Ahituv N (2016) Exonic enhancers: proceed with caution in exome and genome sequencing studies. Genome Med 8:14. https://doi.org/10.1186/s13073-016-0277-0

Article  PubMed  PubMed Central  Google Scholar 

Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for illumina sequence data. Bioinformatics 30:2114–2120. https://doi.org/10.1093/bioinformatics/btu170

Article  PubMed  PubMed Central  Google Scholar 

Consortium EP (2012) An integrated encyclopedia of DNA elements in the human genome. Nature 489:57–74. https://doi.org/10.1038/nature11247

Article  ADS  Google Scholar 

Consortium GT (2013) The Genotype-Tissue Expression (GTEx) project. Nat Genet 45:580–585. https://doi.org/10.1038/ng.2653

Article  Google Scholar 

Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, Chaisson M, Gingeras TR (2013) STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29:15–21. https://doi.org/10.1093/bioinformatics/bts635

Article  PubMed  Google Scholar 

Graham SE, Clarke SL, Wu KH, Kanoni S, Zajac GJM, Ramdas S, Surakka I, Ntalla I, Vedantam S, Winkler TW et al (2021) The power of genetic diversity in genome-wide association studies of lipids. Nature 600:675–679. https://doi.org/10.1038/s41586-021-04064-3

Article  ADS  PubMed  PubMed Central  Google Scholar 

Hasegawa M, Kawai K, Mitsui T, Taniguchi K, Monnai M, Wakui M, Ito M, Suematsu M, Peltz G, Nakamura M, Suemizu H (2011) The reconstituted “humanized liver” in TK-NOG mice is mature and functional. Biochem Biophys Res Commun 405:405–410. https://doi.org/10.1016/j.bbrc.2011.01.042

Article  PubMed  PubMed Central  Google Scholar 

Horn CL, Morales AL, Savard C, Farrell GC, Ioannou GN (2022) Role of cholesterol-associated steatohepatitis in the development of NASH. Hepatol Commun 6:12–35. https://doi.org/10.1002/hep4.1801

Article  PubMed  Google Scholar 

Huang TP, Newby GA, Liu DR (2021) Precision genome editing using cytosine and adenine base editors in mammalian cells. Nat Protoc 16:1089–1128. https://doi.org/10.1038/s41596-020-00450-9

Article  PubMed  Google Scholar 

Johnsson P, Lipovich L, Grander D, Morris KV (2014) Evolutionary conservation of long non-coding RNAs; sequence, structure, function. Biochim Biophys Acta 1840:1063–1071. https://doi.org/10.1016/j.bbagen.2013.10.035

Article  PubMed  Google Scholar 

Klarin D, Damrauer SM, Cho K, Sun YV, Teslovich TM, Honerlaw J, Gagnon DR, DuVall SL, Li J, Peloso GM et al (2018) Genetics of blood lipids among ~300,000 multi-ethnic participants of the Million Veteran Program. Nat Genet 50:1514–1523. https://doi.org/10.1038/s41588-018-0222-9

Article  PubMed  PubMed Central  Google Scholar 

Li H (2011) A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. Bioinformatics 27:2987–2993. https://doi.org/10.1093/bioinformatics/btr509

Article  PubMed  PubMed Central  Google Scholar 

Li P, Ruan X, Yang L, Kiesewetter K, Zhao Y, Luo H, Chen Y, Gucek M, Zhu J, Cao H (2015) A liver-enriched long non-coding RNA, lncLSTR, regulates systemic lipid metabolism in mice. Cell Metab 21:455–467. https://doi.org/10.1016/j.cmet.2015.02.004

Article  PubMed  PubMed Central  Google Scholar 

Liao Y, Smyth GK, Shi W (2013) The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote. Nucleic Acids Res 41:e108. https://doi.org/10.1093/nar/gkt214

Article  PubMed  PubMed Central  Google Scholar 

Love MI, Huber W, Anders S (2014) Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol 15:550. https://doi.org/10.1186/s13059-014-0550-8

Article  PubMed  PubMed Central  Google Scholar 

Mardinoglu A, Wu H, Bjornson E, Zhang C, Hakkarainen A, Rasanen SM, Lee S, Mancina RM, Bergentall M, Pietilainen KH et al (2018) An integrated understanding of the rapid metabolic benefits of a carbohydrate-restricted diet on hepatic steatosis in humans. Cell Metab 27(559–571):e555. https://doi.org/10.1016/j.cmet.2018.01.005

Article  Google Scholar 

Orozco G, Schoenfelder S, Walker N, Eyre S, Fraser P (2022) 3D genome organization links non-coding disease-associated variants to genes. Front Cell Dev Biol 10:995388. https://doi.org/10.3389/fcell.2022.995388

Article  PubMed  PubMed Central  Google Scholar 

Pasquali L, Gaulton KJ, Rodriguez-Segui SA, Mularoni L, Miguel-Escalada I, Akerman I, Tena JJ, Moran I, Gomez-Marin C, van de Bunt M et al (2014) Pancreatic islet enhancer clusters enriched in type 2 diabetes risk-associated variants. Nat Genet 46:136–143. https://doi.org/10.1038/ng.2870

Article  PubMed  PubMed Central  Google Scholar 

Qi G, Chatterjee N (2018) Heritability informed power optimization (HIPO) leads to enhanced detection of genetic associations across multiple traits. PLoS Genet 14:e1007549. https://doi.org/10.1371/journal.pgen.1007549

