agents
In this study, we aim to compare the production of bioengineered RNA (BioRNA) molecules with glycyl versus leucyl htRNA fused hsa-pre-miR-34a carriers, namely BioRNAGly and BioRNALeu, respectively, and perform initial functional assessment. We designed, cloned, overexpressed, and purified a total of 48 new BioRNA/miRNAs, and overall expression levels, final yields, and purities were revealed to be comparable between BioRNAGly and BioRNALeu molecules. Meanwhile, the two versions of BioRNA/miRNAs showed similar activities to inhibit non-small cell lung cancer cell viability. Interestingly, functional analyses using model Bio...
Source: RNA - March 1, 2024 Category: Genetics & Stem Cells Authors: Gavin M Traber Colleen Yi Neelu Batra Meijuan Tu Aiming Yu Source Type: research
Novel RNA molecular bioengineering technology efficiently produces functional miRNA agents
In this study, we aim to compare the production of bioengineered RNA (BioRNA) molecules with glycyl versus leucyl htRNA fused hsa-pre-miR-34a carriers, namely BioRNAGly and BioRNALeu, respectively, and perform initial functional assessment. We designed, cloned, overexpressed, and purified a total of 48 new BioRNA/miRNAs, and overall expression levels, final yields, and purities were revealed to be comparable between BioRNAGly and BioRNALeu molecules. Meanwhile, the two versions of BioRNA/miRNAs showed similar activities to inhibit non-small cell lung cancer cell viability. Interestingly, functional analyses using model Bio...
Source: RNA - March 1, 2024 Category: Genetics & Stem Cells Authors: Gavin M Traber Colleen Yi Neelu Batra Meijuan Tu Aiming Yu Source Type: research
Novel RNA molecular bioengineering technology efficiently produces functional miRNA agents
In this study, we aim to compare the production of bioengineered RNA (BioRNA) molecules with glycyl versus leucyl htRNA fused hsa-pre-miR-34a carriers, namely BioRNAGly and BioRNALeu, respectively, and perform initial functional assessment. We designed, cloned, overexpressed, and purified a total of 48 new BioRNA/miRNAs, and overall expression levels, final yields, and purities were revealed to be comparable between BioRNAGly and BioRNALeu molecules. Meanwhile, the two versions of BioRNA/miRNAs showed similar activities to inhibit non-small cell lung cancer cell viability. Interestingly, functional analyses using model Bio...
Source: RNA - March 1, 2024 Category: Genetics & Stem Cells Authors: Gavin M Traber Colleen Yi Neelu Batra Meijuan Tu Aiming Yu Source Type: research
Novel RNA molecular bioengineering technology efficiently produces functional miRNA agents
In this study, we aim to compare the production of bioengineered RNA (BioRNA) molecules with glycyl versus leucyl htRNA fused hsa-pre-miR-34a carriers, namely BioRNAGly and BioRNALeu, respectively, and perform initial functional assessment. We designed, cloned, overexpressed, and purified a total of 48 new BioRNA/miRNAs, and overall expression levels, final yields, and purities were revealed to be comparable between BioRNAGly and BioRNALeu molecules. Meanwhile, the two versions of BioRNA/miRNAs showed similar activities to inhibit non-small cell lung cancer cell viability. Interestingly, functional analyses using model Bio...
Source: RNA - March 1, 2024 Category: Genetics & Stem Cells Authors: Gavin M Traber Colleen Yi Neelu Batra Meijuan Tu Aiming Yu Source Type: research
Rational design of oligonucleotides for enhanced in vitro transcription of small RNA
RNA. 2024 Feb 29:rna.079923.123. doi: 10.1261/rna.079923.123. Online ahead of print.ABSTRACTAll kinds of RNA molecules can be produced by in vitro transcription using T7 RNA polymerase using DNA templates obtained by solid-phase chemical synthesis, primer extension, PCR or DNA cloning. The oligonucleotide design, however, is a challenge to non-experts as this relies on a set of rules that have been established empirically over time. Here, we describe a Python program to facilitate the Rational design of Oligonucleotides, Calculated with Kinetic parameters for Enhanced in vitro Transcription (ROCKET). The Python tool employ...
Source: RNA - February 29, 2024 Category: Genetics & Stem Cells Authors: Teppei Matsuda Hiroyuki Hori Ryota Yamagami Source Type: research
High-throughput quantitation of protein-RNA UV-crosslinking efficiencies as a predictive tool for high confidence identification of RNA binding proteins
RNA. 2024 Feb 29:rna.079848.123. doi: 10.1261/rna.079848.123. Online ahead of print.ABSTRACTUV-crosslinking has proven to be an invaluable tool for the identification of RNA-protein interactomes. The paucity of methods for distinguishing background from bona fide RNA-protein interactions however makes attribution of RNA binding function on UV-crosslinking alone challenging. To address this need, we previously reported an RNA binding protein (RBP) confidence scoring metric, (RCS), incorporating both signal-to-noise (S:N) and protein abundance determinations to distinguish high and low confidence candidate RBPs. Although RCS...
