Transcription Termination and Antitermination of Bacterial CRISPR Arrays
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB40545 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR4627580_1.fastq.gz | Fastqsanger.gz | |||
| ERR4627580_2.fastq.gz | Fastqsanger.gz | |||
| ERR4627581_1.fastq.gz | Fastqsanger.gz | |||
| ERR4627581_2.fastq.gz | Fastqsanger.gz | |||
| ERR4627582_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 18 |
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Project description:Nus factors prevent premature transcription termination of bacterial CRISPR arrays
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Project description:We used ChIP-seq to map binding of the CRISPR surveillance complex, Cascade, in a Salmonella enterica serovar Typhimurium strain lacking the gene encoding the endonuclease Cas3. We performed ChIP-seq in strains with wild-type and mutant sequences upstream of the two CRISPR arrays, and in strains with wild-type and mutant nusE genes to determine the impact of Nus factor antitermination on CRISPR array function.
2018-10-13 | E-MTAB-7242 | biostudies-arrayexpress
Project description:V. cholerae A50 has a functional CRISPR-cas system with a conserved boxA sequence. Plasmids harboring protospacers that are perfect targets for each spacer of the array are introduced into wt and boxA mutant V. cholerae. After a period of growth without selection, cells are collected and the protospacer plasmids are sequenced in a high throughput manner.
2020-10-08 | E-MTAB-9631 | biostudies-arrayexpress
Project description:A hallmark of CRISPR-Cas immunity systems is the CRISPR array, a genomic locus consisting of short, repeated sequences ('repeats') interspersed with short, variable sequences ('spacers'). CRISPR arrays are transcribed and processed into individual CRISPR RNAs that each include a single spacer, and direct Cas proteins to complementary sequences in invading nucleic acid. Most bacterial CRISPR array transcripts are unusually long for untranslated RNA, suggesting the existence of mechanisms to prevent premature transcription termination by Rho, a conserved bacterial transcription termination factor that rapidly terminates untranslated RNA. We show that Rho can prematurely terminate transcription of bacterial CRISPR arrays, and we identify a widespread antitermination mechanism that antagonizes Rho to facilitate complete transcription of CRISPR arrays. Thus, our data highlight the importance of transcription termination and antitermination in the evolution of bacterial CRISPR-Cas systems.
| S-EPMC7665894 | biostudies-literature
Project description:CRISPR arrays form the physical memory of CRISPR adaptive immune systems by incorporating foreign DNA as spacers that are often AT-rich and derived from viruses. As promoter elements such as the TATA-box are AT-rich, CRISPR arrays are prone to harbouring cryptic promoters. Sulfolobales harbor extremely long CRISPR arrays spanning several kilobases, a feature that is accompanied by the CRISPR-specific transcription factor Cbp1. Aberrant Cbp1 expression modulates CRISPR array transcription, but the molecular mechanisms underlying this regulation are unknown. Here, we characterise the genome-wide Cbp1 binding at nucleotide resolution and characterise the binding motifs on distinct CRISPR arrays, as well as on unexpected non-canonical binding sites associated with transposasons. Cbp1 recruits Cren7 forming together ‘chimeric’ chromatin-like structures at CRISPR arrays. We dissect Cbp1 function in vitro and in vivo and show that the third HTH domain is responsible for Cren7 recruitment, and that Cbp1-Cren7 chromatinization plays a dual role in the transcription of CRISPR arrays. It suppresses spurious transcription from cryptic promoters within CRISPR arrays but enhances CRISPR RNA transcription directed from their cognate promoters in their leader region. Our results show that Cbp1-Cren7 chromatinization drives the productive expression of long CRISPR arrays.
