Genome-wide association studies (GWAS) have reported substantial single-nucleotide polymorphisms (SNPs) associated with major depressive disorder (MDD), but the underlying functional variations in the GWAS risk loci are unclear. Here we show that the European MDD genome-wide risk-associated allele of rs12129573 at 1p31.1 is associated with MDD in Han Chinese, and this SNP is in strong linkage disequilibrium (LD) with a human-unique Alu insertion polymorphism (rs70959274) in the 5′ flanking region of a long non-coding RNA (lncRNA) LINC01360 (Long Intergenic Non-Protein Coding RNA 1360), which is preferably expressed in human testis in the currently available expression datasets. The risk allele at rs12129573 is almost completely linked with the absence of this Alu insertion. The Alu insertion polymorphism (rs70959274) is significantly associated with a lower RNA level of LINC01360 and acts as a transcription silencer likely through modulating the methylation of its internal CpG sites. Luciferase assays confirm that the presence of Alu insertion at rs70959274 suppresses transcriptional activities in human cells, and deletion of the Alu insertion through CRISPR/Cas9-directed genome editing increases RNA expression of LINC01360. Deletion of the Alu insertion in human cells also leads to dysregulation of gene expression, biological processes and pathways relevant to MDD, such as the alterations of mRNA levels of DRD2 and FLOT1, transcription of genes involved in synaptic transmission, neurogenesis, learning or memory, and the PI3K-Akt signaling pathway. In summary, we identify a human-unique DNA repetitive polymorphism in robust LD with the MDD risk-associated SNP at the prominent 1p31.1 GWAS loci, and offer insights into the molecular basis of the illness.
Subscribe to Journal
Get full journal access for 1 year
only $38.38 per issue
All prices are NET prices.
VAT will be added later in the checkout.
Rent or Buy article
Get time limited or full article access on ReadCube.
All prices are NET prices.
Sullivan PF, Neale MC, Kendler KS. Genetic epidemiology of major depression: review and meta-analysis. Am J Psychiatry. 2000;157:1552–62.
Howard DM, Adams MJ, Clarke TK, Hafferty JD, Gibson J, Shirali M, et al. Genome-wide meta-analysis of depression identifies 102 independent variants and highlights the importance of the prefrontal brain regions. Nat Neurosci. 2019;22:343–52.
Li X, Luo Z, Gu C, Hall LS, McIntosh AM, Zeng Y, et al. Common variants on 6q16.2, 12q24.31 and 16p13.3 are associated with major depressive disorder. Neuropsychopharmacology. 2018;43:2146–53.
Wray NR, Ripke S, Mattheisen M, Trzaskowski M, Byrne EM, Abdellaoui A, et al. Genome-wide association analyses identify 44 risk variants and refine the genetic architecture of major depression. Nat Genet. 2018;50:668–81.
Li M, Yue W. VRK2, a candidate gene for psychiatric and neurological disorders. Mol Neuropsychiatry. 2018;4:119–33.
Li H, Chang H, Song X, Liu W, Li L, Wang L, et al. Integrative analyses of major histocompatibility complex loci in the genome-wide association studies of major depressive disorder. Neuropsychopharmacology. 2019;44:1552–61.
Edwards SL, Beesley J, French JD, Dunning AM. Beyond GWASs: illuminating the dark road from association to function. Am J Hum Genet. 2013;93:779–97.
Visscher PM, Wray NR, Zhang Q, Sklar P, McCarthy MI, Brown MA, et al. 10 years of GWAS discovery: biology, function, and translation. Am J Hum Genet. 2017;101:5–22.
Duan J, Shi J, Fiorentino A, Leites C, Chen X, Moy W, et al. A rare functional noncoding variant at the GWAS-implicated MIR137/MIR2682 locus might confer risk to schizophrenia and bipolar disorder. Am J Hum Genet. 2014;95:744–53.
Huo Y, Li S, Liu J, Li X, Luo XJ. Functional genomics reveal gene regulatory mechanisms underlying schizophrenia risk. Nat Commun. 2019;10:670.
Forrest MP, Zhang H, Moy W, McGowan H, Leites C, Dionisio LE, et al. Open chromatin profiling in hiPSC-derived neurons prioritizes functional noncoding psychiatric risk variants and highlights neurodevelopmental loci. Cell Stem Cell. 2017;21:305–18 e8.
Wu Y, Bi R, Zeng C, Ma C, Sun C, Li J, et al. Identification of the primate-specific gene BTN3A2 as an additional schizophrenia risk gene in the MHC loci. EBioMedicine. 2019;44:530–41.
