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Smad4 and Trim33 dependend nodal/activin responsive genes in differentiated mouse ESCs

ABSTRACT: In differentiated mouse ESCs, most of the nodal/activin responsive genes are dependent on both Smad4 and Trim33, some are solely dependent on Smad4, and some are dependent on Trim33. Ebs at Day2.5 from WT, Smad4 null, and Trim33 knock-down ESCs, were treated with activin or SB 431542 for 2 h.

ORGANISM(S): Mus musculus

SUBMITTER: Qiaoran Xi

PROVIDER: E-GEOD-32903 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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A poised chromatin platform for TGF-β access to master regulators.

Xi Qiaoran Q Wang Zhanxin Z Zaromytidou Alexia-Ileana AI Zhang Xiang H-F XH Chow-Tsang Lai-Fong LF Liu Jing X JX Kim Hyesoo H Barlas Afsar A Manova-Todorova Katia K Kaartinen Vesa V Studer Lorenz L Mark Willie W Patel Dinshaw J DJ Massagué Joan J

Cell 20111201 7

Specific chromatin marks keep master regulators of differentiation silent yet poised for activation by extracellular signals. We report that nodal TGF-β signals use the poised histone mark H3K9me3 to trigger differentiation of mammalian embryonic stem cells. Nodal receptors induce the formation of companion Smad4-Smad2/3 and TRIM33-Smad2/3 complexes. The PHD-Bromo cassette of TRIM33 facilitates binding of TRIM33-Smad2/3 to H3K9me3 and H3K18ac on the promoters of mesendoderm regulators Gsc and Mi ...[more]

PMID: 22196728

Similar Datasets

Smad4 and Trim33 dependend nodal/activin responsive genes in differentiated mouse ESCs

Project description:In differentiated mouse ESCs, most of the nodal/activin responsive genes are dependent on both Smad4 and Trim33, some are solely dependent on Smad4, and some are dependent on Trim33.

2012-01-09 | GSE32903 | GEO

Nodal signaling maintains H3K18ac landscape to promote mesendodermal differentiation through TRIM33

Project description:The epigenome of a cell is established and maintained by chromatin modifiers and remodelers, which are recruited to the chromatin by specific transcription factors. In this report, we show that nodal cross-talks with the epigenome through TRIM33-H3K18ac to mediate mesendodermal genes expression. The chromatin accessibility at mesendodermal genes depends on TRIM33. Moreover, histone acetylation is essential for TRIM33 recruitment to many nodal target genes involved in mesendodermal differentiation. The distribution pattern of the H3K18ac mark changes from foci to expanded domains at the mesendodermal genes promoter during embryonic stem cells (ESCs) differentiation to embryoid bodies (EBs). This could be the cue to facilitate TRIM33 colocalized with Smad2/3 at chromatin in EBs but not in ESCs. TRIM33 interacts with the H3K18ac “writer” p300 dependent on nodal signaling, providing a positive feedback to promote activation of mesendodermal genes and association with HDAC1 plays a negative role in activation of mesendodermal genes.

2019-06-01 | GSE115169 | GEO

Recruitment of TRIM33 to cell-context specific PML nuclear bodies regulates Nodal signaling in mESCs

Project description:TRIM33 is a chromatin reader required for mesendoderm differentiation upon activation of Nodal signaling. But, its role in mESCs is still elusive. Here, we found that TRIM33 co-localizes with promyelocytic leukemia nuclear bodies (PML NBs) specifically in mESCs to mediate Nodal signaling-directed transcription of Lefty1/2. We showed that TRIM33 puncta formation in mESCs depends on PML and specific assembly of PML NBs. Moreover, TRIM33 and PML co-regulate Lefty1/2 expression in mESCs. In addition, both PML and mESCs-specific PML NBs are required for TRIM33 recruitment at Lefty1/2 loci. Remarkably, PML NBs directly associate with the Lefty1/2 loci in mESCs. Finally, a TurboID proximity labeling experiment confirmed that TRIM33 is highly enriched in the mESCs-specific PML NBs. Thus, our study provides the mechanistic insight about TRIM33 condensate in regulating Nodal signaling-directed transcription in mESCs, it also reveals that PML NBs recruit distinct sets of client proteins in cell context dependent manner.

2022-12-08 | GSE199738 | GEO

Analysis of chromatin accessibility upon NODAL/Activin signalling reveal mechanisms of SMAD2-regulated transcription

Project description:In this experiment patterns of chromatin accessibility were compared in P19 mouse embryonic teratoma cells treated with either the Nodal/Activin singalling inhibitor SB-431542, or with Activin for 1hr (acute signalling) and 8 hr (prolonged signalling), or left untreated (chronic signalling)

2022-04-10 | GSE178315 | GEO

Mus musculus

Project description:Smad4 and Trim33 dependend nodal/activin responsive genes in differentiated mouse ESCs

| PRJNA146581 | ENA

Tripartite motif-containing 33 (Trim33) determines the pathogenic function of Th17 cells

