DNA methylation-dependent and -independent binding of CDX2 directs activation of distinct developmental and homeostatic genes.
Publication Year:
2024
PubMed ID:
38405700
Funding Grants:
Public Summary:
uring development, our organs form correctly only if the right genes turn on in the right cells at the right times. Special proteins called transcription factors help control this process by attaching to specific spots in our DNA and switching genes on or off. But how these proteins choose just a few targets out of millions of possible DNA sites has remained unclear. In our study, we found that a transcription factor named Cdx2 uses different “DNA cues” in developing tissues than it does in adult tissues. Early in life, Cdx2 prefers to bind to DNA sequences that contain a chemical tag called a methylated CpG, which helps it turn on genes needed for intestinal development. In adults, those same DNA regions lose this chemical tag, preventing Cdx2 from binding where it shouldn’t. Instead, Cdx2 switches to recognizing a more typical DNA sequence to support normal intestinal function. We also show that adding methylation back into adult cells can redirect Cdx2 to its earlier developmental targets. Overall, this work explains how Cdx2 reads chemical signals on DNA to activate the right genes at the right stages of life.
Scientific 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. In turn, DNA and chromatin modifications direct the genomic binding of TFs. However, how TFs navigate various chromatin features and selectively bind a small portion of the millions of possible genomic target loci is still not well understood. Here we show that Cdx2 - a pioneer TF that binds distinct targets in developing versus adult intestinal epithelial cells - has a preferential affinity for a non-canonical CpG-containing motif in vivo. A higher frequency of this motif at embryonic and fetal Cdx2 target loci and the specifically methylated state of the CpG during development allows selective Cdx2 binding and activation of developmental enhancers and linked genes. Conversely, demethylation at these enhancers prohibits ectopic Cdx2 binding in adult cells, where Cdx2 binds its canonical motif without a CpG. This differential Cdx2 binding allows for corecruitment of Ctcf and Hnf4, facilitating the establishment of intestinal superenhancers during development and enhancers mediating adult homeostatic functions, respectively. Induced gain of DNA methylation in the adult mouse epithelium or cultured cells causes ectopic recruitment of Cdx2 to the developmental target loci and facilitates cobinding of the partner TFs. Together, our results demonstrate that the differential CpG motif requirements for Cdx2 binding to developmental versus adult target sites allow it to navigate different DNA methylation profiles and activate cell type-specific genes at appropriate times.
