INO80 complex in the core regulatory network governing ESC self-renewal [728_subunits]
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ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE49251 | GEO | 2014/05/16
SECONDARY ACCESSION(S): PRJNA213414
REPOSITORIES: GEO
Similar Datasets
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: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
2014-05-16 | GSE49250 | GEO
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
2014-05-16 | GSE49137 | GEO
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:Self-renewal and pluripotency in human embryonic stem cells (hESCs) depends upon the function of a remarkably small number of master transcription factors (TFs) that include OCT4, SOX2, and NANOG. Endogenous factors that regulate and maintain the expression of master TFs in hESCs remain largely unknown and/or uncharacterized. We use a genome-wide, proteomics approach to identify proteins associated with the OCT4 enhancer. We identify known OCT4 regulators, plus a subset of potential regulators including a zinc finger protein, ZNF207, that plays diverse roles during development. In hESCs, ZNF207 partners with master pluripotency TFs to govern self-renewal and pluripotency while simultaneously controlling commitment of cells towards ectoderm through direct regulation of neuronal TFs, including OTX2. The distinct roles of ZNF207 during differentiation occur via isoform switching. Thus, a distinct isoform of ZNF207 functions in hESCs at the nexus that balances pluripotency and differentiation to ectoderm.
2018-08-17 | GSE118632 | GEO
Project description:Self-renewal and pluripotency in human embryonic stem cells (hESCs) depends upon the function of a remarkably small number of master transcription factors (TFs) that include OCT4, SOX2, and NANOG. Endogenous factors that regulate and maintain the expression of master TFs in hESCs remain largely unknown and/or uncharacterized. We use a genome-wide, proteomics approach to identify proteins associated with the OCT4 enhancer. We identify known OCT4 regulators, plus a subset of potential regulators including a zinc finger protein, ZNF207, that plays diverse roles during development. In hESCs, ZNF207 partners with master pluripotency TFs to govern self-renewal and pluripotency while simultaneously controlling commitment of cells towards ectoderm through direct regulation of neuronal TFs, including OTX2. The distinct roles of ZNF207 during differentiation occur via isoform switching. Thus, a distinct isoform of ZNF207 functions in hESCs at the nexus that balances pluripotency and differentiation to ectoderm.
2018-08-17 | GSE118637 | GEO
Project description:Self-renewal and pluripotency of the embryonic stem cell (ESC) state is established and maintained by multiple regulatory networks that comprise transcription factors and epigenetic regulators. Although many studies have been performed, the function of epigenetic regulators in these networks is incompletely defined. We conducted a CRISPR-Cas9 mediated loss-of-function genetic screen to target 323 epigenetic and ESC-specific transcription factor genes. This screen identified two new epigenetic regulators—TAF5L and TAF6L—with high confidence for the mouse ESC state. TAF5L and TAF6L are also essential for the efficient somatic reprogramming. In-depth analyses demonstrate that TAF5L and TAF6L belong to and establish a regulatory circuitry with MYC and CORE networks. Moreover, detailed molecular studies reveal TAF5L and TAF6L predominantly regulate their target genes through the c-MYC and MYC regulatory network to control self-renewal of mouse ESCs. Our findings illuminate the multi-layered regulatory networks of TAF5L and TAF6L for gene regulation to maintain the ESC state.
2019-01-01 | GSE113329 | GEO
Project description:Self-renewal and pluripotency of the embryonic stem cell (ESC) state is established and maintained by multiple regulatory networks that comprise transcription factors and epigenetic regulators. Although many studies have been performed, the function of epigenetic regulators in these networks is incompletely defined. We conducted a CRISPR-Cas9 mediated loss-of-function genetic screen to target 323 epigenetic and ESC-specific transcription factor genes. This screen identified two new epigenetic regulators—TAF5L and TAF6L—with high confidence for the mouse ESC state. TAF5L and TAF6L are also essential for the efficient somatic reprogramming. In-depth analyses demonstrate that TAF5L and TAF6L belong to and establish a regulatory circuitry with MYC and CORE networks. Moreover, detailed molecular studies reveal TAF5L and TAF6L predominantly regulate their target genes through the c-MYC and MYC regulatory network to control self-renewal of mouse ESCs. Our findings illuminate the multi-layered regulatory networks of TAF5L and TAF6L for gene regulation to maintain the ESC state.
2019-01-01 | GSE113334 | GEO
Project description:Myc is a master transcription factor that has been demonstrated to be required for embryonic stem cell (ESC) pluripotency, self-renewal, and inhibition of differentiation. Although recent works identified several Myc-targets in ESC the list of Myc binding sites is largely incomplete due to the low sensitivity and specificity of the antibodies available so far. To systematically identify Myc binding sites in mouse ESCs here we used a stringent streptavidin based genome-wide chromatin immunoprecipitation (ChIP-Seq) of a biotin-tagged Myc (Bio-Myc) as well as a ChIP-Seq of the Myc partner Max. This analysis identified 4273 Myc binding sites of which more than 85% co-occupied by Max, overlap with H3K4me3 positive promoters and active enhancers of transcriptional regulators, chromatin modifiers, and genes involved in stem cell self-renewing. The new sites identified were validated experimentally. This study provides a new Myc and Max binding reference in mouse ESCs. ChIP-seq of bio-Myc and Max in E14 and respective controls; Bio-Myc ChIP-seq was performed in a stable clone of E14 mouse embryonic stem cell expressing Biotin-tagged Myc; Mock, Max and IgG were performed in parental wt E14 mESC.
2014-03-05 | E-GEOD-48175 | biostudies-arrayexpress