Trawler: de novo regulatory motif discovery pipeline for chromatin immunoprecipitation

Ettwiller, Laurence; Paten, Benedict; Ramialison, Mirana; Birney, Ewan; Wittbrodt, Joachim

doi:10.1038/nmeth1061

Cited by 69 publications

(78 citation statements)

References 16 publications

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“…Next, we attempted to discover overrepresented motifs in the regions (360 bp) around the peaks identified by each ChIP experiment using the Trawler program (Ettwiller et al, 2007). We found that overrepresented motifs were similar to the PWMs that were determined experimentally (Tbx6b and ZicL) or to those of homologs in other animals (the remaining nine TFs) (see Fig.…”

Section: Research Articlementioning

confidence: 92%

Genomic cis-regulatory networks in the early Ciona intestinalis embryo

et al. 2010

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SUMMARYPrecise spatiotemporal gene expression during animal development is achieved through gene regulatory networks, in which sequence-specific transcription factors (TFs) bind to cis-regulatory elements of target genes. Although numerous cis-regulatory elements have been identified in a variety of systems, their global architecture in the gene networks that regulate animal development is not well understood. Here, we determined the structure of the core networks at the cis-regulatory level in early embryos of the chordate Ciona intestinalis by chromatin immunoprecipitation (ChIP) of 11 TFs. The regulatory systems of the 11 TF genes examined were tightly interconnected with one another. By combining analysis of the ChIP data with the results of previous comprehensive analyses of expression profiles and knockdown of regulatory genes, we found that most of the previously determined interactions are direct. We focused on cis-regulatory networks responsible for the Ciona mesodermal tissues by examining how the networks specify these tissues at the level of their cis-regulatory architecture. We also found many interactions that had not been predicted by simple gene knockdown experiments, and we showed that a significant fraction of TF-DNA interactions make major contributions to the regulatory control of target gene expression.

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Section: Research Articlementioning

confidence: 92%

Genomic cis-regulatory networks in the early Ciona intestinalis embryo

et al. 2010

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“…GO term analysis was performed using GOToolBox (49). Motif enrichment analysis was performed using NestedMICA and Trawler (23,24). For luciferase assays, 40 pg luciferase construct ϩ 0.75 pg pCS2 ϩ Renilla were injected in 1-cell embryos with 150, 450, or 750 pg Ntl mRNA or 150 pg Ntl-VP16 mRNA where indicated.…”

Section: Methodsmentioning

confidence: 99%

“…22). To take advantage of having large-scale in vivo binding data for a T-box factor, we used computational methods to discover an enriched motif associated with Ntl binding in the cis-regulatory modules (CRMs) of target genes (23,24). A CRM was defined as a 500-bp sequence flanking an enriched probe (or the most highly enriched probe in a group), resulting in 233 CRMs being identified.…”

Section: Ntl Binds Mesodermally Expressed Genes Involved In Transcripmentioning

confidence: 99%

A gene regulatory network directed by zebrafish No tail accounts for its roles in mesoderm formation

Morley

Lachani

Keefe

et al. 2009

Proc. Natl. Acad. Sci. U.S.A.

