{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,7,3]],"date-time":"2025-07-03T15:26:54Z","timestamp":1751556414112,"version":"3.37.3"},"reference-count":78,"publisher":"Oxford University Press (OUP)","issue":"19","license":[{"start":{"date-parts":[[2024,7,24]],"date-time":"2024-07-24T00:00:00Z","timestamp":1721779200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"National Institute of Health","award":["R01HD098038"],"award-info":[{"award-number":["R01HD098038"]}]},{"DOI":"10.13039\/100000057","name":"National Institute of General Medical Sciences","doi-asserted-by":"publisher","award":["T32 GM007377"],"award-info":[{"award-number":["T32 GM007377"]}],"id":[{"id":"10.13039\/100000057","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,9,19]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>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\u2009834 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.<\/jats:p>","DOI":"10.1093\/hmg\/ddae111","type":"journal-article","created":{"date-parts":[[2024,7,25]],"date-time":"2024-07-25T02:11:08Z","timestamp":1721873468000},"page":"1711-1725","source":"Crossref","is-referenced-by-count":2,"title":["Integration of CTCF loops, methylome, and transcriptome in differentiating LUHMES as a model for imprinting dynamics of the 15q11-q13 locus in human neurons"],"prefix":"10.1093","volume":"33","author":[{"given":"Orangel J","family":"Gutierrez Fug\u00f3n","sequence":"first","affiliation":[{"name":"University of California Davis Genome Center, Department of Biochemistry and Molecular Medicine, , 451 Health Sciences Dr., Davis, CA 95616, United States"},{"name":"University of California Davis Department of Medical Microbiology and Immunology, School of Medicine, , 1275 Med Science Dr, Davis, CA 95616, United States"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Osman","family":"Sharifi","sequence":"additional","affiliation":[{"name":"University of California Davis Department of Medical Microbiology and Immunology, School of Medicine, , 1275 Med Science Dr, Davis, CA 95616, United States"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nicholas","family":"Heath","sequence":"additional","affiliation":[{"name":"University of California Davis Genome Center, Department of Biochemistry and Molecular Medicine, , 451 Health Sciences Dr., Davis, CA 95616, United States"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6292-655X","authenticated-orcid":false,"given":"Daniela C","family":"Soto","sequence":"additional","affiliation":[{"name":"University of California Davis Genome Center, Department of Biochemistry and Molecular Medicine, , 451 Health Sciences Dr., Davis, CA 95616, United States"},{"name":"University of California Los Angeles Department of Psychiatry and Biobehavioral Sciences, , 757 Westwood Plaza #4, Los Angeles, CA 90095, United States"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"J Antonio","family":"Gomez","sequence":"additional","affiliation":[{"name":"University of California Davis Department of Medical Microbiology and Immunology, School of Medicine, , 1275 Med Science Dr, Davis, CA 95616, United States"},{"name":"Pepperdine University Department of Natural Science, Seaver College, , 24255 Pacific Coast Hwy, Malibu, CA 90263, United States"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Dag H","family":"Yasui","sequence":"additional","affiliation":[{"name":"University of California Davis Department of Medical Microbiology and Immunology, School of Medicine, , 1275 Med Science Dr, Davis, CA 95616, United States"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Aron Judd P","family":"Mendiola","sequence":"additional","affiliation":[{"name":"University of California Davis Department of Medical Microbiology and Immunology, School of Medicine, , 1275 Med Science Dr, Davis, CA 95616, United States"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Henriette","family":"O\u2019Geen","sequence":"additional","affiliation":[{"name":"University of California Davis Genome Center, Department of Biochemistry and Molecular Medicine, , 451 Health Sciences Dr., Davis, CA 95616, United States"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ulrika","family":"Beitnere","sequence":"additional","affiliation":[{"name":"University of California Davis Genome Center, Department of Biochemistry and Molecular Medicine, , 451 Health Sciences Dr., Davis, CA 95616, United States"},{"name":"Max Delbr\u00fcck Center for Molecular Medicine , Robert-R\u00f6ssle-Stra\u00dfe 10, 13125 Berlin, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Marketa","family":"Tomkova","sequence":"additional","affiliation":[{"name":"University of California Davis Genome Center, Department of Biochemistry and Molecular Medicine, , 451 Health Sciences Dr., Davis, CA 95616, United States"},{"name":"University of Oxford Ludwig Cancer Research Center, , Old Road Campus Research Build, Roosevelt Dr, Headington, Oxford OX3 7DQ, United Kingdom"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Viktoria","family":"Haghani","sequence":"additional","affiliation":[{"name":"University of California Davis Department of Medical Microbiology and Immunology, School of Medicine, , 1275 Med Science Dr, Davis, CA 95616, United States"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Greg","family":"Dillon","sequence":"additional","affiliation":[{"name":"Biogen Genetics and Neurodevelopmental Disorders Unit, , 225 Binney Street Cambridge, MA 02142 United 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