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Transcriptome Analysis of Wild Type and HMGB1 knock-out iSLK BAC16 cells

ABSTRACT: Transcriptome Analysis of Wild Type and HMGB1 knock-out iSLK BAC16 cells

PROVIDER: PRJNA660741 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR12564261_1.fastq.gz	Fastqsanger.gz
	SRR12564261_2.fastq.gz	Fastqsanger.gz
	SRR12564262_1.fastq.gz	Fastqsanger.gz
	SRR12564262_2.fastq.gz	Fastqsanger.gz
	SRR12564263_1.fastq.gz	Fastqsanger.gz

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Transcriptome Analysis of HMGB1 knock-out iSLK BAC16 cell (2)

Project description:Transcriptome Analysis of HMGB1 knock-out iSLK BAC16 cell (2)

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Transcriptome Analysis of HMGB1 knock-out iSLK BAC16 cell (2)

Project description:Purpose: RNA sequencing (RNA-seq) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived transcriptome profiling (RNA-seq) to microarray and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis. In addition, we have already registered the transcriptome analysis results of HMGB1 KO iSLK BAC16 cell in GSE157275, and this registration is to reproduce it.

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Project description:Mutant ataxin-1 (Atxn1), which causes spinocerebellar ataxia type 1 (SCA1), binds to and impairs the function of high mobility group box 1 (HMGB1), a critical nuclear protein that regulates DNA architectural changes essential for DNA damage repair and transcription. In this study, we established that transgenic or virus vector-mediated supplementation of HMGB1 ameliorates motor dysfunction and elongates lifespan in mutant Atxn1 knock-in (Atxn1-KI) mice. We identified mitochondrial DNA damage repair by HMGB1 as a novel molecular basis for this effect, in addition to the mechanisms already associated with HMGB1 function, such as nuclear DNA damage repair and nuclear transcription. The dysfunction and the improvement of mitochondrial DNA damage repair functions are tightly associated with the exacerbation and rescue, respectively, of symptoms, supporting the involvement of mitochondrial DNA quality control by HMGB1 in SCA1 pathology. Moreover, we show that the rescue of Purkinje cell dendrites and dendritic spines by HMGB1 could be downstream effects. Although extracellular HMGB1 triggers inflammation mediated by toll-like receptor and receptor for advanced glycation end products, upregulation of intracellular HMGB1 does not induce such side effects. Thus, viral delivery of HMGB1 is a candidate approach by which to modify the disease progression of SCA1 even after its onset.

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