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Measurement of genome-wide gene expression in cyanobacteria grown under simluated natural light conditions [RNA-Seq]

ABSTRACT: Measurement of genome-wide gene expression in cyanobacteria grown under simluated natural light conditions [RNA-Seq]

PROVIDER: PRJNA412032 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR6069380.fastq.gz	Fastqsanger.gz
	SRR6069390.fastq.gz	Fastqsanger.gz
	SRR6069400.fastq.gz	Fastqsanger.gz
	SRR6069410.fastq.gz	Fastqsanger.gz
	SRR6069420.fastq.gz	Fastqsanger.gz

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Measurement of genome-wide gene expression in cyanobacteria grown under simluated natural light conditions [RNA-Seq]

Project description:We used RNA sequencing to measure genome-wide gene expression in the cyanobacterium Synechococcus elongatus PCC 7942 grown under dynamic light regimes that mimic the variation in light intensity seen on a Clear Day in nature, or the rapid changes in light intensity that accompany changes in shading We compare these gene expression dynamics to those of a culture grown under a Low Light condition that mimics the standard laboratory conditions used for study of cyanobacteria. Our analysis reveals that naturally relevant light conditions drastically modify gene expression dynamics in cyanobacteria Notably, the expression of circadian clock-controlled genes is responsive to changes in light intensity, showing modulated dynamics that can allow cyanobacteria to adapt their metabolism to changing environmental conditions

2017-12-16 | GSE104203 | GEO

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Project description:We used ChIP sequencing to measure genome-wide binding of transcription factors in the cyanobacterium Synechococcus elongatus PCC 7942 grown under dynamic light regimes that mimic the rapid changes in light intensity that accompany changes in shading. Our analysis reveals that rapid changes in light intensity modulate the binding of RNA polymerase (RNAP) upstream of genes in a way that correlates with changes in downstream gene expression, suggesting that changes in transcriptional regulation control light-responsive gene expression changes. Also, binding of the circadian clock-controlled transcription factor RpaA and the light-responsive transcription factor RpaB change upstream of genes in a manner correlating with RNAP enrichment and downstream gene expression. This suggests that changes in RpaA and RpaB binding upstream of genes regulate the light-responsive expression of genes in cyanobacteria.

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Measurement of genome-wide gene expression in cyanobacteria grown under simluated natural light conditions

Project description:Measurement of genome-wide gene expression in cyanobacteria grown under simluated natural light conditions

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Measurement of transcription factor binding in cyanobacteria grown under simluated natural light conditions [ChIP-Seq]

Project description:Measurement of transcription factor binding in cyanobacteria grown under simluated natural light conditions [ChIP-Seq]

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Measurement of genome-wide gene expression in cyanobacteria grown under simluated natural light conditions

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

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Project description:Filamentous cyanobacteria of the Nostocaceae family are able to differentiate into multicellular forms to adapt to environmental stresses, and members can establish symbiosis with various embryophytes. Representative laboratory strains are typically grown under continuous light to maintain stable metabolic conditions, however, this departure from a natural diel cycle can result in extended stress. Early genomic examination of Nostoc punctiforme suggests the genetic potential for a circadian clock, but we lack insight into global cellular dynamics through the natural diel cycle for this model organism. Here, we comprehensively assess changes in expression of core cellular processes and the mobilome of accessory genetic elements during diel growth of N. punctiforme PCC 73102. The primary transcriptome confirmed that multicellular cyanobacteria precisely coordinate photosynthesis and carbon assimilation for cell division during the day, while control of DNA recombination and repair appeared to be sequestered to darkness. Moreover, we expanded the known repertoire of light sensing proteins to uncover a putative regulator of circadian rhythm that itself exhibits striking oscillation between day-night expression. This was in sharp contrast to the arrhythmic pattern observed for a homolog of the canonical circadian regulator in unicellular cyanobacteria. Looking beyond cellular coordination of diel growth, we uncovered dynamic mobile elements, and notably, targeted hypermutation by retroelements that are likely maintained to ensure conflict mitigation, which is crucial to a multicellular lifestyle.

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