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Genome-wide maps of Tcf1 binding locations in splenic CD8 T cells.

ABSTRACT: We mapped genome-wide Tcf1 binding locations in mature CD8 T cells to identify its direct target genes.

ORGANISM(S): Mus musculus

PROVIDER: GSE52070 | GEO | 2014/03/05

SECONDARY ACCESSION(S): PRJNA226615

REPOSITORIES: GEO

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Genome-wide maps of Tcf1 binding locations in splenic CD8 T cells.

Project description:We mapped genome-wide Tcf1 binding locations in mature CD8 T cells to identify its direct target genes. This experiment aims to identify genome-wide binding locations for Tcf1 transcription factor in mature CD8 T cells. The CD8 T cells were isolated from wild-type C57BL/6 mice by negative selection. The chromatin fragments were immunoprecipitated by an anti-Tcf1 antiserum or control rabbit serum (without immunization). The immunoprecipitated fragments were then used in high throughput sequencing. Data processing then revealed >3000 high-confidence Tcf1 binding peaks across the CD8 T cell genome. One important finding is that Tcf1 binds directly to Cd4 gene silencer, and thus explain its important role in suppressing the CD4 coreceptor in mature CD8 T cells.

2014-03-05 | E-GEOD-52070 | biostudies-arrayexpress

Impact of Tcf1 and Lef1 deficiency on histone marks and Tcf1 binding in CD8 T cells

Project description:Comparison of epigenome and Tcf1 occupancy between control and Tcf1/Lef1-deficient CD8 T cells Control mice or those are deficient for Tcf1 and Lef1 transcription factors (deleted by CD4-Cre) were used to isolate thymocytes. The thymocytes were surface-stained to identify TCRbeta high, CD69â, CD24â CD8+ subsets. These cells were sorted for ChIPseq analysis of various histone marks. Control mice or those are deficient for Tcf1 (deleted by CD4-Cre) were used to isolate thymocytes. The splenocytes were surface-stained to identify TCRbeta high, CD8+ subsets. These cells were sorted for ChIPseq analysis of Tcf1 binding locations.

2016-02-12 | E-GEOD-73239 | biostudies-arrayexpress

Impact of Tcf1 and Lef1 deficiency on mature CD8 thymocytes

Project description:Comparison of transcriptome between control and Tcf1/Lef1-deficient mature CD8 thymocytes Control mice or those are deficient for Tcf1 and Lef1 transcription factors (deleted by CD4-Cre) were used to isolate thymocytes. The thymocytes were surface-stained to identify TCRbeta high, CD69â, CD24â CD8+ subsets. These cells were sorted for RNAseq analysis.

2016-02-12 | E-GEOD-73238 | biostudies-arrayexpress

Tcf1/Lef1 transcription factors and CD8 T cell identity [ChIP-seq]

Project description:Determine genome-wide binding locations by Tcf1 in naive CD8+ T cells

2021-07-11 | GSE164670 | GEO

Impact of Tcf1 and Lef1 deficiency on mature CD8 thymocytes

Project description:Comparison of transcriptome between control and Tcf1/Lef1-deficient mature CD8 thymocytes

2016-02-12 | GSE73238 | GEO

Impact of Tcf1 and Lef1 deficiency on histone marks and Tcf1 binding in CD8 T cells

Project description:Comparison of epigenome and Tcf1 occupancy between control and Tcf1/Lef1-deficient CD8 T cells

2016-02-12 | GSE73239 | GEO

Tcf1/Lef1 transcription factors and CD8 T cell identity [RNA-seq]

Project description:Comparison of transcriptomes between WT and Tcf1/Lef1-deficient naïve CD8+ T cells

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Tcf1/Lef1 transcription factors and CD8 T cell identity [DNAase-seq]

Project description:Comparison of chromatin accessibility profiles between WT and Tcf1/Lef1-deficient naïve CD8+ T cells

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Tcf1/Lef1 transcription factors and CD8 T cell identity [Hi-C]

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Inverted chromatin immunoprecipitation identifies Tcf1 as a negative regulator of Foxp3 expression

Project description:Regulatory T (Treg) cells are important regulators of the immune system and have versatile functions for the homeostasis and repair of tissues. They express the forkhead box transcription factor Foxp3 as a lineage-defining protein. In mature Treg cells, the Foxp3 core promoter is unmethylated indicating that this area could harbor a transcription factor complex to initiate or repress gene expression, respectively. We used an unbiased method to identify Foxp3-promoter-binding transcription factors (TFs) by inverted chromatin immunoprecipitation (IP) followed by quantitative mass spectrometry. We identified several candidate factors which showed Foxp3-promoter suppressive capacity, one of which was T-cell factor 1 (Tcf1). Using viral overexpression and CRISPR/Cas knockout studies, we identified Tcf1 as a repressor of Foxp3 expression in primary conventional CD4 T cells (Tconv). In Tcf1-deficient animals, increased levels of Foxp3intermediateCD25negative T cells were identified in secondary lymphoid tissues, implicating that Tcf1 protects Foxp3-negative T cells from inadvertent Foxp3 expression.

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