The THO complex regulates pluripotency gene mRNA export to control embryonic stem cell self-renewal and somatic cell reprogramming
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ABSTRACT:
ORGANISM(S): Mus musculus
SUBMITTER: Li Wang
PROVIDER: E-GEOD-51534 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:Embryonic stem cell (ESC) self-renewal and differentiation are governed by a broad-ranging regulatory network. Although the transcriptional regulatory mechanisms involved have been investigated extensively, post-transcriptional regulation is still poorly understood. Here we describe a critical role of the THO complex in ESC self-renewal and differentiation. We show that THO preferentially interacts with pluripotency gene transcripts through Thoc5, and is required for self-renewal at least in part by regulating their export and expression. During differentiation, THO loses its interaction with those transcripts due to reduced Thoc5 expression, leading to decreased expression of pluripotency proteins that facilitates exit from self-renewal. THO is also important for the establishment of pluripotency, as its depletion inhibits somatic cell reprogramming and blastocyst development. Together, our data indicate that THO regulates pluripotency gene mRNA export to control ESC self-renewal and differentiation, and therefore uncover a role for this aspect of post-transcriptional regulation in stem cell fate specification. mouse J1 cells were transfected with non-targeting (NT), Thoc2, and Thoc5 siRNAs. Total RNA was isolated 96 hours after transfection.
2013-11-30 | E-GEOD-51496 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series
2014-05-16 | E-GEOD-49252 | biostudies-arrayexpress
Project description:Embryonic stem cell (ESC) self-renewal and pluripotency is controlled by the coordinated action of transcription factors and chromatin regulators. Compared to the pluripotency transcription factors, the function of the chromatin regulators, especially the ATP-dependent chromatin remodelers, remains poorly understood in ESCs. Here, we show that INO80, a SWI/SNF family chromatin remodeling complex, is essential for ESC self-renewal, pluripotency, somatic cell reprogramming, and embryonic development. Ino80, the ATPase of the complex, forms an auto-regulatory loop with the ESC master transcription factors Oct4, Nanog, and Sox2. More importantly, it co-occupies the enhancer regions of most key pluripotency genes with the master transcription factors, and positively regulates their expression by maintaining an open chromatin structure. Our data suggests that INO80 is an integral component of the pluripotency transcription network, and plays a critical role in both the maintenance and establishment of pluripotency Mouse J1 cells were transfected with non-targeting (NT), Ino80, Ino80b, Ino80c or Ino80e siRNAs, and RNA was isolated 96 hours after transfection. agent: non-targeting siRNA: Mock_1, Mock_2 agent: Ino80 siRNA: Ino80a_1, Ino80a_2 agent: Ino80b siRNA: Ino80b_1, Ino80b_2 agent: Ino80c siRNA: Ino80c_1, Ino80c_2 agent: Ino80e siRNA: Ino80e_1, Ino80e_2 cell line: mouse J1 ESC: Mock_1, Mock_2, Ino80a_1, Ino80a_2, Ino80b_1, Ino80b_2, Ino80c_1, Ino80c_2, Ino80e_1, Ino80e_2 time: 96 hours: Mock_1, Mock_2, Ino80a_1, Ino80a_2, Ino80b_1, Ino80b_2, Ino80c_1, Ino80c_2, Ino80e_1, Ino80e_2 biological replicate: Ino80a_1, Ino80a_2 biological replicate: Ino80b_1, Ino80b_2 biological replicate: Ino80c_1, Ino80c_2 biological replicate: Ino80e_1, Ino80e_2 biological replicate: Mock_1, Mock_2
2014-05-16 | E-GEOD-49251 | biostudies-arrayexpress
Project description:Embryonic stem cell (ESC) self-renewal and pluripotency is controlled by the coordinated action of transcription factors and chromatin regulators. Compared to the pluripotency transcription factors, the function of the chromatin regulators, especially the ATP-dependent chromatin remodelers, remains poorly understood in ESCs. Here, we show that INO80, a SWI/SNF family chromatin remodeling complex, is essential for ESC self-renewal, pluripotency, somatic cell reprogramming, and embryonic development. Ino80, the ATPase of the complex, forms an auto-regulatory loop with the ESC master transcription factors Oct4, Nanog, and Sox2. More importantly, it co-occupies the enhancer regions of most key pluripotency genes with the master transcription factors, and positively regulates their expression by maintaining an open chromatin structure. Our data suggests that INO80 is an integral component of the pluripotency transcription network, and plays a critical role in both the maintenance and establishment of pluripotency Mouse J1 cells were infected with lentiviral-shNT or lentiviral-Ino80, RNA was extracted at 2, 4 or 6 days after infection. agent: non-targeting shRNA: NS_Day_2_1, NS_Day_2_2, NS_Day_4_1, NS_Day_4_2, NS_Day_6_1, NS_Day_6_2 agent: Ino80 shRNA: