ABSTRACT: To investigate the genome-wide binding pattern of Fezf2, we performed ChIP-seq analysis for Fezf2. ChIP-seq of transcription factor in mTECs is difficult because of small number of mTECs or difficulty in gaining ChIP grade antibodies. Then, we generated Fezf2-3Flag knock in mice and performed ChIP-seq analysis by using anti-Flag antibody.
Project description:Fezf2 is highly and specifically expressed in mTECs in mouse thymus and Fezf2 deficiency (Fezf2 KO) in the thymus leads to autoimmunity. However, it is unclear how Fezf2 contributes to thymic gene expression. We collected WT and Fezf2 KO mTECs by FACS, and performed microarrays to determine genes regulated by Fezf2. mTECs were subjected to RNA extraction (from WT or Fezf2 KO mTECs) and hybridization on Affymetrix microarrays.
Project description:Fezf2 is highly and specifically expressed in mTECs in mouse thymus and Fezf2 deficiency (Fezf2 KO) in the thymus leads to autoimmunity. However, it is unclear how Fezf2 contributes to thymic gene expression. We collected WT and Fezf2 KO mTECs by FACS, and performed microarrays to determine genes regulated by Fezf2.
Project description:To integrate the epigenomic landscapes of chromatin accessibility regulated by Chd4 and Fezf2, we performed the assay for transposase-accessible chromatin using sequencing (ATAC-seq) analysis of mTECs from wild type (WT), Chd4 cKO and Fezf2 cKO mTECs.
Project description:ChIP sequencing of Ehf, Fezf2, Elf3 and Klf4 was performed on medullary thymic epithelial cells to analyze the role of Ehf-, Fezf2-, Elf3- and Klf4-dependent gene regulation in mTECs.
Project description:To gain insights into the difference in transcriptional programs regulated by Fezf2, Aire and Chd4, we performed RNA sequencing (RNA-seq) of mTECs from Fezf2-deficient, Aire-deficient and Chd4-deficient mice.
Project description:The goal of the study was to compare gene expression of P0 wild-type, P0 Fezf2-/- cortices, and Fezf2-/-; Fezf2-EnR cortices. Total RNAs were isolated from P0 cortices dissected from wild-type (n=3), Fezf2-/- mice (n=4), and Fezf2-/-; Fezf2-EnR cortices (n=2), following Qiagen RNAeasy kit instruction.Sequence libraries were made following Illumina RNA PolyA library preparation guide.The libaries were pair-end sequenced (150nt per end). Differentially expressed genes were identified by DESEQ.
Project description:We performed ChIP-Seq against histones H3K4me3 and H3K27me3 in medullary thymic epithelial cells (mTECs) of wild-type mice to analysis bivalent epigenetic modifications.