Cellular and genetic drivers of RNA editing variation in the human brain. 2022

Winston H Cuddleston, and Junhao Li, and Xuanjia Fan, and Alexey Kozenkov, and Matthew Lalli, and Shahrukh Khalique, and Stella Dracheva, and Eran A Mukamel, and Michael S Breen
Department of Psychiatry at Mount Sinai, New York, NY, 10029, USA.

Posttranscriptional adenosine-to-inosine modifications amplify the functionality of RNA molecules in the brain, yet the cellular and genetic regulation of RNA editing is poorly described. We quantify base-specific RNA editing across three major cell populations from the human prefrontal cortex: glutamatergic neurons, medial ganglionic eminence-derived GABAergic neurons, and oligodendrocytes. We identify more selective editing and hyper-editing in neurons relative to oligodendrocytes. RNA editing patterns are highly cell type-specific, with 189,229 cell type-associated sites. The cellular specificity for thousands of sites is confirmed by single nucleus RNA-sequencing. Importantly, cell type-associated sites are enriched in GTEx RNA-sequencing data, edited ~twentyfold higher than all other sites, and variation in RNA editing is largely explained by neuronal proportions in bulk brain tissue. Finally, we uncover 661,791 cis-editing quantitative trait loci across thirteen brain regions, including hundreds with cell type-associated features. These data reveal an expansive repertoire of highly regulated RNA editing sites across human brain cell types and provide a resolved atlas linking cell types to editing variation and genetic regulatory effects.

UI MeSH Term Description Entries
D007288 Inosine A purine nucleoside that has hypoxanthine linked by the N9 nitrogen to the C1 carbon of ribose. It is an intermediate in the degradation of purines and purine nucleosides to uric acid and in pathways of purine salvage. It also occurs in the anticodon of certain transfer RNA molecules. (Dorland, 28th ed)
D001921 Brain The part of CENTRAL NERVOUS SYSTEM that is contained within the skull (CRANIUM). Arising from the NEURAL TUBE, the embryonic brain is comprised of three major parts including PROSENCEPHALON (the forebrain); MESENCEPHALON (the midbrain); and RHOMBENCEPHALON (the hindbrain). The developed brain consists of CEREBRUM; CEREBELLUM; and other structures in the BRAIN STEM. Encephalon
D006801 Humans Members of the species Homo sapiens. Homo sapiens,Man (Taxonomy),Human,Man, Modern,Modern Man
D012313 RNA A polynucleotide consisting essentially of chains with a repeating backbone of phosphate and ribose units to which nitrogenous bases are attached. RNA is unique among biological macromolecules in that it can encode genetic information, serve as an abundant structural component of cells, and also possesses catalytic activity. (Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed) RNA, Non-Polyadenylated,Ribonucleic Acid,Gene Products, RNA,Non-Polyadenylated RNA,Acid, Ribonucleic,Non Polyadenylated RNA,RNA Gene Products,RNA, Non Polyadenylated
D017393 RNA Editing A process that changes the nucleotide sequence of mRNA from that of the DNA template encoding it. Some major classes of RNA editing are as follows: 1, the conversion of cytosine to uracil in mRNA; 2, the addition of variable number of guanines at pre-determined sites; and 3, the addition and deletion of uracils, templated by guide-RNAs (RNA, GUIDE, KINETOPLASTIDA). RNA, Messenger, Editing,Editing, RNA,Editings, RNA,RNA Editings
D040641 Quantitative Trait Loci Genetic loci associated with a quantitative trait. Quantitative Trait Loci Genes,Loci, Quantitative Trait,Locus, Quantitative Trait,Quantitative Trait Locus,Trait Loci, Quantitative,Trait Locus, Quantitative

Related Publications

Winston H Cuddleston, and Junhao Li, and Xuanjia Fan, and Alexey Kozenkov, and Matthew Lalli, and Shahrukh Khalique, and Stella Dracheva, and Eran A Mukamel, and Michael S Breen
May 1993, Nature,
Winston H Cuddleston, and Junhao Li, and Xuanjia Fan, and Alexey Kozenkov, and Matthew Lalli, and Shahrukh Khalique, and Stella Dracheva, and Eran A Mukamel, and Michael S Breen
February 2016, Genetics,
Winston H Cuddleston, and Junhao Li, and Xuanjia Fan, and Alexey Kozenkov, and Matthew Lalli, and Shahrukh Khalique, and Stella Dracheva, and Eran A Mukamel, and Michael S Breen
December 2004, Genome research,
Winston H Cuddleston, and Junhao Li, and Xuanjia Fan, and Alexey Kozenkov, and Matthew Lalli, and Shahrukh Khalique, and Stella Dracheva, and Eran A Mukamel, and Michael S Breen
March 2021, Genome biology,
Winston H Cuddleston, and Junhao Li, and Xuanjia Fan, and Alexey Kozenkov, and Matthew Lalli, and Shahrukh Khalique, and Stella Dracheva, and Eran A Mukamel, and Michael S Breen
November 2016, Cell,
Winston H Cuddleston, and Junhao Li, and Xuanjia Fan, and Alexey Kozenkov, and Matthew Lalli, and Shahrukh Khalique, and Stella Dracheva, and Eran A Mukamel, and Michael S Breen
September 2017, Nature medicine,
Winston H Cuddleston, and Junhao Li, and Xuanjia Fan, and Alexey Kozenkov, and Matthew Lalli, and Shahrukh Khalique, and Stella Dracheva, and Eran A Mukamel, and Michael S Breen
August 2016, Nature neuroscience,
Winston H Cuddleston, and Junhao Li, and Xuanjia Fan, and Alexey Kozenkov, and Matthew Lalli, and Shahrukh Khalique, and Stella Dracheva, and Eran A Mukamel, and Michael S Breen
January 1992, Trends in biochemical sciences,
Winston H Cuddleston, and Junhao Li, and Xuanjia Fan, and Alexey Kozenkov, and Matthew Lalli, and Shahrukh Khalique, and Stella Dracheva, and Eran A Mukamel, and Michael S Breen
December 1990, Experientia,
Winston H Cuddleston, and Junhao Li, and Xuanjia Fan, and Alexey Kozenkov, and Matthew Lalli, and Shahrukh Khalique, and Stella Dracheva, and Eran A Mukamel, and Michael S Breen
July 2017, Genome biology,
Copied contents to your clipboard!