ConTra: a promoter alignment analysis tool for identification of transcription factor binding sites across species

Hooghe, Bart; Hulpiau, Paco; Roy, Frans Van; Bleser, Pieter De

doi:10.1093/nar/gkn195

Cited by 59 publications

(53 citation statements)

References 23 publications

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“…SMAD3 binding to a GCCGnCGc element of the bcl2 gene was recently demonstrated (Yang et al, 2006). Furthermore, the promoter alignment analysis tool ConTra (http://bioit.dmbr.ugent.be/ConTra/index.php) predicts binding of high mobility group (HMG) proteins and SP1 to this region of the SNAIL promoter (Hooghe et al, 2008). As shown in Fig.…”

Section: Ikk Controls Tgf-induced Binding Of Smads To the Snail Andmentioning

confidence: 92%

“…Interestingly, we detected TGF-IKK-regulated binding of a SMAD complex to SNAIL and SLUG promoter regions characterized by GC-rich elements. In addition, the promoter alignment analysis tool ConTra predicts binding of HMG proteins and SP1 to both promoter regions (Hooghe et al, 2008). SP1 was recently demonstrated to control the TGF-dependent EMT of Panc1 cells (Jungert et al, 2007).…”

Section: Fig 4 Tgf-dependent Downregulation Of E-cadherin Is Nfb-mentioning

confidence: 99%

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IKKα controls canonical TGFβ–SMAD signaling to regulate genes expressing SNAIL and SLUG during EMT in Panc1 cells

Brandl

Seidler

Haller

et al. 2010

Journal of Cell Science

116

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There was an error published in J. Cell Sci. 123, 4231-4239.In Fig. 4A, the cRel siRNA western blot panel was inadvertently constructed using the wrong images and all three western blots showed incorrect loading controls. The correct images and loading controls are shown in the figure below. The mistake in the figure did not affect the conclusions of the paper.We apologise for this mistake. . TGFb-dependent downregulation of E-cadherin is NFkB-independent. (A) Panc1 cells were transfected with a control or RelA/p65-, RelB-or c-Relspecific siRNA. At 24 hours after the transfection, cells were treated with 10 ng/ml TGFb or were left as an untreated control in DMEM without FCS. After an additional 48 hours, western blots detected RelA/p65, RelB or c-Rel and E-cadherin expression. The membrane was stripped and probed for a-tubulin or b-actin to ensure equal protein loading. (B) Panc1 (upper graph) and MDA-MB231 cells (lower graph) cells were co-transfected with a control or IKKa-specific siRNA and 500 ng of the pGL3control-, NFkB-or SMAD-luciferase reporter gene constructs as indicated. At 24 hours after the transfection, cells were treated with 10 ng/ml TGFb or were left as an untreated control. Luciferase activity was measured 6 hours after the TGFb treatment (Student's t-test: *P,0.05 versus control). (C) Panc1 (upper graph) and MDA-MB231 (lower graph) cells were transfected with a control or IKKa-specific siRNA. At 48 hours after the transfection, cells were stimulated with TGFb (10 ng/ml) for 20 minutes and binding of SMAD3 and SMAD4 to a SMAD consensus oligonucleotide was detected using ABCD assays. Input represents 5% of whole-cell extract of control siRNA-transfected cells. (D) Panc1 cells were treated as in C. Immunoprecipitation was performed with an IKKa-specific antibody or pre-immune serum as a control. Western blots of immunoprecipitates were probed with antibodies against IKKa and SMAD3. Input represents 5% of whole-cell extract of control siRNA-transfected Panc1 cells. (E) MDA-MB231 cells were transfected with a control or IKKa-specific siRNA. At 24 hours after the transfection, cells were treated with 10 ng/ml TGFb or were left as an untreated control in DMEM without FCS. After an additional 48 hours, western blots detected IKKa expression. The membrane was stripped and probed for b-actin to ensure equal protein loading.

