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Transcription Start Site (TSS) mapping and total RNAseq of Streptomyces scabies wild-type (WT) versus Streptomyces scabies ΔbtmL

ABSTRACT: Transcription Start Site (TSS) mapping and total RNAseq of Streptomyces scabies wild-type (WT) versus Streptomyces scabies ΔbtmL

PROVIDER: PRJEB33939 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR3474090.fastq.gz	Fastqsanger.gz
	ERR3474091.fastq.gz	Fastqsanger.gz
	ERR3474092.fastq.gz	Fastqsanger.gz
	ERR3474087.fastq.gz	Fastqsanger.gz
	ERR3474088.fastq.gz	Fastqsanger.gz

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Transcription Start Site (TSS) mapping and total RNAseq of Streptomyces scabies wild-type (WT) versus Streptomyces scabies ΔbtmL

Project description:The aim of this experiment was to map the transcription start sites (TSSs) in the bottromycin biosynthetic gene cluster from Streptomyces scabies, qualitatively assess the expression levels of this cluster within the bacterium's transcriptome and evaluate whether deletion of a potential regulatory gene in the cluster, btmL affects gene cluster expression.

2020-02-19 | E-MTAB-8236 | biostudies-arrayexpress

Comparative analysis of regulatory elements between Escherichia coli and Klebsiella pneumoniae by genome-wide transcription start site profiling [TSS-Seq]

Project description:We report the application of single-molecule-based sequencing technology for high-throughput profiling of transcription start sites for two enterobacteria: Escherichia coli and Klebsiella pneumoniae.By obtaining over fourteen billion bases of sequence from 5' RACE (rapid amplification of cDNA ends) followed by deep sequencing, we generated genome-wide TSS (transcription start site) maps for those two species. With experimentally derived TSS datasets, we examined usage of multiple TSSs, length of 5' UTR (untranslated region), SD (Shine-Dalgarno) sequence motif, promoter sequence motif, and dinucleotide preference near TSS site. In addition, we used the TSS datasets to identify sRNAs (small RNAs) in E. coli and K. pneumoniae. Based on these analysis, we compared regulatory elements including promoter, 5' UTR and sRNAs between two species, and investigated similarities and differences of upstream regulatory regions. Moreover, sRNAs were also compared and analyzed in terms of their sequences and target sequences, presenting possible working mechanisms of K. pneumoniae sRNAs by transferring prior knowledge from E. coli sRNAs. Examination of transcription start sites by biological duplicates from E. coli and K. pneumoniae

2012-07-30 | E-GEOD-35821 | biostudies-arrayexpress

Comparative analysis of regulatory elements between Escherichia coli and Klebsiella pneumoniae by genome-wide transcription start site profiling [TSS-Seq]

2012-07-30 | GSE35821 | GEO

Comparison of genetic differences between Streptomyces scabies and turgidiscabies strains

Project description:Bacteria isolated from potato scab lesions in Finland or northern Sweden were analyzed using microarrays, PCR, and sequencing. Data indicate wide genetic variability in pathogenicity islands among S.turgidiscabies and S.scabies strains. Thirteen Streptomyces scabies and turgidiscabies strains from two different growings, Streptomyces reticulisabiei reference strain DSM41804 and Streptomyces scabies reference strain ATCC49173 were hybridized. Data were analyzed in single channel mode.

2010-06-18 | E-GEOD-18665 | biostudies-arrayexpress

Transcriptional start site mapping of P14 WT and P14 Tbpl2-/- mutant mouse oocytes

Project description:We used SLIC-CAGE to map transcriptional start sites (TSSs) of P14 WT and P14 Tbpl2-/- mutant mouse oocytes. Comparison of WT and Tbpl2-/- oocytes demonstrates that Tbpl2 guides transcriptional start site selection in the growing oocyte. This TSS selection is different compared to the canonical somatic type of TSS selection and depends on TATA-like elements as core promoter motifs, recognised by Tbpl2.

