Comprehensive Analysis of Hippocampal Mirnaomes in Humans and Mice

References

• Chen W , QinC . General hallmarks of microRNAs in brain evolution and development . RNA Biol.12 ( 7 ), 701 – 708 ( 2015 ).
   PubMed Web of Science ®Google Scholar
• Hertel J , LindemeyerM , MissalKet al. The expansion of the metazoan microRNA repertoire . BMC Genomics7 , 25 ( 2006 ).
   PubMed Web of Science ®Google Scholar
• Peterson KJ , DietrichMR , McPeekMA . MicroRNAs and metazoan macroevolution: insights into canalization, complexity, and the Cambrian explosion . BioEssays31 ( 7 ), 736 – 747 ( 2009 ).
   PubMed Web of Science ®Google Scholar
• Meunier J , LemoineF , SoumillonMet al. Birth and expression evolution of mammalian microRNA genes . Genome Res.23 ( 1 ), 34 – 45 ( 2013 ).
   PubMed Web of Science ®Google Scholar
• Kozomara A , Griffiths-JonesS . miRBase: annotating high confidence microRNAs using deep sequencing data . Nucleic Acids Res.42 ( Database issue ), D68 – D73 ( 2014 ).
   PubMed Web of Science ®Google Scholar
• Krichevsky AM , KingKS , DonahueCP , KhrapkoK , KosikKS . A microRNA array reveals extensive regulation of microRNAs during brain development . RNA9 ( 10 ), 1274 – 1281 ( 2003 ).
   PubMed Web of Science ®Google Scholar
• Miska EA , Alvarez-SaavedraE , TownsendMet al. Microarray analysis of microRNA expression in the developing mammalian brain . Genome Biol.5 ( 9 ), R68 ( 2004 ).
   PubMed Web of Science ®Google Scholar
• Sempere LF , FreemantleS , Pitha-RoweI , MossE , DmitrovskyE , AmbrosV . Expression profiling of mammalian microRNAs uncovers a subset of brain-expressed microRNAs with possible roles in murine and human neuronal differentiation . Genome Biol.5 ( 3 ), R13 ( 2004 ).
   PubMed Web of Science ®Google Scholar
• Shinde S , AroraN , BhadraU . A complex network of microRNAs expressed in brain and genes associated with amyotrophic lateral sclerosis . Int. J. Genomics 2013 , 383024 ( 2013 ).
   PubMed Web of Science ®Google Scholar
• Cembrowski MS , WangL , SuginoK , ShieldsBC , SprustonN . Hipposeq: a comprehensive RNA-seq database of gene expression in hippocampal principal neurons . eLife5 , e14997 ( 2016 ).
   PubMed Web of Science ®Google Scholar
• Lewis BP , BurgeCB , BartelDP . Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets . Cell120 ( 1 ), 15 – 20 ( 2005 ).
   PubMed Web of Science ®Google Scholar
• Somel M , GuoS , FuNet al. MicroRNA, mRNA, and protein expression link development and aging in human and macaque brain . Genome Res.20 ( 9 ), 1207 – 1218 ( 2010 ).
   PubMed Web of Science ®Google Scholar
• Wu X , ZhangD , LiG . Insights into the regulation of human CNV-miRNAs from the view of their target genes . BMC Genomics13 , 707 ( 2012 ).
   PubMed Web of Science ®Google Scholar
• Smibert P , MiuraP , WestholmJOet al. Global patterns of tissue-specific alternative polyadenylation in Drosophila . Cell Rep.1 ( 3 ), 277 – 289 ( 2012 ).
   PubMed Web of Science ®Google Scholar
• Miura P , ShenkerS , Andreu-AgulloC , WestholmJO , LaiEC . Widespread and extensive lengthening of 3′ UTRs in the mammalian brain . Genome Res.23 ( 5 ), 812 – 825 ( 2013 ).
   PubMed Web of Science ®Google Scholar
• Bak M , SilahtarogluA , MollerMet al. MicroRNA expression in the adult mouse central nervous system . RNA14 ( 3 ), 432 – 444 ( 2008 ).
   PubMed Web of Science ®Google Scholar
• Coolen M , ThieffryD , DrivenesO , BeckerTS , Bally-CuifL . miR-9 controls the timing of neurogenesis through the direct inhibition of antagonistic factors . Dev. Cell22 ( 5 ), 1052 – 1064 ( 2012 ).
   PubMed Web of Science ®Google Scholar
• Davila JL , GoffLA , RicuperoCLet al. A positive feedback mechanism that regulates expression of miR-9 during neurogenesis . PLoS ONE9 ( 4 ), e94348 ( 2014 ).
