Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA322677 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR3584174.fastq.gz | Fastqsanger.gz | |||
| SRR3584175.fastq.gz | Fastqsanger.gz | |||
| SRR3584176.fastq.gz | Fastqsanger.gz | |||
| SRR3584177.fastq.gz | Fastqsanger.gz |
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Project description:SIRT7 is an RNA-activated protein lysine deacylase [RIP ribosomal RNA]
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Project description:SIRT7 is an RNA-activated protein lysine deacylase
| PRJNA322675 | ENA
Project description:We report that RNA can increase the catalytic efficiency of SIRT7 and that SIRT7 can remove long chain fatty acyl groups more efficiently than removing acetyl groups. Truncation and mutagenesis studies revealed residues at both the amino and carboxyl termini of SIRT7 that are involved in RNA-binding and important for activity. RNA immunoprecipitation-sequencing (RIP-seq) identified ribosomal RNA (rRNA) as the predominant RNA binding partners of SIRT7. The associated RNA was able to effectively activate the deacetylase and defatty-acylase activities of SIRT7. These findings provide important insights into the biological functions of SIRT7, as well as an improved platform to develop SIRT7 modulators.
2017-02-17 | GSE81840 | GEO
Project description:We report that RNA can increase the catalytic efficiency of SIRT7 and that SIRT7 can remove long chain fatty acyl groups more efficiently than removing acetyl groups. Truncation and mutagenesis studies revealed residues at both the amino and carboxyl termini of SIRT7 that are involved in RNA-binding and important for activity. RNA immunoprecipitation-sequencing (RIP-seq) identified ribosomal RNA (rRNA) as the predominant RNA binding partners of SIRT7. The associated RNA was able to effectively activate the deacetylase and defatty-acylase activities of SIRT7. These findings provide important insights into the biological functions of SIRT7, as well as an improved platform to develop SIRT7 modulators.
2017-02-17 | GSE81839 | GEO
Project description:Methods: RNA-sequencing was performed on matched samples obtained across several different gene expression measurement methods including: (a) fresh-frozen (FF) RNA samples by mRNA-seq, Ribo-zero and DSN and (b) FFPE samples by Ribo-zero and DSN. We also assayed the matched samples with Agilent microarray. RNA-seq data was compared on the rRNA-removal efficiency, genome profile, library complexity, coverage uniformity and quantitative cosinstency across protocols and with microarray data. Results: Compared to mRNA-seq, Ribo-zero provides equivalent percentage of rRNA component, genome-based mapped reads, and consistent quantification of transcripts. Moreover, Ribo-zero and DSN protocols achieve concordant transcript profiling in FFPE samples, and provide substantially more information on non-poly(A) RNA, which cannot be captured by mRNA-seq. Therefore, our study provides evidence that RNA-sequencing can generate accurate and reproducible transcript quantification using FFPE tissues.
2014-08-20 | GSE51783 | GEO
Project description:Methods: RNA-sequencing was performed on matched samples obtained across several different gene expression measurement methods including: (a) fresh-frozen (FF) RNA samples by mRNA-seq, Ribo-zero and DSN and (b) FFPE samples by Ribo-zero and DSN. We also assayed the matched samples with Agilent microarray. RNA-seq data was compared on the rRNA-removal efficiency, genome profile, library complexity, coverage uniformity and quantitative cosinstency across protocols and with microarray data. Results: Compared to mRNA-seq, Ribo-zero provides equivalent percentage of rRNA component, genome-based mapped reads, and consistent quantification of transcripts. Moreover, Ribo-zero and DSN protocols achieve concordant transcript profiling in FFPE samples, and provide substantially more information on non-poly(A) RNA, which cannot be captured by mRNA-seq. Therefore, our study provides evidence that RNA-sequencing can generate accurate and reproducible transcript quantification using FFPE tissues. mRNA profile of 11 breast tumors were assayed by Agilent microarray, and by RNA-sequencing on libraries including: (a) fresh-frozen (FF) RNA samples by mRNA-seq, Ribo-zero and DSN and (b) FFPE samples by Ribo-zero and DSN, using Illunia HiSeq2000 2x50bp. RNA-Seq raw data is to be made available through dbGaP (controlled access) due to patient privacy concerns: http://www.ncbi.nlm.nih.gov/gap/?term=phs000676
2014-08-20 | E-GEOD-51783 | biostudies-arrayexpress
Project description:We used RNA-seq to examine circular RNAs from RNase R treated ribo-zero RNAs in HeLa cells.
2019-09-13 | GSE119938 | GEO
Project description:SIRT7 is an NAD+-dependent protein deacetylase with important roles in ribosome biogenesis and cell proliferation. Previous studies have established that SIRT7 is associated with RNA polymerase I, interacts with pre-rRNA and promotes rRNA synthesis. Here we show that SIRT7 is also associated with snoRNAs that are involved in pre-rRNA processing and rRNA maturation. Knockdown of SIRT7 impairs U3 snoRNA-dependent early cleavage steps that are necessary for generation of 18S rRNA. Mechanistically, SIRT7 deacetylates U3-55k, a core component of the U3 snoRNP complex, and reversible acetylation of U3-55k modulates the association of U3-55k with U3 snoRNA. Deacetylation by SIRT7 enhances U3-55k binding to U3 snoRNA, which is a prerequisite for pre-rRNA processing. Under stress conditions, SIRT7 is released from nucleoli, leading to hyperacetylation of U3-55k and attenuation of prerRNA processing. The results reveal a multifaceted role of SIRT7 in ribosome biogenesis, regulating both transcription and processing of rRNA. CLIP-seq was performed in Flag-SIRT7-293T cells.
2016-01-07 | E-GEOD-76578 | biostudies-arrayexpress
Project description:Sirtuin proteins regulate diverse cellular pathways that influence genomic stability, metabolism, and ageing. SIRT7 is a mammalian sirtuin whose biochemical activity, molecular targets, and physiologic functions have been unclear. Here we show that SIRT7 is an NAD+-dependent, histone H3 acetyl-lysine 18 (H3K18Ac) deacetylase that stabilizes the transformed state of cancer cells. Genome-wide binding studies reveal that SIRT7 binds to promoters of a specific set of gene targets, where it deacetylates H3K18Ac and promotes transcriptional repression. The spectrum of SIRT7 target genes is defined in part by interaction of SIRT7 with the cancer-related ETS transcription factor ELK4, and comprises numerous genes with links to tumour suppression. Notably, selective hypoacetylation of H3K18Ac has recently been linked to oncogenic transformation, and in patients, is associated with aggressive tumour phenotypes and poor prognosis. We find that deacetylation of H3K18Ac by SIRT7 is necessary for maintaining essential features of human cancer cells including anchorage independent growth and escape from contact inhibition. Moreover, SIRT7 is necessary for a global hypoacetylation of H3K18Ac associated with cellular transformation by viral oncoproteins. Finally, SIRT7 depletion markedly reduces the tumourigenicity of human cancer cell xenografts in mice. Together, our work establishes SIRT7 as the first known site-specific H3K18Ac deacetylase and demonstrates a pivotal role for SIRT7 in chromatin regulation, cellular transformation programs, and tumour formation in vivo. SIRT7 ChIP-seq was performed in K562 cell lines under normal conditions. Two replicates were performed for both the SIRT7 ChIP as well as input control.
2012-05-06 | E-GEOD-28149 | biostudies-arrayexpress