An etiologic regulatory mutation in IRF6 with loss- and gain-of-function effects

Fakhouri, Walid D.; Rahimov, Fedik; Attanasio, Catia; Kouwenhoven, Evelyn N.; Lima, Renata Lacerda; Félix, Têmis Maria; Nitschke, Larissa; Huver, David; Barrons, Julie; Kousa, Youssef A.; Leslie, Elizabeth J.; Pennacchio, Len A.; Bokhoven, Hans van; Visel, Axel; Zhou, Huiqing; Murray, Jeffrey C.; Schutte, Brian C.

doi:10.1093/hmg/ddt664

Cited by 62 publications

(80 citation statements)

References 36 publications

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“…One scenario is that the binding of p63 may mark epithelial lineage-related regulatory elements as a placeholder during epithelial commitment, and the recruitment of different sets of co-regulators is required for gene regulation in an epithelial-related tissue- and stage-specific manner. This hypothesis is supported by previous reports that p63 binding sites identified in epidermal keratinocytes have been found to be associated with limb and palate development and with relevant diseases, split hand/foot malformation [18] and van der Woude syndrome where cleft lip/palate is one of the major features [60, 61]. The placeholder paradigm of transcription factor-mediated regulation has been reported for a group of transcription factors such as FoxA and GATA proteins in lineage progenitor cells [62].…”

Section: Discussionsupporting

confidence: 82%

Transcription factor p63 bookmarks and regulates dynamic enhancers during epidermal differentiation

et al. 2015

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The transcription factor p63 plays a pivotal role in keratinocyte proliferation and differentiation in the epidermis. However, how p63 regulates epidermal genes during differentiation is not yet clear. Using epigenome profiling of differentiating human primary epidermal keratinocytes, we characterized a catalog of dynamically regulated genes and p63-bound regulatory elements that are relevant for epithelial development and related diseases. p63-bound regulatory elements occur as single or clustered enhancers, and remarkably, only a subset is active as defined by the co-presence of the active enhancer mark histone modification H3K27ac in epidermal keratinocytes. We show that the dynamics of gene expression correlates with the activity of p63-bound enhancers rather than with p63 binding itself. The activity of p63-bound enhancers is likely determined by other transcription factors that cooperate with p63. Our data show that inactive p63-bound enhancers in epidermal keratinocytes may be active during the development of other epithelial-related structures such as limbs and suggest that p63 bookmarks genomic loci during the commitment of the epithelial lineage and regulates genes through temporal- and spatial-specific active enhancers.

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Section: Discussionsupporting

confidence: 82%

Transcription factor p63 bookmarks and regulates dynamic enhancers during epidermal differentiation

et al. 2015

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“…Mutations in regulatory elements are already described in cancer [48,49] or in developmental disorders such as Van der Woude syndrome [50] or isolated pancreatic agenesis [51]. To test the hypothesis of a mutated regulatory element, we constructed reporter systems using a pTAL-Luc plasmid in which the wild-type and mutated sequences were linked to a firefly luciferase reporter gene with a promoter (S2 Fig).…”

Section: Resultsmentioning

confidence: 99%

A Point Mutation in a lincRNA Upstream of GDNF Is Associated to a Canine Insensitivity to Pain: A Spontaneous Model for Human Sensory Neuropathies

