Agirre E, Oldfield AJ, Bellora N, Segelle A, Luco RF (2021) Splicing-associated chromatin signatures: a combinatorial and position-dependent role for histone marks in splicing definition. Nat Commun 12(1):682. https://doi.org/10.1038/s41467-021-20979-x
Article ADS CAS PubMed PubMed Central Google Scholar
Bekku Y, Vargova L, Goto Y, Vorisek I, Dmytrenko L, Narasaki M, Ohtsuka A, Fassler R, Ninomiya Y, Sykova E, Oohashi T (2010) Bral1: its role in diffusion barrier formation and conduction velocity in the CNS. J Neurosci 30(8):3113–3123. https://doi.org/10.1523/JNEUROSCI.5598-09.2010
Article CAS PubMed PubMed Central Google Scholar
Berkel TDM, Pandey SC (2017) Emerging role of epigenetic mechanisms in alcohol addiction. 41:666–680. https://doi.org/10.1111/acer.13338
Blencowe BJ (2006) Alternative splicing: new insights from global analyses. Cell 126(1):37–47. https://doi.org/10.1016/j.cell.2006.06.023
Article CAS PubMed Google Scholar
Bogenpohl JW, Smith ML, Farris SP, Dumur CI, Lopez MF, Becker HC, Grant KA, Miles MF (2019) Cross-species co-analysis of prefrontal cortex chronic ethanol transcriptome responses in mice and monkeys. Front Mol Neurosci 12:197. https://doi.org/10.3389/fnmol.2019.00197
Article CAS PubMed PubMed Central Google Scholar
Busch A, Bruggemann M, Ebersberger S, Zarnack K (2020) iCLIP data analysis: a complete pipeline from sequencing reads to RBP binding sites. Methods 178:49–62. https://doi.org/10.1016/j.ymeth.2019.11.008
Article CAS PubMed Google Scholar
Carvalho L, Chen H, Maienschein-Cline M, Glover EJ, Pandey SC, Lasek AW (2023) Conserved role for PCBP1 in altered RNA splicing in the hippocampus after chronic alcohol exposure. Mol Psychiatry. https://doi.org/10.1038/s41380-023-02184-y
Article PubMed PubMed Central Google Scholar
Casteels T, Bajew S, Reinis J, Enders L, Schuster M, Fontaine F, Muller AC, Wagner BK, Bock C, Kubicek S (2022) SMNDC1 links chromatin remodeling and splicing to regulate pancreatic hormone expression. Cell Rep 40(9):111288. https://doi.org/10.1016/j.celrep.2022.111288
Article CAS PubMed Google Scholar
Cates HM, Heller EA, Lardner CK, Purushothaman I, Pena CJ, Walker DM, Cahill ME, Neve RL, Shen L, Bagot RC, Nestler EJ (2018) Transcription factor E2F3a in nucleus accumbens affects cocaine action via transcription and alternative splicing. Biol Psychiatry 84(3):167–179. https://doi.org/10.1016/j.biopsych.2017.11.027
Article CAS PubMed Google Scholar
Donadoni M, Cicalese S, Sarkar DK, Chang SL, Sariyer IK (2019) Alcohol exposure alters pre-mRNA splicing of antiapoptotic Mcl-1L isoform and induces apoptosis in neural progenitors and immature neurons. Cell Death Dis 10(6):447. https://doi.org/10.1038/s41419-019-1673-3
Article PubMed PubMed Central Google Scholar
Feng J, Wilkinson M, Liu X, Purushothaman I, Ferguson D, Vialou V, Maze I, Shao N, Kennedy P, Koo J, Dias C, Laitman B, Stockman V, LaPlant Q, Cahill ME, Nestler EJ, Shen L (2014) Chronic cocaine-regulated epigenomic changes in mouse nucleus accumbens. Genome Biol 15(4):R65. https://doi.org/10.1186/gb-2014-15-4-r65
Article CAS PubMed PubMed Central Google Scholar
Galante PA, Sakabe NJ, Kirschbaum-Slager N, de Souza SJ (2004) Detection and evaluation of intron retention events in the human transcriptome. RNA 10(5):757–765. https://doi.org/10.1261/rna.5123504
Article CAS PubMed PubMed Central Google Scholar
Gatta E, Auta J, Gavin DP, Bhaumik DK, Grayson DR, Pandey SC, Guidotti A (2017) Emerging role of one-carbon metabolism and DNA methylation enrichment on delta-containing GABAA receptor expression in the cerebellum of subjects with alcohol use disorders (AUD). Int J Neuropsychopharmacol 20(12):1013–1026. https://doi.org/10.1093/ijnp/pyx075
Article CAS PubMed PubMed Central Google Scholar
Hu Q, Kim EJ, Feng J, Grant GR, Heller EA (2017) Histone posttranslational modifications predict specific alternative exon subtypes in mammalian brain. PLoS Comput Biol 13(6):e1005602. https://doi.org/10.1371/journal.pcbi.1005602
Article ADS CAS PubMed PubMed Central Google Scholar
Huggett SB, Ikeda AS, McGeary JE, Kaun KR, Palmer RHC (2022) Opioid use disorder and alternative mRNA splicing in reward circuitry. Genes (Basel). https://doi.org/10.3390/genes13061045
Huggett SB, Ikeda AS, Yuan Q, Benca-Bachman CE, Palmer RHC (2023) Genome- and transcriptome-wide splicing associations with alcohol use disorder. Sci Rep 13(1):3950. https://doi.org/10.1038/s41598-023-30926-z
Article ADS CAS PubMed PubMed Central Google Scholar