107

118

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Using chromatin immunoprecipitation combined with genomic microarrays we have identified targets of No tail (Ntl), a zebrafish Brachyury ortholog that plays a central role in mesoderm formation. We show that Ntl regulates a downstream network of other transcription factors and identify an in vivo Ntl binding site that resembles the consensus T-box binding site (TBS) previously identified by in vitro studies. We show that the notochord-expressed gene floating head ( flh) is a direct transcriptional target of Ntl and that a combination of TBSs in the flh upstream region are required for Ntl-directed expression. Using our genome-scale data we have assembled a preliminary gene regulatory network that begins to describe mesoderm formation and patterning in the early zebrafish embryo.brachyury ͉ chromatin immunopreciptitation ͉ microarray E mbryonic development proceeds through a series of progressively more restricted cell states in which sets of state-specific genes are expressed in a finely controlled temporal and spatial order. This coordination of gene expression is brought about by the integration of signaling inputs and binding of transcription factors at cis-regulatory modules (CRMs) associated with target genes, and can be described by a gene regulatory network (GRN). Such GRNs have been useful in understanding how development proceeds in the early lineages of sea urchins and ascidians (1, 2). However, although GRNs using data from single gene studies have been used to describe aspects of Xenopus mesendoderm and lamprey neural crest development (3, 4) a systematic approach to building a GRN by genome-scale analysis has not yet been used to describe early cell fate commitment in developing vertebrate embryos. Understanding how transcriptional regulation drives cell fate commitment in vertebrates is essential not only in understanding their development, but also for informing future efforts to recapitulate cell restriction to different tissue lineages for stem cell-based replacement therapies (5). We have thus set out to assemble a GRN that can describe vertebrate mesoderm development using zebrafish as a model system to identify targets of a key transcriptional regulator, No tail (Ntl).Ntl is a zebrafish ortholog of Brachyury, a T-domain transcription factor that is expressed as an early response to mesoderm induction and plays a central role in mesoderm development in all vertebrates. For instance, studies in mice, Xenopus, and zebrafish reveal that Brachyury orthologs influence many aspects of mesoderm specification and patterning, being required for formation of the notochord and posterior somites, for normal cell movements during gastrulation and tail outgrowth, and for establishment of left-right asymmetry (reviewed in refs. 6, 7).Here, we use chromatin immunoprecipitation combined with zebrafish genomic microarrays (ChIP-chip) to survey binding of Ntl at promoter regions. We show that Ntl binds the promoters of transcription factors implicated in posterior identity, muscle specification, cell movements, ...

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“…We used the Trawler program (Ettwiller et al, 2007;Haudry et al, 2010) to identify conserved over-represented motifs in each node of the hierarchical clustering tree. Trawler was run with the default options and the number of occurrences (K) was calculated according to the number of genes composing each node (n) as: Kn/2.…”

Section: Motif Searchmentioning

confidence: 99%

“…We hypothesised that: (1) if all the genes within an SG are regulated by the same t-AF, we would expect them to harbour a common DNA sequence (or motif) in their regulatory regions that represents the binding site of the t-AF; and (2) this shared motif should be enriched in the set of genes within the same SG, as compared with its occurrence in the regulatory regions of other genes. Using the Trawler program (Ettwiller et al, 2007;Haudry et al, 2010), we systematically searched for common sequence motifs that represent likely t-AF footprints within the non-coding 5 kb upstream of the transcription start site (TSS) of genes encompassed in the 74 co-expressed TRN mountains or mountain ranges.…”

Section: Shared Biological Processes Of Co-expressed Genesmentioning

confidence: 99%

Cis-regulatory properties of medaka synexpression groups

et al. 2012

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SUMMARYDuring embryogenesis, tissue specification is triggered by the expression of a unique combination of developmental genes and their expression in time and space is crucial for successful development. Synexpression groups are batteries of spatiotemporally co-expressed genes that act in shared biological processes through their coordinated expression. Although several synexpression groups have been described in numerous vertebrate species, the regulatory mechanisms that orchestrate their common complex expression pattern remain to be elucidated. Here we performed a pilot screen on 560 genes of the vertebrate model system medaka (Oryzias latipes) to systematically identify synexpression groups and investigate their regulatory properties by searching for common regulatory cues. We find that synexpression groups share DNA motifs that are arranged in various combinations into cis-regulatory modules that drive co-expression. In contrast to previous assumptions that these genes are located randomly in the genome, we discovered that genes belonging to the same synexpression group frequently occur in synexpression clusters in the genome. This work presents a first repertoire of synexpression group common signatures, a resource that will contribute to deciphering developmental gene regulatory networks.

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Trawler: de novo regulatory motif discovery pipeline for chromatin immunoprecipitation

Cited by 69 publications

References 16 publications

Genomic cis-regulatory networks in the early Ciona intestinalis embryo

Genomic cis-regulatory networks in the early Ciona intestinalis embryo

A gene regulatory network directed by zebrafish No tail accounts for its roles in mesoderm formation

Cis-regulatory properties of medaka synexpression groups

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