Yang CP, Li X, Wu Y, Shen Q, Zeng Y, Xiong Q, et al. Comprehensive integrative analyses identify GLT8D1 and CSNK2B as schizophrenia risk genes. Nat Commun. 2018;9:838.
Payer LM, Steranka JP, Yang WR, Kryatova M, Medabalimi S, Ardeljan D, et al. Structural variants caused by Alu insertions are associated with risks for many human diseases. Proc Natl Acad Sci USA. 2017;114:E3984–E92.
Song JHT, Lowe CB, Kingsley DM. Characterization of a human-specific tandem repeat associated with bipolar disorder and schizophrenia. Am J Hum Genet. 2018;103:421–30.
Marshall CR, Howrigan DP, Merico D, Thiruvahindrapuram B, Wu W, Greer DS, et al. Contribution of copy number variants to schizophrenia from a genome-wide study of 41,321 subjects. Nat Genet. 2017;49:27–35.
Yang Z, Zhou D, Li H, Cai X, Liu W, Wang L, et al. The genome-wide risk alleles for psychiatric disorders at 3p21.1 show convergent effects on mRNA expression, cognitive function and mushroom dendritic spine. Mol Psychiatry. 2020;25:48–66.
Yang Z, Cai X, Qu N, Zhao L, Zhong BL, Zhang SF, et al. Identification of a functional 339-bp Alu polymorphism in the schizophrenia-associated locus at 10q24.32. Zool Res. 2020;41:84–9.
Li M, Jaffe AE, Straub RE, Tao R, Shin JH, Wang Y, et al. A human-specific AS3MT isoform and BORCS7 are molecular risk factors in the 10q24.32 schizophrenia-associated locus. Nat Med. 2016;22:649–56.
Deininger P. Alu elements: know the SINEs. Genome Biol. 2011;12:236.
Stoneking M, Fontius JJ, Clifford SL, Soodyall H, Arcot SS, Saha N, et al. Alu insertion polymorphisms and human evolution: evidence for a larger population size in Africa. Genome Res. 1997;7:1061–71.
Zhang C, Wu Z, Zhao G, Wang F, Fang Y. Identification of IL6 as a susceptibility gene for major depressive disorder. Sci Rep. 2016;6:31264.
Xiao X, Zheng F, Chang H, Ma Y, Yao YG, Luo XJ, et al. The Gene Encoding Protocadherin 9 (PCDH9), a novel risk factor for major depressive disorder. Neuropsychopharmacology. 2018;43:1128–37.
Aljanabi SM, Martinez I. Universal and rapid salt-extraction of high quality genomic DNA for PCR-based techniques. Nucleic Acids Res. 1997;25:4692–3.
Li M, Luo XJ, Xiao X, Shi L, Liu XY, Yin LD, et al. Analysis of common genetic variants identifies RELN as a risk gene for schizophrenia in Chinese population. World J Biol Psychiatry. 2013;14:91–9.
Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MA, Bender D, et al. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet. 2007;81:559–75.
Pruim RJ, Welch RP, Sanna S, Teslovich TM, Chines PS, Gliedt TP, et al. LocusZoom: regional visualization of genome-wide association scan results. Bioinformatics. 2010;26:2336–7.
GTEx Consortium, Laboratory Data Analysis, Coordinating Center-Analysis Working Group, Statistical Methods groups-Analysis Working Group, Enhancing GTEx groups, NIH Common Fund. et al. Genetic effects on gene expression across human tissues. Nature. 2017;550:204–13.
Barrett JC, Fry B, Maller J, Daly MJ. Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics. 2005;21:263–5.
Genomes Project Consortium, Auton A, Brooks LD, Durbin RM, Garrison EP, Kang HM, et al. A global reference for human genetic variation. Nature. 2015;526:68–74.
Ward LD, Kellis M. HaploReg: a resource for exploring chromatin states, conservation, and regulatory motif alterations within sets of genetically linked variants. Nucleic Acids Res. 2012;40:D930–4.
Encode Project Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature. 2012;489:57–74.
Ritchie GR, Dunham I, Zeggini E, Flicek P. Functional annotation of noncoding sequence variants. Nat Methods. 2014;11:294–6.
Wingender E, Dietze P, Karas H, Knuppel R. TRANSFAC: a database on transcription factors and their DNA binding sites. Nucleic Acids Res. 1996;24:238–41.
Larsen F, Gundersen G, Lopez R, Prydz H. CpG islands as gene markers in the human genome. Genomics. 1992;13:1095–107.
Haeussler M, Schonig K, Eckert H, Eschstruth A, Mianne J, Renaud JB, et al. Evaluation of off-target and on-target scoring algorithms and integration into the guide RNA selection tool CRISPOR. Genome Biol. 2016;17:148.
