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Kim HG, Rosenfeld JA, Scott DA, Bénédicte G, Labonne JD, Brown J, McGuire M, Mahida S, Naidu S, Gutierrez J, Lesca G, des Portes V, Bruel AL, Sorlin A, Xia F, Capri Y, Muller E, McKnight D, Torti E, Rüschendorf F, Hummel O, Islam Z, Kolatkar PR, Layman LC, Ryu D, Kong IK, Madan-Khetarpal S, Kim CH. Disruption of PHF21A causes syndromic intellectual disability with craniofacial anomalies, epilepsy, hypotonia, and neurobehavioral problems including autism. Mol Autism 2019; 10:35. [PMID: 31649809 PMCID: PMC6805429 DOI: 10.1186/s13229-019-0286-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 09/01/2019] [Indexed: 02/02/2023] Open
Abstract
Background PHF21A has been associated with intellectual disability and craniofacial anomalies based on its deletion in the Potocki-Shaffer syndrome region at 11p11.2 and its disruption in three patients with balanced translocations. In addition, three patients with de novo truncating mutations in PHF21A were reported recently. Here, we analyze genomic data from seven unrelated individuals with mutations in PHF21A and provide detailed clinical descriptions, further expanding the phenotype associated with PHF21A haploinsufficiency. Methods Diagnostic trio whole exome sequencing, Sanger sequencing, use of GeneMatcher, targeted gene panel sequencing, and MiSeq sequencing techniques were used to identify and confirm variants. RT-qPCR was used to measure the normal expression pattern of PHF21A in multiple human tissues including 13 different brain tissues. Protein-DNA modeling was performed to substantiate the pathogenicity of the missense mutation. Results We have identified seven heterozygous coding mutations, among which six are de novo (not maternal in one). Mutations include four frameshifts, one nonsense mutation in two patients, and one heterozygous missense mutation in the AT Hook domain, predicted to be deleterious and likely to cause loss of PHF21A function. We also found a new C-terminal domain composed of an intrinsically disordered region. This domain is truncated in six patients and thus likely to play an important role in the function of PHF21A, suggesting that haploinsufficiency is the likely underlying mechanism in the phenotype of seven patients. Our results extend the phenotypic spectrum of PHF21A mutations by adding autism spectrum disorder, epilepsy, hypotonia, and neurobehavioral problems. Furthermore, PHF21A is highly expressed in the human fetal brain, which is consistent with the neurodevelopmental phenotype. Conclusion Deleterious nonsense, frameshift, and missense mutations disrupting the AT Hook domain and/or an intrinsically disordered region in PHF21A were found to be associated with autism spectrum disorder, epilepsy, hypotonia, neurobehavioral problems, tapering fingers, clinodactyly, and syndactyly, in addition to intellectual disability and craniofacial anomalies. This suggests that PHF21A is involved in autism spectrum disorder and intellectual disability, and its haploinsufficiency causes a diverse neurological phenotype. Electronic supplementary material The online version of this article (10.1186/s13229-019-0286-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hyung-Goo Kim
- 1Neurological Disorders Research Center, Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Doha, Qatar
| | - Jill A Rosenfeld
- 2Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - Daryl A Scott
- 2Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA.,3Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX USA
| | - Gerard Bénédicte
- 4Laboratoires de Diagnostic Génétique, Unité de génétique moléculaire, Nouvel Hôpital Civil, Strasbourg Cedex, France
| | - Jonathan D Labonne
- 5Section of Reproductive Endocrinology, Infertility & Genetics, Department of Obstetrics & Gynecology, Augusta University, Augusta, GA USA
| | - Jason Brown
- 5Section of Reproductive Endocrinology, Infertility & Genetics, Department of Obstetrics & Gynecology, Augusta University, Augusta, GA USA
| | | | | | | | - Jacqueline Gutierrez
- 3Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX USA
| | - Gaetan Lesca
- 8Department of Medical Genetics, Lyon University Hospital, Lyon, France
| | - Vincent des Portes
- 9Department of Pediatric Neurology, Lyon University Hospital, Lyon, France
| | - Ange-Line Bruel
- 10Équipe Génétique des Anomalies du Développement (GAD), INSERM, Dijon, France
| | - Arthur Sorlin
- Centre de Génétique, CHU Dijon Bourgogne, Dijon, France
