DNA-binding Sequence Specificity of DUX4

Overview

Journal Skelet Muscle

Specialty Physiology

Date 2016 Jan 30

PMID 26823969

Citations 25

Authors

Yu Zhang

John K Lee

Erik A Toso

Joslynn S Lee

Si Ho Choi

Matthew Slattery

Hideki Aihara

Michael Kyba

Affiliations

Soon will be listed here.

Abstract

Background: Misexpression of the double homeodomain transcription factor DUX4 results in facioscapulohumeral muscular dystrophy (FSHD). A DNA-binding consensus with two tandem TAAT motifs based on chromatin IP peaks has been discovered; however, the consensus has multiple variations (flavors) of unknown relative activity. In addition, not all peaks have this consensus, and the Pitx1 promoter, the first DUX4 target sequence mooted, has a different TAAT-rich sequence. Furthermore, it is not known whether and to what extent deviations from the consensus affect DNA-binding affinity and transcriptional activation potential.

Results: Here, we take both unbiased and consensus sequence-driven approaches to determine the DNA-binding specificity of DUX4 and its tolerance to mismatches at each site within its consensus sequence. We discover that the best binding and the greatest transcriptional activation are observed when the two TAAT motifs are separated by a C residue. The second TAAT motif in the consensus sequence is actually (T/C)AAT. We find that a T is preferred here. DUX4 has no transcriptional activity on "half-sites", i.e., those bearing only a single TAAT motif. We further find that DUX4 does not bind to the TAATTA motif in the Pitx1 promoter, that Pitx1 sequences have no competitive band shift activity, and that the Pitx1 sequence is transcriptionally inactive, calling into question PITX1 as a DUX4 target gene. Finally, by multimerizing binding sites, we find that DUX4 transcriptional activation demonstrates tremendous synergy and that at low DNA concentrations, at least two motifs are necessary to detect a transcriptional response.

Conclusions: These studies illuminate the DNA-binding sequence preferences of DUX4.

Citing Articles

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DUX4 Role in Normal Physiology and in FSHD Muscular Dystrophy.

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Analysis of genes regulated by DUX4 via oxidative stress reveals potential therapeutic targets for treatment of facioscapulohumeral dystrophy.

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A Deoxyribonucleic Acid Decoy Trapping DUX4 for the Treatment of Facioscapulohumeral Muscular Dystrophy.

Mariot V, Joubert R, Marsollier A, Hourde C, Voit T, Dumonceaux J Mol Ther Nucleic Acids. 2020; 22:1191-1199.

PMID: 33312755 PMC: 7701011. DOI: 10.1016/j.omtn.2020.10.028.

References

Geng L, Yao Z, Snider L, Fong A, Cech J, Young J . DUX4 activates germline genes, retroelements, and immune mediators: implications for facioscapulohumeral dystrophy. Dev Cell. 2012; 22(1):38-51. PMC: 3264808. DOI: 10.1016/j.devcel.2011.11.013. View

Wilson D, Sheng G, Lecuit T, Dostatni N, Desplan C . Cooperative dimerization of paired class homeo domains on DNA. Genes Dev. 1993; 7(11):2120-34. DOI: 10.1101/gad.7.11.2120. View

Young J, Whiddon J, Yao Z, Kasinathan B, Snider L, Geng L . DUX4 binding to retroelements creates promoters that are active in FSHD muscle and testis. PLoS Genet. 2013; 9(11):e1003947. PMC: 3836709. DOI: 10.1371/journal.pgen.1003947. View

Dandapat A, Bosnakovski D, Hartweck L, Arpke R, Baltgalvis K, Vang D . Dominant lethal pathologies in male mice engineered to contain an X-linked DUX4 transgene. Cell Rep. 2014; 8(5):1484-96. PMC: 4188423. DOI: 10.1016/j.celrep.2014.07.056. View

Dandapat A, Hartweck L, Bosnakovski D, Kyba M . Expression of the human FSHD-linked DUX4 gene induces neurogenesis during differentiation of murine embryonic stem cells. Stem Cells Dev. 2013; 22(17):2440-8. PMC: 3749711. DOI: 10.1089/scd.2012.0643. View

Czerny T, Busslinger M . DNA-binding and transactivation properties of Pax-6: three amino acids in the paired domain are responsible for the different sequence recognition of Pax-6 and BSAP (Pax-5). Mol Cell Biol. 1995; 15(5):2858-71. PMC: 230517. DOI: 10.1128/MCB.15.5.2858. View