Chang H, Yi B, Ma R, Zhang X, Zhao H, Xi Y. CRISPR/cas9, a novel genomic tool to knock down microRNA in vitro and in vivo. Sci Rep. 2016;6:22312.
Zhao L, Chang H, Zhou DS, Cai J, Fan W, Tang W, et al. Replicated associations of FADS1, MAD1L1, and a rare variant at 10q26.13 with bipolar disorder in Chinese population. Transl Psychiatry. 2018;8:270.
Liu W, Yan H, Zhou D, Cai X, Zhang Y, Li S, et al. The depression GWAS risk allele predicts smaller cerebellar gray matter volume and reduced SIRT1 mRNA expression in Chinese population. Transl Psychiatry. 2019;9:333.
Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30:2114–20.
Kim D, Langmead B, Salzberg SL. HISAT: a fast spliced aligner with low memory requirements. Nat Methods. 2015;12:357–60.
Liao Y, Smyth GK, Shi W. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics. 2014;30:923–30.
Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15:550.
Yu G, Wang LG, Han Y, He QY. clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS. 2012;16:284–7.
Yu G, Li F, Qin Y, Bo X, Wu Y, Wang S. GOSemSim: an R package for measuring semantic similarity among GO terms and gene products. Bioinformatics. 2010;26:976–8.
Jaffe AE, Straub RE, Shin JH, Tao R, Gao Y, Collado-Torres L, et al. Developmental and genetic regulation of the human cortex transcriptome illuminate schizophrenia pathogenesis. Nat Neurosci. 2018;21:1117–25.
Fromer M, Roussos P, Sieberts SK, Johnson JS, Kavanagh DH, Perumal TM, et al. Gene expression elucidates functional impact of polygenic risk for schizophrenia. Nat Neurosci. 2016;19:1442–53.
Ng B, White CC, Klein HU, Sieberts SK, McCabe C, Patrick E, et al. An xQTL map integrates the genetic architecture of the human brain’s transcriptome and epigenome. Nat Neurosci. 2017;20:1418–26.
Fullard JF, Giambartolomei C, Hauberg ME, Xu K, Voloudakis G, Shao Z, et al. Open chromatin profiling of human postmortem brain infers functional roles for non-coding schizophrenia loci. Hum Mol Genet. 2017;26:1942–51.
Hasler J, Strub K. Alu elements as regulators of gene expression. Nucleic Acids Res. 2006;34:5491–7.
Fornes O, Castro-Mondragon JA, Khan A, van der Lee R, Zhang X, Richmond PA, et al. JASPAR 2020: update of the open-access database of transcription factor binding profiles. Nucleic Acids Res. 2020;48:D87–92.
Hu H, Miao YR, Jia LH, Yu QY, Zhang Q, Guo AY. AnimalTFDB 3.0: a comprehensive resource for annotation and prediction of animal transcription factors. Nucleic Acids Res. 2019;47:D33–8.
Zhong J, Li S, Zeng W, Li X, Gu C, Liu J, et al. Integration of GWAS and brain eQTL identifies FLOT1 as a risk gene for major depressive disorder. Neuropsychopharmacology. 2019;44:1542–51.
Grace AA. Dysregulation of the dopamine system in the pathophysiology of schizophrenia and depression. Nat Rev Neurosci. 2016;17:524–32.
Dunlop BW, Nemeroff CB. The role of dopamine in the pathophysiology of depression. Arch Gen Psychiatry. 2007;64:327–37.
Cai N, Chang S, Li Y, Li Q, Hu J, Liang J, et al. Molecular signatures of major depression. Curr Biol. 2015;25:1146–56.
Shao L, Martin MV, Watson SJ, Schatzberg A, Akil H, Myers RM, et al. Mitochondrial involvement in psychiatric disorders. Ann Med. 2008;40:281–95.
Wang Q, Dwivedi Y. Transcriptional profiling of mitochondria associated genes in prefrontal cortex of subjects with major depressive disorder. World J Biol Psychiatry. 2017;18:592–603.
Penzes P, Cahill ME, Jones KA, VanLeeuwen JE, Woolfrey KM. Dendritic spine pathology in neuropsychiatric disorders. Nat Neurosci. 2011;14:285–93.
Forrest MP, Parnell E, Penzes P. Dendritic structural plasticity and neuropsychiatric disease. Nat Rev Neurosci. 2018;19:215–34.
Duman RS, Aghajanian GK, Sanacora G, Krystal JH. Synaptic plasticity and depression: new insights from stress and rapid-acting antidepressants. Nat Med. 2016;22:238–49.
