Gene Activity in Early Development

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Type I-regulated Dorsal enhancers receive high levels of Dorsal, contain low-affinity Dorsal sites and drive expression in ventral mesodermal domains e. Type II enhancers receive intermediate levels of Dorsal and drive expression in mediolateral domains of different sizes e. This system has been studied so intensively that the level of knowledge is sufficient for quantitative modeling of cis -regulatory interactions Zinzen et al. It was therefore of interest to determine whether our global analysis could reveal new insights into this process.

Gene-Environment Interaction

The boundaries of Twist binding are in remarkable agreement with the limits of characterized minimal enhancers e. More importantly, we were very surprised to identify new CRMs for several of these well-characterized genes Fig. Identification of novel enhancers for genes differentially expressed along the D—V axis. A—G Schematic diagrams indicating the target locus exons in gray, introns in orange together with Twist-enriched sequences red bars, top : 2—4 h, bottom : 4—6 h , the location of known regulatory sequence green bars , and the novel enhancer region tested double-headed arrow.

H Schematic overview of a transverse section through a stage 5 embryo. The nuclear Dorsal gradient red activates Twist expression blue on the ventral side of the embryo. Twist binds to CRMs associated with targets expressed in ventral e. I Twist regulates components of the Dorsal network; schematic model of the subcircuit leading to collaborative activation of targets in the ventral blastoderm. Twist binds to CRMs of all genes with a red border. Dashed lines indicate indirect regulation.

Mechanical Forces Can Contribute to Gene Expression During Development

K Twist also binds to CRMs regulating known components red border of the repressive complex associated with Dorsal. Seven novel enhancers for D—V patterning genes reveal the regulatory complexity of Twist-bound CRMs: The cactus , stumps , and wntD enhancers drive expression in a domain overlapping Twist within the ventral blastoderm Fig. While the regulation of zygotic cactus expression was previously not understood, our data reveals a Twist-bound CRM that is sufficient to drive expression in the presumptive mesoderm Fig.

The stumps CRM is expressed in a subset of Twist-expressing cells, yielding a salt and pepper pattern that may reflect the requirement for a second, partially redundant enhancer e. The wntD CRM is highly expressed at the anterior and posterior poles of the ventral blastoderm, but is very weakly expressed within the central region Fig. This mirrors the transient expression of the endogenous gene at this stage of development Fig.

This single enhancer reflects the regulatory logic deduced from genetic studies: The inputs from Twist and Dorsal activate WntD, while Snail represses its transcription within the presumptive mesoderm Fig. The CRM for crumbs reproduces the endogenous genes expression Fig. This bp region can function as an enhancer in the ectoderm while acting as a silencer within the ventral blastoderm.

Therefore, even at the same stage of development, these four Twist-bound CRMs drive expression in different spatial patterns within a small population of cells.

Gene expression in early development | Nature Genetics

This complexity is clearly mediated by context-dependent integration of additional inputs. Dorsal and its associated corepressors Cut, Retained, and Capicua recruit Groucho to repress dpp , confining its expression to the dorsal blastoderm Valentine et al. Interestingly, Twist binds to regulatory regions of all three Dorsal corepressors Fig.

Overall, our exhaustive map of new CRMs for D—V patterning genes greatly extends our previous knowledge and will likely improve predictive models for this system. Twist is not only required for D—V patterning. The direct target genes are significantly enriched in functional groups of genes involved in cell communication, signal transduction, cell motility, and cell adhesion Fig.

Genes in these categories are essential for multiple aspects of development, including gastrulation and directed migration of mesodermal cells.


Genetic studies have demonstrated a requirement for twist in these processes Leptin and Grunewald ; however, the molecular mechanism remained ill-defined. Twist targets functional cassettes required for diverse developmental processes. Genes with a red border were identified as direct Twist targets. The present study highlights a new direct connection between Twist and many key components involved in cell cycle progression and cell growth Fig. In many cases, Twist binds to several CRMs of these genes e. This surprising link between Twist and the cell cycle is highly likely to be of regulatory significance; twist mutant embryos have proliferative defects that can be genetically separated from the block in mesoderm gastrulation Arora and Nusslein-Volhard Twist orchestrates early mesoderm development by binding to CRMs of virtually all genes within functional groups essential for gastrulation, mesoderm proliferation, migration, and specification.

In contrast, few CRMs for genes involved in terminal differentiation e. Among these are TFs essential for mesoderm development, including gap hb , hkb , kr , kni , pair rule eve , slp , opa , odd , prd , run , and segmentation genes en , hh , ptc , wg , as well as homeotic genes pb , Scr , Antp , Abd-A , Abd-B , Ubx. These classes of target genes implicate a new role for Twist in the establishment or maintenance of anterior—posterior patterning within the mesoderm in addition to its known role in D—V axis formation.

