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MGA-seq is an efficient tool for genetic variants and extrachromosomal DNA detection in cancer cell [RNA-Seq]

ABSTRACT: MGA-seq is an efficient tool for genetic variants and extrachromosomal DNA detection in cancer cell [RNA-Seq]

PROVIDER: PRJNA844316 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR19504687.fastq.gz	Fastqsanger.gz
	SRR19504688.fastq.gz	Fastqsanger.gz
	SRR19504689.fastq.gz	Fastqsanger.gz

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MGA-seq is an efficient tool for genetic variants and extrachromosomal DNA detection in cancer cell [MGA-Seq]

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Project description:This SuperSeries is composed of the SubSeries listed below.

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M6 Mga+ vs Mga-

Project description:The transcriptional regulator Mga of Streptococcus pyogenes (the group A streptococcus, GAS) is known to directly activate several virulence genes important for colonization and immune evasion during exponential growth. Transcriptome analysis comparing two mga-1 serotypes (M1 SF370, M6 JRS4) and one mga-2 serotype (M4 GA40634) against their isogenic mga-inactivated strains uncovered a broader Mga regulon profile containing both activated and repressed genes with predicted functions primarily related to the uptake and metabolism of sugars. Although the divergent M1 and M4 Mga profiles were similar in size and content, the M6 JRS4 strain was clearly distinct, even from other M6 strains. Real-time RT-PCR and northern blot analysis validated our microarray results and confirmed that established core Mga regulon genes directly activated by Mga (emm, scpA, sof, fba) exhibited the highest activation levels across all strains tested. A novel ORF (Spy2036) encoding a cytosolic hypothetical protein was highly activated in all three serotypes and was called gene regulated by Mga or grm. Mga was shown to bind directly to Pgrm, which overlaps the Mga-regulated Psof in OF+ strains, suggesting that grm is part of the core Mga regulon and is able to activate two divergently transcribed genes from a single site in a class II background. Both class and serotype specific Mga-regulated genes, such as speB, were apparent. In fact, Mga activated speB as long as it was expressed in the wild type strain, although direct binding of Mga to the PspeB promoter could not be demonstrated. Thus, Mga is able to both directly and indirectly regulate genes shown to be important for virulence and the metabolic homeostasis of GAS. Keywords: Wild-type vs Mga-

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