Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR5957680.fastq.gz | Fastqsanger.gz | |||
| SRR5957690.fastq.gz | Fastqsanger.gz | |||
| SRR5957700.fastq.gz | Fastqsanger.gz | |||
| SRR5957710.fastq.gz | Fastqsanger.gz | |||
| SRR5957720.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:In bacteria and archaea, CRISPR loci confer adaptive, sequence-based immunity against viruses and plasmids. CRISPR interference is specified by CRISPR RNAs (crRNAs) that are transcribed and processed from CRISPR spacers and repeats. Pre-crRNA processing is essential for CRISPR interference in all systems studied thus far. Here we examine crRNA biogenesis and CRISPR interference in naturally competent Neisseria spp., including the human pathogen N. meningitidis. Our studies reveal a unique crRNA maturation pathway in which crRNA transcription is driven by promoters that are embedded within each repeat, yielding crRNA 5’ ends are not formed by processing. Although crRNA 3’ end formation occurs through RNase III cleavage of a pre-crRNA/tracrRNA duplex, as in other Type II CRISPR systems, this processing event is dispensable for interference. The meningococcal pathway is the most streamlined CRISPR/cas system characterized to date. Endogenous CRISPR spacers frequently target genomic sequences of other Neisseria strains and so limit natural transformation, which is the primary source of genetic variation that contributes to immune evasion, antibiotic resistance, and virulence in N. meningitidis. dRNA-seq approach for RNA samples from cultures of N. lactamica 020-06, harvested at mid-log. Two cDNA libraries from total RNA were prepared to distinguish between transcripts with either primary orprocessed 5’ ends: one library is generated from untreated RNA, whereas the other is treated with terminator exonuclease (TEX),
2013-04-23 | E-GEOD-44582 | biostudies-arrayexpress
Project description:To gain a global view on the impact of the collateral activity on protein expression levels, mass spectrometry was used for proteomics analysis of HEK 293T cells when PspCas13b was co-expressed with non-targeted (NT) crRNA or targeting (T) crRNA, which targets the BCR-ABL1 mRNA breakpoint. There was no evidence of off-target protein degradation by T crRNA compared to the non-targeting crRNA. The only significantly repressed proteins were the target BCR-ABL1 p190 (81% reduction) and eGFP (89% reduction) that are encoded on the same mRNA expression construct and encoded mRNA. Catalytic dead Cas13 (dCas13) and crRNA only were used as negative control.
2024-05-20 | PXD051089 | Pride
Project description:The associated experiments document the production of small RNA (sRNA) during the expression of Cas13 and crRNA, crRNA alone, or controls from agrobacterium spot infiltration in Nicotiana benthamiana. We document the specific production of sRNA corresponding to the guide sequence of the targeted mRNA. In cases where a multi-guide crRNA or a hairpin were expressed, abundent sRNA are produced correspinding to the target mRNA, but outside of the corresponding guide sequence site.
2021-12-07 | GSE171980 | GEO
Project description:In bacteria and archaea, CRISPR loci confer adaptive, sequence-based immunity against viruses and plasmids. CRISPR interference is specified by CRISPR RNAs (crRNAs) that are transcribed and processed from CRISPR spacers and repeats. Pre-crRNA processing is essential for CRISPR interference in all systems studied thus far. Here we examine crRNA biogenesis and CRISPR interference in naturally competent Neisseria spp., including the human pathogen N. meningitidis. Our studies reveal a unique crRNA maturation pathway in which crRNA transcription is driven by promoters that are embedded within each repeat, yielding crRNA 5’ ends are not formed by processing. Although crRNA 3’ end formation occurs through RNase III cleavage of a pre-crRNA/tracrRNA duplex, as in other Type II CRISPR systems, this processing event is dispensable for interference. The meningococcal pathway is the most streamlined CRISPR/cas system characterized to date. Endogenous CRISPR spacers frequently target genomic sequences of other Neisseria strains and so limit natural transformation, which is the primary source of genetic variation that contributes to immune evasion, antibiotic resistance, and virulence in N. meningitidis.
