Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

54 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ChIP-seq experiment of mouse embryonic stem cells (mESCs), assessing beta-catenin DNA binding in wild type mESCs and TCF/LEF quadruple knock-out mESCs.

ABSTRACT: Mouse embryonic stem cells (mESCs), derived from pre-implantation blastocyst cells, can be maintained in vitro in defined N2B27 medium supplemented with two chemical inhibitors for GSK3 and MEK (2i) and the cytokine leukemia inhibitory factor (LIF), which act synergistically to promote self-renewal and pluripotency. Many efforts have been devoted to identify genes that promote exit from the pluripotent state and the transition to a primed state of differentiation. One of the first identified players in this process was the Wnt/b-catenin effector TCF7L1 (previously referred to as TCF3), belonging to the family of four TCF/LEF transcription factors, which acts as pro-differentiation factor by repressing pluripotency genes. Of note, there is little evidence that the genetic abrogation of the mechanisms required for the exit from the pluripotent state is sufficient to enable self-renewal in the absence of 2iL. Here, we found that complete loss-of-function of Tcf7, Lef1, Tcf7l1 and Tcf7l2, the genes encoding for the four TCF/LEF transcription factors, (refered to as qKO) allows mESCs to become fully 2iL-independent and to propagate in basal N2B27. In addition to RNA-seq data deposited under accession number E-MTAB-10564, chromatin immunoprecipitation followed by deep DNA sequencing (ChIP-seq) has been performed in CHIR-stimulated mESCs. Here, the DNA binding landscape of β-catenin has been analyzed to assess its possible connection to TCF/LEF-mediated pluripotency.

INSTRUMENT(S): Illumina HiSeq 4000

ORGANISM(S): Mus musculus

SUBMITTER: Simon Söderholm

PROVIDER: E-MTAB-10575 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

TCF/LEF dependent and independent regulation of Wnt/beta-catenin transcription

Project description:During canonical Wnt signalling the activity of nuclear beta-catenin is largely mediated by the TCF/LEF family of transcription factors. To challenge this view we used the CRISPR/Cas9 genome editing approach to generate HEK 293T cell clones simultaneously carrying loss-of-function alleles of all four TCF/LEF genes. Exploiting unbiased whole transcriptome sequencing studies, we found that a subset of beta-catenin transcriptional targets did not require TCF/LEF factors for their regulation. Consistent with this finding, we observed in a genome-wide analysis that beta-catenin occupied specific genomic regions in the absence of TCF/LEF. Finally, we revealed the existence of a transcriptional activity of beta-catenin that specifically appears when TCF/LEF factors are absent, and refer to this as beta-catenin-GHOST response. Collectively, this study uncovers a previously neglected modus operandi of beta-catenin that bypasses the TCF/LEF transcription factors.

2018-11-22 | E-MTAB-7028 | biostudies-arrayexpress

RNA-seq experiment of mouse embryonic stem cells (mESCs), comparing TCF/LEF quadruple knock-out cells with wild type cells

Project description:Mouse embryonic stem cells (mESCs), derived from pre-implantation blastocyst cells, can be maintained in vitro in defined N2B27 medium supplemented with two chemical inhibitors for GSK3 and MEK (2i) and the cytokine leukemia inhibitory factor (LIF), which act synergistically to promote self-renewal and pluripotency. Many efforts have been devoted to identify genes that promote exit from the pluripotent state and the transition to a primed state of differentiation. One of the first identified players in this process was the Wnt/b-catenin effector TCF7L1 (previously referred to as TCF3), belonging to the family of four TCF/LEF transcription factors, which acts as pro-differentiation factor by repressing pluripotency genes. Of note, there is little evidence that the genetic abrogation of the mechanisms required for the exit from the pluripotent state is sufficient to enable self-renewal in the absence of 2iL. Here, we found that complete loss-of-function of Tcf7, Lef1, Tcf7l1 and Tcf7l2, the genes encoding for the four TCF/LEF transcription factors, (refered to as qKO) allows mESCs to become fully 2iL-independent and to propagate in basal N2B27. To understand the genetic program that allows qKO cells to achieve 2iL-independent self-renewal, we performed RNA sequencing (RNA-seq) of qKO and wild type mESCs.

