Conservation of RET Regulatory Function from Human to Zebrafish Without Sequence Similarity

Fisher, Shannon; Grice, Elizabeth A.; Vinton, Ryan M.; Bessling, Seneca L.; McCallion, Andrew S.

doi:10.1126/science.1124070

Cited by 342 publications

(324 citation statements)

References 27 publications

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“…Other works have indicated that mammalian enhancers can drive expression to zebrafish embryos in the absence of overt sequence conservation [39,43,74,75], but in these studies it was not clear whether the mammalian enhancers had originated de novo in the mammalian lineage or if they were divergent orthologues to those of zebrafish. As indicated by the work of Taher et al [45], which used NCEs of the amphibian Xenopus as an intermediate species to find divergent mammalian and zebrafish NCEs, orthologous vertebrate enhancers can become so dissimilar by extensive mutations in TFBSs and intervening sequences that computer algorithms may fail to identify them.…”

Section: Discussion (A) Conservation Of Function By Non-homologous Enmentioning

confidence: 99%

Enhancer turnover and conserved regulatory function in vertebrate evolution

Domené

Bumaschny

Souza

et al. 2013

Phil. Trans. R. Soc. B

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Mutations in regulatory regions including enhancers are an important source of variation and innovation during evolution. Enhancers can evolve by changes in the sequence, arrangement and repertoire of transcription factor binding sites, but whole enhancers can also be lost or gained in certain lineages in a process of turnover. The proopiomelanocortin gene ( Pomc ), which encodes a prohormone, is expressed in the pituitary and hypothalamus of all jawed vertebrates. We have previously described that hypothalamic Pomc expression in mammals is controlled by two enhancers—nPE1 and nPE2—that are derived from transposable elements and that presumably replaced the ancestral neuronal Pomc regulatory regions. Here, we show that nPE1 and nPE2, even though they are mammalian novelties with no homologous counterpart in other vertebrates, nevertheless can drive gene expression specifically to POMC neurons in the hypothalamus of larval and adult transgenic zebrafish. This indicates that when neuronal Pomc enhancers originated de novo during early mammalian evolution, the newly created cis- and trans- codes were similar to the ancestral ones. We also identify the neuronal regulatory region of zebrafish pomca and confirm that it is not homologous to the mammalian enhancers. Our work sheds light on the process of gene regulatory evolution by showing how a locus can undergo enhancer turnover and nevertheless maintain the ancestral transcriptional output.

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Section: Discussion (A) Conservation Of Function By Non-homologous Enmentioning

confidence: 99%

Enhancer turnover and conserved regulatory function in vertebrate evolution

Domené

Bumaschny

Souza

et al. 2013

Phil. Trans. R. Soc. B

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“…Although many of the key enzymes responsible for deposition and maintenance of H3K27me3 are known, it is likely that we do not have a complete catalog of all the elements of all PREs (Delest et al 2012), nor do we know the exact spatial or orientation requirements of the involved binding sites (if indeed there are any). However, the extreme conservation of H3K27me3 across distantly related species leads to the question of how a cis-regulatory element composed of relatively degenerate sequence motifs could persist functionally over such a long period of time (Ruvinsky and Ruvkun 2003;Fisher et al 2006).…”

Section: H3k27me3 Conservation Bypassed By Gene Duplicationmentioning

confidence: 99%

Evolution of H3K27me3-marked chromatin is linked to gene expression evolution and to patterns of gene duplication and diversification

Arthur

Slattery

et al. 2014

Genome Res.

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Histone modifications are critical for the regulation of gene expression, cell type specification, and differentiation. However, evolutionary patterns of key modifications that regulate gene expression in differentiating organisms have not been examined. Here we mapped the genomic locations of the repressive mark histone 3 lysine 27 trimethylation (H3K27me3) in four species of Drosophila, and compared these patterns to those in C. elegans. We found that patterns of H3K27me3 are highly conserved across species, but conservation is substantially weaker among duplicated genes. We further discovered that retropositions are associated with greater evolutionary changes in H3K27me3 and gene expression than tandem duplications, indicating that local chromatin constraints influence duplicated gene evolution. These changes are also associated with concomitant evolution of gene expression. Our findings reveal the strong conservation of genomic architecture governed by an epigenetic mark across distantly related species and the importance of gene duplication in generating novel H3K27me3 profiles.[Supplemental material is available for this article.]While transcriptional regulation has long been recognized as a significant target of evolutionary change (King and Wilson 1975), the specific mechanisms behind regulatory divergence have been difficult to dissect (Carroll 2008). In most cases, research has focused on recognizable cis-elements where transcription factors bind in a sequence-specific manner (Borneman et al. 2007;Bradley et al. 2010;Dowell 2010;Ni et al. 2012). Changes to either a transcription factor's DNA-binding properties or transcription factor binding sites (TFBS) enable the evolution of differential regulation, and numerous examples of this phenomenon have been observed (Ludwig et al. 2005;Shultzaberger et al. 2012).Whereas changes in cis-regulatory elements have been implicated in phenotypic and specifically morphological changes (Carroll 2008;Stern and Orgogozo 2008), other components of transcriptional regulation such as the chromatin environment have been scarcely explored (Lenhard et al. 2012). Histone modifications, which are chemical alterations of the histone spools upon which DNA is threaded, constitute one of the best-described elements of chromatin state (Zhou et al. 2011). These modifications can act directly or indirectly (through recruited enzymes) to alter DNA accessibility, thereby controlling other DNA-protein interactions (Campos and Reinberg 2009). Unlike TFBSs, however, histone modifications are not necessarily easily localizable to particular sequence elements, making their evolution difficult to study (Delest et al. 2012).Histone 3 lysine 27 trimethylation (H3K27me3) is one of the best-known histone modifications, in terms of both its biogenesis and effects. H3K27me3 is associated with complex cis-regulatory elements called Polycomb Response Elements (PREs) (Delest et al. 2012). Unlike TFBSs, PREs are compound regulatory elements composed of multiple, sometimes partially redundant, sequen...