Project description:We report that Tripartite motif-containing 33 (Trim33), a protein that was previously associated with TGF-beta signaling, determines the pathogenic function of Th17 cells. Trim33 deficiency in T cells resulted in resistance to an autoimmune disease model. Lack of Trim33 did not impact TGF-beta signaling in mediating Foxp3 gene expression but greatly reduced TGF-beta induction of IL-17 production during Th17 cell differentiation. Importantly, we found TGF-beta not only increased IL-17 but also suppressed IL-10 expression; absence of Trim33 or Smad2 but not Smad4 in T cells enhanced IL-10 expression. In a Smad2-dependent manner, Trim33 was recruited to Il17 and Il10 gene loci and was crucial in appropriate histone modification accompanying Th17 differentiation. Our study thus demonstrates that Trim33, a non-canonical branch of TGF-beta signaling, programs the pro-inflammatory function of Th17 differentiation by promoting IL-17 and suppressing IL-10 expression. As a critical switch of pathogenic versus regulatory phenotype of T cells, Trim33 may be targeted in treating human autoimmune diseases.

2018-05-02 | GSE113925 | GEO

Activin/Nodal-dependent N6-methyladenosine (m6A) deposition in human pluripotent stem cells

Project description:This experiment was designed to probe the function of Activin/Nodal signalling in the deposition of m6A in human pluripotent stem cells (hPSCs). hPSCs were cultured in presence of Activin or subjected to short-term inhibition of Activin/Nodal signalling for 2h using the receptor antagonist SB-431542 (IP). The global abundance of m6A was then measured by nuclear-enriched methylated RNA immunoprecipitation followed by deep sequencing (NeMeRIP-seq). Pre-NeMeRIP input RNA was used as control to normalise for the changes in gene expression in the two conditions.

2017-12-26 | E-MTAB-5229 | biostudies-arrayexpress

RNA-seq of WTAP knockdown human pluripotent stem cells during the exit from pluripotency induced by Activin/Nodal inhibition

Project description:This experiment was designed to monitor the gene expression changes induced by the knockdown of WTAP in human pluripotent stem cells (hPSCs) during the exit from pluripotency induced by the inhibition of Activin/Nodal signalling. hPSCs carrying a tetracycline-inducible short hairpin RNA (shRNA) against WTAP were cultured in control conditions or in presence of tetracycline (TET) to drive gene knockdown. Cells were monitored by RNA-seq in the pluripotent state (culture conditions containing Activin), or at various time points after inhibition of Activin/Nodal signalling with the receptor antagonist SB-431542 (SB). Samples were collected after 2h, 8h and 32h.

2018-01-04 | E-MTAB-5230 | biostudies-arrayexpress

Dynamics of TRIM33 binding in macrophages and effects of TRIM33 deletion on chromatin state during activation of primary macrophages.

Project description:To get insight into TRIM33 functions, TRIM33 ChIP-seq was carried out in murine macrophage cell line (RAW) and in bone marrow-derived macrophages (BMDM). The results showed that, in addition to its role in hematopoietic differentiation, TRIM33 may modulate PU.1 transcriptional activity during macrophage development and/or activation.To characterize the role of TRIM33 in macrophages, we bred TRIM33fl/fl mice with Lyz-Cre mice where the Cre recombinase gene is under the regulatory sequences of the Lyz gene that is expressed only in mature myeloid cells. Bone marrow cells from LyzCre/Trim33+/+ mice and LyzCre/Trim33flox/flox mice were differentiated in macrophages and treated during 0h, 4h, 12h and 24h with LPS. Using ChIP-seq, we provide a link between TRIM33 binding and H3K4me3 spreading on inflammatory genes in macrophages. Chromatin immunoprecipitations of TRIM33 and H3K4Me3 followed by multiparallel sequencing performed in murine bone marrow-derived macrophages (BMDM).

2015-11-23 | E-GEOD-43654 | biostudies-arrayexpress

A role for the Trim33 ubiquitin ligase in cellular response to replicative stress

Project description:Deregulation of RNA polymerase II (RNAPII) by oncoproteins, such as transcription factor Myc, interferes with DNA replication and is a major source of DNA damage and genomic instability. Ubiquitination is a key pathway controlling RNAPII activity via modification of RNAPII subunits or associated regulatory proteins. We uncover a mechanism for genome maintenance by ubiquitin ligase Trim33 and transcription factor E2f4. We show that Trim33 promotes E2f4 protein turnover, restricting interactions of E2f4 with chromatin and with the Recql DNA helicase. Replicative stress blunts Trim33-dependent regulation, which stimulates E2f4 and Recql recruitment to chromatin and facilitates recovery of DNA replication. Deletion of Trim33 triggers chronic recruitment of Recql to chromatin and accelerates DNA replication under stress, accompanied by compromised DDR signaling and DNA repair. Depletion of Trim33 in Myc-overexpressing cells leads to accumulation of replication-associated DNA damage and delays Myc-driven tumorigenesis. We propose that the Trim33-E2f4-Recql axis provides a mechanism to control DNA replication at transcriptionally active chromatin to maintain genome integrity.

2023-07-24 | PXD037854 | Pride

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