Analysis of the Teashirt Target Genes in Ureteric Bud Development

  • Laurent FasanoEmail author
  • Irene Sanchez-Martin
  • Xavier Caubit
Part of the Methods in Molecular Biology book series (MIMB, volume 1926)


Microarrays and RNA-seq (RNA sequencing) are powerful techniques to assess transcript abundance in biological samples and to improve our understanding of the relationship between genotype and phenotype. Tshz3+/− heterozygous mouse is a model for a human 19q12 syndrome characterized by autistic traits and renal tract defects (Caubit et al., Nat Genet 48:1359–1369, 2016). To unravel renal tract pathological mechanisms, we took advantage of Tshz3 mouse and performed comparative genome-wide expression profiling on embryonic ureter and/or kidney.

Key words

Microarray RNA-seq Mouse Ureter Kidney Tshz3 


  1. 1.
    Caubit X, Gubellini P, Andrieux J, Roubertoux PL, Metwaly M, Jacq B, Fatmi A, Had-Aissouni L, Kwan KY, Salin P, Carlier M, Lieden A, Rudd E, Shinawi M, Vincent-Delorme C, Cuisset JM, Lemaitre MP, Abderrehamane F, Duban B, Lemaitre JF, Woolf AS, Bockenhauer D, Severac D, Dubois E, Zhu Y, Sestan N, Garratt AN, Kerkerian-Le Goff L, Fasano L (2016) TSHZ3 deletion causes an autism syndrome and defects in cortical projection neurons. Nat Genet 48(11):1359–1369. Scholar
  2. 2.
    Schena M, Shalon D, Davis RW, Brown PO (1995) Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270(5235):467–470CrossRefPubMedCentralGoogle Scholar
  3. 3.
    Lashkari DA, DeRisi JL, McCusker JH, Namath AF, Gentile C, Hwang SY, Brown PO, Davis RW (1997) Yeast microarrays for genome wide parallel genetic and gene expression analysis. Proc Natl Acad Sci U S A 94(24):13057–13062CrossRefPubMedCentralGoogle Scholar
  4. 4.
    Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B (2008) Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 5(7):621–628. Scholar
  5. 5.
    Nagalakshmi U, Wang Z, Waern K, Shou C, Raha D, Gerstein M, Snyder M (2008) The transcriptional landscape of the yeast genome defined by RNA sequencing. Science 320(5881):1344–1349. Scholar
  6. 6.
    Wilhelm BT, Marguerat S, Watt S, Schubert F, Wood V, Goodhead I, Penkett CJ, Rogers J, Bahler J (2008) Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution. Nature 453(7199):1239–1243. Scholar
  7. 7.
    Caubit X, Lye CM, Martin E, Core N, Long DA, Vola C, Jenkins D, Garratt AN, Skaer H, Woolf AS, Fasano L (2008) Teashirt 3 is necessary for ureteral smooth muscle differentiation downstream of SHH and BMP4. Development 135(19):3301–3310. Scholar
  8. 8.
    Martin E, Caubit X, Airik R, Vola C, Fatmi A, Kispert A, Fasano L (2013) TSHZ3 and SOX9 regulate the timing of smooth muscle cell differentiation in the ureter by reducing myocardin activity. PLoS One 8(5):e63721. Scholar
  9. 9.
    Jenkins D, Caubit X, Dimovski A, Matevska N, Lye CM, Cabuk F, Gucev Z, Tasic V, Fasano L, Woolf AS (2010) Analysis of TSHZ2 and TSHZ3 genes in congenital pelvi-ureteric junction obstruction. Nephrol Dial Transplant 25(1):54–60CrossRefPubMedCentralGoogle Scholar
  10. 10.
    Costantini F, Watanabe T, Lu B, Chi X, Srinivas S (2011) Dissection of embryonic mouse kidney, culture in vitro, and imaging of the developing organ. Cold Spring Harb Protoc 2011(5):pdb prot5613. Scholar
  11. 11.
    Staack A, Donjacour AA, Brody J, Cunha GR, Carroll P (2003) Mouse urogenital development: a practical approach. Differentiation 71(7):402–413. Scholar
  12. 12.
    Wang Z, Wang DZ, Pipes GC, Olson EN (2003) Myocardin is a master regulator of smooth muscle gene expression. Proc Natl Acad Sci U S A 100(12):7129–7134. Scholar
  13. 13.
    Oliveros JC (2007–2015) Venny. An interactive tool for comparing lists with Venn’s diagrams.

Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  • Laurent Fasano
    • 1
    Email author
  • Irene Sanchez-Martin
    • 1
  • Xavier Caubit
    • 1
  1. 1.Aix Marseille University, CNRS, IBDMMarseilleFrance

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