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“…All sequences were tested for enhancer activity in the Hb using our established zebrafish transgenesis pipeline (Fisher et al 2006;McGaughey et al 2008). We define hindbrain expression as any expression in the CNS region that is posterior to the midbrain …”

Section: Genome-wide Predictions Identify Novel Hindbrain Enhancersmentioning

confidence: 99%

“…Short fragment sequences for HB01 and HB16 were synthesized as double-stranded oligos, A overhangs added, then cloned as predicted enhancers. At least 100 embryos were injected per construct at the two-cell stage with tol2 transposase as previously described (Fisher et al 2006). Injected embryos were screened for GFP expression in the CNS at 24 and 48 hpf.…”

Section: Hindbrain Genesmentioning

confidence: 99%

Systematic elucidation and in vivo validation of sequences enriched in hindbrain transcriptional control

et al. 2012

Self Cite

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Illuminating the primary sequence encryption of enhancers is central to understanding the regulatory architecture of genomes. We have developed a machine learning approach to decipher motif patterns of hindbrain enhancers and identify 40,000 sequences in the human genome that we predict display regulatory control that includes the hindbrain. Consistent with their roles in hindbrain patterning, MEIS1, NKX6-1, as well as HOX and POU family binding motifs contributed strongly to this enhancer model. Predicted hindbrain enhancers are overrepresented at genes expressed in hindbrain and associated with nervous system development, and primarily reside in the areas of open chromatin. In addition, 77 (0.2%) of these predictions are identified as hindbrain enhancers on the VISTA Enhancer Browser, and 26,000 (60%) overlap enhancer marks (H3K4me1 or H3K27ac). To validate these putative hindbrain enhancers, we selected 55 elements distributed throughout our predictions and six low scoring controls for evaluation in a zebrafish transgenic assay. When assayed in mosaic transgenic embryos, 51/55 elements directed expression in the central nervous system. Furthermore, 30/34 (88%) predicted enhancers analyzed in stable zebrafish transgenic lines directed expression in the larval zebrafish hindbrain. Subsequent analysis of sequence fragments selected based upon motif clustering further confirmed the critical role of the motifs contributing to the classifier. Our results demonstrate the existence of a primary sequence code characteristic to hindbrain enhancers. This code can be accurately extracted using machine-learning approaches and applied successfully for de novo identification of hindbrain enhancers. This study represents a critical step toward the dissection of regulatory control in specific neuronal subtypes.[Supplemental material is available for this article.]In metazoans, precise spatiotemporal patterns of gene expression are modulated by the exquisite contributions of transcriptional regulatory sequences. These include enhancers that activate transcription in a manner frequently observed to be independent of distance, position, and orientation with respect to the promoter of their target genes (Banerji et al. 1981). Empirically validated enhancers are typically a few hundred base pairs long and comprise binding sites for multiple transcription factors (TFs). In turn, TFs bound to these sequences also interact with common co-activators, communicating with the basal transcription machinery assembled at the promoter, and increasing the rate of transcription (Bulger and Groudine 2011). Identifying the combinatorial protein-DNA and protein-protein interactions that determine spatial and temporal enhancer function is crucial to understanding how distinct cellular and developmental programs are established.The systematic discovery of enhancers has proven challenging, since they are often located at great genomic distances from the genes they regulate (Lettice et al. 2003). The classical approach to enhancer identification invo...

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Conservation of RET Regulatory Function from Human to Zebrafish Without Sequence Similarity

Cited by 342 publications

References 27 publications

Enhancer turnover and conserved regulatory function in vertebrate evolution

Enhancer turnover and conserved regulatory function in vertebrate evolution

Evolution of H3K27me3-marked chromatin is linked to gene expression evolution and to patterns of gene duplication and diversification

Systematic elucidation and in vivo validation of sequences enriched in hindbrain transcriptional control

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