Lisa Dailey

Modulation of the Activity of Multiple Transcriptional Activation Domains by the DNA Binding Domains Mediates the Synergistic Action of Sox2 and Oct-3 on the Fibroblast Growth Factor-4Enhancer

Fibroblast growth factor(FGF)-4 gene expression in the inner cell mass of the blastocyst and in EC cells requires the combined activity of two transcriptional regulators, Sox2 and Oct-3, which bind to adjacent sites on the FGF-4 enhancer DNA and synergistically activate transcription. Sox2 and Oct-3 bind cooperatively to the enhancer DNA through their DNA-binding, high mobility group and POU domains, respectively. These two domains, however, are not sufficient to activate transcription. We have analyzed a number of Sox2 and Oct-3 deletion mutants to identify the domains within each protein that contribute to the activity of the Sox2·Oct-3 complex. Within Oct-3, we have identified two activation domains, the N-terminal AD1 and the C-terminal AD2, that play a role in the activity of the Sox2·Oct-3 complex. AD1 also displays transcriptional activation functions in the absence of Sox2 while AD2 function was only detected within the Sox2·Oct-3 complex. In Sox2, we have identified three activation domains within its C terminus: R1, R2, and R3. R1 and R2 can potentiate weak activation by Sox2 in the absence of Oct-3 but their deletion has no effect on the Sox2·Oct-3 complex. In contrast, R3 function is only observed when Sox2 is complexed with Oct-3. In addition, analysis of Oct-1/Oct-3 chimeras indicates that the Oct-3 homeodomain also plays a critical role in the formation of a functional Sox2·Oct-3 complex. Our results are consistent with a model in which the synergistic action of Sox2 and Oct-3 results from two major processes. Cooperative binding of the factors to the enhancer DNA, mediated by their binding domains, stably tethers each factor to DNA and increases the activity of intrinsic activation domains within each protein. Protein-protein and protein-DNA interactions then may lead to reciprocal conformational changes that expose latent activation domains within each protein. These findings define a mechanism that may also be utilized by other Sox·POU protein complexes in gene activation.

A network of transcriptional and signaling events is activated by FGF to induce chondrocyte growth arrest and differentiation.

Activating mutations in FGF receptor 3 (FGFR3) cause several human dwarfism syndromes by affecting both chondrocyte proliferation and differentiation. Using microarray and biochemical analyses of FGF-treated rat chondrosarcoma chondrocytes, we show that FGF inhibits chondrocyte proliferation by initiating multiple pathways that result in the induction of antiproliferative functions and the down-regulation of growth-promoting molecules. The initiation of growth arrest is characterized by the rapid dephosphorylation of the retinoblastoma protein (pRb) p107 and repression of a subset of E2F target genes by a mechanism that is independent of cyclin E–Cdk inhibition. In contrast, hypophosphorylation of pRb and p130 occur after growth arrest is first detected, and may contribute to its maintenance. Importantly, we also find a number of gene expression changes indicating that FGF promotes many aspects of hypertrophic differentiation, a notion supported by in situ analysis of developing growth plates from mice expressing an activated form of FGFR3. Thus, FGF may coordinate the onset of differentiation with chondrocyte growth arrest in the developing growth plate.

Coevolution of HMG domains and homeodomains and the generation of transcriptional regulation by Sox/POU complexes

The highly conserved homeodomains and HMG domains are components of a large number of proteins that play a role in the transcriptional regulation of gene expression during embryogenesis. Both the HMG domain and the homeodomain serve as interfaces for factor interactions with DNA, as well as with other proteins, and it is likely that the high degree of structural and sequence conservation within these domains reflects the conservation of basic aspects of these interactions. Classical HMG domain proteins have an ancient origin, being found in all eukaryotes, and are thought to have given rise to the metazoan‐specific class of HMG domain proteins called the Sox proteins. Similarly, the metazoan‐specific POU domain proteins are thought to have arisen from genes encoding ancestral homeodomain proteins. In this review, we summarize several examples of different HMG‐homeodomain interactions that illustrate not only the ancient origin of each of these protein families, but also their relationship to each other, and discuss how coevolution of HMG and homeodomains may have lead to creation of the specialized Sox/POU protein complexes. Using the FGF‐4 gene as an example, we also speculate on how coevolution of regulatory Sox/POU target DNA sequences may have occurred, and how the summation of these changes may have lead to the emergence of new developmental pathways.