Although the function of many of the remaining TFs is unknown, our data links these regulators to mesoderm development. The sheer number of TFs regulated by Twist does not support a simple hierarchical network, where Twist regulates a small set of TFs, which in turn control another layer of regulators, and so forth. Rather, our data suggests a model for Twist contributing to the regulation of the majority of TFs involved in every aspect of early mesoderm development. Although Twist is expressed during both developmental time periods assayed, it binds to CRMs in a temporally regulated manner.

Approximately half of the enhancer regions are detected at both time periods, indicating continuous binding of Twist throughout these developmental stages Fig. This dynamic occupancy reveals that the ability of Twist to bind to CRMs is tightly controlled beyond the mere presence of a suitable binding site, and is likely regulated by other TFs that aid or inhibit binding.

To identify additional regulators that could differentiate between temporally bound CRMs, we searched for overrepresented sequence motifs, using two complementary computational approaches: statistical enrichment of position weight matrices PWMs for characterized TFs, and the de novo detection of overrepresented motifs Supplemental Material.

Twist occupies enhancers in a temporally regulated manner with Dorsal and Tinman. About one-quarter of all detected regions are specific to either the early green or late red time periods. Both known control sites underlined, left as well as all seven novel sites tested are significantly bound by Dorsal in vivo.

The X -axis indicates the region tested; the Y -axis displays the level of enrichment as the ratio of enrichment using primers against the region of interest compared with primers covering a negative control region. All but one predicted site are significantly bound by Tinman in vivo.

In contrast, Dorsal motifs are exclusively enriched in the early-bound CRMs, and not in the late group. A number of other motifs were also uncovered Supplementary Fig. Our data reveals Twist binding to almost all previously characterized Dorsal enhancers Fig.

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Twist and Dorsal are known to interact physically and to coregulate enhancers in the early, but not the late, time window of our experiment Shirokawa and Courey We therefore hypothesized that Dorsal may be coregulating many of the newly discovered Twist CRMs, in keeping with the specific enrichment of Dorsal consensus motifs within these enhancers. Significant binding of Dorsal was detected by quantitative real-time PCR to all seven predicted sites tested Fig.

Similarly, as Tinman consensus sites were significantly enriched in 4—6-h CRMs, we tested the in vivo occupancy of predicted sites by Tinman at this stage of development. ChIP experiments detected significant binding of Tinman to 10 of 11 sites tested Fig. Given the large number of early and late CRMs, the enrichment of these motifs highlights extensive combinatorial binding of Dorsal and Twist at 2—4 h, and Tinman and Twist at 4—6 h.

To delineate the combinatorial relationships between Twist and other TFs, we generated an initial transcriptional network for early mesoderm development.

Online Developmental Biology: Analyzing Gene Expression

The temporal binding map for Twist was integrated with in vivo binding data for Mef2, Dorsal, and Tinman. Our previous study of Mef2-bound enhancers Sandmann et al. As it is difficult to visualize all Twist target genes, we focused on TFs whose CRMs are cobound by two or more regulators during these stages of development Fig.

Therefore, all links in this network represent direct connections to the same CRM at the same stages of development. A core transcriptional network for early mesoderm development. The regulatory connections for CRMs fulfilling these criteria are shown for all genes coding for TFs. Color code: Dorsal dark blue, known regulation; light blue, predicted interaction , Twist gray , Mef2 red , and Tinman dark green, known regulation; light green, predicted interaction.

The direction of regulation, if known, is indicated by pointed or bar-ended arrows. Feed-forward loops and combinatorial regulation of downstream regulators are dominant features controlling early mesoderm development. The resulting core network of 51 TFs is already relatively complex, with nine genes [ nau , E spl , eve , bap , Ubx , lbe , odd , hth , and Ptx1 ] being targeted by three out of the four examined regulators. The topology of the network provides several insights into how Twist functions to regulate multiple aspects of early mesoderm development. Extensive combinatorial binding and feed-forward regulation are abundant features.

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  • Dorsal activates twist , which in turn coregulates the majority of known direct Dorsal targets. Depending on the logical inputs from the two upstream regulators transcriptional repression or activation , feed-forward loops can aid in cellular decision making by filtering out noisy regulatory inputs Mangan et al.

    For example, early gene expression in the mesoderm e. This data, in combination with in vivo binding data for other TFs, lays the foundation of a transcriptional network describing early mesoderm development. Our data revealed extensive Twist binding to characterized Dorsal enhancers and also, surprisingly, to Dorsal-regulated silencers e. Moreover, many of the new regulatory regions we identified for D—V patterning genes can function either as enhancers or integrated enhancer-silencer modules e. This ability of Twist to act within the context of silencers, as well as enhancers, may partially explain the widespread recruitment of Twist to many regulatory regions and its ability to regulate diverse developmental processes.