Ontology highlight
ABSTRACT:
PROVIDER: PRJNA819988 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Bacteria defend themselves from viral infection using diverse immune systems, many of which sense and target foreign nucleic acids. Defense-associated reverse transcriptase (DRT) systems provide an intriguing counterpoint to this immune strategy by instead leveraging DNA synthesis, but the identities and functions of their DNA products remain largely unknown. Here we show that DRT2 systems execute an unprecedented immunity mechanism that involves de novo gene synthesis via rolling-circle reverse transcription of a non-coding RNA (ncRNA). Unbiased profiling of RT-associated RNA and DNA ligands in DRT2-expressing cells revealed that reverse transcription generates concatenated cDNA repeats through programmed template jumping on the ncRNA. The presence of phage then triggers second-strand cDNA synthesis, leading to the production of long double-stranded DNA. Remarkably, this DNA product is efficiently transcribed, generating messenger RNAs that encode a stop codon-less, never-ending ORF (neo) whose translation causes potent growth arrest. Phylogenetic analyses and screening of diverse DRT2 homologs further revealed broad conservation of rolling-circle reverse transcription and Neo protein function. Our work highlights an elegant expansion of genome coding potential through RNA-templated gene creation, and challenges conventional paradigms of genetic information encoded along the one-dimensional axis of genomic DNA.
2024-06-18 | MSV000095071 | MassIVE
Project description:Bacteria defend themselves from viral predation using diverse immune systems, many of which sense and target foreign nucleic acids. Defense-associated reverse transcriptase (DRT) systems provide an intriguing counterpoint to this immune strategy by instead leveraging DNA synthesis, but the identities and functions of their DNA products remain largely unknown. Here we show that DRT2 systems execute an unprecedented immunity mechanism that involves de novo gene synthesis via rolling-circle reverse transcription of a non-coding RNA (ncRNA). Unbiased profiling of RT-associated RNA and DNA ligands uncovered constitutive synthesis of concatenated cDNA repeats through programmed template jumping on the ncRNA. The presence of phage then triggers second-strand cDNA synthesis, leading to the production of long double-stranded DNA. Remarkably, this nascent ‘gene’ is efficiently transcribed, generating messenger RNAs that encode a stop codon-less, never-ending ORF (neo) whose translation causes potent growth arrest. Phylogenetic analyses and screening of diverse DRT2 homologs further revealed broad conservation of rolling-circle reverse transcription and Neo protein function. Our work highlights an elegant expansion of genome coding potential through RNA-templated gene creation, and challenges conventional paradigms of genetic information encoded along the one-dimensional axis of genomic DNA.
2024-08-11 | GSE270162 | GEO
Project description:Bacteria defend themselves from viral predation using diverse immune systems, many of which sense and target foreign nucleic acids. Defense-associated reverse transcriptase (DRT) systems provide an intriguing counterpoint to this immune strategy by instead leveraging DNA synthesis, but the identities and functions of their DNA products remain largely unknown. Here we show that DRT2 systems execute an unprecedented immunity mechanism that involves de novo gene synthesis via rolling-circle reverse transcription of a non-coding RNA (ncRNA). Unbiased profiling of RT-associated RNA and DNA ligands uncovered constitutive synthesis of concatenated cDNA repeats through programmed template jumping on the ncRNA. The presence of phage then triggers second-strand cDNA synthesis, leading to the production of long double-stranded DNA. Remarkably, this nascent ‘gene’ is efficiently transcribed, generating messenger RNAs that encode a stop codon-less, never-ending ORF (neo) whose translation causes potent growth arrest. Phylogenetic analyses and screening of diverse DRT2 homologs further revealed broad conservation of rolling-circle reverse transcription and Neo protein function. Our work highlights an elegant expansion of genome coding potential through RNA-templated gene creation, and challenges conventional paradigms of genetic information encoded along the one-dimensional axis of genomic DNA.