2013-04-23 | GSE44582 | GEO
Project description:To evaluate the specificity of CRISPR activation by vgdCas12a on a genome-wide scale, we carried out whole-transcriptome RNA-seq of HEK293T cells with the TRE3G-GFP reporter transfected with either WT dCas12a or vgdCas12a combined with the TRE3G-targeting crRNA. We also included a non-targeting crRNA as negative control for each case.
2022-01-14 | GSE166817 | GEO
Project description:Many bacteria and archaea use CRISPR-Cas systems, which provide RNA-based, adaptive, and inheritable immune defenses against invading viruses and other foreign genetic elements. The proper processing of CRISPR guide RNAs (crRNAs) is a crucial step in the maturation of the defense complexes and is frequently performed by specialized ribonucleases encoded by cas genes. However, some systems employ enzymes associated with degradosome or housekeeping functions, such as RNase III or the endoribonuclease RNase E. Here, the endo- and 5´-exoribonuclease RNase J was identified as additional enzyme involved in crRNA maturation, acting jointly with RNase E in the crRNA maturation of a type III-Bv CRISPR-Cas system, and possibly together with a further RNase. Co-IP experiments revealed a small set of proteins that were co-enriched with RNase J, among them PNPase. Despite a measured, strong 3’ exonucleolytic activity of the recombinant enzyme, PNPase was not confirmed to contribute to crRNA maturation. However, the co-IP results indicate that PNPase is a component of the cyanobacterial degradosome that can recruit either RNase E or RNase J, together with additional enriched proteins.
2025-10-06 | PXD060866 | Pride
Project description:By a robust unbiased ChIP-seq approach, we demonstrated that CRISPR/Cas9 had crRNA-specific off-target binding activities in human genome. However, most of those binding off-targets could not be efficiently cleaved both in vivo and in vitro which suggested the cleavage off-target activity of CRISPR/Cas9 in human genome is very limited. We provided a valuable tool to further investigate the molecular mechanism of CRISPR/Cas9 and to optimize its in vivo targeting sgRNA binding sites were identified with ChipSeq by using GFP antibody (there are 2 replicates for egfa-t1 sgRNA,emx1 sgRNA and control without sgRNA in Hek293T cells, one egfa-t1 sgRNA,emx1 sgRNA and control without sgRNA in HeLaS3 cells)
2014-06-18 | E-GEOD-58511 | biostudies-arrayexpress
Project description:Prokaryotes create adaptive immune memories by acquiring foreign DNA snippets, known as spacers, into the CRISPR array1. In type II CRISPR-Cas systems, the RNA-guided effector Cas9 also assists the acquisition machinery by selecting spacers from protospacer adjacent motif (PAM)-flanked DNA2,3. Here, we uncover the first biological role for Cas9 that is independent of its dual RNA partners. Following depletion of crRNA and/or tracrRNA, Neisseria apoCas9 stimulates spacer acquisition efficiency. Physiologically, Cas9 senses low levels of crRNA in cells with short CRISPR arrays – such as those undergoing array neogenesis or natural array contractions – and dynamically upregulates acquisition to quickly expand the small immune memory banks. As the CRISPR array expands, rising crRNA abundance in turn reduces apoCas9 availability, thereby dampening acquisition to mitigate autoimmunity risks associate with elevated acquisition. While apoCas9’s nuclease lobe alone suffices for stimulating acquisition, only full-length Cas9 responses to crRNA levels to boost acquisition in cells with low immunity depth. Finally, we show that this activity is evolutionarily conserved across multiple type II-C Cas9 orthologs. Altogether, we establish an auto-replenishing feedback mechanism in which apoCas9 safeguards CRISPR immunity depth by acting as both a crRNA sensor and a regulator of spacer acquisition.
2025-08-29 | GSE302092 | GEO