Genome-wide analysis of canonical Wnt target gene regulation in Xenopus tropicalis challenges β-catenin paradigm

We would like to thank Ken Cho, Ira Blitz, Kris Vleminckx and Aaron Zorn for discussion and Adam Lynch for comments on the manuscript. The research of the authors is supported by the UK Biotechnology and Biological Sciences Research Council (BB/M001695/1).Peer reviewe

WNT and BMP regulate roadblocks toward cardiomyocyte differentiation : lessons learned from embryos inform human stem cell differentiation

Funding: A Münsterberg acknowledges research grant funding from BHF (PG/15/77/31761) and BBSRC (BB/N002326/1). Research in the SH laboratory is supported by BHF (PG/12/75/29851).Peer reviewedPublisher PD

Genome-wide transcriptomics analysis identifies sox7 and sox18 as specifically regulated by gata4 in cardiomyogenesis

This work was supported by British Heart Foundation (BHF Project Grant no PG/13/23/30080 to B.A.A and S.H.), Biotechnology and Biological Sciences Research Council (BB/M001695/1 to S.H.) and the University of Aberdeen (for A.T.L). Acknowledgements We’re grateful to Ms Yvonne Turnbull and Ms Kate Watt for technical assistance and lab management. We would like to thank Professor Cedric Blanpain and Dr Xionghui Li from Université Libre de Bruxelles for providing training of ES cell manipulation and Mesp1/Gata4 cell lines. We are grateful to Professor Todd Evans from Weill Cornell Medical College for generously providing iGata ES cell lines. We also would like to thank Professor Aaron Zorn and Scott Rankin for providing Xsox18 plasmid.Peer reviewedPublisher PD

A mathematical modelling portrait of Wnt signalling in early vertebrate embryogenesis

Acknowledegements We would like to express our gratitude to Dr Yasushi Saka for training and encouragement. Funding was received from the BHF (RG/18/8/33673 to CVG and SH) and BBSRC (BB/N021924/1; BB/M001695/1; BB/S018190/1 to SH). S.H. was a Royal Society/Leverhulme Trust Senior Research Fellow (SRF\R1\191017).Peer reviewedPublisher PD

Evolutionary diversification of the canonical Wnt signaling effector TCF/LEF in chordates

This work was supported by the Biotechnology and Biological Sciences Research Council (BBSRC), linked projects, references BB/S016856/1 and BB/S020640/1.Wnt signaling is essential during animal development and regeneration, but also plays an important role in diseases such as cancer and diabetes. The canonical Wnt signaling pathway is one of the most conserved signaling cascades in the animal kingdom, with the T-cell factor/lymphoid enhancer factor (TCF/LEF) proteins the major mediators of Wnt/β-catenin-regulated gene expression. In comparison to invertebrates, vertebrates possess a high diversity of TCF/LEF family genes, implicating this as a possible key change to Wnt signaling at the evolutionary origin of vertebrates. However, the precise nature of this diversification is only poorly understood. The aim of this study is to clarify orthology, paralogy and isoform relationships within the TCF/LEF gene family within chordates via in silico comparative study of TCF/LEF gene structure, molecular phylogeny and gene synteny. Our results support the notion that the four TCF/LEF paralog subfamilies in jawed vertebrates (gnathostomes) evolved via the two rounds of whole-genome duplication that occurred during early vertebrate evolution. Importantly, gene structure comparisons and synteny analysis of jawless vertebrate (cyclostome) TCFs suggest that a TCF7L2-like form of gene structure is a close proxy for the ancestral vertebrate structure. In conclusion, we propose a detailed evolutionary path based on a new pre-whole-genome duplication vertebrate TCF gene model. This ancestor gene model highlights the chordate and vertebrate innovations of TCF/LEF gene structure, providing the foundation for understanding the role of Wnt/β-catenin signaling in vertebrate evolution.Publisher PDFPeer reviewe

Tissue- and stage-specific Wnt target gene expression is controlled subsequent to β-catenin recruitment to cis-regulatory modules

Acknowledgements We thank Saartje Hontelez (Radboud University, Nijmegen), Sylvie Janssens and Kris Vleminckx (Vlaams Instituut voor Biotechnologie, Universiteit Gent) and Shelby Blythe (Princeton University) for advice on ChIP experiments; Caroline Hill (CRUK, LRI) for discussion on BMP signalling; Juan Larraín (Pontificia Universitad Católica de Chile) and Susan Fairley (European Bioinformatics Institute) for advice on RNA-seq experiments; Yvonne Turnbull (IMSARU, University of Aberdeen) for technical assistance; Alasdair MacKenzie (University of Aberdeen) for discussion and suggestions on the manuscript; Hajime Ogino (Nagahama Institute of Bio-Science and Technology) and Atsushi Suzuki (Hiroshima University) for plasmids; Pierre McCrea (University of Texas MD Anderson Cancer Center) for anti-Xenopus β-catenin antibody; The Genome Analysis Centre (TGAC, BBSRC, Norwich) for high-throughput sequencing; and Xenbase (http://www.xenbase.org) for reference database access. Funding This work was supported by the Biotechnology and Biological Sciences Research Council [BB/I003746/1 to S.H., BB/M001695/1 to S.H. and Y.N.]. Deposited in PMC for immediate release.Peer reviewedPublisher PD

