R-loop formation and chromatin decondensation at the PWS critical locus

Prader-Willi syndrome (PWS) is a neurodevelopmental disorder with a known genetic etiology but a complex epigenetic basis. PWS is an imprinted disorder, meaning that genes expressed only on the paternal but not the maternal chromosome 15 are responsible. Furthermore, unlike genetic mutations that affect protein-coding genes, the smallest genetic deletions causing PWS only affect noncoding transcripts of RNA. At the heart of the minimally deleted region in PWS are two types of noncoding RNAs. First, the HBII-85/SNORD116 snoRNAs localize to the nucleolus, a subnuclear structure that enlarges in mature neurons and serves as a cellular factory for ribosomes. Second, the host gene surrounding the snoRNA components surprisingly stays in the nucleus and forms a large RNA cloud-like structure that increases in size with neuronal maturity. While most of the focus in the PWS field has been on understanding the function of the snoRNA components, the host snoRNA-lncRNA may be of equal if not greater importance to understanding and treating PWS. In this proposal, we seek to test the hypothesis that the host snoRNAlncRNA directly alters the structure of the PWS genetic locus by forming an RNA:DNA structure called an R-loop during neurodevelopment, creating a highly active nuclear domain important for neuronal maturity. The approaches include novel imaging methods to observe RNA and DNA structural changes in individual neuronal nuclei in mouse and human brain, novel mouse-human chromosome 15 hybrid cell lines, and novel molecular R-loop detection methods. Results from these investigations are expected to improve understanding of the epigenetic basis of PWS and may enable epigenetic therapy for PWS by reactivating inactive transcripts through noncoding RNA-based therapies.

Research Outcomes: Project Summary

Topotecan treatment stabilizes the formation of RNA:DNA hybrids (R-loops) at G-skewed repeat elements within paternal SNORD116, resulting in increased chromatin decondensation and inhibition of Ube3a-ATS expression. 116HG forms a subnuclear RNA cloud that remains tethered to the site of its transcription, and increases in size in postnatal neurons.

Research Outcomes: Publications

Epigenetics in Prader-Willi Syndrome. Mendiola A.J.P., LaSalle J.M.  Frontiers in Genetics, 2021. DOI:10.3389/fgene.2021.624581

Epigenetics of Circadian Rhythms in Imprinted Neurodevelopmental Disorders. Coulson RL, LaSalle J. Progress in Molecular Biology and Translational Science 2018.

Prader-Willi locus Snord116 RNA processing requires an active endogenous allele and neuron-specific splicing by Rbfox3/NeuN. Coulson RL, Powell WT, Yasui DH, Dileep G, Resnick J and LaSalle J.  Human Molecular Genetics, 2018.

R-loop formation at Snord116 mediates topotecan inhibition of Ube3a-antisense and allele-specific chromatin decondensation. Powell WT, Coulson RL, Gonzales ML, Crary FK, Wong SS, Adams S, Ach RA, Tsang P, Yamada NA, Yasui DH, Chédin F, LaSalle. Proceedings of the National Academy of Sciences of the United States of America.110(34):13938-43, 2013.

A Prader-Willi locus lncRNA cloud modulates diurnal genes and energy expenditure. Powell WT, Coulson RL, Crary FK, Wong SS, Ach RA, Tsang P, Alice Yamada N, Yasui DH,LasalleJM.   Human Molecular Genetics. 22(21):4318-28, 2013.

Imprinting in the CNS and neurodevelopment disorders. Powell W, LaSalle JM.  Epigenetic regulation in the nervous system: Basic mechanisms and clinical impact. Edited by Nestler E, Sweatt D, Meaney M, Akbarian S. Elsevier Press. 267-279, 2013.

Funded Year:


Awarded to:

Janine LaSalle




University of California Davis


Janine LaSalle

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