FIREWACh: high-throughput functional detection of transcriptional regulatory modules in mammalian cells

Promoters and enhancers establish precise gene transcription patterns. The development of functional approaches for their identification in mammalian cells has been complicated by the size of these genomes. Here we report a high-throughput functional assay for directly identifying active promoter and enhancer elements called FIREWACh (Functional Identification of Regulatory Elements Within Accessible Chromatin), which we used to simultaneously assess over 80,000 DNA fragments derived from nucleosome-free regions within the chromatin of embryonic stem cells (ESCs) and identify 6,364 active regulatory elements. Many of these represent newly discovered ESC-specific enhancers, showing enriched binding-site motifs for ESC-specific transcription factors including SOX2, POU5F1 (OCT4) and KLF4. The application of FIREWACh to additional cultured cell types will facilitate functional annotation of the genome and expand our view of transcriptional network dynamics.

Downregulation of akt activity contributes to the growth arrest induced by FGF in chondrocytes

Unregulated FGF signaling produced by activating FGFR3 mutations causes several forms of dwarfism‐associated chondrodysplasias in humans and mice. FGF signaling inhibits chondrocyte proliferation by activating multiple signal transduction pathways that all contribute to chondrocyte growth arrest and induction of some aspects of differentiation. Previous studies had identified the Stat1 pathway, dephosphorylation of the Rb family proteins p107 and p130, induction of p21 expression and sustained activation of MAP kinases as playing a role in the FGF response of chondrocytes. We have examined the role of Akt (PKB) in the response of chondrocytes to FGF signaling. Differently from what is observed in many other cell types, FGF does not activate Akt in chondrocytes, and Akt phosphorylation is actually downregulated after FGF treatment. By expressing a constitutively activated, myristylated form of Akt (myr‐Akt) in the RCS chondrosarcoma cell line, we show that Akt activation partially counteracts the inhibitory effect of FGF signaling. The response of myr‐Akt expressing cells to FGF is identical to parental RCS in the first few hours after treatment, but then diverges as myr‐Akt cells show decreased p130 phosphorylation, increased cyclin E/cdk2 activity and continue to proliferate at a slow rate. Constitutive Akt activation does not affect p21 expression but appears to influence directly cdk/cyclin activity. On the other hand, the induction of differentiation‐related genes is unchanged in myr‐Akt cells. These results identify Akt downregulation as an important aspect of the response of chondrocytes to FGF that, however, only affects chondrocyte proliferation and not the ability of FGF to induce differentiation genes. J. Cell. Physiol.

Identification of active transcriptional regulatory modules by the functional assay of DNA from nucleosome-free regions

The identification of transcriptional regulatory modules within mammalian genomes is a prerequisite to understanding the mechanisms controlling regulated gene expression. While high-throughput microarray- and sequencing-based approaches have been used to map the genomic locations of sites of nuclease hypersensitivity or target DNA sequences bound by specific protein factors, the identification of regulatory elements using functional assays, which would provide important complementary data, has been relatively rare. Here we present a method that permits the functional identification of active transcriptional regulatory modules using a simple procedure for the isolation and analysis of DNA derived from nucleosome-free regions (NFRs), the 2% of the cellular genome that contains these elements. The more than 100 new active regulatory DNAs identified in this manner from F9 cells correspond to both promoter-proximal and distal elements, and display several features predicted for endogenous transcriptional regulators, including localization within DNase-accessible chromatin and CpG islands, and proximity to expressed genes. Furthermore, comparison with published ChIP-seq data of ES-cell chromatin shows that the functional elements we identified correspond with genomic regions enriched for H3K4me3, a histone modification associated with active transcriptional regulatory elements, and that the correspondence of H3K4me3 with our promoter-distal elements is largely ES-cell specific. The majority of the distal elements exhibit enhancer activity. Importantly, these functional DNA fragments are an average 149 bp in length, greatly facilitating future applications to identify transcription factor binding sites mediating their activity. Thus, this approach provides a tool for the high-resolution identification of the functional components of active promoters and enhancers.