Krom Y, Dumonceaux J, Mamchaoui K, den Hamer B, Mariot V, Negroni E . Generation of isogenic D4Z4 contracted and noncontracted immortal muscle cell clones from a mosaic patient: a cellular model for FSHD. Am J Pathol. 2012; 181(4):1387-401. PMC: 3463638. DOI: 10.1016/j.ajpath.2012.07.007. View

Zeng W, de Greef J, Chen Y, Chien R, Kong X, Gregson H . Specific loss of histone H3 lysine 9 trimethylation and HP1gamma/cohesin binding at D4Z4 repeats is associated with facioscapulohumeral dystrophy (FSHD). PLoS Genet. 2009; 5(7):e1000559. PMC: 2700282. DOI: 10.1371/journal.pgen.1000559. View

van Overveld P, Lemmers R, Sandkuijl L, Enthoven L, Winokur S, Bakels F . Hypomethylation of D4Z4 in 4q-linked and non-4q-linked facioscapulohumeral muscular dystrophy. Nat Genet. 2003; 35(4):315-7. DOI: 10.1038/ng1262. View

10.

de Greef J, Lemmers R, van Engelen B, Sacconi S, Venance S, Frants R . Common epigenetic changes of D4Z4 in contraction-dependent and contraction-independent FSHD. Hum Mutat. 2009; 30(10):1449-59. DOI: 10.1002/humu.21091. View

11.

Thijssen P, Balog J, Yao Z, Pham T, Tawil R, Tapscott S . DUX4 promotes transcription of FRG2 by directly activating its promoter in facioscapulohumeral muscular dystrophy. Skelet Muscle. 2015; 4:19. PMC: 4364343. DOI: 10.1186/2044-5040-4-19. View

12.

Bosnakovski D, Xu Z, Gang E, Galindo C, Liu M, Simsek T . An isogenetic myoblast expression screen identifies DUX4-mediated FSHD-associated molecular pathologies. EMBO J. 2008; 27(20):2766-79. PMC: 2572182. DOI: 10.1038/emboj.2008.201. View

13.

Snider L, Geng L, Lemmers R, Kyba M, Ware C, Nelson A . Facioscapulohumeral dystrophy: incomplete suppression of a retrotransposed gene. PLoS Genet. 2010; 6(10):e1001181. PMC: 2965761. DOI: 10.1371/journal.pgen.1001181. View

14.

van Deutekom J, Wijmenga C, van Tienhoven E, Gruter A, Hewitt J, Padberg G . FSHD associated DNA rearrangements are due to deletions of integral copies of a 3.2 kb tandemly repeated unit. Hum Mol Genet. 1993; 2(12):2037-42. DOI: 10.1093/hmg/2.12.2037. View

15.

Wallace L, Garwick S, Mei W, Belayew A, Coppee F, Ladner K . DUX4, a candidate gene for facioscapulohumeral muscular dystrophy, causes p53-dependent myopathy in vivo. Ann Neurol. 2011; 69(3):540-52. PMC: 4098764. DOI: 10.1002/ana.22275. View

16.

Seale P, Sabourin L, Girgis-Gabardo A, Mansouri A, Gruss P, Rudnicki M . Pax7 is required for the specification of myogenic satellite cells. Cell. 2000; 102(6):777-86. DOI: 10.1016/s0092-8674(00)00066-0. View

17.

Jones T, Chen J, Rahimov F, Homma S, Arashiro P, Beermann M . Facioscapulohumeral muscular dystrophy family studies of DUX4 expression: evidence for disease modifiers and a quantitative model of pathogenesis. Hum Mol Genet. 2012; 21(20):4419-30. PMC: 3459465. DOI: 10.1093/hmg/dds284. View

18.

Schaap M, Lemmers R, Maassen R, van der Vliet P, Hoogerheide L, van Dijk H . Genome-wide analysis of macrosatellite repeat copy number variation in worldwide populations: evidence for differences and commonalities in size distributions and size restrictions. BMC Genomics. 2013; 14:143. PMC: 3599962. DOI: 10.1186/1471-2164-14-143. View

19.

Dixit M, Ansseau E, Tassin A, Winokur S, Shi R, Qian H . DUX4, a candidate gene of facioscapulohumeral muscular dystrophy, encodes a transcriptional activator of PITX1. Proc Natl Acad Sci U S A. 2007; 104(46):18157-62. PMC: 2084313. DOI: 10.1073/pnas.0708659104. View

20.

Gabriels J, Beckers M, Ding H, De Vriese A, Plaisance S, van der Maarel S . Nucleotide sequence of the partially deleted D4Z4 locus in a patient with FSHD identifies a putative gene within each 3.3 kb element. Gene. 1999; 236(1):25-32. DOI: 10.1016/s0378-1119(99)00267-x. View