Diverse LEF/TCF Expression in Human Colorectal Cancer Correlates with Altered Wnt-Regulated Transcriptome in a Meta-Analysis of Patient Biopsies

Funding: CM acknowledges funding from the Scottish Government: Rural & Environment Science & Analytical Services. (RESAS). SH is a Royal Society/Leverhulme Trust Senior Research Fellow (SRF\R1\191017) and acknowledges research funding from the Biotechnology and Biological Sciences Research Council (BB/S018190/1, BB/M001695/1). Author Contributions: C.-D.M. and S.H. had conceived and supervised this project; C.-D.M. curated the data and carried out some analysis; S.M.L.G., carried out most of the analysis; F.A. wrote an original draft together with Stefan Hoppler. All authors have read and agreed to the published version of the manuscript. Supplementary Materials: The following are available online at www.mdpi.com/2073-4425/11/5/538/s1: Figure S1: Principal Component Analysis of selected studies, Figure S2: Principal Component Analysis of de-selected study, Table S1: Transcriptomics Data (Correlation Coefficients) Table S1A: Transcript correlation between eight selected genes (TCF7, LEF1, TCF7L1, TCF7L2, AXIN2, DKK1, FZD7, LGR5); Table S1B: The TCF7-correlated transcriptome; Table S1C: The LEF1correlated transcriptome; Table S1D: The TCF7L1-correlated transcriptome; Table S1E: The TCF7L2-correlated transcriptome; Table S1F: The AXIN2-correlated transcriptome; Table S1G: The DKK1-correlated transcriptome; Table S1H: The FZD7-correlated transcriptome; Table S1I: The LGR5-correlated transcriptome; Table S1J: Differences in LEF/TCF-correlated transcriptomes; Table S1K: Differences between AXIN2- and LEF/TCF-correlated transcriptomes, Table S2: Correlated Transcriptome in normal and tumor tissue, Table S3: Comparison of LEF/TCF-correlated transcriptomes, Table S4: Differences between AXIN1- and LEF/TCF-correlated transcriptomes.Peer reviewedPublisher PD

Positive feedback regulation of fzd7 expression robustly shapes a steep Wnt gradient in Xenopus heart development, together with sFRP1 and heparan sulfate

Acknowledgements We thank Dr. Yukio Nakamura (Aberdeen University, UK; Present address: Repertoire Genesis Inc., Japan.) and Dr. Masanori Taira (Chuo University, Japan) for their help in initiating this project; Dr. Takehiko Nakamura (Seikagaku Corporation, Japan) for NAH46 antibody and hybridoma; Dr. Osamu Yoshie (Kindai University, Japan) for HepSS-1 hybridoma; Dr. Makoto Matsuyama (Shigei Medical Research Institute, Japan) for the contribution to the generation of NAH46 and HepSS-1 antibody from the hybridomas; Dr. Steven D. Aird for technical editing of the manuscript. This international collaboration was supported in part by Daiwa Anglo-Japanese Foundation (12969/13787 to T.Y., B.A., T.M., and S.H.); with additional research support in Japan from MEXT/JSPS KAKENHI (19K16138 to T.Y., 18K06244/21K06183 to T.Y. and T.M.); and in the United Kingdom from BHF (RG/18/8/33673 to S.H.) and BBSRC (BB/N021924/1; BB/M001695/1 to S.H.). S.H. was a Royal Society/Leverhulme Trust Senior Research Fellow (SRF\R1\191017).Peer reviewedPublisher PD

Distinctive Roles of Canonical and Noncanonical Wnt Signaling in Human Embryonic Cardiomyocyte Development

Open Access funded by British Heart Foundation Under a Creative Commons license Acknowledgments Our thanks go to Gioia Polidori Francisco for training and discussions, Kate Watt and Yvonne Turnbull for technical and laboratory managerial support, Kadri Oras and Laura Ferguson for experimental support, Po-Lin So and Bruce Conklin (Gladstone Institutes) for providing their unpublished protocols, and Yukio Nakamura for discussion. This research is supported by the British Heart Foundation (PG/12/75/29851) and the Institute of Medical Sciences. A.S.B. was supported by the British Heart Foundation (FS/12/37/29516).Peer reviewedPublisher PD

Genome-wide transcriptomics analysis of genes regulated by GATA4, 5 and 6 during cardiomyogenesis in Xenopus laevis

Funding sources This work was supported by British Heart Foundation (BHF Project Grant no PG/13/23/30080 to B.A.A and S.H.), Biotechnology and Biological Sciences Research Council (BB/M001695/1 to S.H.) and the University of Aberdeen (for A.T.L).Peer reviewedPublisher PD