   PubMed Web of Science ®Google Scholar
• Giusti SA , VoglAM , BrockmannMMet al. MicroRNA-9 controls dendritic development by targeting REST . eLife3 ( 2014 ).
   PubMed Web of Science ®Google Scholar
• Yao H , MaR , YangLet al. MiR-9 promotes microglial activation by targeting MCPIP1 . Nat. Commun.5 , 4386 ( 2014 ).
   PubMed Web of Science ®Google Scholar
• Li Y , PengT , LiLet al. MicroRNA-9 regulates neural apoptosis in methylmalonic acidemia via targeting BCL2L11 . Int. J. Dev. Neurosci.36 , 19 – 24 ( 2014 ).
   PubMed Web of Science ®Google Scholar
• Liu W , LiuC , ZhuJet al. MicroRNA-16 targets amyloid precursor protein to potentially modulate Alzheimer’s-associated pathogenesis in SAMP8 mice . Neurobiol. Aging33 ( 3 ), 522 – 534 ( 2012 ).
   PubMed Web of Science ®Google Scholar
• An YW , JhangKA , WooSY , KangJL , ChongYH . Sulforaphane exerts its anti-inflammatory effect against amyloid-β peptide via STAT-1 dephosphorylation and activation of Nrf2/HO-1 cascade in human THP-1 macrophages . Neurobiol. Aging38 , 1 – 10 ( 2016 ).
   PubMed Web of Science ®Google Scholar
• Li YY , CuiJG , HillJM , BhattacharjeeS , ZhaoY , LukiwWJ . Increased expression of miRNA-146a in Alzheimer’s disease transgenic mouse models . Neurosci. Lett.487 ( 1 ), 94 – 98 ( 2011 ).
   PubMed Web of Science ®Google Scholar
• Kaalund SS , VenoMT , BakMet al. Aberrant expression of miR-218 and miR-204 in human mesial temporal lobe epilepsy and hippocampal sclerosis-convergence on axonal guidance . Epilepsia55 ( 12 ), 2017 – 2027 ( 2014 ).
   PubMed Web of Science ®Google Scholar
• Lett TA , ChakravartyMM , FelskyDet al. The genome-wide supported microRNA-137 variant predicts phenotypic heterogeneity within schizophrenia . Mol. Psychiatr.18 ( 4 ), 443 – 450 ( 2013 ).
   PubMed Web of Science ®Google Scholar
• Kohen R , DobraA , TracyJH , HaugenE . Transcriptome profiling of human hippocampus dentate gyrus granule cells in mental illness . Transl. Psychiatry.4 , e366 ( 2014 ).
   PubMed Web of Science ®Google Scholar
• Clark RE , SquireLR . Similarity in form and function of the hippocampus in rodents, monkeys, and humans . Proc. Natl Acad. Sci. USA110 ( Suppl. 2 ), 10365 – 10370 ( 2013 ).
   PubMedGoogle Scholar
• Ashbrook DG , WilliamsRW , LuLet al. Joint genetic analysis of hippocampal size in mouse and human identifies a novel gene linked to neurodegenerative disease . BMC Genomics15 , 850 ( 2014 ).
   PubMed Web of Science ®Google Scholar
• Sahay A , ScobieKN , HillASet al. Increasing adult hippocampal neurogenesis is sufficient to improve pattern separation . Nature472 ( 7344 ), 466 – 470 ( 2011 ).
   PubMed Web of Science ®Google Scholar
• Chen W , XiaX , SongNet al. Cross-species analysis of gene expression and function in prefrontal cortex, hippocampus and striatum . PLoS ONE11 ( 10 ), e0164295 ( 2016 ).
   PubMed Web of Science ®Google Scholar
• Wang Z , WangN , LiZ , XiaoF , DaiJ . Human high intelligence is involved in spectral redshift of biophotonic activities in the brain . Proc. Natl Acad. Sci. USA113 ( 31 ), 8753 – 8758 ( 2016 ).
   PubMed Web of Science ®Google Scholar
• Ziemka-Nalecz M , ZalewskaT . Transient forebrain ischemia effects FAK-coupled signaling in gerbil hippocampus . Neurochem. Int.51 ( 6–7 ), 405 – 411 ( 2007 ).
   PubMed Web of Science ®Google Scholar
• Li R , LiY , KristiansenK , WangJ . SOAP: short oligonucleotide alignment program . Bioinformatics24 ( 5 ), 713 – 714 ( 2008 ).
   PubMed Web of Science ®Google Scholar
• Rice P , LongdenI , BleasbyA . EMBOSS: the European Molecular Biology Open Software Suite . Trends Genet.16 ( 6 ), 276 – 277 ( 2000 ).