2021-06-15 | E-MTAB-10564 | biostudies-arrayexpress

Chromatin immunoprecipitation of ectopic FLAG-tagged TCF7L1 followed by Mass Spectrome-try in H9-TCF7L1 Human Embryonic Stem Cells

Project description:TCF7L1 is a member of the T cell factor/Lymphoid enhancer factor (TCF/LEF) family of tran-scription factors that are part of the WNT/beta-CATENIN signaling pathway. TCF7L1 modulates transcription by interacting with other regulators on chromatin. TCF7L1 has been shown to be one of the key factors in maintaining pluripotency in human embryonic stem cells (ESCs). We previously demonstrated that the absence of TCF71 causes H9 hESCs to differentiate sponta-neously (Sierra et al., 2018 Development 145(4).pii:dev161075). Mechanistically, how TCF7L1 inhibits differentiation and keeps cells in the pluripotent state is not clear. Identifying transcrip-tional regulators on chromatin is a critical step to elucidating one of several molecular mecha-nisms controlled by TCF7L1. We previously developed a FLAG tagged TCF7L1 transgene that is controlled by a doxycycline-inducible TET-ON system and generated the H9-TCF7L1 line (Sier-ra et al., 2018 Development 145(4).pii:dev161075). Here we used the H9-TCF7L1 line and em-ployed the method called rapid immunoprecipitation (IP) mass spectrometry of endogenous pro-tein (RIME) (Mohammed et al., 2016 Nat Protoc 11(2):316-26) to identify TCF7L1-associated proteins on chromatin. Coupling of these two methods (the FLAG tagged TETON inducible sys-tem and RIME) allowed us to control the level of TCF7L1 expression in hESCs, immunopreci-pate TCF7L1 using an anti-FLAG antibody and capture TCF7L1-bound associated complexes on chromatin. Our MS analysis identified some known proteins that have been shown to associate with the WNT/beta-CATENIN/TCF/LEF pathway, as well as novel complexes that have not been linked with TCF7L1. Gene Ontology analysis suggest these proteins function in chromatin modi-fication, splicing, and RNA processing. Our data could create new ideas for in-depth studies of TCF7L1 controlling pluripotency in human ESCs and for understanding how TCF7L1 may act in other cell types.

2024-06-16 | PXD047582 | Pride

TCF/LEF dependent and independent regulation of Wnt/beta-catenin transcription

2018-11-02 | E-MTAB-7029 | biostudies-arrayexpress

CUT&RUN LoV-U of beta-catenin, TCF/LEF transcription factors and histone modifications in HEK293T and mouse embryonic hindlimb tissue at 11.5 days post coitum

Project description:In our attempts to profile different regulators of the WNT/b-catenin transcriptional complex, CUT&RUN failed to produce consistent binding patterns of the non-DNA-binding b-catenin. We developed a modified CUT&RUN protocol, which we refer to as LoV-U (Low Volume and Urea), that enables the generation of robust and reproducible b-catenin binding profiles. CUT&RUN-LoV-U can profile all classes of chromatin regulators tested, as shown by datasets targeting the TCF/LEF transcription factors and various histone modifications. CUT&RUN-LoV-U uncovers direct WNT/β-catenin target genes in human cells, as well as in ex vivo cells isolated from developing mouse tissue.

2022-07-16 | E-MTAB-11951 | biostudies-arrayexpress

Ascl2 acts as an R-spondin/Wnt responsive switch to control stemness in intestinal crypts [ChIP-seq]