Source: RNA - February 29, 2024 Category: Genetics & Stem Cells Authors: Johncarlo Kristofich Christopher Nicchitta Source Type: research
Rational design of oligonucleotides for enhanced in vitro transcription of small RNA
RNA. 2024 Feb 29:rna.079923.123. doi: 10.1261/rna.079923.123. Online ahead of print.ABSTRACTAll kinds of RNA molecules can be produced by in vitro transcription using T7 RNA polymerase using DNA templates obtained by solid-phase chemical synthesis, primer extension, PCR or DNA cloning. The oligonucleotide design, however, is a challenge to non-experts as this relies on a set of rules that have been established empirically over time. Here, we describe a Python program to facilitate the Rational design of Oligonucleotides, Calculated with Kinetic parameters for Enhanced in vitro Transcription (ROCKET). The Python tool employ...
Source: RNA - February 29, 2024 Category: Genetics & Stem Cells Authors: Teppei Matsuda Hiroyuki Hori Ryota Yamagami Source Type: research
High-throughput quantitation of protein-RNA UV-crosslinking efficiencies as a predictive tool for high confidence identification of RNA binding proteins
RNA. 2024 Feb 29:rna.079848.123. doi: 10.1261/rna.079848.123. Online ahead of print.ABSTRACTUV-crosslinking has proven to be an invaluable tool for the identification of RNA-protein interactomes. The paucity of methods for distinguishing background from bona fide RNA-protein interactions however makes attribution of RNA binding function on UV-crosslinking alone challenging. To address this need, we previously reported an RNA binding protein (RBP) confidence scoring metric, (RCS), incorporating both signal-to-noise (S:N) and protein abundance determinations to distinguish high and low confidence candidate RBPs. Although RCS...
Source: RNA - February 29, 2024 Category: Genetics & Stem Cells Authors: Johncarlo Kristofich Christopher Nicchitta Source Type: research
A side-by-side comparison of peptide-delivered antisense antibiotics employing different nucleotide mimics
RNA. 2024 Feb 27:rna.079969.124. doi: 10.1261/rna.079969.124. Online ahead of print.ABSTRACTAntisense oligomer (ASO)-based antibiotics that target mRNAs of essential bacterial genes have great potential for counteracting antimicrobial resistance and for precision microbiome editing. To date, the development of such antisense antibiotics has primarily focused on using phosphorodiamidate morpholino (PMO) and peptide nucleic acid (PNA) backbones, largely ignoring the growing number of chemical modalities that have spurred the success of ASO-based human therapy. Here, we directly compare the activities of seven chemically dist...
Source: RNA - February 27, 2024 Category: Genetics & Stem Cells Authors: Chandradhish Ghosh Linda Popella V Dhamodharan Jakob Jung Julia Dietzsch Lars Barquist Claudia H öbartner J örg Vogel Source Type: research
A side-by-side comparison of peptide-delivered antisense antibiotics employing different nucleotide mimics
RNA. 2024 Feb 27:rna.079969.124. doi: 10.1261/rna.079969.124. Online ahead of print.ABSTRACTAntisense oligomer (ASO)-based antibiotics that target mRNAs of essential bacterial genes have great potential for counteracting antimicrobial resistance and for precision microbiome editing. To date, the development of such antisense antibiotics has primarily focused on using phosphorodiamidate morpholino (PMO) and peptide nucleic acid (PNA) backbones, largely ignoring the growing number of chemical modalities that have spurred the success of ASO-based human therapy. Here, we directly compare the activities of seven chemically dist...
Source: RNA - February 27, 2024 Category: Genetics & Stem Cells Authors: Chandradhish Ghosh Linda Popella V Dhamodharan Jakob Jung Julia Dietzsch Lars Barquist Claudia H öbartner J örg Vogel Source Type: research
High-resolution RNA tertiary structures in Zika virus stem-loop A for the development of inhibitory small molecules
RNA. 2024 Feb 21:rna.079796.123. doi: 10.1261/rna.079796.123. Online ahead of print.ABSTRACTFlaviviruses such as Zika (ZIKV) and dengue virus (DENV) are positive-sense RNA viruses belonging to Flaviviridae. The flavivirus genome contains a 5' end stem-loop promoter sequence known as stem-loop A (SLA) that is recognized by the flavivirus polymerase NS5 during viral RNA synthesis and 5' guanosine cap methylation. The crystal structures of ZIKV and DENV SLAs show a well-defined fold, consisting of a bottom stem, side loop, and top stem-loop, providing unique interaction sites for small-molecule inhibitors to disrupt the promo...
Source: RNA - February 21, 2024 Category: Genetics & Stem Cells Authors: Jerricho Tipo Keerthi Gottipati Kyung H Choi Source Type: research
High-resolution RNA tertiary structures in Zika virus stem-loop A for the development of inhibitory small molecules
RNA. 2024 Feb 21:rna.079796.123. doi: 10.1261/rna.079796.123. Online ahead of print.ABSTRACTFlaviviruses such as Zika (ZIKV) and dengue virus (DENV) are positive-sense RNA viruses belonging to Flaviviridae. The flavivirus genome contains a 5' end stem-loop promoter sequence known as stem-loop A (SLA) that is recognized by the flavivirus polymerase NS5 during viral RNA synthesis and 5' guanosine cap methylation. The crystal structures of ZIKV and DENV SLAs show a well-defined fold, consisting of a bottom stem, side loop, and top stem-loop, providing unique interaction sites for small-molecule inhibitors to disrupt the promo...
Source: RNA - February 21, 2024 Category: Genetics & Stem Cells Authors: Jerricho Tipo Keerthi Gottipati Kyung H Choi Source Type: research