Plassais¹,

Lagoutte²,

Correard³

et al. 2016

PLoS Genet

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Human Hereditary Sensory Autonomic Neuropathies (HSANs) are characterized by insensitivity to pain, sometimes combined with self-mutilation. Strikingly, several sporting dog breeds are particularly affected by such neuropathies. Clinical signs appear in young puppies and consist of acral analgesia, with or without sudden intense licking, biting and severe self-mutilation of the feet, whereas proprioception, motor abilities and spinal reflexes remain intact. Through a Genome Wide Association Study (GWAS) with 24 affected and 30 unaffected sporting dogs using the Canine HD 170K SNP array (Illumina), we identified a 1.8 Mb homozygous locus on canine chromosome 4 (adj. p-val = 2.5x10-6). Targeted high-throughput sequencing of this locus in 4 affected and 4 unaffected dogs identified 478 variants. Only one variant perfectly segregated with the expected recessive inheritance in 300 sporting dogs of known clinical status, while it was never present in 900 unaffected dogs from 130 other breeds. This variant, located 90 kb upstream of the GDNF gene, a highly relevant neurotrophic factor candidate gene, lies in a long intergenic non-coding RNAs (lincRNA), GDNF-AS. Using human comparative genomic analysis, we observed that the canine variant maps onto an enhancer element. Quantitative RT-PCR of dorsal root ganglia RNAs of affected dogs showed a significant decrease of both GDNF mRNA and GDNF-AS expression levels (respectively 60% and 80%), as compared to unaffected dogs. We thus performed gel shift assays (EMSA) that reveal that the canine variant significantly alters the binding of regulatory elements. Altogether, these results allowed the identification in dogs of GDNF as a relevant candidate for human HSAN and insensitivity to pain, but also shed light on the regulation of GDNF transcription. Finally, such results allow proposing these sporting dog breeds as natural models for clinical trials with a double benefit for human and veterinary medicine.

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“…Antibodies were obtained from Dr. Satrajit Sinha, State University of NY Buffalo [ΔNp63, (Romano et al, )], Dr. James. Wahl, UNMC (E‐Cadherin, [Keim et al, ]), Dr. Brian Schutte, Michigan State University (IRF6 for immunofluorescence, [Fakhouri et al, ]), Imgenex (IMG 3484; IRF6 for WB), Santa Cruz Biotechnology (TAp63 [sc‐8608]; TGFβ3 [sc‐82]; E‐Cadherin [sc‐7870]), Cell Signaling (K17 [4543]; PCNA [2586]), Abcam (K14 [Ab7800]) and Millipore (ApopTag® Fluorescein Direct In Situ Apoptosis Detection Kit).…”

Section: Methodsmentioning

confidence: 99%

TGFβ3 Regulates Periderm Removal Through ΔNp63 in the Developing Palate

Liu

et al. 2015

Journal Cellular Physiology

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The periderm is a flat layer of epithelium created during embryonic development. During palatogenesis, the periderm forms a protective layer against premature adhesion of the oral epithelia, including the palate. However, the periderm must be removed in order for the medial edge epithelia (MEE) to properly adhere and form a palatal seam. Improper periderm removal results in a cleft palate. Although the timing of transforming growth factor β3 (TGFβ3) expression in the MEE coincides with periderm degeneration, its role in periderm desquamation is not known. Interestingly, murine models of knockout (-/-) TGFβ3, interferon regulatory factor 6 (IRF6) (-/-), and truncated p63 (ΔNp63) (-/-) are born with palatal clefts because of failure of the palatal shelves to adhere, suggesting that these genes regulate palatal epithelial differentiation. However, despite having similar phenotypes in null mouse models, no studies have analyzed the possible association between the TGFβ3 signaling cascade and the IRF6/ΔNp63 genes during palate development. Recent studies indicate that regulation of ΔNp63, which depends on IRF6, facilitates epithelial differentiation. We performed biochemical analysis, gene activity and protein expression assays with palatal sections of TGFβ3 (-/-), ΔNp63 (-/-), and wild-type (WT) embryos, and primary MEE cells from WT palates to analyze the association between TGFβ3 and IRF6/ΔNp63. Our results suggest that periderm degeneration depends on functional TGFβ3 signaling to repress ΔNp63, thereby coordinating periderm desquamation. Cleft palate occurs in TGFβ3 (-/-) because of inadequate periderm removal that impedes palatal seam formation, while cleft palate occurs in ΔNp63 (-/-) palates because of premature fusion.

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An etiologic regulatory mutation in IRF6 with loss- and gain-of-function effects

Cited by 62 publications

References 36 publications

Transcription factor p63 bookmarks and regulates dynamic enhancers during epidermal differentiation

Transcription factor p63 bookmarks and regulates dynamic enhancers during epidermal differentiation

A Point Mutation in a lincRNA Upstream of GDNF Is Associated to a Canine Insensitivity to Pain: A Spontaneous Model for Human Sensory Neuropathies

TGFβ3 Regulates Periderm Removal Through ΔNp63 in the Developing Palate

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