Deciphering the molecular mechanisms underlying the binding of the TWIST1/E12 complex to regulatory E-box sequences

Bouard, Charlotte; Terreux, Raphaël; Honorat, Mylène; Manship, Brigitte; Ansieau, Stéphane; Vigneron, Arnaud; Puisieux, Alain; Payen, Léa

doi:10.1093/nar/gkw334

Cited by 20 publications

(30 citation statements)

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“…Although the 3-D structure of TWIST1 has not been solved, transcription factors with available elucidated 3-D structures that share high sequence similarity with TWIST1 can be served as applicable models for TWIST1 structure prediction. Using this strategy, previous study has modeled the dimerization of TWIST1 DNA binding domain with E2A, together with the E-Box DNA target 31 ( Supplementary Fig. 4).…”

Section: Resultsmentioning

confidence: 99%

“…The p.F191S mutation impairs the E2A/Twist1 transcriptional activity but not E2A/Twist1 interaction. Previously, the E2A-dependent Twist1 transcriptional activity has been characterized through both biochemical assay and computational analysis 19,31 . In order to know whether our mutation influences the transcriptional activity, we employed the E-box promoter assay 31,37 .…”

Section: Resultsmentioning

confidence: 99%

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An ENU-induced mutation in Twist1 transactivation domain causes hindlimb polydactyly with complete penetrance and dominant-negatively impairs E2A-dependent transcription

Chen

Cheng

Tan

et al. 2020

Sci Rep

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Twist1 encodes a basic helix-loop-helix transcription factor (TF), which forms homodimer or heterodimer with other TFs, like E2A, to regulate target genes' expression. Mutations in TWIST1 are associated with Saethre-Chotzen syndrome (SCS), a rare congenital disorder characterized with osteogenesis abnormalities. However, how dysfunction of TWIST1 leads to SCS is still largely unknown. Here, using an unbiased ENU-induced mutagenesis screening, we identified a novel Twist1 mutation and the mutant mouse phenocopies some features of SCS in a dominant manner. Physically, our mutation p.F191S lies at the edge of a predicted α-helix in Twist1 transactivation (TA) domain. Adjacent to F191, a consecutive three-residue (AFS) has been hit by 3 human and 2 mouse disease-associated mutations, including ours. Unlike previously reported mouse null and p.S192P alleles that lead to hindlimb polydactyly with incomplete penetrance but a severe craniofacial malformation, our p.F191S causes the polydactyly (84.2% bilateral and 15.8% unilateral) with complete penetrance but a mild craniofacial malformation. Consistent with the higher penetrance, p.F191S has stronger impairment on E2A-dependent transcription than p.S192P. Although human p.A186T and mouse p.S192P disease mutations are adjacent to ours, these three mutations function differently to impair the E2A-dependent transcription. Unlike p.A186T and p.S192S that disturb local protein conformation and unstabilize the mutant proteins, p.F191S keeps the mutant protein stable and its interaction with E2A entire. Therefore, we argue that p.F191S we identified acts in a dominant-negative manner to impair E2Adependent transcription and to cause the biological consequences. In addition, the mutant mouse we provided here could be an additional and valuable model for better understanding the disease mechanisms underlying SCS caused by TWIST1 dysfunction.The function of TWIST1 in osteogenesis has been reflected by the identification of the TWIST1 mutations in Saethre-Chotzen syndrome (SCS), a rare congenital disorder often associated with cone-shaped head, asymmetrical face, hand and foot malformation, and even mental retardation 1-3 . Further studies demonstrated that Twist1 is also involved in epithelial-mesenchymal transition and cell migration during embryonic development and contributes to the invasion of carcinoma cells and tumor metastasis 4-7 .Twist1 encodes a basic helix-loop-helix (bHLH) transcription factor and Twist1 DNA-binding capability essential for its functions has been intensively studied previously [8][9][10][11][12][13] . Twist1 either functions as homodimer or DiscussionIdentification of a novel Twist1 mutation responsible for hindlimb polydactyly. In ENU-induced mutagenesis, mutations that generate stop codon (nonsense), disrupt splicing site, or change amino acid (missense) are most likely disease-causing 22,23 . Among our 160 mutations identified by our exome-sequencing, no stop-gain and splicing site mutation was found. Instead, we identified 16 nonsynonymous mutati...

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

An ENU-induced mutation in Twist1 transactivation domain causes hindlimb polydactyly with complete penetrance and dominant-negatively impairs E2A-dependent transcription

Chen

Cheng

Tan

et al. 2020

Sci Rep

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“…Based on recent findings [4], we studied the particular involvement of the (1), (1*), (−1) and (−1*) DNA bases in the establishment of H-bond interactions between the wild-type or R154P mutated TE complex and the E-box sequence (Fig. 5a, b and c).…”

Section: Resultsmentioning

confidence: 99%

“…Using MD simulations and biochemical assays, we and others also highlighted the pivotal function of the R118H/Q/C, R120P, S144R, and K145E/Q residues in the molecular binding of the TE complex [4, 10–12, 18, 23, 28, 32, 33]. Mutations affecting these residues, as observed in SCS, lead to a decrease in the binding affinity of the dimer with the regulatory E-box sequences, and likely modify the transactivation functions of TWIST1 [12, 15, 20], resulting in an imbalance in the TWIST1/TWIST1 homodimer and in the TE heterodimer during the developmental process [6].…”

