Trans-splicing in human embryonic stem cells
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: Chun Yu
PROVIDER: E-GEOD-32503 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:CHQ5B primary human myoblasts obtained from Dr V. Mouly (Paris, France) have been described previously (Faulkner et al., 1999). Ankrd2 is upregulated on differentiation of myoblasts. The change in gene expression was studied in cells silenced for Ankrd2 (infected with AAV-shAnkrd2), control cells (infected with AAV-shLuc) and control cells uninfected.
2011-12-31 | E-MEXP-2949 | biostudies-arrayexpress
Project description:The histone variant macroH2A generally associates with transcriptionally inert chromatin, however the factors that regulate its chromatin incorporation remain elusive. Here, we identify the SWI/SNF helicase, ATRX, as a novel macroH2A interacting protein. Unlike its role in assisting H3.3 chromatin deposition, ATRX acts as a negative regulator of macroH2A’s chromatin association. In human erythroleukemic cells deficient for ATRX, ChIP-sequencing studies reveal that macroH2A accumulates at the HBA gene cluster on the subtelomere of chromosome 16, coinciding with the loss of α globin expression. Collectively, our results implicate deregulation of macroH2A’s distribution as a contributing factor to the α thalassemia phenotype of ATRX syndrome. Mononucleosomes from K562 cells bearing integrated lentiviral shRNA constructs targeting either luciferase (shluc) or ATRX (sh92) were isolated and ChIP'd with mH2A1 antibody. DNA from shluc Input and the two mH2A1 ChIPs were isolated and sequenced on Illumina's Hiseq.
2012-03-08 | E-GEOD-35339 | biostudies-arrayexpress
Project description:Glucocorticoid resistance is a major driver of therapeutic failure in T-cell acute lymphoblastic leukemia (T-ALL). Here we identify the AKT1 kinase as a signaling factor driving glucocorticoid resistance in T-ALL. Mechanistically, AKT1 directly phosphorylates the glucocorticoid receptor NR3C1 protein and blocks glucocorticoid-induced NR3C1 transcription by inhibiting glucocorticoid-induced NT3C1 translocation to the nucleus. Consistently, pharmacologic inhibition of AKT1 increases the response of T-ALL cells to glucocorticoid therapy and effectively reverses glucocorticoid resistance in vitro and in vivo. These results warrant the clinical testing of AKT1 inhibitors and glucocorticoids in combination for the treatment of T-ALL. Gene Expression Analysis of DND41 cell lines infected with shPTEN or shLUC and treated with 1M-BM-5M Dexamethasone vs DMSO for 24h, in triplicate.
2013-10-01 | E-GEOD-41062 | biostudies-arrayexpress
Project description:The heterotic hybrid offspring of Arabidopsis accessions C24 and Landsberg erecta have altered methylomes. Changes occur most frequently at loci where parental methylation levels are different. There are context-specific biases in the non-additive methylation patterns with mCG generally increased and mCHH decreased relative to the parents. These changes are a result of two main mechanisms, Trans Chromosomal Methylation (TCM) and Trans Chromosomal deMethylation (TCdM), where the methylation level of one parental allele alters to resemble that of the other parent. Regions of altered methylation are enriched around genic regions and are often correlated with changes in siRNA levels. We identified examples of genes with altered expression likely to be due to methylation changes and suggest that in crosses between the C24 and Ler accessions, epigenetic controls can be important in the generation of altered transcription levels which may contribute to the increased biomass of the hybrids. C24, Ler, and C24 x Ler
2012-02-05 | E-GEOD-35542 | biostudies-arrayexpress
Project description:Trans-splicing occurs post-transcriptionally and generates transcripts that are orderly inconsistent with their corresponding DNA templates. Until recently only exceedingly rare trans-splicing events have been experimentally characterized in the mammalian transcriptomes. Although hundreds to thousands of trans-spliced RNA candidates have been nominated by bioinformatics- or NGS (next-generation sequencing)-based approaches, these candidates unavoidably suffered from potential false positives arising from genetic rearrangement events or in vitro artifacts. Here we develop a pipeline (TSscan) based on NGS transcriptome data to identify trans-splicing in human embryonic stem cells (ESCs). TSscan integrates RNA sequencing data derived from different NGS platforms (i.e., Roche 454, SOLiD, and Illumina) and different human ESC lines (i.e., H1 and H9) as well as several in silico filters to minimize these two types of potential false positives. Our result shows that a tremendous amount of apparent experimental artifacts are indeed present in NGS data, which may be the most major false positives of trans-splicing detection. TSscan totally identified 10 trans-spliced RNA candidates in human ESCs, four of which are experimentally validated to be true. Further experiments reveal that these four events represent differential expression during the transition of pluripotent status to differentiate statuses. Especially, we observe that one event (the trans-spliced isoform of NCRMS), which is also a large intergenic non-coding RNA, tends to be specifically transcribed in ESCs and induced pluripotent stem cells and can conspicuously affect the pluripotency maintenance of ESCs. As far as we know, TSscan is the first pipeline for systematic identification of trans-splicing that utilizes NGS data in the human transcriptome, opening up an important class of post-transcriptional events for comprehensive characterization. human embryonic stem cell H9