shIno80_Day_2_1, shIno80_Day_2_2, shIno80_Day_4_1, shIno80_Day_4_2, shIno80_Day_6_1, shIno80_Day_6_2 time: 48 hours: NS_Day_2_1, NS_Day_2_2, shIno80_Day_2_1, shIno80_Day_2_2 time: 96 hours: NS_Day_4_1, NS_Day_4_2, shIno80_Day_4_1, shIno80_Day_4_2 time: 144 hours: NS_Day_6_1, NS_Day_6_2, shIno80_Day_6_1, shIno80_Day_6_2 cell line: mouse J1 ESC: NS_Day_2_1, NS_Day_2_2, shIno80_Day_2_1, shIno80_Day_2_2, NS_Day_4_1, NS_Day_4_2, shIno80_Day_4_1, shIno80_Day_4_2, NS_Day_6_1, NS_Day_6_2, shIno80_Day_6_1, shIno80_Day_6_2 biological replicate: shIno80_Day_2_1, shIno80_Day_2_2 biological replicate: shIno80_Day_4_1, shIno80_Day_4_2 biological replicate: shIno80_Day_6_1, shIno80_Day_6_2 biological replicate: NS_Day_2_1, NS_Day_2_2 biological replicate: NS_Day_4_1, NS_Day_4_2 biological replicate: NS_Day_6_1, NS_Day_6_2
2014-05-16 | E-GEOD-49250 | biostudies-arrayexpress
Project description:Embryonic stem cell (ESC) self-renewal and differentiation is governed by a comprehensive regulatory network. Although the transcriptional regulation has been extensively investigated, post-transcriptional mechanisms controlling the ESC state are poorly understood. Here we describe a critical role of the THO complex in ESC self-renewal and differentiation. We show that THO preferentially interacts with pluripotency gene transcripts through Thoc5, and is required for self-renewal by regulating their export and expression. During differentiation, THO loses its interaction with those transcripts due to reduced Thoc5 expression, which leads to decreased expression of pluripotency proteins and facilitates differentiation. Finally, THO is also important for the establishment of pluripotency, as its depletion inhibits somatic cell reprogramming and blastocyst development. Together, our data indicates that THO regulates pluripotency gene mRNA export to control ESC self-renewal and differentiation, and uncovers a novel mechanism of post-transcriptional regulation in stem cell fate specification. RNA IP was conducted by use of antibody against Thoc2, the precipitated RNA was used to generate library using illumina Kit, and subsequently sequenced by miSeq
2013-11-30 | E-GEOD-48436 | biostudies-arrayexpress
Project description:Embryonic stem cell (ESC) self-renewal and pluripotency is controlled by the coordinated action of transcription factors and chromatin regulators. Compared to the pluripotency transcription factors, the function of the chromatin regulators, especially the ATP-dependent chromatin remodelers, remains poorly understood in ESCs. Here, we show that INO80, a SWI/SNF family chromatin remodeling complex, is essential for ESC self-renewal, pluripotency, somatic cell reprogramming, and embryonic development. Ino80, the ATPase of the complex, forms an auto-regulatory loop with the ESC master transcription factors Oct4, Nanog, and Sox2. More importantly, it co-occupies the enhancer regions of most key pluripotency genes with the master transcription factors, and positively regulates their expression by maintaining an open chromatin structure. Our data suggests that INO80 is an integral component of the pluripotency transcription network, and plays a critical role in both the maintenance and establishment of pluripotency Identification of Ino80 localization in mouse embryonic stem cells
2014-05-16 | E-GEOD-49137 | biostudies-arrayexpress
Project description:Single-cell transcriptomics has recently emerged as a powerful technology to explore gene expression heterogeneity amongst single cells. Here we identify two major sources of technical variability, sampling noise and global cell-to-cell variation in sequencing efficiency. We propose noise models to correct for this and after validation by single-molecule FISH experiments, we apply these models to demonstrate that growing mES cells in 2i instead of serum/LIF globally reduces gene expression variability. J1 mouse embryonic stem cells (mESCs) were cutured in 2i or in serum medium. Cells were dissociated into a single cell suspension and picked under a stereomicroscope using a 30μm glass capillary and mouth pipette. Picked cells were deposited in the lid of an 0.5ml LoBind eppendorf tube and snap frozen in liquid nitrogen. For the pool and split controls, approximately 1 million cells were lysed, the amount of RNA was quantified on a bioanalyzer (Agilent) using the Eukaryote Total RNA pico kit. 20pg aliquots of total RNA were used for each pool and split control. Single cells and controls were processed using the previously described CEL-seq technique, with a few alterations. A 4bp random barcode as unique molecular identifier (UMI) was added to the primer in between the cell specific barcode and the poly T stretch. Libraries were sequenced on an Illumina HighSeq 2500 using 50bp paired end sequencing. For cells and controls, two libraries were sequenced on two lanes in total for each condition.
