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Set7: ERCC bulk short-read RNA-seq by Illumina NextSeq platform, additional samples

ABSTRACT: Set7: ERCC bulk short-read RNA-seq by Illumina NextSeq platform, additional samples

PROVIDER: PRJNA1123717 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR29399300_1.fastq.gz	Fastqsanger.gz
	SRR29399300_2.fastq.gz	Fastqsanger.gz
	SRR29399301_1.fastq.gz	Fastqsanger.gz
	SRR29399301_2.fastq.gz	Fastqsanger.gz
	SRR29399302_1.fastq.gz	Fastqsanger.gz

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Set7: ERCC bulk short-read RNA-seq by Illumina NextSeq platform, additional samples

Project description:DNA sequencing is a critical tool in modern biology. Over the last two decades, it has been revolutionized by the advent of massively parallel sequencing, leading to significant advances in genome and transcriptome sequencing of various organisms. Nevertheless, challenges such as accuracy, lack of competitive options and prohibitive costs associated with high throughput parallel short-read sequencing persist. Here, we conduct a comparative analysis between the Element Biosciences AVITI platform and its counterpart the Illumina NextSeq platform, testing DNA and RNA short-read sequencing, as well as synthetic long-read sequencing for single cells and RNA transcripts.

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Set2: ERCC bulk short-read RNA-seq by Illumina NextSeq platform

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Set1: ERCC bulk short-read RNA-seq by Element Biosciences AVITI platform

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Deep sequencing reveals novel Set7 networks

Project description:Methyl-dependent regulation of transcription has expanded from a traditional focus on histones to encompass transcription factor modulation. While the Set7 lysine methyltransferase is associated with pro-inflammatory gene expression in vascular endothelial cells, genome-wide regulatory roles remain to be investigated. From initial characterization of Set7 as specific for methyl-lysine 4 of H3 histones (H3K4m1), biochemical activity toward non-histone substrates has revealed additional mechanisms of gene regulation. mRNA-Seq revealed transcriptional deregulation of over 8,000 genes in an endothelial model of Set7 knockdown. Gene ontology identified up-regulated pathways involved in developmental processes and extracellular matrix remodeling, whereas pathways regulating the inflammatory response as well as nitric oxide signaling were down-regulated. Chromatin maps derived from ChIP-Seq profiling of H3K4m1 identified several hundred loci with loss of H3K4m1 at gene regulatory elements associated with an unexpectedly subtle effect on gene expression. Transcription factor network analysis implicated six previously described Set7 substrates in mRNA-Seq changes, and we predict that Set7 post-translationally regulates other transcription factors associated with vascular endothelial gene expression through the presence of Set7 amino acid methylation motifs. We describe a role for Set7 in regulating developmental pathways and response to stimuli (inflammation/immune response) in human endothelial cells of vascular origin. Set7-dependent gene expression changes that occurred independent of H3K4m1 may involve transcription factor lysine methylation events. The method of mapping measured transcriptional changes to transcription factors to identify putative substrates with strong associations to functional changes is applicable to substrate prediction for other broad-substrate histone modifiers.

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