A cis-Regulatory Signature in Ascidians and Flies, Independent of Transcription Factor Binding Sites

Khoueiry, Pierre; Rothbächer, Ute; Ohtsuka, Yukio; Daian, Fabrice; Frangulian, Eric; Roure, Agnès; Dubchak, Inna; Lemaire, Patrick

doi:10.1016/j.cub.2010.03.063

Cited by 57 publications

(82 citation statements)

References 47 publications

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“…Promoters with low levels of binding (#50th percentile of promoters) despite the presence of nearby TAGteam motifs had less accessible chromatin (;10-fold) than did promoters with high levels of binding ($95th percentile). These results are compatible with recent findings that many Ciona intestinalis and Drosophila CRMs contain sequence signatures, independent of transcription factor binding sites, predicted to promote nucleosome depletion (Khoueiry et al 2010). …”

Section: Org Downloaded Fromsupporting

confidence: 93%

The TAGteam motif facilitates binding of 21 sequence-specific transcription factors in the Drosophila embryo

Satija¹,

Bradley²

2012

Genome Res.

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Highly overlapping patterns of genome-wide binding of many distinct transcription factors have been observed in worms, insects, and mammals, but the origins and consequences of this overlapping binding remain unclear. While analyzing chromatin immunoprecipitation data sets from 21 sequence-specific transcription factors active in the Drosophila embryo, we found that binding of all factors exhibits a dose-dependent relationship with ''TAGteam'' sequence motifs bound by the zinc finger protein Vielfaltig, also known as Zelda, a recently discovered activator of the zygotic genome. TAGteam motifs are present and well conserved in highly bound regions, and are associated with transcription factor binding even in the absence of canonical recognition motifs for these factors. Furthermore, levels of binding in promoters and enhancers of zygotically transcribed genes are correlated with RNA polymerase II occupancy and gene expression levels. Our results suggest that Vielfaltig acts as a master regulator of early development by facilitating the genome-wide establishment of overlapping patterns of binding of diverse transcription factors that drive global gene expression.[Supplemental material is available for this article.]Genome-wide chromatin immunoprecipitation (ChIP) experiments in diverse metazoans have shown that many transcription factors bind thousands of highly overlapping loci in undifferentiated cells (Boyer et al.

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Section: Org Downloaded Fromsupporting

confidence: 93%

The TAGteam motif facilitates binding of 21 sequence-specific transcription factors in the Drosophila embryo

Satija¹,

Bradley²

2012

Genome Res.

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“…These cells are progenitors of the anterior (a-line) and posterior (b-line) neural lineages. Although Nodal is similarly regulated (Khoueiry et al, 2010;Ohta and Satou, 2013), Foxa.a additionally represses Nodal in the anterior lineage (Imai et al, 2006), and Nodal is therefore expressed only in the posterior neural lineage (Fig. S1B).…”

Section: Introductionmentioning

confidence: 98%

“…As a result, Otx expression is induced in two pairs of cells at the 32-cell stage (Fig. S1A,B) (Bertrand et al, 2003;Hudson et al, 2003;Hudson and Lemaire, 2001;Khoueiry et al, 2010;Ohta and Satou, 2013;Ohta et al, 2015). These cells are progenitors of the anterior (a-line) and posterior (b-line) neural lineages.…”

Section: Introductionmentioning

confidence: 98%

Tfap2 and Sox1/2/3 cooperatively specify ectodermal fates in ascidian embryos

et al. 2016

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Epidermis and neural tissues differentiate from the ectoderm in animal embryos. Although epidermal fate is thought to be induced in vertebrate embryos, embryological evidence has indicated that no intercellular interactions during early stages are required for epidermal fate in ascidian embryos. To test this hypothesis, we determined the gene regulatory circuits for epidermal and neural specification in the ascidian embryo. These circuits started with Tfap2-r.b and Sox1/2/3, which are expressed in the ectodermal lineage immediately after zygotic genome activation. Tfap2-r.b expression was diminished in the neural lineages upon activation of fibroblast growth factor signaling, which is known to induce neural fate, and sustained only in the epidermal lineage. Tfap2-r. b specified the epidermal fate cooperatively with Dlx

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“…The genome browser screen-shot in Figure 2A shows the upstream region of the KH transcript model for Ci-MYT (first three exons, in orange, and two introns are visible). Different genome browser tracks annotate functional genome data predicted for this region, such as chromatin immunoprecipitation (ChIP) data 14 (here shown for ZicL, Ci-zinc finger of the cerebellum L), sequence conservation between two related Ciona species 15,24 or nucleosome occupancy 16,17 (from top to bottom in Figure 2A). Generally, exonic protein coding regions are highly conserved (alignment track in Figure 2A).…”

Section: Electroporation For Efficient Gene Functional and Enhancer Smentioning

confidence: 99%

“…Additional high conservation peaks appear in non-coding regions upstream and in the first intron. Two of these are predicted to be nucleosome free according to a sequence based algorithm 16,17 (red frames in Figure 2A) suggesting accessibility to transcription factors. Indeed, Chip-on-ChIP signals 14 for Ci-ZicL transcription factor binding (green bars in Figure 2A) are enriched in these two conserved regions.…”

Section: Electroporation For Efficient Gene Functional and Enhancer Smentioning

confidence: 99%

Embryo Microinjection and Electroporation in the Chordate <em>Ciona intestinalis</em>

Kari

Zeng

Zitzelsberger

et al. 2016

JoVE

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Simple model organisms are instrumental for in vivo studies of developmental and cellular differentiation processes. Currently, the evolutionary distance to man of conventional invertebrate model systems and the complexity of genomes in vertebrates are critical challenges to modeling human normal and pathological conditions. The chordate Ciona intestinalis is an invertebrate chordate that emerged from a common ancestor with the vertebrates and may represent features at the interface between invertebrates and vertebrates. A common body plan with much simpler cellular and genomic composition should unveil gene regulatory network (GRN) links and functional genomics readouts explaining phenomena in the vertebrate condition. The compact genome of Ciona, a fixed embryonic lineage with few divisions and large cells, combined with versatile community tools foster efficient gene functional analyses in this organism. Here, we present several crucial methods for this promising model organism, which belongs to the closest sister group to vertebrates. We present protocols for transient transgenesis by electroporation, along with microinjection-mediated gene knockdown, which together provide the means to study gene function and genomic regulatory elements. We extend our protocols to provide information on how community databases are utilized for in silico design of gene regulatory or gene functional experiments. An example study demonstrates how novel information can be gained on the interplay, and its quantification, of selected neural factors conserved between Ciona and man. Furthermore, we show examples of differential subcellular localization in embryonic cells, following DNA electroporation in Ciona zygotes. Finally, we discuss the potential of these protocols to be adapted for tissue specific gene interference with emerging gene editing methods. The in vivo approaches in Ciona overcome major shortcomings of classical model organisms in the quest of unraveling conserved mechanisms in the chordate developmental program, relevant to stem cell research, drug discovery, and subsequent clinical application.

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A cis-Regulatory Signature in Ascidians and Flies, Independent of Transcription Factor Binding Sites

Cited by 57 publications

References 47 publications

The TAGteam motif facilitates binding of 21 sequence-specific transcription factors in the Drosophila embryo

The TAGteam motif facilitates binding of 21 sequence-specific transcription factors in the Drosophila embryo

Tfap2 and Sox1/2/3 cooperatively specify ectodermal fates in ascidian embryos

Embryo Microinjection and Electroporation in the Chordate <em>Ciona intestinalis</em>

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