2020-11-12 | E-MTAB-8866 | biostudies-arrayexpress

Transcription start site positioning is not affected by +1 nucleosome depletion

Project description:The relationship between the positioning of nucleosomes and transcription start sites (TSSs) is unclear. Here, we report that deletion of the Fun30 class chromatin remodelers Fft2 and Fft3 leads to depletion of +1 nucleosome occupancy. Strikingly, in the vast majority of cases, this depletion had no impact on the placement of the TSS, favoring a model where TSS placement is primarily DNA sequence-driven.

2018-06-30 | GSE85046 | GEO

Tur1 regulates alternative TSS usage in Cryptococcus

Project description:Cryptococcus neoformans is a life-threatening basidiomycete fungal pathogen responsible for meningoencephalitis in immunocompromised patients. This yeast can adapt to diverse habitats, efficiently produces virulence factors, and escapes immune surveillance. This implies intricate mechanisms underlying its gene regulation networks, which are yet to be comprehensively understood. Alternative transcription usage regulation has been identified as the major mean for gene expression regulation in metazoans. However, in fungi, its impact remains elusive as its study has thus far been restricted to model yeasts. We here re-analysed transcription start site (TSS)-seq data to define genuine TSS clusters in two species of pathogenic Cryptococcus. We identified two types of TSS clusters associated with specific DNA sequence motifs. Our analysis also revealed that alternative TSS usage regulation in response to environmental cues is widespread in Cryptococcus, altering gene expression and protein targeting. Importantly, we performed a forward genetic screen to identify a unique transcription factor (TF) named Tur1, which regulates aTSS usage genome-wide when cells switch from exponential phase to stationary phase. Tur1 has been previously shown to be essential for virulence in C. neoformans. Accordingly, we demonstrated here that a tur1Δ mutant strain is more sensitive to superoxide stress and phagocytosed more efficiently by macrophages than the Wild-type (WT) strain.

2024-07-03 | PXD045272 | Pride

Transcription start site analysis of Streptococcus agalactiae strain BM110

Project description:Streptococcus agalactiae, also known as Group B streptococcus, emerged in the 1960s as a leading cause of septicemia and meningitis in neonates. It is also an increasing cause of infections in adults with underlying diseases. To characterize transcription start sites (TSS) in the hypervirulent ST17 lineage (strain BM110) we used a differential RNA-seq strategy, based on selective Tobacco Acid Pyrophosphatase (TAP) treatment and adapter ligation, which differentiates primary transcripts and processed RNAs

2021-08-23 | GSE158048 | GEO

TE-TSS: an integrated data resource of human and mouse transposable element (TE)-derived transcription start site (TSS).

Project description:Transposable elements (TEs) are abundant in the genome and serve as crucial regulatory elements. Some TEs function as epigenetically regulated promoters, and these TE-derived transcription start sites (TSSs) play a crucial role in regulating genes associated with specific functions, such as cancer and embryogenesis. However, the lack of an accessible database that systematically gathers TE-derived TSS data is a current research gap. To address this, we established TE-TSS, an integrated data resource of human and mouse TE-derived TSSs (http://xozhanglab.com/TETSS). TE-TSS has compiled 2681 RNA sequencing datasets, spanning various tissues, cell lines and developmental stages. From these, we identified 5768 human TE-derived TSSs and 2797 mouse TE-derived TSSs, with 47% and 38% being experimentally validated, respectively. TE-TSS enables comprehensive exploration of TSS usage in diverse samples, providing insights into tissue-specific gene expression patterns and transcriptional regulatory elements. Furthermore, TE-TSS compares TE-derived TSS regions across 15 mammalian species, enhancing our understanding of their evolutionary and functional aspects. The establishment of TE-TSS facilitates further investigations into the roles of TEs in shaping the transcriptomic landscape and offers valuable resources for comprehending their involvement in diverse biological processes.

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The murine 900 kb downsteam region from Gata3 interacts to the transciption start site and three enhancers in Th2 cells.

Project description:Murine counterpart of the region (mG900 region), in which SNPs associated with human asthma are enriched, is located 900 kb downstream from the transcription start site (TSS) of Gata3. Gata3-TSS interacted with mG900 region in only cultured Th2 cells but not in naive CD4 T cells or cultured Th0 cells. The mG900-deficient Th2 cells exhibited reduced interaction between Gata3-TSS and three enhancers.

2024-07-17 | GSE241990 | GEO

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