Program Specificity for Ptf1a in Pancreas versus Neural Tube Development Correlates with Distinct Collaborating Cofactors and Chromatin Accessibility

Abstract

The lineage-specific basic helix-loop-helix transcription factor Ptf1a is a critical driver for development of both the pancreas and nervous system. How one transcription factor controls diverse programs of gene expression is a fundamental question in developmental biology. To uncover molecular strategies for the program-specific functions of Ptf1a, we identified bound genomic regions in vivo during development of both tissues. Most regions bound by Ptf1a are specific to each tissue, lie near genes needed for proper formation of each tissue, and coincide with regions of open chromatin. The specificity of Ptf1a binding is encoded in the DNA surrounding the Ptf1a-bound sites, because these regions are sufficient to direct tissue-restricted reporter expression in transgenic mice. Fox and Sox factors were identified as potential lineage-specific modifiers of Ptf1a binding, since binding motifs for these factors are enriched in Ptf1a-bound regions in pancreas and neural tube, respectively. Of the Fox factors expressed during pancreatic development, Foxa2 plays a major role. Indeed, Ptf1a and Foxa2 colocalize in embryonic pancreatic chromatin and can act synergistically in cell transfection assays. Together, these findings indicate that lineage-specific chromatin landscapes likely constrain the DNA binding of Ptf1a, and they identify Fox and Sox gene families as part of this process.

The nuclear hormone receptor family member NR5A2 controls aspects of multipotent progenitor cell formation and acinar differentiation during pancreatic organogenesis

“…These sites have functional marks of active transcriptional control regions: co-localization of other acinar specific factors (PTF1A and RBPJL) and enrichment of H3K4me2 and RNApol2. This 1.2-kb region is sufficient to direct pancreatic acinar-specific expression in transgenic mouse embryos (Meredith et al, 2013).…”

“…The regions of these genes bound by NR5A2 are active pancreas-specific transcriptional enhancers in transgenic mice (Masui et al, 2007Rojas et al, 2009;Meredith et al, 2013) (Mei Jiang, T.G.D., G.H.S. and R.J.M., unpublished).…”

“…RNA-Seq analysis of the E17.5 pancreas has been reported previously (Masui et al, 2010;Meredith et al, 2013). Differentially expressed genes were identified using edgeR (McCarthy et al, 2012).…”

“…Preparation of mouse pancreatic chromatin, immunoprecipitation, quantification, preparation of Illumina sequencing libraries and their analysis were performed as described previously (Meredith et al, 2013), with details and modifications described in the supplementary material methods.…”

Transcriptional Maintenance of Pancreatic Acinar Identity, Differentiation, and Homeostasis by PTF1A

“…The heterodimer has little, if any, transactivating potential and requires an RBP subunit for its known functions (21,25). The three-subunit complex binds DNA cooperatively; it is unable to bind a lone E-box and requires an RBP recognition sequence (TC-box; TTCCCA) spaced one, two, or three DNA turns away from an E-box (21,26). RBPJ (RBPJ/ CSL) is also the obligate transcription factor of the canonical vertebrate Notch signaling pathway (27,28).…”