title: Remotely acting SMCHD1 gene regulatory elements: in silico prediction and identification of potential regulatory variants in patients with FSHD.
abstract: BACKGROUND
  Facioscapulohumeral dystrophy (FSHD) is commonly associated with contraction of the D4Z4 macro-satellite repeat on chromosome 4q35 (FSHD1) or mutations in the SMCHD1 gene (FSHD2). Recent studies have shown that the clinical manifestation of FSHD1 can be modified by mutations in the SMCHD1 gene within a given family. The absence of either D4Z4 contraction or SMCHD1 mutations in a small cohort of patients suggests that the disease could also be due to disruption of gene regulation. In this study, we postulated that mutations responsible for exerting a modifier effect on FSHD might reside within remotely acting regulatory elements that have the potential to interact at a distance with their cognate gene promoter via chromatin looping. To explore this postulate, genome-wide Hi-C data were used to identify genomic fragments displaying the strongest interaction with the SMCHD1 gene. These fragments were then narrowed down to shorter regions using ENCODE and FANTOM data on transcription factor binding sites and epigenetic marks characteristic of promoters, enhancers and silencers.
  
  
  RESULTS
  We identified two regions, located respectively ~14 and ~85 kb upstream of the SMCHD1 gene, which were then sequenced in 229 FSHD/FSHD-like patients (200 with D4Z4 repeat units <11). Three heterozygous sequence variants were found ~14 kb upstream of the SMCHD1 gene. One of these variants was found to be of potential functional significance based on DNA methylation analysis. Further functional ascertainment will be required in order to establish the clinical/functional significance of the variants found.
  
  
  CONCLUSIONS
  In this study, we propose an improved approach to predict the possible locations of remotely acting regulatory elements that might influence the transcriptional regulation of their associated gene(s). It represents a new way to screen for disease-relevant mutations beyond the immediate vicinity of the specific disease gene. It promises to be useful for investigating disorders in which mutations could occur in remotely acting regulatory elements.
authors.affiliation: School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham, NG11 8NS, UK.
authors.forename: Mary B
authors.initials: MB
authors.lastname: Mayes
authors.affiliation: Institute of Medical Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK.
authors.forename: Taniesha
authors.initials: T
authors.lastname: Morgan
authors.affiliation: Institute of Medical Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK.
authors.forename: Jincy
authors.initials: J
authors.lastname: Winston
authors.affiliation: School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham, NG11 8NS, UK.
authors.forename: Daniel S
authors.initials: DS
authors.lastname: Buxton
authors.affiliation: School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham, NG11 8NS, UK.|Present address: Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK.
authors.forename: Mihir Anant
authors.initials: MA
authors.lastname: Kamat
authors.affiliation: Blood Sciences Department and Bristol Genetics Laboratory, Southmead Hospital, Westbury-on-Trym, Bristol, BS10 5NB, UK.
authors.forename: Debbie
authors.initials: D
authors.lastname: Smith
authors.affiliation: Blood Sciences Department and Bristol Genetics Laboratory, Southmead Hospital, Westbury-on-Trym, Bristol, BS10 5NB, UK.
authors.forename: Maggie
authors.initials: M
authors.lastname: Williams
authors.affiliation: School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham, NG11 8NS, UK.
authors.forename: Rebecca L
authors.initials: RL
authors.lastname: Martin
authors.affiliation: MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK.
authors.forename: Dirk A
authors.initials: DA
authors.lastname: Kleinjan
authors.affiliation: Institute of Medical Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK.
authors.forename: David N
authors.initials: DN
authors.lastname: Cooper
authors.affiliation: Institute of Medical Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK.
authors.forename: Meena
authors.initials: M
authors.lastname: Upadhyaya
authors.affiliation: School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham, NG11 8NS, UK. nadia.chuzhanova@ntu.ac.uk.
authors.forename: Nadia
authors.initials: N
authors.lastname: Chuzhanova
mesh_terms: D001483:Base Sequence; D002868:Chromosomal Proteins, Non-Histone / Q000235:genetics*; D003198:Computer Simulation; D019175:DNA Methylation / Q000235:genetics*; D044127:Epigenesis, Genetic; D005260:Female; D006801:Humans; D008297:Male; D020391:Muscular Dystrophy, Facioscapulohumeral / Q000235:genetics* / Q000473:pathology; D009154:Mutation / Q000235:genetics; D010375:Pedigree; D012045:Regulatory Sequences, Nucleic Acid / Q000235:genetics*
chemical_list: D002868:Chromosomal Proteins, Non-Histone; C578241:SMCHD1 protein, human