2014-02-03 | E-GEOD-30557 | biostudies-arrayexpress
Project description:ES cell pluripotency is thought to be regulated in part by H3K4 methylation. However, it is unclear how H3K4 demethylation contributes to ES cell function and participates in iPS cell reprogramming. Here, we show that KDM5B, which demethylates H3K4, is important for ES cell differentiation, and presents a barrier to the reprogramming process. Depletion of Kdm5b leads to an extension in the self-renewal of ES cells in the absence of LIF. Transcriptome analysis revealed the persistent expression of pluripotency-genes and underexpression of developmental genes during differentiation in the absence of Kdm5b, suggesting that KDM5B plays a key role in cellular fate changes. We also observed accelerated reprogramming of differentiated cells in the absence of Kdm5b, demonstrating that KDM5B is a barrier to the reprogramming process. Expression analysis revealed that mesenchymal master regulators associated with epithelial-to-mesenchymal transition (EMT) are downregulated during reprogramming in the absence of Kdm5b. Moreover, global analysis of H3K4me3/2 revealed that enhancers of fibroblast genes are rapidly deactivated in the absence of Kdm5b, and genes associated with EMT lose H3K4me3/2 during the early reprogramming process. These findings provide functional insight into the role for KDM5B in regulating ES cell differentiation and as a barrier to the reprogramming process. ChIP-Seq for H3K4me3 and H3K4me2 in murine shLuc and shKdm5b 4TF-MEFs (tetO-Pou5f1,-Sox2,-Klf4,-c-Myc) at 48h.
2013-10-14 | E-GEOD-47123 | biostudies-arrayexpress
Project description:Microarray analyses revealed distinct gene expression alterations in the luminal and basal epithelial compartments in the absence of Ror2 with marked alterations observed in genes associated with actin filament-based processes and the actin cytoskeletal network. Given that Ror2 expression resides in both basal and luminal epithelial cells, we wanted to identify compartment-specific functions for Ror2 in coordinating development. Accordingly, luminal and basal epithelial cell populations from shLUC and shRor2 outgrowths were isolated by FACS separation on the basis of CD24 and CD29 surface marker expression and gene expression analysis was subsequently performed using Agilent microarrays.
2015-01-09 | E-GEOD-57985 | biostudies-arrayexpress
Project description:Trans-splicing occurs post-transcriptionally and generates transcripts that are orderly inconsistent with their corresponding DNA templates. Until recently only exceedingly rare trans-splicing events have been experimentally characterized in the mammalian transcriptomes. Although hundreds to thousands of trans-spliced RNA candidates have been nominated by bioinformatics- or NGS (next-generation sequencing)-based approaches, these candidates unavoidably suffered from potential false positives arising from genetic rearrangement events or in vitro artifacts. Here we develop a pipeline (TSscan) based on NGS transcriptome data to identify trans-splicing in human embryonic stem cells (ESCs). TSscan integrates RNA sequencing data derived from different NGS platforms (i.e., Roche 454, SOLiD, and Illumina) and different human ESC lines (i.e., H1 and H9) as well as several in silico filters to minimize these two types of potential false positives. Our result shows that a tremendous amount of apparent experimental artifacts are indeed present in NGS data, which may be the most major false positives of trans-splicing detection. TSscan totally identified 10 trans-spliced RNA candidates in human ESCs, four of which are experimentally validated to be true. Further experiments reveal that these four events represent differential expression during the transition of pluripotent status to differentiate statuses. Especially, we observe that one event (the trans-spliced isoform of NCRMS), which is also a large intergenic non-coding RNA, tends to be specifically transcribed in ESCs and induced pluripotent stem cells and can conspicuously affect the pluripotency maintenance of ESCs. As far as we know, TSscan is the first pipeline for systematic identification of trans-splicing that utilizes NGS data in the human transcriptome, opening up an important class of post-transcriptional events for comprehensive characterization.
2014-02-03 | GSE30557 | GEO
Project description:Transcriptome profiling of undifferentiated H1 hESCs cultured on Matrigel, 293BM and 1112BM Biomatrices
2015-10-01 | E-MTAB-1647 | biostudies-arrayexpress
Project description:In order to investigate the gene expression changes in human embryonic stem cells (hESCs) during differentiation, we performed a microarray analysis from RNAs isolated from undifferentiated hESCs and their differentiated cells incubated for 1 week or 2 weeks in ESC medium. Human SNUhES3 ESCs (Seoul National University Hospital, Seoul, Korea) were cultured on mitotically-arrested STO feeder cells (ATCC, Manassas, USA) in DMEM/F12 supplemented with 20% knockout serum replacement (KSR). The embryoid bodies were incubated for 1 or 2 weeks in the above ESC medium without bFGF. Cells were then lysed and RNA was isolated.
2012-12-31 | E-GEOD-36255 | biostudies-arrayexpress