The FoxA factors in organogenesis and differentiation

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The genetic analysis of the Foxa genes in both total and conditional mutant mice has clearly established that organogenesis of multiple systems is controlled by this subfamily of winged helix transcription factors. These discoveries followed the establishment of the conceptional framework of the mechanism of action of the FoxA proteins as ‘pioneer factors’ that can engage chromatin before other transcription factors. Recent molecular and genomic studies have also shown that FoxA proteins can facilitate binding of several nuclear receptors to their respective targets in a context-dependent manner, greatly increasing the range and importance of FoxA factors in biology.

Introduction

The late 1980s were the heyday for the discovery of tissue-specific, or at least tissue-enriched, transcriptional regulators. Using the recently invented technologies of promoter-reporter assays and DNA-affinity chromatography and the rat liver as abundant and relatively homogeneous source of biomaterial, in short succession multiple Hepatocyte Nuclear Factors, or HNF's, were purified and cloned [1]. Among these, the HNF-3 proteins, discovered by Costa and Lai in James Darnell's group, constituted a whole new class of DNA-binding proteins, as they did not contain any of the DNA contact motifs, such as Zinc-fingers, known at the time [2, 3]. In a wonderful example of convergence of distant scientific disciplines, at the same time the mutation responsible for the homeotic transformations in the Drosophila mutant forkhead was cloned, and was discovered to share a central, highly conserved motif with the HNF-3 proteins [4, 5].

This 100 amino acid so-called forkhead box was shown by X-ray crystallography to form a variant of the helix–loop–helix fold, with two large loops, giving it the appearance of a ‘winged helix’ [6]. This structural information, and the striking similarity with the DNA binding motif of linker histones, led to elegant studies by the Zaret lab, which demonstrated that HNF-3alpha can replace linker histones and affect chromatin structure directly, a rare feat among DNA binding proteins [7]. This property of the HNF-3 proteins is crucial to their proposed role as pioneer factors in the initiation of organ-specific transcriptional programs, which will be discussed below.

Subsequent to the discovery of the HNF-3 proteins as homologues of Drosophila forkhead, hundreds of related genes were cloned in species ranging from yeast to human [8]. Mammalian genomes contain more than forty winged helix transcription factors, which have been classified into 19 subclasses or clades, based on sequence conservation [9]. In the year 2000, the rather confusing nomenclature of the vertebrate winged helix genes was streamlined, with all genes renamed as Fox, for Forkhead Box, with a letter indicating the subclass [8]. Thus, the unlinked HNF-3 genes are now named Foxa1, Foxa2 and Foxa3.

Section snippets

Foxa2: first in axial patterning

From invertebrates to vertebrates, the genome was duplicated and reduplicated. This is exemplified best by the four homeobox gene clusters in vertebrate genomes, all derived from one ancient cluster. Thus, one would expect four Foxa genes as orthologues of the Drosophila forkhead; however, the putative ‘Foxa4’ gene was lost in evolution. So how is it that duplicated genes retain their relevance and contribute to fitness? One common mechanism is via attainment of new expression domains, and thus

Foxa1 and Foxa2: cooperating in organogenesis

The cooperation of Foxa1 and Foxa2 in organ development is striking, and apparent in every system that has been studied genetically thus far. When the two genes are missing from the foregut endoderm, hepatic specification is blocked completely [17, 18]. This finding was the first genetic validation of the competency model of liver development proposed by Zaret and colleagues who had shown that FoxA proteins can open chromatinized DNA templates in vitro, and enable subsequent access for other

Cell-type and stage-specific gene regulation by Foxa factors

A clue to this question came from chromatin immunoprecipitation assays with chromatin isolated from different stages of pancreatic development [27••]. These data showed that the occupancy of different cis-regulatory elements by FoxA is stage-dependent. Current work is aiming to determine the molecular basis for this phenomenon using global location analysis. ChIP-on-Chip studies, that is chromatin immunoprecipitation followed by hybridization of the transcription factor bound DNA to tiled

FoxA factors and nuclear receptors

Over the past few years, genomic approaches have supported and expanded the concept of cooperation of hormone or signal-dependent transcription factors, such as nuclear receptors, and cell-type specific factors, in ensuring that hormone dependent gene activation occurs only in the intended cell type. As discussed below, the FoxA factors play a major role in gene activation by the glucocorticoid, androgen, and estrogen receptors.

Almost twenty years ago, Schütz and colleagues asked the question

Conclusions

The genetic analysis of the Foxa genes using both total and conditional alleles has clearly established that organogenesis of multiple systems is controlled by this small subfamily of winged helix transcription factors. These discoveries followed the establishment of the conceptional framework of the mechanism of action of these proteins by the Zaret lab, who had used biochemical tools to provide evidence for the function of the FoxA factors as ‘pioneer factors’. Recent genome-wide location

References and recommended reading

Papers of particular interest, published within the period of review, have been highlighted as:

  • • of special interest

  • •• of outstanding interest

Acknowledgement

Related work in my lab is supported in part through NIH grants DK-049210 and DK-055342.

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