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DNA Methylation dependent and independent binding of CDX2 imparts distinct developmental and homeostatic functions. [nativeChIPseq]

ABSTRACT: Precise spatiotemporal and cell type-specific gene expression is essential for proper tissue development and function. Transcription factors (TFs) guide this process by binding to developmental stage-specific targets and establishing an appropriate enhancer landscape. DNA and chromatin modifications form barriers to the genomic binding of TFs, however, the details of how TFs navigate various chromatin features and selectively bind a small portion of the millions of possible genomic target loci remain unknown. Here we show that Cdx2, a pioneer TF that binds distinct targets in developing and adult intestinal epithelial cells, has a preferential affinity to a non-canonical CpG-containing motif in vivo. A higher frequency of this motif at the embryonic and fetal target loci of Cdx2 and the methylated state of the CpG particularly during development allows its selective binding and activation of developmental enhancers and linked genes. Conversely, demethylation at these enhancers prohibits ectopic Cdx2 binding in adult cells, where Cdx2 binds the canonical motif without a CpG. This distinct Cdx2 binding allows corecruitment of Ctcf and Hnf4 facilitating the establishment of intestinal superenhancers during development and enhancers activating adult tissue functions, respectively. Induced gain of DNA methylation in the adult epithelium in vivo or in cultured cells causes recruitment of Cdx2 to the developmental target loci and cobinding of the partner TFs. Our results demonstrate that the distinct propensities of Cdx2 to bind motifs with and without CpGs and the divergent distribution of these motifs at developmental and adult target sites allow Cdx2 to navigate distinct DNA methylation profiles and activate cell type-specific enhancers and genes.

ORGANISM(S): Mus musculus

PROVIDER: GSE253726 | GEO | 2024/11/29

REPOSITORIES: GEO

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Project description:The family of Zic transcription factors (TFs) are required for cerebellar development, and their binding is highly enriched at developmentally regulated enhancers active in cerebellar granule neurons at the progenitor stage around postnatal day 7 (P7) and the mature adult stage at P60 in the mouse cerebellum. Interestingly, Zic1/2 ChIP-seq data reveal that the Zics change their binding profile over time. To characterize these differences in Zic targeting between early and late cerebellar maturation, we compared the sequence underlying Zic Peaks, their relationship with active chromatin and gene expression at P7 and P60. From this we found Zic peaks tend to be large and bind open-active chromatin. Strikingly, Zic peaks shift from binding at promoter proximal regions at P7 to distal enhancer regions at P60. We hypothesize that other TFs collaborate with the Zic TFs to change their binding targets and affect their regulatory activity. A multi-tiered approach was used to predict TF binding at those Zic ChIP sites. We assessed motif enrichment (HOMER) and in-vivo TF binding profiles (BART) to determine putative TFs collaborating with Zic to drive this regulation. We then validated the presence of the predicted TFs in granule neurons using gene expression. This workflow identified known and novel distinct collaborators of Zic between early and late development. Early collaborates of Zic includes bHLH factors and chromatin remodelers whereas late collaborators of Zic are activity regulated TFs which are markers of synaptic maturation. To identify Zic’s developmental gene targets in cerebellar maturation, we used H3K4me3 PLAC-seq data, which captures promoter-enhancer loops from the adult mouse cerebellum and Hi-C data from the young mouse cerebellum to map genes to Zic bound enhancers. This revealed Zic as a transcriptional activator of late developmental genes in the cerebellum. Using this same approach with in vitro Zic KD, we were able to identify Zic dependent developmental gene targets which have functions in axonogenesis, axon guidance, and ion channel signaling, which are integral in proper maturation of a neuron. These integrated analyses reveal how Zic and other TFs regulate temporal expression of CGN developmental genes and provides information that will enhance our understanding of the molecular mechanisms that regulate the mode of TF function at enhancers.

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DNA Methylation dependent and independent binding of CDX2 imparts distinct developmental and homeostatic functions. [nativeChIPseq]

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