Kang HJ, Voleti B, Hajszan T, Rajkowska G, Stockmeier CA, Licznerski P, et al. Decreased expression of synapse-related genes and loss of synapses in major depressive disorder. Nat Med. 2012;18:1413–7.
Duman RS, Aghajanian GK. Synaptic dysfunction in depression: potential therapeutic targets. Science. 2012;338:68–72.
Li S, Zong L, Hou Y, Zhang W, Zhou L, Yang Q, et al. Altered DNA methylation of the AluY subfamily in schizophrenia and bipolar disorder. Epigenomics. 2019;11:581–6.
Li S, Yang Q, Hou Y, Jiang T, Zong L, Wang Z, et al. Hypomethylation of LINE-1 elements in schizophrenia and bipolar disorder. J Psychiatr Res. 2018;107:68–72.
Li M, Wu DD, Yao YG, Huo YX, Liu JW, Su B, et al. Recent positive selection drives the expansion of a schizophrenia risk nonsynonymous variant at SLC39A8 in Europeans. Schizophr Bull. 2016;42:178–90.
Keller MC. Evolutionary perspectives on genetic and environmental risk factors for psychiatric disorders. Annu Rev Clin Psychol. 2018;14:471–93.
Uher R. The role of genetic variation in the causation of mental illness: an evolution-informed framework. Mol Psychiatry. 2009;14:1072–82.
Giltay EJ, van der Mast RC, Lauwen E, Heijboer AC, de Waal MWM, Comijs HC. Plasma testosterone and the course of major depressive disorder in older men and women. Am J Geriatr Psychiatry. 2017;25:425–37.
Walther A, Breidenstein J, Miller R. Association of testosterone treatment with alleviation of depressive symptoms in men: a systematic review and meta-analysis. JAMA Psychiatry. 2019;76:31–40.
Tao R, Cousijn H, Jaffe AE, Burnet PW, Edwards F, Eastwood SL, et al. Expression of ZNF804A in human brain and alterations in schizophrenia, bipolar disorder, and major depressive disorder: a novel transcript fetally regulated by the psychosis risk variant rs1344706. JAMA Psychiatry. 2014;71:1112–20.
Birnbaum R, Jaffe AE, Hyde TM, Kleinman JE, Weinberger DR. Prenatal expression patterns of genes associated with neuropsychiatric disorders. Am J Psychiatry. 2014;171:758–67.
Walker RL, Ramaswami G, Hartl C, Mancuso N, Gandal MJ, de la Torre-Ubieta L, et al. Genetic control of expression and splicing in developing human brain informs disease mechanisms. Cell. 2019;179:750–71 e22.
Kanton S, Boyle MJ, He Z, Santel M, Weigert A, Sanchis-Calleja F, et al. Organoid single-cell genomic atlas uncovers human-specific features of brain development. Nature. 2019;574:418–22.
Zhong S, Zhang S, Fan X, Wu Q, Yan L, Dong J, et al. A single-cell RNA-seq survey of the developmental landscape of the human prefrontal cortex. Nature. 2018;555:524–8.
Larsen PA, Lutz MW, Hunnicutt KE, Mihovilovic M, Saunders AM, Yoder AD, et al. The Alu neurodegeneration hypothesis: a primate-specific mechanism for neuronal transcription noise, mitochondrial dysfunction, and manifestation of neurodegenerative disease. Alzheimers Dement. 2017;13:828–38.
Pardinas AF, Holmans P, Pocklington AJ, Escott-Price V, Ripke S, Carrera N, et al. Common schizophrenia alleles are enriched in mutation-intolerant genes and in regions under strong background selection. Nat Genet. 2018;50:381–9.
The authors declare no competing interests.
Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
About this article
Cite this article
Liu, W., Li, W., Cai, X. et al. Identification of a functional human-unique 351-bp Alu insertion polymorphism associated with major depressive disorder in the 1p31.1 GWAS risk loci. Neuropsychopharmacol. 45, 1196–1206 (2020). https://doi.org/10.1038/s41386-020-0659-2
Massively Parallel Reporter Assays: Defining Functional Psychiatric Genetic Variants Across Biological Contexts
Biological Psychiatry (2020)
Functional Genomics Identify a Regulatory Risk Variation rs4420550 in the 16p11.2 Schizophrenia-Associated Locus
Biological Psychiatry (2020)
A Human-Specific Schizophrenia Risk Tandem Repeat Affects Alternative Splicing of a Human-Unique Isoform AS3MTd2d3 and Mushroom Dendritic Spine Density
Schizophrenia Bulletin (2020)