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Section: Ikk Controls Tgf-induced Binding Of Smads To the Snail Andmentioning

confidence: 92%

Section: Fig 4 Tgf-dependent Downregulation Of E-cadherin Is Nfb-mentioning

confidence: 99%

IKKα controls canonical TGFβ–SMAD signaling to regulate genes expressing SNAIL and SLUG during EMT in Panc1 cells

Brandl

Seidler

Haller

et al. 2010

Journal of Cell Science

116

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“…Consensus lef1/tcf binding sites were determined and evaluated for conservation by using the UCSC Genome Browser (genome.ucsc.edu) (Kent et al, 2002), the Match tool of TRANSFAC (Biobase) (Kel et al, 2003) and the alignment tool Contra (Hooghe et al, 2008). ChIP assays were performed according to the method described before (Blythe et al, 2009) but with minor modifications: we used gastrula X. tropicalis embryos at stage 11 and cross-linking time was 45 min.…”

Section: Chromatin Immunoprecipitationmentioning

confidence: 99%

The Wnt signaling mediator tcf1 is required for expression of foxd3 during Xenopus gastrulation

Janssens¹,

Broek²,

Davenport³

et al. 2013

Int. J. Dev. Biol.

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TCF1 belongs to the family of LEF1/TCF transcription factors that regulate gene expression downstream of Wnt/b-catenin signaling, which is crucial for embryonic development and is involved in adult stem cell regulation and tumor growth. In early Xenopus embryos, tcf1 plays an important role in mesoderm induction and patterning. Foxd3 emerged as a potential tcf1 target gene in a microarray analysis of gastrula stage embryos. Because foxd3 and tcf1 are coexpressed during gastrulation, we investigated whether foxd3 is regulated by tcf1. By using morpholino-mediated knockdown, we show that during gastrulation foxd3 expression is dependent on tcf1. By chromatin immunoprecipitation, we also demonstrate direct interaction of b-catenin/tcf complexes with the foxd3 gene locus. Hence, our results indicate that tcf1 acts as an essential activator of foxd3, which is critical for dorsal mesoderm formation in early embryos.

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“…With these so-called phylogenetic footprinting approaches, conserved regions that point to the presence of important functionality, i.e., TFBSs (and also RNAP/ribosome binding sites), are identified (30,131). The most basic methodology is to construct a global multiple sequence alignment of the orthologous promoter sequences using an alignment tool such as ClustalW (292) and then to manually identify conserved regions within this alignment (Fig.…”

Section: In Silico Prediction Of Tfbssmentioning

confidence: 99%

Mechanisms and Evolution of Control Logic in Prokaryotic Transcriptional Regulation

Hijum

Medema

Kuipers

2009

Microbiol Mol Biol Rev

139

149

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SUMMARY A major part of organismal complexity and versatility of prokaryotes resides in their ability to fine-tune gene expression to adequately respond to internal and external stimuli. Evolution has been very innovative in creating intricate mechanisms by which different regulatory signals operate and interact at promoters to drive gene expression. The regulation of target gene expression by transcription factors (TFs) is governed by control logic brought about by the interaction of regulators with TF binding sites (TFBSs) in cis-regulatory regions. A factor that in large part determines the strength of the response of a target to a given TF is motif stringency, the extent to which the TFBS fits the optimal TFBS sequence for a given TF. Advances in high-throughput technologies and computational genomics allow reconstruction of transcriptional regulatory networks in silico. To optimize the prediction of transcriptional regulatory networks, i.e., to separate direct regulation from indirect regulation, a thorough understanding of the control logic underlying the regulation of gene expression is required. This review summarizes the state of the art of the elements that determine the functionality of TFBSs by focusing on the molecular biological mechanisms and evolutionary origins of cis-regulatory regions.

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ConTra: a promoter alignment analysis tool for identification of transcription factor binding sites across species

Cited by 59 publications

References 23 publications

IKKα controls canonical TGFβ–SMAD signaling to regulate genes expressing SNAIL and SLUG during EMT in Panc1 cells

IKKα controls canonical TGFβ–SMAD signaling to regulate genes expressing SNAIL and SLUG during EMT in Panc1 cells

The Wnt signaling mediator tcf1 is required for expression of foxd3 during Xenopus gastrulation

Mechanisms and Evolution of Control Logic in Prokaryotic Transcriptional Regulation

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