| | - Fan Xia
- 2Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
| | - Yline Capri
- Service de Génétique Clinique, CHU Robert Debré, Paris, France
| | - Eric Muller
- 13Clinical Genetics, Stanford Children's Health at CPMC, San Francisco, CA USA
| | | | | | | | - Oliver Hummel
- 15Max Delbrück Center (MDC) for Molecular Medicine, Berlin, Germany
| | - Zeyaul Islam
- 16Diabetes Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University, Doha, Qatar
| | - Prasanna R Kolatkar
- 16Diabetes Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University, Doha, Qatar
| | - Lawrence C Layman
- 5Section of Reproductive Endocrinology, Infertility & Genetics, Department of Obstetrics & Gynecology, Augusta University, Augusta, GA USA.,17Department of Neuroscience and Regenerative Medicine, Augusta University, Augusta, GA USA
| | - Duchwan Ryu
- 18Department of Statistics and Actuarial Science, Northern Illinois University, DeKalb, IL USA
| | - Il-Keun Kong
- 19Department of Animal Science, Division of Applied Life Science (BK21plus), Gyeongsang National University, Jinju, Korea
| | | | - Cheol-Hee Kim
- 21Department of Biology, Chungnam National University, Daejeon, Korea
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Vera DL, Madzima TF, Labonne JD, Alam MP, Hoffman GG, Girimurugan SB, Zhang J, McGinnis KM, Dennis JH, Bass HW. Differential nuclease sensitivity profiling of chromatin reveals biochemical footprints coupled to gene expression and functional DNA elements in maize. Plant Cell 2014; 26:3883-93. [PMID: 25361955 PMCID: PMC4247582 DOI: 10.1105/tpc.114.130609] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Revised: 10/03/2014] [Accepted: 10/14/2014] [Indexed: 05/19/2023]
Abstract
The eukaryotic genome is organized into nucleosomes, the fundamental units of chromatin. The positions of nucleosomes on DNA regulate protein-DNA interactions and in turn influence DNA-templated events. Despite the increasing number of genome-wide maps of nucleosome position, how global changes in gene expression relate to changes in nucleosome position is poorly understood. We show that in nucleosome occupancy mapping experiments in maize (Zea mays), particular genomic regions are highly susceptible to variation introduced by differences in the extent to which chromatin is digested with micrococcal nuclease (MNase). We exploited this digestion-linked variation to identify protein footprints that are hypersensitive to MNase digestion, an approach we term differential nuclease sensitivity profiling (DNS-chip). Hypersensitive footprints were enriched at the 5' and 3' ends of genes, associated with gene expression levels, and significantly overlapped with conserved noncoding sequences and the binding sites of the transcription factor KNOTTED1. We also found that the tissue-specific regulation of gene expression was linked to tissue-specific hypersensitive footprints. These results reveal biochemical features of nucleosome organization that correlate with gene expression levels and colocalize with functional DNA elements. This approach to chromatin profiling should be broadly applicable to other species and should shed light on the relationships among chromatin organization, protein-DNA interactions, and genome regulation.
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Affiliation(s)
- Daniel L Vera
- Department of Biological Science, Florida State University, Tallahassee, Florida 32306-4295
| | - Thelma F Madzima
- Department of Biological Science, Florida State University, Tallahassee, Florida 32306-4295
| | - Jonathan D Labonne
- Department of Biological Science, Florida State University, Tallahassee, Florida 32306-4295
| | - Mohammad P Alam
- Department of Biological Science, Florida State University, Tallahassee, Florida 32306-4295
| | - Gregg G Hoffman
- Department of Biological Science, Florida State University, Tallahassee, Florida 32306-4295
| | - S B Girimurugan
- Department of Statistics, Florida State University, Tallahassee, Florida 32306
| | - Jinfeng Zhang
- Department of Statistics, Florida State University, Tallahassee, Florida 32306
| | - Karen M McGinnis
- Department of Biological Science, Florida State University, Tallahassee, Florida 32306-4295
| | - Jonathan H Dennis
- Department of Biological Science, Florida State University, Tallahassee, Florida 32306-4295
| | - Hank W Bass
- Department of Biological Science, Florida State University, Tallahassee, Florida 32306-4295
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