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Disorders with similar clinical phenotypes reveal underlying genetic interaction: SATB2 acts as an activator of the UPF3B gene

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Abstract

Two syndromic cognitive impairment disorders have very similar craniofacial dysmorphisms. One is caused by mutations of SATB2, a transcription regulator and the other by heterozygous mutations leading to premature stop codons in UPF3B, encoding a member of the nonsense-mediated mRNA decay complex. Here we demonstrate that the products of these two causative genes function in the same pathway. We show that the SATB2 nonsense mutation in our patient leads to a truncated protein that localizes to the nucleus, forms a dimer with wild-type SATB2 and interferes with its normal activity. This suggests that the SATB2 nonsense mutation has a dominant negative effect. The patient’s leukocytes had significantly decreased UPF3B mRNA compared to controls. This effect was replicated both in vitro, where siRNA knockdown of SATB2 in HEK293 cells resulted in decreased UPF3B expression, and in vivo, where embryonic tissue of Satb2 knockout mice showed significantly decreased Upf3b expression. Furthermore, chromatin immunoprecipitation demonstrates that SATB2 binds to the UPF3B promoter, and a luciferase reporter assay confirmed that SATB2 expression significantly activates gene transcription using the UPF3B promoter. These findings indicate that SATB2 activates UPF3B expression through binding to its promoter. This study emphasizes the value of recognizing disorders with similar clinical phenotypes to explore underlying mechanisms of genetic interaction.

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Abbreviations

BSA:

Bovine serum albumin

ChIP:

Chromatin immunoprecipitation

DMEM:

Dulbecco’s modified Eagle medium

E:

Embryonic day

HEK:

Human embryonic kidney

h:

Hours

HRP:

Horseradish peroxidase

MAR:

Matrix attachment regions

min:

Minutes

Mt:

Mutant/truncated

NLS:

Nuclear localization signal

NMD:

Nonsense-mediated mRNA decay

PBS:

Phosphate buffered saline

PSG:

Penicillin-streptomycin-glutamine

SATB2:

Special AT-rich Sequence Binding 2

SDS:

Sodium dodecyl sulfate

siRNA:

Small interfering RNA

UPF3B :

UPF3 regulator of nonsense transcripts homolog B

Wt:

Wild type

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Acknowledgments

We like to thank Drs. Gergana Dobreva and Rudolph Grosschedl (Max Planck Institution for Immunobiology and Epigenetics, Freiburg, Germany) for kindly providing the pfos-luc-Wt SATB2 plasmid and Satb2 knockout mice. This study was supported by the Royal Golden Jubilee Ph.D. Program to PL (Grant No PHD/0026/2549); the Intramural Research Program of the National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA; The Thailand Research Fund; Ratchadapiseksomphot Fund (RES560530177-HR), Chulalongkorn University Centenary Academic Development Project (CU56-HR05), and the Higher Education Research Promotion and National Research University Project of Thailand, Office of the Higher Education Commission (HR1163A).

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Authors and Affiliations

  1. Biomedical Science Program, Faculty of Graduate School, Chulalongkorn University, Bangkok, Thailand

    Petcharat Leoyklang

  2. Department of Pediatrics, Faculty of Medicine, The Center of Excellence for Medical Genetics, Chulalongkorn University, Bangkok, Thailand

    Petcharat Leoyklang, Kanya Suphapeetiporn, Chalurmpon Srichomthong, Siraprapa Tongkobpetch & Vorasuk Shotelersuk

  3. Excellence Center for Medical Genetics, King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Bangkok, Thailand

    Petcharat Leoyklang, Kanya Suphapeetiporn, Chalurmpon Srichomthong, Siraprapa Tongkobpetch & Vorasuk Shotelersuk

  4. Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, 10 Center Drive, Building 10, Room 10C103, Bethesda, MD, 20892-1851, USA

    Petcharat Leoyklang, Heidi Dorward, Andrew R. Cullinane, William A. Gahl & Marjan Huizing

  5. Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108, Freiburg, Germany

    Stefanie Fietze

  6. Division of Medical Genetics and Metabolism, Department of Pediatrics, King Chulalongkorn Memorial Hospital, Sor Kor Building 11th Floor, Bangkok, 10330, Thailand

    Kanya Suphapeetiporn

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  1. Petcharat Leoyklang
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  2. Kanya Suphapeetiporn
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  5. Stefanie Fietze
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  6. Heidi Dorward
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  7. Andrew R. Cullinane
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  8. William A. Gahl
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  9. Marjan Huizing
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  10. Vorasuk Shotelersuk
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Correspondence to Kanya Suphapeetiporn or Marjan Huizing.

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Leoyklang, P., Suphapeetiporn, K., Srichomthong, C. et al. Disorders with similar clinical phenotypes reveal underlying genetic interaction: SATB2 acts as an activator of the UPF3B gene. Hum Genet 132, 1383–1393 (2013). https://doi.org/10.1007/s00439-013-1345-9

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  • DOI: https://doi.org/10.1007/s00439-013-1345-9

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