TY - JOUR
T1 - Multi-omics approach dissects cis-regulatory mechanisms underlying North Carolina macular dystrophy, a retinal enhanceropathy
AU - van de Sompele, Stijn
AU - Small, Kent W.
AU - Cicekdal, Munevver Burcu
AU - Soriano, V. ctor L. pez
AU - D'haene, Eva
AU - Shaya, Fadi S.
AU - Agemy, Steven
AU - van der Snickt, Thijs
AU - Rey, Alfredo Dueñas
AU - Rosseel, Toon
AU - van Heetvelde, Mattias
AU - Vergult, Sarah
AU - Balikova, Irina
AU - Bergen, Arthur A.
AU - Boon, Camiel J. F.
AU - de Zaeytijd, Julie
AU - Inglehearn, Chris F.
AU - Kousal, Bohdan
AU - Leroy, Bart P.
AU - Rivolta, Carlo
AU - Vaclavik, Veronika
AU - van den Ende, Jenneke
AU - van Schooneveld, Mary J.
AU - Gómez-Skarmeta, José Luis
AU - Tena, Juan J.
AU - Martinez-Morales, Juan R.
AU - Liskova, Petra
AU - Vleminckx, Kris
AU - de Baere, Elfride
N1 - Funding Information: This work was supported by grants from Ghent University Special Research Fund (BOF20/GOA/023) (E.D.B., K.V., B.P.L.); Ghent University Hospital Innovation Fund NucleUZ (E.D.B.); JED Foundation (E.D.B.); H2020 Marie Sklodowska-Curie Innovative Training Networks (ITN) StarT (grant No. 813490 ) (E.D.B., K.V., J.L.G.-S., J.J.T., J.R.M.-M.); EJP RD Solve-RET EJPRD19-234 (E.D.B., P.L., B.K., C.R., J.L.G.-S., J.J.T., J.R.M.-M.), SNSF grant # 204285 (C.R.), and Foundation Fighting Blindness in Columbia, MD (grant #: BR-GE-1216-0715-CSH ). S.V.d.S. ( 1145719N ) is PhD fellow of the Research Foundation Flanders (FWO), E.D.B. ( 1802220N ) and B.P.L. ( 1803816N ) are FWO Senior Clinical Investigators; M.B.C., V.L.S., and A.D.R. are Early Starting Researcher of ITN StarT (grant # 813490 ). B.K., B.P.L., C.J.F.B., E.D.B., P.L., and V.V. are members of ERN-EYE (Framework Partnership Agreement No 739534-ERN-EYE). K.W.S. received an unrestricted grant from The Molecular Insight Research Foundation . Publisher Copyright: © 2022
PY - 2022/11/3
Y1 - 2022/11/3
N2 - North Carolina macular dystrophy (NCMD) is a rare autosomal-dominant disease affecting macular development. The disease is caused by non-coding single-nucleotide variants (SNVs) in two hotspot regions near PRDM13 and by duplications in two distinct chromosomal loci, overlapping DNase I hypersensitive sites near either PRDM13 or IRX1. To unravel the mechanisms by which these variants cause disease, we first established a genome-wide multi-omics retinal database, RegRet. Integration of UMI-4C profiles we generated on adult human retina then allowed fine-mapping of the interactions of the PRDM13 and IRX1 promoters and the identification of eighteen candidate cis-regulatory elements (cCREs), the activity of which was investigated by luciferase and Xenopus enhancer assays. Next, luciferase assays showed that the non-coding SNVs located in the two hotspot regions of PRDM13 affect cCRE activity, including two NCMD-associated non-coding SNVs that we identified herein. Interestingly, the cCRE containing one of these SNVs was shown to interact with the PRDM13 promoter, demonstrated in vivo activity in Xenopus, and is active at the developmental stage when progenitor cells of the central retina exit mitosis, suggesting that this region is a PRDM13 enhancer. Finally, mining of single-cell transcriptional data of embryonic and adult retina revealed the highest expression of PRDM13 and IRX1 when amacrine cells start to synapse with retinal ganglion cells, supporting the hypothesis that altered PRDM13 or IRX1 expression impairs interactions between these cells during retinogenesis. Overall, this study provides insight into the cis-regulatory mechanisms of NCMD and supports that this condition is a retinal enhanceropathy.
AB - North Carolina macular dystrophy (NCMD) is a rare autosomal-dominant disease affecting macular development. The disease is caused by non-coding single-nucleotide variants (SNVs) in two hotspot regions near PRDM13 and by duplications in two distinct chromosomal loci, overlapping DNase I hypersensitive sites near either PRDM13 or IRX1. To unravel the mechanisms by which these variants cause disease, we first established a genome-wide multi-omics retinal database, RegRet. Integration of UMI-4C profiles we generated on adult human retina then allowed fine-mapping of the interactions of the PRDM13 and IRX1 promoters and the identification of eighteen candidate cis-regulatory elements (cCREs), the activity of which was investigated by luciferase and Xenopus enhancer assays. Next, luciferase assays showed that the non-coding SNVs located in the two hotspot regions of PRDM13 affect cCRE activity, including two NCMD-associated non-coding SNVs that we identified herein. Interestingly, the cCRE containing one of these SNVs was shown to interact with the PRDM13 promoter, demonstrated in vivo activity in Xenopus, and is active at the developmental stage when progenitor cells of the central retina exit mitosis, suggesting that this region is a PRDM13 enhancer. Finally, mining of single-cell transcriptional data of embryonic and adult retina revealed the highest expression of PRDM13 and IRX1 when amacrine cells start to synapse with retinal ganglion cells, supporting the hypothesis that altered PRDM13 or IRX1 expression impairs interactions between these cells during retinogenesis. Overall, this study provides insight into the cis-regulatory mechanisms of NCMD and supports that this condition is a retinal enhanceropathy.
KW - IRX1
KW - North Carolina macular dystrophy, NCMD
KW - PRDM13
KW - UMI-4C
KW - cis-regulatory elements, CREs
KW - enhanceropathy
KW - human retina
KW - multi-omics
KW - non-coding single-nucleotide variants, SNVs
KW - whole-genome sequencing
UR - http://www.scopus.com/inward/record.url?scp=85140979264&partnerID=8YFLogxK
U2 - https://doi.org/10.1016/j.ajhg.2022.09.013
DO - https://doi.org/10.1016/j.ajhg.2022.09.013
M3 - Article
C2 - 36243009
SN - 0002-9297
VL - 109
SP - 2029
EP - 2048
JO - American journal of human genetics
JF - American journal of human genetics
IS - 11
ER -