2014-04-20 | E-GEOD-54695 | biostudies-arrayexpress
Project description:Hepatocellular carcinoma (HCC) is a frequent cancer with poor prognosis and with limited possibilities for anti-cancer treatment. Evidence has recently accumulated suggesting that multiple signaling pathways are activated in human cancer. It has been recently shown by exosome sequencing of HCC that 161 putative driver genes are associated with 11 recurrently altered pathways, suggesting that we need to inhibit these multiple pathways for HCC therapy. THOC5, a member of transcription/export (TREX) complex, that plays a role in less than 1% of mRNA processing in normal cells such as fibroblasts or macrophages, is not required for maintenance of mature hepatocytes. In this study, we have examined the role of THOC5 in human HCC. Enhanced THOC5 expression was not observed in differentiation grading 1 (G1) human HCC, but 78% of G2 and G3 exhibited increased levels of THOC5. Furthermore, the 50% depletion of THOC5 in hepatocellular carcinoma cell lines, Huh7 and HepG2 causes lipid accumulation and apoptosis. Transcriptome analysis using THOC5 depleted Huh7 and HepG2 cells revealed that 1049 and 837 genes were downregulated upon depletion of THOC5 in Huh7 and HepG2 cells, respectively. Among these genes, 396 were commonly downregulated in both cell lines. Some of these, such as tissue inhibitor of metalloproteinase 3 (TIMP3), tripartite motif containing 24 (TRIM24), ribosomal protein S6 kinase polypeptide 3 (RPS6KA3) and transmembrane emp24-like trafficking protein 10 (TMED10) are known to be fine tuners for several signal transduction pathways. The expression of these proteins was correlated with the THOC5 expression level in HCC. To inhibit multiple signaling pathways we are currently examining the effects of a combination of siRNAs against THOC5 target genes in HCC cell lines. Our data suggest that THOC5, which controls a set of genes that are involved in HCC malignancy can be a potential biomarker for HCC. In addition, THOC5 target gene, TMED10 may also be a novel biomarker of HCC. Furthermore, the suppression of the THOC5 gene per se or multiple THOC5 target genes may represent a novel strategy for cancer therapy. Huh7 and HepG2 cells were infected with lentiviral THOC5 and control shRNAs. Five days after infection, total RNAs were isolated and subjected to microarray analysis.
2015-11-02 | E-GEOD-70178 | biostudies-arrayexpress
Project description:Transcription termination has important regulatory functions, impacting mRNA stability, localization and translation potential. Failure to appropriately terminate transcription can also lead to read-through transcription and the synthesis of antisense RNAs which can have profound impact on gene expression. The Transcription-Export (THO/TREX) protein complex plays an important role in coupling transcription with splicing and export of mRNA. However, little is known about the role of the THO/TREX complex in the control of transcription termination. In this work, we show that two proteins of the THO/TREX complex, namely TREX COMPONENT 1 (TEX1 or THO3) and HYPER RECOMBINATION1 (HPR1 or THO1) contribute to the correct transcription termination at several loci in Arabidopsis thaliana. We first demonstrate this by showing defective termination in tex1 and hpr1 mutants at the nopaline synthase (NOS) terminator present in a T-DNA inserted between exon 1 and 3 of the PHO1 locus in the pho1-7 mutant. Read-through transcription beyond the NOS terminator and splicing-out of the T-DNA resulted in the generation of a near full-length PHO1 mRNA (minus exon 2) in the tex1 pho1-7 and hpr1 pho1-7 double mutants, with enhanced production of a truncated PHO1 protein that retained phosphate export activity. Consequently, the strong reduction of shoot growth associated with the severe phosphate deficiency of the pho1-7 mutant was alleviated in the tex1 pho1-7 and hpr1 pho1-7 double mutants. Additionally, we show that RNA termination defects in tex1 and hpr1 mutants leads to 3'UTR extensions in several endogenous genes. These results demonstrate that THO/TREX complex contributes to the regulation of transcription termination.
| S-EPMC7179932 | biostudies-literature
Project description:Transcription termination of mRNAs transcribed from a given locus has a decisive role in regulating the gene function as it determines the coding potential and inclusion of regulatory sequence elements. Failure in appropriate transcription termination leads to read-through transcription, resulting in the synthesis of antisense RNAs which can have profound impact on overall gene expression. However, molecular mechanisms which regulate transcription termination and chimeric RNA formation are poorly understood. We explored the regulatory function of transcription and export complex (THO/TREX) in transcription termination. We show that two members of THO/TREX complex, TREX COMPONENT 1 (TEX1) and HYPER RECOMBINATION1(HPR1) are critical for the correct transcription termination in Arabidopsis. We first demonstrate this by showing defective termination of the bacterial nopaline synthase (NOS) terminator on a transgene in tex1 and hpr1 mutants. Additionally, we show that RNA termination defects in tex1 and hpr1 mutants are widespread at the whole genome levels leading to 3’UTR extensions, truncations and in some cases in the formation of intergenic chimeric transcripts. Chromatin immunoprecipitation coupled with quantitative PCR experiments confirmed the presence of RNA polymerase II beyond the canonical termination sites on genes with defective RNA termination in tex1 and hpr1 mutants. These results demonstrate that THO/TREX complex is a novel regulator of transcription termination in Arabidopsis.
2020-03-24 | GSE128877 | GEO