Amplification and excision of integrated polyoma DNA sequences require a functional origin of replication

Cells transformed by Polyoma virus (Py) can undergo a high rate of excision or amplification of integrated viral DNA sequences, and these phenomena require the presence of homology (i.e., repeats) within the viral insertion as well as a functional viral large T antigen (T-Ag). To determine whether the main role of large T-Ag in excision and amplification was replicative or recombination-promoting, we studied transformed rat cell lines containing tandem insertions of a ts-a Py molecule (encoding a thermolabile large T-Ag) with a deletion of the origin of viral DNA replication. Culturing of these cells at the temperature permissive for large T-Ag function did not result in any detectable excision or amplification of integrated Py sequences. We then introduced into origin-defective lines a recombinant plasmid containing the viral origin of replication and the gene coding for resistance to the antibiotic G418. All G418-resistant clones analyzed readily amplified the integrated plasmid molecules when grown under conditions permissive for large T-Ag function, showing that these cells produced viral large T-Ag capable of promoting amplification in trans of DNA sequences containing the Py origin. These observations strongly suggest that Polyoma large T antigen promotes excision or amplification of viral DNA by initiating replication at the integrated origin, providing a favorable substrate for subsequent recombination.

High throughput technologies for the functional discovery of mammalian enhancers: new approaches for understanding transcriptional regulatory network dynamics.

Completion of the human and mouse genomes has inspired new initiatives to obtain a global understanding of the functional regulatory networks governing gene expression. Enhancers are primary regulatory DNA elements determining precise spatio- and temporal gene expression patterns, but the observation that they can function at any distance from the gene(s) they regulate has made their genome-wide characterization challenging. Since traditional, single reporter approaches would be unable to accomplish this enormous task, high throughput technologies for mapping chromatin features associated with enhancers have emerged as an effective surrogate for enhancer discovery. However, the last few years have witnessed the development of several new innovative approaches that can effectively screen for and discover enhancers based on their functional activation of transcription using massively parallel reporter systems. In addition to their application for genome annotation, these new high throughput functional approaches open new and exciting avenues for modeling gene regulatory networks.

The evolution of polyoma-transformed rat cell lines during propagation in vitro

Abstract We have previously shown that the presence of a functional viral large T antigen in polyoma-transformed rat cells results in instability of the integrated viral DNA, as manifest by free viral DNA production, excision, and amplification of the integrated viral molecules. It has also been observed that polyoma tumors or transformed cell lines often do not produce functional large T antigen. To determine if an evolution toward the loss of large T-Ag function took place in vitro in polyoma-transformed cell lines, we studied the changes occurring in the integrated viral DNA sequences of a ts-a Py-transformed rat cell line, ts-a H3, upon propagation under conditions permissive (33°) or nonpermissive (39°) for large T function. H3 contains a single insertion of a partial tandem of ∼1.2 viral genomes, and at 33° produces free viral DNA and also undergoes a high frequency of excision and amplification, involving recombination between homologous portions of viral DNA. While the integrated arrangement of viral DNA sequences remains unchanged at 39°, in two independent experiments long-term propagation of H3 at 33° resulted in the emergence of a fully transformed cell population which no longer produced free viral DNA and whose integrated viral DNA pattern was modified. In one of these populations, H3 ∗ , interruption of the integrated viral coding sequences unique to large T antigen by a segment of host DNA resulted in the loss of large T antigen function. In another population, H3A ∗ -3, the integrated viral DNA had undergone some rearrangement which, however, did not apparently affect large T Ag coding sequences. Since the latter cell population did not produce free viral DNA and was unable to “rescue” integrated viral DNA sequences from a T-Ag-negative Py-transformed cell line after cell fusion, the large T antigen produced by H3A ∗ -3 is probably nonfunctional. These results are consistent with the hypothesis that the presence of large T antigen leads to instability of the viral DNA integration and that this instability is responsible for the selection of large T antigen-negative cells from Py-transformed populations. Possible mechanisms underlying this type of evolution are presented.

Isolation and Analysis of DNA Derived from Nucleosome-Free Regions

Precise regulation of the levels and timing of gene expression is fundamental to all biological processes and is largely determined by the activity of cis-regulatory modules, containing the binding sites for transcription factors, within promoters and enhancers. The global identification of these transcriptional regulatory elements within mammalian genomes, and understanding when and where they are active, is an important effort that will require the development and implementation of several different technologies. Here we detail a means for the identification of transcriptional regulatory elements using functional assays. The success of this approach relies on focusing the functional assay on DNA derived from nucleosome-free regions (NFRs), i.e., the 2% of the genome within a given cell in which regulatory elements reside. Accordingly, we present a simple method for isolating NFR DNA, and a functional assay that can be used for the identification of promoter and enhancers components within this population.