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Integration of CTCF loops, methylome, and transcriptome in differentiating LUHMES as a model for imprinting dynamics of the 15q11-q13 locus in human neurons

Year: 2024
Type: article
Abstract: Human cell line models, including the neuronal precursor line LUHMES, are important for investigating developmental transcriptional dynamics within imprinted regions, particularly the 15q11-q13 Angelman (AS) and Prader-Willi (PWS) syndrome locus. AS results from loss of maternal UBE3A in neurons, where the paternal allele is silenced by a convergent antisense transcript UBE3A-ATS, a lncRNA that terminates at PWAR1 in non-neurons. qRT-PCR analysis confirmed the exclusive and progressive increase in UBE3A-ATS in differentiating LUHMES neurons, validating their use for studying UBE3A silencing. Genome-wide transcriptome analyses revealed changes to 11 834 genes during neuronal differentiation, including the upregulation of most genes within the 15q11-q13 locus. To identify dynamic changes in chromatin loops linked to transcriptional activity, we performed a HiChIP validated by 4C, which identified two neuron-specific CTCF loops between MAGEL2-SNRPN and PWAR1-UBE3A. To determine if allele-specific differentially methylated regions (DMR) may be associated with CTCF loop anchors, whole genome long-read nanopore sequencing was performed. We identified a paternally hypomethylated DMR near the SNRPN upstream loop anchor exclusive to neurons and a paternally hypermethylated DMR near the PWAR1 CTCF anchor exclusive to undifferentiated cells, consistent with increases in neuronal transcription. Additionally, DMRs near CTCF loop anchors were observed in both cell types, indicative of allele-specific differences in chromatin loops regulating imprinted transcription. These results provide an integrated view of the 15q11-q13 epigenetic landscape during LUHMES neuronal differentiation, underscoring the complex interplay of transcription, chromatin looping, and DNA methylation. They also provide insights for future therapeutic approaches for AS and PWS.
DOI: 10.1093/hmg/ddae111
Authors: Orangel J Gutierrez Fugón, Osman Sharifi, Nicholas Heath, Daniela C Soto, J Antonio Gomez, Dag H Yasui, Aron Judd P Mendiola, Henriette O’Geen, Ulrika Beitnere, Marketa Tomkova, Viktoria Haghani, Greg Dillon, David J Segal, Janine M LaSalle
Institutions: University of California, Davis, University of California, Los Angeles, Pepperdine University, Max Delbrück Center, University of Oxford, Ludwig Cancer Research, Biogen (United States)
Language: English
Subfield: Genetics
Open Access status: hybrid
Estimated APC paid: $4,610
Funders: Biogen, Foundation for Angelman Syndrome Therapeutics, National Institutes of Health, University of California, Davis, National Institute of General Medical Sciences, National Institute of Environmental Health Sciences, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Genome Center, University of California, Davis
Awards: Training Program in Molecular and Cellular Biology, G3304377175, Acquisition of Covaris E220 and Sciclone G3 systems for high throughput sequencin, Imprinted snoRNA loci and circadian entrainment, G7736640793, UC Davis Environmental Health Sciences Core Center, Placental identified NHIP regulating neuronal oxidative stress in autism
OpenAlex ID: W4400967904
FWCI: 0.59
Cites: 118
Cited by: 3
Related to: 10