2023-03-24 | GSE226026 | GEO
Project description:Transcription termination of mRNAs transcribed from a given locus has a decisive role in regulating the gene function as it determines the coding potential and inclusion of regulatory sequence elements. Failure in appropriate transcription termination leads to read-through transcription, resulting in the synthesis of antisense RNAs which can have profound impact on overall gene expression. However, molecular mechanisms which regulate transcription termination and chimeric RNA formation are poorly understood. We explored the regulatory function of transcription and export complex (THO/TREX) in transcription termination. We show that two members of THO/TREX complex, TREX COMPONENT 1 (TEX1) and HYPER RECOMBINATION1(HPR1) are critical for the correct transcription termination in Arabidopsis. We first demonstrate this by showing defective termination of the bacterial nopaline synthase (NOS) terminator on a transgene in tex1 and hpr1 mutants. Additionally, we show that RNA termination defects in tex1 and hpr1 mutants are widespread at the whole genome levels leading to 3’UTR extensions, truncations and in some cases in the formation of intergenic chimeric transcripts. Chromatin immunoprecipitation coupled with quantitative PCR experiments confirmed the presence of RNA polymerase II beyond the canonical termination sites on genes with defective RNA termination in tex1 and hpr1 mutants. These results demonstrate that THO/TREX complex is a novel regulator of transcription termination in Arabidopsis.
2020-03-24 | GSE128877 | GEO
Project description:Rho dependent transcription termination is a dominant mechanism of transcription termination in Mycobacterium tuberculosis
2017-08-01 | GSE97559 | GEO
Project description:Canonical bacterial intrinsic terminators do not require additional factors for efficient transcription termination, although the general transcription elongation factor NusA was known to increase the termination efficiency slightly in vitro. We found that the effect of NusA varies widely among different terminators and identified a subclass of weak non-canonical terminators that largely depend on NusA for recognition by RNA polymerase. Using genome-wide 3’ end-mapping on an engineered Bacillus subtilis NusA depletion strain, we identified >2000 intrinsic terminators, hundreds of which are NusA-dependent. Our in vitro and in vivo characterization showed that terminators with weak RNA hairpins and distal U-tract interruptions tend to be NusA-dependent. Our observations indicate that the lethality associated with deletion of nusA is caused by global readthrough of NusA-dependent terminators, resulting in misregulation of physiologically important downstream genes. We also show that nusA expression is autoregulated by a transcription attenuation mechanism that is mediated by NusA-dependent termination.
2016-01-01 | GSE67058 | GEO
Project description:Transcription termination determines the ends of transcriptional units and thereby ensures integrity of gene regulation. Here we perform genome-wide investigation of RNA polymerase II (Pol II) transcription termination in Caenorhabditis elegans and observe two distinct modes of termination. Whereas a subset of genes requires the exoribonuclease XRN2, a known termination factor, termination of other genes appears independent of, and refractory to, XRN2. Unexpectedly, promoters instruct the choice of termination mode, but XRN2-independent termination additionally requires a compatible region downstream of the 3’ end cleavage site. Hence, different termination mechanisms may affect different configurations of Pol II complexes dictated by promoters.
2018-02-05 | GSE97775 | GEO
Project description:Canonical bacterial intrinsic terminators do not require additional factors for efficient transcription termination, although the general transcription elongation factor NusA was known to increase the termination efficiency slightly in vitro. We found that the effect of NusA varies widely among different terminators and identified a subclass of weak non-canonical terminators that largely depend on NusA for recognition by RNA polymerase. Using genome-wide 3â end-mapping on an engineered Bacillus subtilis NusA depletion strain, we identified >2000 intrinsic terminators, hundreds of which are NusA-dependent. Our in vitro and in vivo characterization showed that terminators with weak RNA hairpins and distal U-tract interruptions tend to be NusA-dependent. Our observations indicate that the lethality associated with deletion of nusA is caused by global readthrough of NusA-dependent terminators, resulting in misregulation of physiologically important downstream genes. We also show that nusA expression is autoregulated by a transcription attenuation mechanism that is mediated by NusA-dependent termination. 3' end-mapping and mRNA profiling of stationary phase B. subtilis NusA-depletion (PLBS802) strain in NusA expressing and depleted conditions, 6 replicates each.
2016-07-03 | E-GEOD-67058 | biostudies-arrayexpress