Regulatory variants of FOXG1 in the context of its topological domain organisation

Abstract

FOXG1 syndrome is caused by FOXG1 intragenic point mutations, or by long-range position effects (LRPE) of intergenic structural variants. However, the size of the FOXG1 regulatory landscape is uncertain, because the associated topologically associating domain (TAD) in fibroblasts is split into two domains in embryonic stem cells (hESC). Indeed, it has been suggested that the pathogenetic mechanism of deletions that remove the stem-cell-specific TAD boundary may be enhancer adoption due to ectopic activity of enhancer(s) located in the distal hESC-TAD. Herein we map three de novo translocation breakpoints to the proximal regulatory domain of FOXG1. The classical FOXG1 syndrome in these and in other translocation patients, and in a patient with an intergenic deletion that removes the hESC-specific TAD boundary, do not support the hypothesised enhancer adoption as a main contributor to the FOXG1 syndrome. Also, virtual 4 C and HiC-interaction data suggest that the hESC-specific TAD boundary may not be critical for FOXG1 regulation in a majority of human cells and tissues, including brain tissues and a neuronal progenitor cell line. Our data support the importance of a critical regulatory region (SRO) proximal to the hESC-specific TAD boundary. We further narrow this critical region by a deletion distal to the hESC-specific boundary, associated with a milder clinical phenotype. The distance from FOXG1 to the SRO ( > 500 kb) highlight a limitation of ENCODE DNase hypersensitivity data for functional prediction of LRPE. Moreover, the SRO has little overlap with a cluster of frequently associating regions (FIREs) located in the proximal hESC-TAD.

Modeling the Pathological Long-Range Regulatory Effects of Human Structural Variation with Patient-Specific hiPSCs

“…However, due to technical and ethical reasons, the etiologically relevant embryonic cell types involved in human congenital disorders (e.g., NCCs in BOFS) are extremely difficult to isolate from human patients. Consequently, the exact long-range regulatory mechanisms whereby balanced SVs cause human congenital disease remain in many cases theoretical and mostly supported by correlative observations (Kleinjan and van Heyningen, 2005;Mehrjouy et al, 2018;Redin et al, 2017;Zepeda-Mendoza et al, 2018).…”

“…Deletion and duplications spanning TAD boundaries can result in the ''fusion'' of neighboring TADs or in the appearance of ''neo-TADs,'' respectively, which can lead to the emergence of ectopic enhancer-gene interactions (i.e., enhancer adoption or hijacking) and gains in gene expression (Franke et al, 2016;Grö schel et al, 2014;Lupiá ñ ez et al, 2015). Translocations and inversions that cross TAD boundaries can result in the ''shuffling'' of TADs that are normally spatially separated, causing gains in gene expression by enhancer adoption or gene silencing through either position effect variegation (PEV) or loss of endogenous enhancer-gene interactions (i.e., enhancer disconnection; Goubau et al, 2013;Kleinjan and van Heyningen, 2005;Kleinjan et al, 2001;Lettice et al, 2002;Mehrjouy et al, 2018;Redin et al, 2017;Zepeda-Mendoza et al, 2018).…”

Transcription and Beyond: Delineating FOXG1 Function in Cortical Development and Disorders

“…A subsequent report mapping seven patients with severe encephalopathies revealed five cis-acting regulatory elements: one neural tube-specific enhancer and four silencers affecting FOXG1 at genomic and transcriptional levels (Allou et al, 2012), supporting the presence of long-range regulatory interactions between these regulatory elements and FOXG1 expression. Mapping of additional translocations with virtual 4C and Hi-C DNA-DNA analysis identified regulatory regions across topologically associated domains (TAD) boundaries associated with different clinical phenotypes (Mehrjouy et al, 2018), providing a genome-wide landscape of FOXG1 regulators at chromosomal levels.…”

Interpreting the impact of noncoding structural variation in neurodevelopmental disorders

“…This regulatory structure is disrupted by translocations and deletions distal to FOXG1 in multiple patients with similar Rett-like features (Fig. 3b), likely caused by either enhancer deletion/translocation or a rewiring of interactions due to the deletion of TAD boundary elements 69,97 . SVs in the 5q14.3 region upstream of MEF2C result in a Rett-like syndrome as well (Fig.…”