BRF1 mutations alter RNA polymerase III-dependent transcription and cause neurodevelopmental anomalies

Genome Res. 2015 Feb;25(2):155-66. doi: 10.1101/gr.176925.114.

Guntram Borck ¹, Friederike Hög ², Maria Lisa Dentici ³, Perciliz L Tan ⁴, Nadine Sowada ⁵, Ana Medeira ⁶, Lucie Gueneau ⁷, Holger Thiele ⁸, Maria Kousi ⁴, Francesca Lepri ³, Larissa Wenzeck ², Ian Blumenthal ⁹, Antonio Radicioni ¹⁰, Tito Livio Schwarzenberg ¹¹, Barbara Mandriani ¹², Rita Fischetto ¹³, Deborah J Morris-Rosendahl ¹⁴, Janine Altmüller ¹⁵, Alexandre Reymond ⁷, Peter Nürnberg ¹⁶, Giuseppe Merla ¹⁷, Bruno Dallapiccola ³, Nicholas Katsanis ⁴, Patrick Cramer ¹⁸, Christian Kubisch ¹⁹

Affiliations

1 Institute of Human Genetics, University of Ulm, 89081 Ulm, Germany; [email protected].
2 Gene Center Munich and Department of Biochemistry, Center for Integrated Protein Science CIPSM, Ludwig-Maximilians-Universität München, 81377 Munich, Germany;
3 Bambino Gesù Children's Hospital, IRCCS, 00165 Rome, Italy;
4 Center for Human Disease Modeling, Duke University, Durham, North Carolina 27710, USA;
5 Institute of Human Genetics, University of Ulm, 89081 Ulm, Germany;
6 Serviço de Genética, Departamento de Pediatria, Hospital S. Maria, CHLN, 1649-035 Lisboa, Portugal;
7 Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland;
8 Cologne Center for Genomics (CCG), University of Cologne, 50931 Cologne, Germany;
9 Molecular Neurogenetics Unit and Psychiatric and Neurodevelopmental Genetics Unit, Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts 02114, USA;
10 Department of Experimental Medicine, Sapienza University, 00161 Rome, Italy;
11 Department of Neonatology, Sapienza University, 00161 Rome, Italy;
12 IRCCS Casa Sollievo Della Sofferenza, Medical Genetics Unit, 71013 San Giovanni Rotondo, Italy; PhD Program, Molecular Genetics applied to Medical Sciences, University of Brescia, 25121 Brescia, Italy;
13 U.O. Malattie Metaboliche PO Giovanni XXIII, AOU Policlinico Consorziale, 70120 Bari, Italy;
14 Genomic Medicine, National Heart and Lung Institute, Imperial College, London SW3 6LY, United Kingdom;
15 Cologne Center for Genomics (CCG), University of Cologne, 50931 Cologne, Germany; Institute for Human Genetics, University of Cologne, 50931 Cologne, Germany;
16 Cologne Center for Genomics (CCG), University of Cologne, 50931 Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, 50674 Cologne, Germany; Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany;
17 IRCCS Casa Sollievo Della Sofferenza, Medical Genetics Unit, 71013 San Giovanni Rotondo, Italy;
18 Max Planck Institute for Biophysical Chemistry, Department of Molecular Biology, 37077 Göttingen, Germany;
19 Institute of Human Genetics, University of Ulm, 89081 Ulm, Germany; Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany.

PMID: 25561519 DOI: 10.1101/gr.176925.114

Abstract

RNA polymerase III (Pol III) synthesizes tRNAs and other small noncoding RNAs to regulate protein synthesis. Dysregulation of Pol III transcription has been linked to Cancer, and germline mutations in genes encoding Pol III subunits or tRNA processing factors cause neurogenetic disorders in humans, such as hypomyelinating leukodystrophies and pontocerebellar hypoplasia. Here we describe an autosomal recessive disorder characterized by cerebellar hypoplasia and intellectual disability, as well as facial dysmorphic features, short stature, microcephaly, and dental anomalies. Whole-exome sequencing revealed biallelic missense alterations of BRF1 in three families. In support of the pathogenic potential of the discovered alleles, suppression or CRISPR-mediated deletion of brf1 in zebrafish embryos recapitulated key neurodevelopmental phenotypes; in vivo complementation showed all four candidate mutations to be pathogenic in an apparent isoform-specific context. BRF1 associates with BDP1 and TBP to form the transcription factor IIIB (TFIIIB), which recruits Pol III to target genes. We show that disease-causing mutations reduce Brf1 occupancy at tRNA target genes in Saccharomyces cerevisiae and impair cell growth. Moreover, BRF1 mutations reduce Pol III-related transcription activity in vitro. Taken together, our data show that BRF1 mutations that reduce protein activity cause neurodevelopmental anomalies, suggesting that BRF1-mediated Pol III transcription is required for normal cerebellar and cognitive development.

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