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Glycolytic body (G body) RIP-sequencing

ABSTRACT: Glycolytic body (G body) RIP-sequencing

PROVIDER: PRJNA608654 | ENA |

REPOSITORIES: ENA

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Glycolytic body (G body) RIP-sequencing

Project description:Glycolytic (G) bodies were purified from hypoxic yeast using differential centrifugation and immunoprecipitation by Pfk2-GFP-Flag in order to determine the RNAs that localize to G bodies by determining the enrichment of RNAs copurified with G bodies over both the flow through and total RNA fractions. We find significant overlap between enriched RNAs and RNAs bound by glycolysis enzymes in normoxic conditions. Our study determined that RNA is an integral component of G bodies and is required for G body formation. Specific mRNAs are only slightly enriched in G bodies.

2020-04-27 | GSE145881 | GEO

Glycolytic Enzyme Coalesce in G bodies Under Hypoxic Stress

Project description:Glycolysis is upregulated in cells under specific conditions, such as hypoxia and high energy demand, to achieve the metabolic requirements for continued cell proliferation. However, the mechanism of this increased glycolytic rate remains poorly understood. In the budding yeast Saccharomyces cerevisiae, we discovered that hypoxia induces concentration of many glycolytic enzymes, including the Pfk2p subunit of the ratelimiting enzyme, phosphofructokinase, into a single, non-membrane-bound granule that we define as the "glycolytic body" or "G body". Pfk2p localization to G bodies depends on its N-terminal, intrinsically disordered region. In order to identify factors important for G body formation, we conducted a yeast kinome screen and identified the AMP kinase ortholog, Snf1p, to be required for the localization of multiple glycolytic enzymes to G bodies. Further, proteomic analyses of purified G bodies identified a core set of resident factors, many of which are essential for G body integrity. Cells incapable of forming G bodies in hypoxic conditions display abnormal cell division and produce inviable daughter cells. Conversely, cells that form G bodies show increased glucose consumption and decreased levels of glycolytic intermediates. Importantly, G bodies also form in human, hepatocarcinoma cells upon hypoxic stress. Together, our results suggest that G body formation is a conserved, adaptive response to increase glycolytic output during hypoxia or tumorigenesis.

2017-07-24 | PXD006686 | Pride

RIP sequencing in L02 cells

Project description:RIP sequencing in L02 cells

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RIP sequencing in L02 cells

Project description:RIP-SEQ was performed in L02 cells

2020-11-04 | GSE160743 | GEO

RNA-binding protein immunoprecipitation (RIP)and RNA sequencing

Project description:We report the result of lncRNAs binding to Hes1 in colon cancer SW480 cells using Magna RIP™ RNA-Binding Protein Immunoprecipitation Kit (Millipore, MD, USA) following the manufacturer's instructions, the RNAs were analyzed by Illumina HiSeq 2500 Sequencing.

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RNA immunoprecipitation sequencing (RIP-seq) in four types of cancer cell lines

Project description:The ribosomal protein S6 (RPS6) antibody used for RIP to measure the landscape associated RNA by sequencing

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RIP-seq data for CCNT1

Project description:To demonstrate RIPSeeker program that is developed for RIP-seq analyses, we generated RIP-seq data corresponding to the protein CCNT1 in HEK293 cell line using standard RIP-seq protocols described in Zhao et al., (2010). We performed two in-house RIP-seq experiments both for CCNT1 in human HEK293 cells. Briefly, we generated tagged CCNT1 using a triple tag system that supports lentiviral stable expression and mammalian affinity purification (MAPLE) Mak et al (2010). The HEK293 cells stably expressing tagged CCNT1 was purified by M2 agarose beads, followed by RNA extraction by Trizol. The library synthesis was carried out according to the RIP-seq protocol described in Zhao et al., (2010) except that one of the two experiments was done with non-strand-specific sequencing.

2012-12-28 | E-GEOD-43170 | biostudies-arrayexpress

Mettl3-RIP-sequencing of NK cells

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Identification of YAP-associated lncRNAs via RNA-binding protein immunoprecipitation sequencing (RIP-seq) experiments

Project description:The analysis of the RNA-binding protein immunoprecipitation sequencing (RIP-seq) experiment is performed to identified YAP-specific binding lncRNAs.

2019-10-29 | GSE129535 | GEO

RIP-sequencing reveals that X-ray irradiation infection ELAVL1 binding RNA sites

Project description:We report the application of RIP-sequencing technology for high-throughput profiling of ELAVL1 protein on the effect of lncRNA an mRNA in WS1 cells after 5 Gy X-ray irradiation

2018-07-20 | GSE102146 | GEO

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