In Vitro Site Selection of a Consensus Binding Site for the Drosophila Melanogaster Tbx20 Homolog Midline

Overview

Journal PLoS One

Specialties General Medicine
Science

Date 2012 Nov 8

PMID 23133562

Citations 3

Authors

Nima Najand

Jae-Ryeon Ryu

William J Brook

Affiliations

Soon will be listed here.

Abstract

We employed in vitro site selection to identify a consensus binding sequence for the Drosophila melanogaster Tbx20 T-box transcription factor homolog Midline. We purified a bacterially expressed T-box DNA binding domain of Midline, and used it in four rounds of precipitation and polymerase-chain-reaction based amplification. We cloned and sequenced 54 random oligonucleotides selected by Midline. Electromobility shift-assays confirmed that 27 of these could bind the Midline T-box. Sequence alignment of these 27 clones suggests that Midline binds as a monomer to a consensus sequence that contains an AGGTGT core. Thus, the Midline consensus binding site we define in this study is similar to that defined for vertebrate Tbx20, but differs from a previously reported Midline binding sequence derived through site selection.

Citing Articles

midline represses Dpp signaling and target gene expression in Drosophila ventral leg development.

Phillips L, Atienza M, Ryu J, Svendsen P, Kelemen L, Brook W Biol Open. 2022; 11(5).

PMID: 35608103 PMC: 9167623. DOI: 10.1242/bio.059206.

Dynamics of promoter bivalency and RNAP II pausing in mouse stem and differentiated cells.

Mantsoki A, Devailly G, Joshi A BMC Dev Biol. 2018; 18(1):2.

PMID: 29458328 PMC: 5819258. DOI: 10.1186/s12861-018-0163-7.

The expression of the T-box selector gene midline in the leg imaginal disc is controlled by both transcriptional regulation and cell lineage.

Svendsen P, Ryu J, Brook W Biol Open. 2015; 4(12):1707-14.

PMID: 26581591 PMC: 4736030. DOI: 10.1242/bio.013565.

References

Buescher M, Svendsen P, Tio M, Miskolczi-McCallum C, Tear G, Brook W . Drosophila T box proteins break the symmetry of hedgehog-dependent activation of wingless. Curr Biol. 2004; 14(19):1694-702. DOI: 10.1016/j.cub.2004.09.048. View

Nusslein-Volhard C, Wieschaus E, Kluding H . Mutations affecting the pattern of the larval cuticle inDrosophila melanogaster : I. Zygotic loci on the second chromosome. Wilehm Roux Arch Dev Biol. 2017; 193(5):267-282. DOI: 10.1007/BF00848156. View

Messenger N, Kabitschke C, Andrews R, Grimmer D, Miguel R, Blundell T . Functional specificity of the Xenopus T-domain protein Brachyury is conferred by its ability to interact with Smad1. Dev Cell. 2005; 8(4):599-610. DOI: 10.1016/j.devcel.2005.03.001. View

Sebe-Pedros A, de Mendoza A, Lang B, Degnan B, Ruiz-Trillo I . Unexpected repertoire of metazoan transcription factors in the unicellular holozoan Capsaspora owczarzaki. Mol Biol Evol. 2010; 28(3):1241-1254. PMC: 4342549. DOI: 10.1093/molbev/msq309. View

Lamolet B, Pulichino A, Lamonerie T, Gauthier Y, Brue T, Enjalbert A . A pituitary cell-restricted T box factor, Tpit, activates POMC transcription in cooperation with Pitx homeoproteins. Cell. 2001; 104(6):849-59. DOI: 10.1016/s0092-8674(01)00282-3. View

Carlson J, Chakravarty A, DeZiel C, Gross R . SCOPE: a web server for practical de novo motif discovery. Nucleic Acids Res. 2007; 35(Web Server issue):W259-64. PMC: 1933170. DOI: 10.1093/nar/gkm310. View

Liu Q, Hiramoto M, Ueda H, Gojobori T, Hiromi Y, Hirose S . Midline governs axon pathfinding by coordinating expression of two major guidance systems. Genes Dev. 2009; 23(10):1165-70. PMC: 2685537. DOI: 10.1101/gad.1774209. View

Singh R, Horsthuis T, Farin H, Grieskamp T, Norden J, Petry M . Tbx20 interacts with smads to confine tbx2 expression to the atrioventricular canal. Circ Res. 2009; 105(5):442-52. DOI: 10.1161/CIRCRESAHA.109.196063. View

Homann O, Johnson A . MochiView: versatile software for genome browsing and DNA motif analysis. BMC Biol. 2010; 8:49. PMC: 2867778. DOI: 10.1186/1741-7007-8-49. View

10.

Naiche L, Harrelson Z, Kelly R, Papaioannou V . T-box genes in vertebrate development. Annu Rev Genet. 2005; 39:219-39. DOI: 10.1146/annurev.genet.39.073003.105925. View

11.

Carreira S, Dexter T, Yavuzer U, Easty D, Goding C . Brachyury-related transcription factor Tbx2 and repression of the melanocyte-specific TRP-1 promoter. Mol Cell Biol. 1998; 18(9):5099-108. PMC: 109095. DOI: 10.1128/MCB.18.9.5099. View

12.

Shen T, Aneas I, Sakabe N, Dirschinger R, Wang G, Smemo S . Tbx20 regulates a genetic program essential to adult mouse cardiomyocyte function. J Clin Invest. 2011; 121(12):4640-54. PMC: 3223071. DOI: 10.1172/JCI59472. View

13.

White P, Chapman D . Dll1 is a downstream target of Tbx6 in the paraxial mesoderm. Genesis. 2005; 42(3):193-202. DOI: 10.1002/gene.20140. View

14.

Muller C, Herrmann B . Crystallographic structure of the T domain-DNA complex of the Brachyury transcription factor. Nature. 1998; 389(6653):884-8. DOI: 10.1038/39929. View

15.

Stirnimann C, Ptchelkine D, Grimm C, Muller C . Structural basis of TBX5-DNA recognition: the T-box domain in its DNA-bound and -unbound form. J Mol Biol. 2010; 400(1):71-81. DOI: 10.1016/j.jmb.2010.04.052. View

16.

Coll M, Seidman J, Muller C . Structure of the DNA-bound T-box domain of human TBX3, a transcription factor responsible for ulnar-mammary syndrome. Structure. 2002; 10(3):343-56. DOI: 10.1016/s0969-2126(02)00722-0. View

17.

Buescher M, Tio M, Tear G, Overton P, Brook W, Chia W . Functions of the segment polarity genes midline and H15 in Drosophila melanogaster neurogenesis. Dev Biol. 2006; 292(2):418-29. DOI: 10.1016/j.ydbio.2006.01.016. View

18.

Kispert A, Koschorz B, Herrmann B . The T protein encoded by Brachyury is a tissue-specific transcription factor. EMBO J. 1995; 14(19):4763-72. PMC: 394574. DOI: 10.1002/j.1460-2075.1995.tb00158.x. View

19.

Papapetrou C, Putt W, Fox M, Edwards Y . The human TBX6 gene: cloning and assignment to chromosome 16p11.2. Genomics. 1999; 55(2):238-41. DOI: 10.1006/geno.1998.5646. View

20.

Ghosh T, PACKHAM E, Bonser A, Robinson T, Cross S, Brook J . Characterization of the TBX5 binding site and analysis of mutations that cause Holt-Oram syndrome. Hum Mol Genet. 2001; 10(18):1983-94. DOI: 10.1093/hmg/10.18.1983. View