50 - Regulatory Mutations of FOXG1 in the Context of Topological Domains

Abstract

Recent HiC proximity mapping have revealed a 3D-organization of the human genome where cis-regulatory interactions occur within megabase-sized topological associating domains (TADs) ( 1 Dixon J.R. Selvaraj S. Yue F. et al. Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature. 2012; 485: 376-380 Crossref PubMed Scopus (3953) Google Scholar ). TADs are separated by boundaries (TDB) which are enriched in Transcriptional Start Sites (TSS), housekeeping genes, binding sites for CTCF insulator factor and SINE elements ( 1 Dixon J.R. Selvaraj S. Yue F. et al. Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature. 2012; 485: 376-380 Crossref PubMed Scopus (3953) Google Scholar ). Different structural variations like deletions and translocations may interfere with the TAD organization. Translocations with breakpoints outside of TAD boundaries (the majority) will invariably interfere with TAD organization, creating fusion domains, whereas deletions may or may not, depending on position and size. Although the majority of TADs are identical in human embryonic cells (hESC) and IMR90 fibroblast, some loci display a differential pattern in the two cell lines. This is exemplified by the Forkhead box G1 (FOXG1) gene on 14q12, located within a 2 Mb sized TAD in IMR90 cells which is split into two TADs in hESC. FOXG1 encodes a winged-helix transcriptional repressor critical for early telencephalon development. Coding mutations of FOXG1 causes a congenital variant of the severe neurodevelopmental disorder Rett syndrome2. Balanced chromosomal rearrangements with breakpoints downstream of FOXG1 have been shown to cause the same phenotype as coding mutations ( 2 Alosi D. Klitten L.L. Bak M. et al. Dysregulation of FOXG1 by ring chromosome 14. Mol Cytogenet. 2015; 8: 24 Crossref PubMed Scopus (6) Google Scholar , 3 Shoichet S.A. Kunde S.A. Viertel P. et al. Haploinsufficiency of novel FOXG1B variants in a patient with severe mental retardation and microcephaly. Hum Genet. 2005; 117: 536-544 Crossref PubMed Scopus (79) Google Scholar ). Such long range position effects (LRPE) are presumably caused by the removal of cis-acting regulatory elements. The LRPE critical region at the FOXG1 locus is not defined, and intra-TAD deletions that remove the hESC-specific TAD boundary distal to FOXG1 have been suggested to exemplify enhancer adoption ( 4 Lettice L.A. Daniels S. Sweeney E. et al. Enhancer-adoption as a mechanism of human developmental disease. Hum Mutat. 2011; 32: 1492-1499 Crossref PubMed Scopus (78) Google Scholar ), with the establishment of new deleterious enhancer-target gene interactions ( 5 Ibn-Salem J. Köhler S. Love M.I. et al. Deletions of chromosomal regulatory boundaries are associated with congenital disease. Genome Biol. 2014; 15: 423 Crossref PubMed Scopus (95) Google Scholar ). Herein we have mapped two new LRPE-associated translocations by mate-pair sequencing, which we use together with additional microdeletions distal to FOXG1 to define the critical LRPE-region and the evidence for or against enhancer adoption as a major feature of the FOXG1-locus.