2024-08-11 | GSE270161 | GEO
Project description:Bacteria defend themselves from viral predation using diverse immune systems, many of which sense and target foreign nucleic acids. Defense-associated reverse transcriptase (DRT) systems provide an intriguing counterpoint to this immune strategy by instead leveraging DNA synthesis, but the identities and functions of their DNA products remain largely unknown. Here we show that DRT2 systems execute an unprecedented immunity mechanism that involves de novo gene synthesis via rolling-circle reverse transcription of a non-coding RNA (ncRNA). Unbiased profiling of RT-associated RNA and DNA ligands uncovered constitutive synthesis of concatenated cDNA repeats through programmed template jumping on the ncRNA. The presence of phage then triggers second-strand cDNA synthesis, leading to the production of long double-stranded DNA. Remarkably, this nascent ‘gene’ is efficiently transcribed, generating messenger RNAs that encode a stop codon-less, never-ending ORF (neo) whose translation causes potent growth arrest. Phylogenetic analyses and screening of diverse DRT2 homologs further revealed broad conservation of rolling-circle reverse transcription and Neo protein function. Our work highlights an elegant expansion of genome coding potential through RNA-templated gene creation, and challenges conventional paradigms of genetic information encoded along the one-dimensional axis of genomic DNA.
2024-08-11 | GSE270160 | GEO
Project description:We present Smart-Seq2 Rolling Circle to Concatemeric Consensus (Smar2C2) for the identification and quantification of transcription start sites. Smar2C2 allows for the identification of upwards of 70 million unique transcription start sites from a single sample with as little as 40 pg of RNA input.
2022-10-04 | GSE197144 | GEO
Project description:We report isoCirc, a long-read sequencing strategy coupled with an integrated computational pipeline to characterize full-length circular RNA (circRNA isoforms) using rolling circle amplification (RCA) followed by long-read sequencing. Applying isoCirc to 12 human tissues, we determined full-length structures and examined tissue specificities of circRNA isoforms in human transcriptomes.
2020-09-12 | GSE141693 | GEO
Project description:This study investigated changes in the transcriptome of outdoor grown leafy spurge crown buds as they progress from paradormancy in August and September into endo dormancy in October through to ecodormancy in November and December. Keywords: Dormancy leafy spurge adventitious-buds A series of balanced dyeswap rolling circle hybiridizations were used with each year representing s seperate circle and with direction of the circles reversing on alternate years. Note, the Aug-Sep 04 hybridization failed and is missing from the dataset
2007-08-23 | E-GEOD-8849 | biostudies-arrayexpress
Project description:Circular RNA (circRNA) has recently gained attention for its emerging biological activities, relevance to disease, and potential as biomarkers. Furthermore, the growing prominence of RNA vaccines has brought circRNAs into the spotlight as a promising alternative modality due to their enhanced stability compared to linear RNA. Nevertheless, sequencing circRNAs has presented challenges. In this context, we introduce a novel circRNA sequencing method called Induro-RT mediated circRNA-sequencing (IMCR-seq), which relies on a group II intron reverse transcriptase with robust rolling circle reverse transcription activity. The IMCR-seq protocol eliminates the need for conventional circRNA enrichment methods such as rRNA depletion and RNaseR digestion yet achieved the highest circRNA enrichment and detected 6-1000 times more circRNAs for the benchmarked human samples compared to other methods. IMCR-seq is applicable to any organism, capable of detecting circRNAs of more than 7,000 nucleotides, and is effective using as little as 10 ng of total RNA. These enhancements render IMCR-seq suitable for clinical samples, including disease tissues and liquid biopsies. To demonstrate IMCR-seq's clinical relevance, we applied it to lung tumor tissue and plasma samples from a healthy individual and a lung cancer patient and detected cancer-specific circRNAs as potential biomarkers. In summary, IMCR-seq presents an efficient and versatile circRNA sequencing method with high potential for research and clinical applications.
2024-06-01 | GSE248303 | GEO