   PubMed Web of Science ®Google Scholar
• Jones-Rhoades MW , BartelDP . Computational identification of plant microRNAs and their targets, including a stress-induced miRNA . Mol. Cell14 ( 6 ), 787 – 799 ( 2004 ).
   PubMed Web of Science ®Google Scholar
• Denman RB . Using RNAFOLD to predict the activity of small catalytic RNAs . Biotechniques15 ( 6 ), 1090 – 1095 ( 1993 ).
   PubMed Web of Science ®Google Scholar
• Agarwal V , BellGW , NamJW , BartelDP . Predicting effective microRNA target sites in mammalian mRNAs . eLife4 ( 2015 ).
   Web of Science ®Google Scholar
• Baek D , VillenJ , ShinC , CamargoFD , GygiSP , BartelDP . The impact of microRNAs on protein output . Nature455 ( 7209 ), 64 – 71 ( 2008 ).
   PubMed Web of Science ®Google Scholar
• Huang da W , ShermanBT , LempickiRA . Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources . Nat. Protoc.4 ( 1 ), 44 – 57 ( 2009 ).
   PubMed Web of Science ®Google Scholar
• Vlachos IS , ZagganasK , ParaskevopoulouMDet al. DIANA-miRPath v3.0: deciphering microRNA function with experimental support . Nucleic Acids Res.43 ( W1 ), W460 – W466 ( 2015 ).
   PubMed Web of Science ®Google Scholar
• Paraskevopoulou MD , GeorgakilasG , KostoulasNet al. DIANA-microT web server v5.0: service integration into miRNA functional analysis workflows . Nucleic Acids Res.41 ( Web Server issue ), W169 – W173 ( 2013 ).
   PubMed Web of Science ®Google Scholar
• Vlachos IS , ParaskevopoulouMD , KaragkouniDet al. DIANA-TarBase v7.0: indexing more than half a million experimentally supported miRNA:mRNA interactions . Nucleic Acids Res.43 ( Database issue ), D153 – D159 ( 2015 ).
   PubMedGoogle Scholar
• Naeem H , KuffnerR , CsabaG , ZimmerR . miRSel: automated extraction of associations between microRNAs and genes from the biomedical literature . BMC Bioinformatics11 , 135 ( 2010 ).
   PubMedGoogle Scholar
• Robinson MD , McCarthyDJ , SmythGK . edgeR: a bioconductor package for differential expression analysis of digital gene expression data . Bioinformatics26 ( 1 ), 139 – 140 ( 2010 ).
   PubMed Web of Science ®Google Scholar
• Ewing B , GreenP . Base-calling of automated sequencer traces using phred. II. Error probabilities . Genome Res.8 ( 3 ), 186 – 194 ( 1998 ).
   PubMed Web of Science ®Google Scholar
• Tam S , de BorjaR , TsaoMS , McPhersonJD . Robust global microRNA expression profiling using next-generation sequencing technologies . Lab. Invest.94 ( 3 ), 350 – 358 ( 2014 ).
   PubMed Web of Science ®Google Scholar
• Miller JA , DingSL , SunkinSMet al. Transcriptional landscape of the prenatal human brain . Nature508 ( 7495 ), 199 – 206 ( 2014 ).
   PubMed Web of Science ®Google Scholar
• Juhila J , SipilaT , IcayKet al. MicroRNA expression profiling reveals miRNA families regulating specific biological pathways in mouse frontal cortex and hippocampus . PLoS ONE6 ( 6 ), e21495 ( 2011 ).
   PubMed Web of Science ®Google Scholar
• Ludwig N , LeidingerP , BeckerKet al. Distribution of miRNA expression across human tissues . Nucleic Acids Res.44 ( 8 ), 3865 – 3877 ( 2016 ).
   PubMed Web of Science ®Google Scholar
• Tomita H , VawterMP , WalshDMet al. Effect of agonal and postmortem factors on gene expression profile: quality control in microarray analyses of postmortem human brain . Biol. Psychiatry55 ( 4 ), 346 – 352 ( 2004 ).
   PubMed Web of Science ®Google Scholar
• Hu HY , HeL , FominykhKet al. Evolution of the human-specific microRNA miR-941 . Nat. Comm.3 , 1145 ( 2012 ).
   PubMed Web of Science ®Google Scholar
• Lopez JP , LimR , CruceanuCet al. miR-1202 is a primate-specific and brain-enriched microRNA involved in major depression and antidepressant treatment . Nat. Med.20 ( 7 ), 764 – 768 ( 2014 ).
   PubMed Web of Science ®Google Scholar