Section: Discussionmentioning

confidence: 99%

Destabilization of the TWIST1/E12 complex dimerization following the R154P point-mutation of TWIST1: an in silico approach

et al. 2017

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BackgroundThe bHLH transcription factor TWIST1 plays a key role in the embryonic development and in tumorigenesis. Some loss-of-function mutations of the TWIST1 gene have been shown to cause an autosomal dominant craniosynostosis, known as the Saethre-Chotzen syndrome (SCS). Although the functional impacts of many TWIST1 mutations have been experimentally reported, little is known on the molecular mechanisms underlying their loss-of-function. In a previous study, we highlighted the predictive value of in silico molecular dynamics (MD) simulations in deciphering the molecular function of TWIST1 residues.ResultsHere, since the substitution of the arginine 154 amino acid by a glycine residue (R154G) is responsible for the SCS phenotype and the substitution of arginine 154 by a proline experimentally decreases the dimerizing ability of TWIST1, we investigated the molecular impact of this point mutation using MD approaches. Consistently, MD simulations highlighted a clear decrease in the stability of the α-helix during the dimerization of the mutated R154P TWIST1/E12 dimer compared to the wild-type TE complex, which was further confirmed in vitro using immunoassays.ConclusionsOur study demonstrates that MD simulations provide a structural explanation for the loss-of-function associated with the SCS TWIST1 mutation and provides a proof of concept of the predictive value of these MD simulations. This in silico methodology could be used to determine reliable pharmacophore sites, leading to the application of docking approaches in order to identify specific inhibitors of TWIST1 complexes.Electronic supplementary materialThe online version of this article (doi:10.1186/s12900-017-0076-x) contains supplementary material, which is available to authorized users.

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“…Instead, For five of the 12 distinct combinations of smoothing half-window κ and spatial window λ investigated using SArKS, the k-mer CCACCTGC was identified at the positions s i with maximal values ofŷ i (the k-mers GCACACCTT, TGGAACTCACT, CCTGGAAC, and CAGCCTGG (identified using two distinct parameter combinations at the same suffix index i) were associated the highestŷ i values using the remaining seven parameter combinations). The octamer CCACCTGC contains the canonical core recognition E-box sequence CANNTG (specifically, the E12-box variant CACCTG (Bouard et al, 2016); we note that the significant SArKS peak set contains many peaks corresponding to the 7-mer CACCTGC as well as the longer octamer adding the extra initial C). Comparison of CCACCTGC with known motifs from the JASPAR database using tomtom finds some evidence of similarity to 10 TF-binding motifs (SNAI2, MAX, SCRT2, SCRT1, TCF3, MNT, Id2, MAX::MYC, TCF4, and FIGLA; q-values of 0.14 for each), though no similarities significant at q ≤ 0.1.…”

Section: S3222 Top Motifs Identified In Sequences Upstream Of Tssmentioning

confidence: 93%

SArKS:de novodiscovery of gene expression regulatory motifs and domains by suffix array kernel smoothing

Wylie

Hofmann

Zemelman

2017

Preprint

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Experiments designed to assess differential gene expression represent a rich resource for discovering how DNA regulatory sequences influence transcription. Results derived from such experiments are usually quantified as continuous scores, such as fold changes, test statistics and p-values. We present a de novo motif discovery algorithm, SArKS, which uses a nonparametric kernel smoothing approach to identify promoter motifs correlated with elevated differential expression scores. SArKS has the capability to smooth over both motif sequence similarity and, in a second pass, over spatial proximity of multiple motifs to identify longer regions enriched in correlative motifs. We applied SArKS to simulated data, illustrating how SArKS can be used to find motifs embedded in random background sequences, and to two published RNA-seq expression data sets, one probing S. cerevisiae transcriptional response to anti-fungal agents and the other comparing gene expression profiles among cortical neuron subtypes in M. musculus. For both RNA-seq sets we successfully identified motifs whose kernel-smoothed scores were significantly elevated compared to the permutation-estimated background distributions. We found strong similarities between these identified motifs and known, biologically meaningful sequence elements which may help to provide additional context for the results previously published regarding these data sets. Finally, because eukaryotic transcription regulation is highly combinatorial, we also outline how SArKS methods might be extended to discover synergistic motifs.

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Deciphering the molecular mechanisms underlying the binding of the TWIST1/E12 complex to regulatory E-box sequences

Cited by 20 publications

References 56 publications

An ENU-induced mutation in Twist1 transactivation domain causes hindlimb polydactyly with complete penetrance and dominant-negatively impairs E2A-dependent transcription

An ENU-induced mutation in Twist1 transactivation domain causes hindlimb polydactyly with complete penetrance and dominant-negatively impairs E2A-dependent transcription

Destabilization of the TWIST1/E12 complex dimerization following the R154P point-mutation of TWIST1: an in silico approach

SArKS:de novodiscovery of gene expression regulatory motifs and domains by suffix array kernel smoothing

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