Kawasawa YI, Mohammad S, Son AI, Morizono H, Basha A, Salzberg AC, Torii M, Hashimoto-Torii K (2017) Genome-wide profiling of differentially spliced mRNAs in human fetal cortical tissue exposed to alcohol. Alcohol 62:1–9. https://doi.org/10.1016/j.alcohol.2017.05.001
Article CAS PubMed PubMed Central Google Scholar
Krapacher FA, Fernandez-Suarez D, Andersson A, Carrier-Ruiz A, Ibanez CF (2022) Convergent dopamine and ALK4 signaling to PCBP1 controls FosB alternative splicing and cocaine behavioral sensitization. EMBO J 41(15):e110721. https://doi.org/10.15252/embj.2022110721
Article CAS PubMed PubMed Central Google Scholar
Kyzar EJ, Zhang H, Pandey SC (2019) Adolescent alcohol exposure epigenetically suppresses amygdala arc enhancer RNA expression to confer adult anxiety susceptibility. 85:904–914. https://doi.org/10.1016/j.biopsych.2018.12.021
Leung SK, Jeffries AR, Castanho I, Jordan BT, Moore K, Davies JP, Dempster EL, Bray NJ, O’Neill P, Tseng E, Ahmed Z, Collier DA, Jeffery ED, Prabhakar S, Schalkwyk L, Jops C, Gandal MJ, Sheynkman GM, Hannon E, Mill J (2021) Full-length transcript sequencing of human and mouse cerebral cortex identifies widespread isoform diversity and alternative splicing. Cell Rep 37(7):110022. https://doi.org/10.1016/j.celrep.2021.110022
Article CAS PubMed PubMed Central Google Scholar
Lev Maor G, Yearim A, Ast G (2015) The alternative role of DNA methylation in splicing regulation. Trends Genet 31(5):274–280. https://doi.org/10.1016/j.tig.2015.03.002
Article CAS PubMed Google Scholar
Li R, Reiter JL, Chen AB, Chen SX, Foroud T, Edenberg HJ, Lai D, Liu Y (2023) RNA alternative splicing impacts the risk for alcohol use disorder. Mol Psychiatry. https://doi.org/10.1038/s41380-023-02111-1
Article PubMed PubMed Central Google Scholar
Liu Y, Zhang H (2022) RNA m6A modification changes in postmortem nucleus accumbens of subjects with alcohol use disorder: a pilot study. Genes (Basel). https://doi.org/10.3390/genes13060958
Article PubMed PubMed Central Google Scholar
Luco RF, Allo M, Schor IE, Kornblihtt AR, Misteli T (2011) Epigenetics in alternative pre-mRNA splicing. 144:16–26. https://doi.org/10.1016/J.CELL.2010.11.056
Lusk R, Hoffman PL, Mahaffey S, Rosean S, Smith H, Silhavy J, Pravenec M, Tabakoff B, Saba LM (2022) Beyond genes: inclusion of alternative splicing and alternative polyadenylation to assess the genetic architecture of predisposition to voluntary alcohol consumption in brain of the HXB/BXH recombinant inbred rat panel. Front Genet 13:821026. https://doi.org/10.3389/fgene.2022.821026
Article CAS PubMed PubMed Central Google Scholar
Matera AG, Wang Z (2014) A day in the life of the spliceosome. Nat Rev Mol Cell Biol 15(2):108–121. https://doi.org/10.1038/nrm3742
Article CAS PubMed PubMed Central Google Scholar
Maunakea AK, Chepelev I, Cui K, Zhao K (2013) Intragenic DNA methylation modulates alternative splicing by recruiting MeCP2 to promote exon recognition. Cell Res 23(11):1256–1269. https://doi.org/10.1038/cr.2013.110
Article CAS PubMed PubMed Central Google Scholar
Mews P, Egervari G, Nativio R, Sidoli S, Donahue G, Lombroso SI, Alexander DC, Riesche SL, Heller EA, Nestler EJ, Garcia BA, Berger SL (2019) Alcohol metabolism contributes to brain histone acetylation. Nature 574(7780):717–721. https://doi.org/10.1038/s41586-019-1700-7
Article ADS CAS PubMed PubMed Central Google Scholar
Nestler EJ, Lüscher C (2019) The molecular basis of drug addiction: linking epigenetic to synaptic and circuit mechanisms. 102:48–59. https://doi.org/10.1016/j.neuron.2019.01.016
Nik S, Bowman TV (2019) Splicing and neurodegeneration: insights and mechanisms. Wiley Interdiscipl Rev RNA 10(4):e1532. https://doi.org/10.1002/wrna.1532
O’Brien MA, Weston RM, Sheth NU, Bradley S, Bigbee J, Pandey A, Williams RW, Wolstenholme JT, Miles MF (2018) Ethanol-induced behavioral sensitization alters the synaptic transcriptome and exon utilization in DBA/2J mice. Front Genet 9:402. https://doi.org/10.3389/fgene.2018.00402
Article CAS PubMed PubMed Central Google Scholar
Palmisano M, Pandey SC (2017) Epigenetic mechanisms of alcoholism and stress-related disorders. 60:7–18. https://doi.org/10.1016/j.alcohol.2017.01.001
Pandey SC, Ugale R, Zhang H, Tang L, Prakash A (2008) Brain chromatin remodeling: a novel mechanism of alcoholism. J Neurosci 28(14):3729–3737. https://doi.org/10.1523/JNEUROSCI.5731-07.2008
Article CAS PubMed PubMed Central Google Scholar
Pepke S, Wold B, Mortazavi A (2009) Computation for ChIP-seq and RNA-seq studies. Nat Methods 6(11 Suppl):S22-32.
Comments (0)