Project description:Wnt signals control three functions of intestinal crypts: maintenance of Lgr5 stem cells, proliferation of transit-amplifying daughters and formation of Paneth cells. Here, we study how the Wnt effector Î²-catenin/Tcf4 cooperates with the Wnt-activated transcription factor Ascl2 to control a stem cell transcription program. DNA elements that are co-occupied and synergistically regulated by Ascl2 and Tcf4 specifically map to stem cell genes. In vitro, Tcf4-/- mini-guts are rescued by Ascl2 expression, while Ascl2-/- organoids are rescued by Wnt signaling. A direct auto-activatory loop leads to an on/off expression pattern of Ascl2 with a threshold that depends on the previous state. Wnt/R-spondin1 activates this loop. This mechanism interprets Wnt levels in crypts and translates this continuous signal into a discrete Ascl2 âonâ or âoffâ decision. In turn Ascl2, together with Î²-catenin/Tcf, activates stem cell genes. Thus, Ascl2 forms a transcriptional 'stemness switch' that is both Wnt-responsive and Wnt-dependent Examination of Tcf4, B-catenin and Ascl2 DNA occupancy in murine intestinal organoids and human colorectal cancer cell lines *** Original raw files unavailable due to loss during backup ***

2016-07-15 | E-GEOD-84456 | biostudies-arrayexpress

TCF7L1 regulates colorectal cancer cell migration and invasion by repressing GAS1 expression (RNA-Seq)

Project description:Dysregulation of the canonical Wnt/β-catenin signaling pathway is a hallmark of colorectal cancer (CRC). The T-cell factor/lymphoid enhancer factor (TCF/LEF; hereafter, TCF) family of transcription factors are critical regulators of canonical Wnt/β-catenin target gene expression. Despite similarity across DNA-binding and protein-binding domains, TCF family members differentially regulate target gene expression in CRC. Of the four TCF family members, TCF7L1 predominantly functions as a transcriptional repressor and it has an oncogenic role in CRC. Despite this role, few target genes regulated by TCF7L1 in CRC have been identified. Through RNA-sequencing of transcripts differentially expressed in control and TCF7L1-overexpressing HCT116 cells, we identified 397 genes that were repressed directly, or indirectly, by TCF7L1. Gene set enrichment analysis found genes associated with epithelial-mesenchymal transition amongst those that are differentially expressed. By silencing and overexpressing TCF7L1 in CRC cell lines, we found that TCF7L1 promoted migration, invasion, and adhesion in vitro. Chromatin immunoprecipitation followed by sequencing (ChIP-sequencing) localized 3661 TCF7L1 binding sites within the CRC genome. Comparison of genes whose expression was downregulated by TCF7L1 and genes with TCF7L1 binding sites revealed 41 novel targets directly regulated by TCF7L1. Among these, we localized a TCF7L1 promoter-proximal binding site within the growth arrest specific 1 (GAS1) gene. We found that ectopic GAS1 expression rescued the TCF7L1-mediated increase in migration and invasion in CRC cells. These findings uncover a novel role for TCF7L1 in repressing GAS1 expression to promote migration and invasion of CRC cells in vitro.

2024-06-05 | GSE241025 | GEO

TCF7L1 regulates colorectal cancer cell migration and invasion by repressing GAS1 expression (ChIP-Seq)

2024-06-05 | GSE241026 | GEO

ChIP-seq experiment of mouse embryonic stem cells (mESCs), assessing beta-catenin DNA binding in wild type mESCs and TCF/LEF quadruple knock-out mESCs.

Project description:ChIP-seq experiment of mouse embryonic stem cells (mESCs), assessing beta-catenin DNA binding in wild type mESCs and TCF/LEF quadruple knock-out mESCs.

| PRJEB45562 | ENA

Identification of beta-catenin binding regions in SW480 cells

Project description:Deregulation of canonical Wnt/beta-catenin pathway is one of the earliest events in the pathogenesis of colon cancer. Mutations in APC or CTNNB1 (beta-catenin gene) are highly frequent in colon cancer and cause aberrant stabilization of b-catenin, which activates the transcription of Wnt target genes by binding to chromatin via the TCF/LEF transcription factors. Here we report an integrative analysis of genome-wide chromatin occupancy of b-catenin by chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-seq) and gene expression profiling by microarray analysis upon RNAi-mediated knockdown of beta-catenin in colon cancer cells (GSE53656). Immunoprecipitated samples from human colon cancer SW480 cells with antibodies against beta-catenin and control IgG respectively were used for ChIP-seq experiments.

2014-03-12 | E-GEOD-53927 | 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