Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Regulation of highly expressed hCINAP on translatome

ABSTRACT: hCINAP is essential for human 18S rRNA processing and ribosome assembly. hCINAP is highly expressed in human cancers and promotes cancer cell growth. To connect the role of hCINAP in ribosome biogenesis and tumor growth, genome-wide polysome profiling was performed to detect the regulation of hCINAP on ribosome assembly and translation control. The results showed taht hihgly expressed hCINAP promotes ribosome biogenesis and selectively modulates cancer-associated translatome to promote malignancy. This result provides important insights into the molecular mechanism underlying the role of hCINAP in tumorigenesis. For the transcriptional profile, MCF7 cells transfected with control vector or GFP-hCINAP were collected and total RNA was extracted. For the polysoem profile, MCF7 cells with stably expressed GFP or GFP-hCINAP were subjected to surcose gradient fractionation. Ribosome profiles were obtained by measuring the absorbance of the sucrose gradient at a wavelength of 254 nm using a BioComp Gradient Fractionator. The fractions corresponding to subpolysome and polysome were collected and RNA was extracted. The cDNA library was generated and sequenced via Illumina HiSeqTM 2000. The clean reads were mapped to the UCSC hg19 reference genome and FPKM was assigned to calculate expression levels. The recruitment to polysome of each mRNA was calculated according to their FPKM values in the monsome and polysome.

ORGANISM(S): Homo sapiens

SUBMITTER: Dongmei Bai

PROVIDER: E-GEOD-81469 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Estrogen Coordinates Translation and Transcription Revealing a Role for NRSF in Human Breast Cancer Cells

Project description:Analysis of estrogen receptor (ER)-positive MCF7 cell total RNA expression and polysome-assiciated RNA expression following treatment with estradiol (E2) and vehicle (etoh). We used expression microarrays to measure polysome association and total RNA abundance in E2 treated MCF7. These data, along with previously published data, show that genes that are upregulated by estrogen treatment are biased towards association with polysomes. MCF7 cells were grown in hormone depleted media for three days before a 1 hour treatment with E2 or 0.1 % ethanol (vehicle). Total RNA was collected using standard methods and polysome-association RNA from the same cells were collected using sucrose gradient fractionation. Both RNA populations were purified, labeled, and hybridized to Affymetrix Human Genest arrays.

2010-05-07 | E-GEOD-18592 | biostudies-arrayexpress

Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and rea1 mutant total and polysome-bound Transcriptomes

Project description:Analysis of gene expression level. The hypothesis tested in the present study was that rea1 mutant influence the translation level of translation and nucleosome assembly associated genes. Results provide important information of the gene translation level regulation of ribosome proteins, elongation factors, histones and genes associated with other biological processes. Endosperm total and polysome-bound mRNA profiles of 15DAP wild type (WT) and rea1 mutant were generated by deep sequencing, in triplicate, using Illumina Hiseq 2500 (Zea mays).

2015-04-25 | E-GEOD-67083 | biostudies-arrayexpress

Regulation of highly expressed hCINAP on translatome

Project description:hCINAP is essential for human 18S rRNA processing and ribosome assembly. hCINAP is highly expressed in human cancers and promotes cancer cell growth. To connect the role of hCINAP in ribosome biogenesis and tumor growth, genome-wide polysome profiling was performed to detect the regulation of hCINAP on ribosome assembly and translation control. The results showed taht hihgly expressed hCINAP promotes ribosome biogenesis and selectively modulates cancer-associated translatome to promote malignancy. This result provides important insights into the molecular mechanism underlying the role of hCINAP in tumorigenesis.

2016-07-18 | GSE81469 | GEO

Heat shock of procyclic T. brucei

Project description:Ransom of polysome gradient, input and light fractions 39 degrees.

2016-06-13 | E-MTAB-4575 | biostudies-arrayexpress

Polysome-associated mRNA profiling of cancer cells in response to CXCL12 and IGF1

Project description:CXCL12 and IGF1 are key secreting molecules produced by cancer-associated fibroblasts in breast cancer. These factors promote the survival of disseminated cancer cells in the bone marrow. To assess the combined responses elicited by CXCL12 and IGF1, we examined the translating transcriptome of cancer cells in response to these two factors by Translating Ribosome Affinity Purification (TRAP)-RNAseq. MDA-MB-231 cells were engineered to express an EGFP-tagged version of ribosomal protein L10a. This allows the retrieval of polysome-associated mRNA by anti-GFP pull down (TRAP) and profiling the translating transcriptome by RNAseq. EGFP-L10a+ cancer cells were serum starved (0.2% serum) for 24 hours, and then treated with CXCL12 (30ng/mL) + IGF1 (10ng/mL) or CXCL12 (300ng/mL) + IGF1 (100ng/mL) for 6hrs. Two biological replicates were profiled for each condition.

2013-11-01 | E-GEOD-43296 | biostudies-arrayexpress

Separation and Paired Proteome Profiling of Plant Chloroplast and Cytoplasmic Ribosomes

Project description:Conventional preparation methods of plant ribosomes fail to resolve non-translating chloroplast or cytoplasmic ribosome subunits from translating fractions. We established preparation of these ribosome complexes from Arabidopsis thaliana leaf, root, and seed tissues by optimized sucrose density gradient centrifugation of protease protected plant extracts. The method co-purified non-translating 30S and 40S ribosome subunits, separated non-translating 50S from 60S subunits, and resolved assembled monosomes from low oligomeric polysomes. Combining ribosome fractionation with microfluidic rRNA analysis and proteomics, we characterized the rRNA and ribosomal protein (RP) composition. The identity of cytoplasmic and chloroplast ribosome complexes and the presence of ribosome biogenesis factors in the 60S - 80S sedimentation interval were verified. In vivo cross-linking of leaf tissue stabilized ribosome biogenesis complexes but induced polysome run-off. Omitting cross-linking, the established paired fractionation and proteome analysis monitored relative abundances of plant chloroplast and cytoplasmic ribosome fractions and enabled analysis of RP composition and ribosome associated proteins including transiently associated biogenesis factors.