Article  PubMed  PubMed Central  Google Scholar 

Reed BD, Charos AE, Szekely AM, Weissman SM, Snyder M (2008) Genome-wide occupancy of SREBP1 and its partners NFY and SP1 reveals novel functional roles and combinatorial regulation of distinct classes of genes. PLoS Genet 4:e1000133. https://doi.org/10.1371/journal.pgen.1000133

Article  PubMed  PubMed Central  Google Scholar 

Roadmap Epigenomics C, Kundaje A, Meuleman W, Ernst J, Bilenky M, Yen A, Heravi-Moussavi A, Kheradpour P, Zhang Z, Wang J et al (2015) Integrative analysis of 111 reference human epigenomes. Nature 518:317–330. https://doi.org/10.1038/nature14248

Article  Google Scholar 

Ruan X, Li P, Cangelosi A, Yang L, Cao H (2016) A long non-coding RNA, lncLGR, regulates hepatic glucokinase expression and glycogen storage during fasting. Cell Rep 14:1867–1875. https://doi.org/10.1016/j.celrep.2016.01.062

Article  PubMed  PubMed Central  Google Scholar 

Ruan X, Li P, Chen Y, Shi Y, Pirooznia M, Seifuddin F, Suemizu H, Ohnishi Y, Yoneda N, Nishiwaki M et al (2020) In vivo functional analysis of non-conserved human lncRNAs associated with cardiometabolic traits. Nat Commun 11:45. https://doi.org/10.1038/s41467-019-13688-z

Article  ADS  PubMed  PubMed Central  Google Scholar 

Ruan X, Li P, Ma Y, Jiang CF, Chen Y, Shi Y, Gupta N, Seifuddin F, Pirooznia M, Ohnishi Y et al (2021) Identification of human long noncoding RNAs associated with nonalcoholic fatty liver disease and metabolic homeostasis. J Clin Invest. https://doi.org/10.1172/JCI136336

Article  PubMed  PubMed Central  Google Scholar 

Sakaue S, Kanai M, Tanigawa Y, Karjalainen J, Kurki M, Koshiba S, Narita A, Konuma T, Yamamoto K, Akiyama M et al (2021) A cross-population atlas of genetic associations for 220 human phenotypes. Nat Genet 53:1415–1424. https://doi.org/10.1038/s41588-021-00931-x

Article  PubMed  Google Scholar 

Sallam T, Jones M, Thomas BJ, Wu X, Gilliland T, Qian K, Eskin A, Casero D, Zhang Z, Sandhu J et al (2018) Transcriptional regulation of macrophage cholesterol efflux and atherogenesis by a long noncoding RNA. Nat Med 24:304–312. https://doi.org/10.1038/nm.4479

Article  PubMed  PubMed Central  Google Scholar 

Sollis E, Mosaku A, Abid A, Buniello A, Cerezo M, Gil L, Groza T, Gunes O, Hall P, Hayhurst J et al (2023) The NHGRI-EBI GWAS Catalog: knowledgebase and deposition resource. Nucleic Acids Res 51:D977–D985. https://doi.org/10.1093/nar/gkac1010

Article  PubMed  Google Scholar 

Suppli MP, Rigbolt KTG, Veidal SS, Heeboll S, Eriksen PL, Demant M, Bagger JI, Nielsen JC, Oro D, Thrane SW et al (2019) Hepatic transcriptome signatures in patients with varying degrees of nonalcoholic fatty liver disease compared with healthy normal-weight individuals. Am J Physiol Gastrointest Liver Physiol 316:G462–G472. https://doi.org/10.1152/ajpgi.00358.2018

Article  PubMed  Google Scholar 

Thuronyi BW, Koblan LW, Levy JM, Yeh WH, Zheng C, Newby GA, Wilson C, Bhaumik M, Shubina-Oleinik O, Holt JR, Liu DR (2019) Continuous evolution of base editors with expanded target compatibility and improved activity. Nat Biotechnol 37:1070–1079. https://doi.org/10.1038/s41587-019-0193-0

Article  PubMed  PubMed Central  Google Scholar 

Toth PP, Potter D, Ming EE (2012) Prevalence of lipid abnormalities in the United States: the National Health and Nutrition Examination Survey 2003–2006. J Clin Lipidol 6:325–330. https://doi.org/10.1016/j.jacl.2012.05.002

Article  PubMed  Google Scholar 

Vosa U, Claringbould A, Westra HJ, Bonder MJ, Deelen P, Zeng B, Kirsten H, Saha A, Kreuzhuber R, Yazar S et al (2021) Large-scale cis- and trans-eQTL analyses identify thousands of genetic loci and polygenic scores that regulate blood gene expression. Nat Genet 53:1300–1310. https://doi.org/10.1038/s41588-021-00913-z

Article  PubMed  PubMed Central  Google Scholar 

Wang Y, Viscarra J, Kim SJ, Sul HS (2015) Transcriptional regulation of hepatic lipogenesis. Nat Rev Mol Cell Biol 16:678–689. https://doi.org/10.1038/nrm4074

Article  PubMed  PubMed Central  Google Scholar 

Yang L, Li P, Yang W, Ruan X, Kiesewetter K, Zhu J, Cao H (2016) Integrative transcriptome analyses of metabolic responses in mice define pivotal LncRNA metabolic regulators. Cell Metab 24:627–639. https://doi.org/10.1016/j.cmet.2016.08.019

Article  PubMed  PubMed Central  Google Scholar 

Zhao XY, Li S, Wang GX, Yu Q, Lin JD (2014) A long noncoding RNA transcriptional regulatory circuit drives thermogenic adipocyte differentiation. Mol Cell 55:372–382. https://doi.org/10.1016/j.molcel.2014.06.004

Article  PubMed