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Transcriptome profiling of Mesoplasma florum strain L1 using RNA sequencing (RNA-Seq) and genome-wide 5'-rapid amplification of cDNA ends (5'-RACE)

ABSTRACT: Transcriptome profiling of Mesoplasma florum strain L1 using RNA sequencing (RNA-Seq) and genome-wide 5'-rapid amplification of cDNA ends (5'-RACE)

PROVIDER: PRJNA641121 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR12068546.fastq.gz	Fastqsanger.gz
	SRR12068547_1.fastq.gz	Fastqsanger.gz
	SRR12068547_2.fastq.gz	Fastqsanger.gz
	SRR12068548_1.fastq.gz	Fastqsanger.gz
	SRR12068548_2.fastq.gz	Fastqsanger.gz

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Transcriptome profiling of Mesoplasma florum strain L1 using RNA sequencing (RNA-Seq) and genome-wide 5'-rapid amplification of cDNA ends (5'-RACE)

Project description:Mesoplasma florum is a near-minimal bacterium belonging to the Mollicutes class particularly characterized by its small genome, fast growth rate, and lack of pathogenic potential. Here, we report the first genome-wide transcriptomic analysis of this microorganism using directional RNA sequencing (RNA-Seq) and 5'-rapid amplification of cDNA ends (5'-RACE). 5'-RACE sequencing reads were used to identify 605 putative transcription start sites (TSSs), of which more than 400 could be associated to a conserved promoter sequence. Along with terminator predictions, these TSSs allowed the reconstruction of M. florum transcription units, covering more than 90% of annotated genes. We evaluated the expression level of all M. florum protein coding genes using paired-end RNA-Seq reads according to the number of fragments per kilobase per million of mapped reads (FPKM). FPKM values were converted to absolute transcript abundances using biomass quantification data. These efforts aim at reaching a deep understanding of global cellular mechanisms in M. florum and will guide future genome engineering projects in this simple organism.

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Project description:The near-minimal bacterium Mesoplasma florum constitutes an interesting model for synthetic genomics and systems biology studies due to its small genome, fast growth rate, and lack of pathogenic potential. However, some fundamental aspects of its biology remain largely unexplored. Here, we report a broad yet remarkably detailed characterization of M. florum by combining a wide variety of experimental approaches. More specifically, we investigated several physical and physiological aspects of this bacterium, and performed the first genome-wide analysis of its transcriptome and proteome using RNA sequencing techniques and two-dimensional liquid chromatography-tandem mass spectrometry. These analyses notably revealed the M. florum consensus promoter, a first experimental cartography of transcription units, as well as the transcription and expression levels of all annotated genes. We also converted gene transcription and expression levels into absolute molecular abundances using biomass quantification results, generating an unprecedented view of the M. florum cellular composition and functions. These characterization efforts will provide an experimental foundation for the development of a genome-scale metabolic model for M. florum and will guide future genome engineering endeavours in this simple organism.

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Project description:Long non-coding RNAs (lncRNA) constitute a large fraction of mammalian transcriptomes that still remains unexplored, mainly due to the lack of comprehensive, high-quality lncRNA annotation that limits the possibility to fully explore their functional capacity. We have developed RACE-seq, an experimental workflow based on RACE (Rapid Amplification of cDNA Ends) and long read RNA sequencing, aimed at both rare isoform discovery and better definition of gene boundaries. We applied 3â and 5â RACE-seq on 398 low-expressed GENCODE v7 lncRNA genes in seven human tissues (brain, testis, heart, kidney, liver, lung and spleen). The sequences obtained led to the discovery of 2,641 on-target, previously unknown alternative transcripts. Novel isoforms extended 60% of the 398 targeted lncRNA loci further in either 5' or 3', and often reached genome hallmarks typical of gene boundaries. In parallel, we used nested RACE-seq, and confirmed that nested RACE-seq has overwhelmingly better sensitivity than its standard counterpart.

2016-06-01 | E-MTAB-3912 | biostudies-arrayexpress

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GENCODE Batch VIII b: determining lncRNA transcript 5' and 3'-ends by RACE-PCR / 454 sequencing

Project description:As part of the ENCODE consortium the GENCODE project is producing a reference gene set through manual and automated gene prediction. In the current phase of ENCODE we have found strong evidence that many lncRNAs transcript termini are still unknown. This experiment aims to set up an experimental validation strategy to accurately determine the 5' and 3' ends of transcripts, which is based on semi-nested RACE extensions of annotated 5' and 3' ends followed by high throughput sequencing. A total of 400 highly expressed lncRNA transcript models from Gencode 7 which did not have any CAGE/PET support were selected as the test set whereas 25 transcripts with transcript start site (TSS) supported by CAGE tags and transcript termination site (TTS) supported by PET ditags formed the positive control set. Transcript ends were amplified by RACE-PCR from brain and testis RNA samples and sequenced using the Roche 454 platform. The sequencing was performed at the Centre for Genomic Regulation (CRG), Barcelona, Spain.

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