2021-09-09 | PXD019329 | Pride

Mouse cardiac tissue, polysomes and monosomes: Vehicle treated control vs. 25mg/kg DMNQ

Project description:Translational profiling of mouse cardiac tissue treated with 25mg/kg DMNQ in 10 ml/kg arachis oil over an acute time course (0.5-120 hours) compared to time matched control animals treated with 10ml/kg saline Two colour microarrays with time matched controls vs 25mg/kg DMNQ cardiac tissue. Before microarray analysis RNA separated on a sucrose density gradient into those mRNAs activitly undergoing translation (polysomes) and those not (monosomes) with control monosomes and treated monosomes on one set of arrays, and polysome control and polysome treated on another set of microarrays. The normalized Log2 of the monosomes was subtracted from the respective Log2 of the polysomes (on Series record). Time points studied were 0.5, 1, 2, 12, 24 and 120 hours following dosing, biological replicates n=3 independent animals at each time point, technical replicates (reverse labelling) n<1. One array printed onto two slides (A and B), one replicate per array.

2010-08-06 | E-GEOD-17830 | biostudies-arrayexpress

Mouse cardiac tissue, polysomes and monosomes: Vehicle treated control vs. 15mg/kg doxorubicin

Project description:Translational profiling of mouse cardiac tissue treated with 15mg/kg doxorubicin in 10 ml/kg saline over an acute time course (0.5-120 hours) compared to time matched control animals treated with 10ml/kg saline. Two colour microarrays with time matched controls vs 15mg/kg doxorubicin cardiac tissue. Before microarray analysis, RNA is separated on a sucrose density gradient into those mRNAs activity undergoing translation (polysomes) and those not (monosomes) with control monosomes and treated monosomes on one set of arrays, and polysome control and polysome treated on another set of microarrays. Thealized Log2 of the monosomes was subtracted from the respective Log2 of the polysomes (on Series record). Time points studied were 0.5, 1, 2, 12, 24 and 120 hours following dosing, biological replicates n=3 independent animals at each time point, technical replicates (reverse labelling) n<1. One array printed onto two slides (A and B), one replicate per array.

2010-08-05 | E-GEOD-17823 | biostudies-arrayexpress

Cap analysis of gene expression (CAGE) of polysome-associated RNA against total RNA from human HEK293 cell line

Project description:In this study, we used CAGE followed by deep sequencing to globally profile the transcript 5’ isoforms in the translatome (i.e., polysome-associated RNA) and transcriptome (i.e., total RNA) of human HEK293 cells at single-nucleotide resolution. After removing low-quality sequencing reads, we obtained approximately 18 million and 14 million CAGE tags respectively for the translatome and transcriptome of HEK293 cells. These tags were then mapped to the human genome (assembly GRCh37) using bowtie with two mismatches allowed. Tags mapped to rRNA were less than 17.9% for translatome and 7.5% for transcriptome, indicating high quality of the two CAGE libraries. By comparing CAGE tags between HEK293's translatome and transcriptome, we revealed selective usage of the TSS-derived 5’ ends by polysome.

2019-06-13 | E-MTAB-7382 | biostudies-arrayexpress

Global regulation of mRNA translation and stability in the early Drosophila embryo by the Smaug RNA-binding protein- Polysome gradient/microarray study

Project description:To gain a panoramic view of Smaug function in the early embryo we identified mRNAs that are bound to Smaug using RNA co-immunoprecipitation followed by hybridization to DNA microarrays. We also identified the mRNAs that are translationally repressed by Smaug using polysome gradients and microarrays. Comparison of the bound mRNAs to those that are translationally repressed by Smaug and those that require Smaug for their degradation suggests that a large fraction of Smaug?s target mRNAs are both translationally repressed and degraded by Smaug. Smaug directly regulates components of the TRiC/CCT chaperonin, the proteasome regulatory particle and lipid droplets as well as many metabolic enzymes, including several glycolytic enzymes. Embryos laid by wild-type or smaug1 homozygous mothers were collected 0-2 hours post-egglaying and lysed in an equal volume of polysome lysis buffer. The lysate was applied to polysome gradients that were fractionated into four fractions. mRNA was extracted from each fraction and converted to cDNA that was applied on custom-designed Nimblegen arrays. Three biological replicates were performed for each of the four fraction in each of the two genotypes. To demonstrate that the presence of mRNAs at the bottom of the gradient were the result of translation, we performed a puromycin experiment. smaug1 homozygous mothers were collected 0-2 hours post-egglaying and lysed in an equal volume of puromycin lysis buffer and then treated either with cycloheximide or puromycin. The lysate from each condition was applied to separate polysome gradients that were each fractionated into four fractions. mRNA was extracted from each fraction and converted to cDNA that was applied on custom-designed Nimblegen arrays. Two biological replicates were performed for each of the four fraction from each of the two conditions.

2013-12-03 | E-GEOD-50026 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data