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Volumn 34, Issue 5, 2017, Pages 1217-1229

Differential Gene Expression in the Human Brain Is Associated with Conserved, but Not Accelerated, Noncoding Sequences

Author keywords

Brain; Conserved noncoding sequence; Gene expression

Indexed keywords

ACCELERATION; ADULT; BRAIN REGION; DNA STRUCTURE; GENE EXPRESSION; HUMAN; PROBABILITY; SPECIES; UPREGULATION; ANIMAL; BRAIN; CONSERVED SEQUENCE; GENE EXPRESSION REGULATION; GENETICS; METABOLISM; NUCLEOTIDE SEQUENCE; OPEN READING FRAME;

EID: 85019126732     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msx076     Document Type: Article
Times cited : (9)

References (76)
  • 1
    • 33745626459 scopus 로고    scopus 로고
    • Improved scoring of functional groups from gene expression data by decorrelating go graph structure
    • Alexa A, Rahnenführer J, Lengauer T. (2006). Improved scoring of functional groups from gene expression data by decorrelating GO graph structure. Bioinformatics 22: 1600-1607
    • (2006) Bioinformatics , vol.22 , pp. 1600-1607
    • Alexa, A.1    Rahnenführer, J.2    Lengauer, T.3
  • 2
    • 84892554083 scopus 로고    scopus 로고
    • Heterogeneous tempo and mode of conserved noncoding sequence evolution among four mammalian orders
    • Babarinde IA, Saitou N. (2013). Heterogeneous tempo and mode of conserved noncoding sequence evolution among four mammalian orders. Genome Biol Evol. 5: 2330-2343
    • (2013) Genome Biol Evol , vol.5 , pp. 2330-2343
    • Babarinde, I.A.1    Saitou, N.2
  • 3
    • 85016147805 scopus 로고    scopus 로고
    • Genomic locations of conserved noncoding sequences and their proximal protein-coding genes in mammalian expression dynamics
    • Babarinde IA, Saitou N. (2016). Genomic locations of conserved noncoding sequences and their proximal protein-coding genes in mammalian expression dynamics. Mol Biol Evol. 33: 1807-1817
    • (2016) Mol Biol Evol , vol.33 , pp. 1807-1817
    • Babarinde, I.A.1    Saitou, N.2
  • 7
    • 3042740671 scopus 로고    scopus 로고
    • Comparative genomics at the vertebrate extremes
    • Boffelli D, Nobrega MA, Rubin EM. (2004). Comparative genomics at the vertebrate extremes. Nat Rev Genet. 5: 456-465
    • (2004) Nat Rev Genet , vol.5 , pp. 456-465
    • Boffelli, D.1    Nobrega, M.A.2    Rubin, E.M.3
  • 10
    • 46149104377 scopus 로고    scopus 로고
    • Evo-devo and an expanding evolutionary syn thesis a genetic theory of morphological evolution
    • Carroll SB. (2008). Evo-devo and an expanding evolutionary synthesis: A genetic theory of morphological evolution. Cell 134: 25-36
    • (2008) Cell , vol.134 , pp. 25-36
    • Carroll, S.B.1
  • 11
    • 84866453386 scopus 로고    scopus 로고
    • Genomic context analysis reveals dense interaction network between vertebrate ultraconserved non-coding elements
    • Dimitrieva S, Bucher P. (2012). Genomic context analysis reveals dense interaction network between vertebrate ultraconserved non-coding elements. Bioinformatics 28: i395-i401
    • (2012) Bioinformatics , vol.28 , pp. i395-i401
    • Dimitrieva, S.1    Bucher, P.2
  • 13
    • 33645833857 scopus 로고    scopus 로고
    • Conservation of RET regulatory function from human to zebrafish without sequence similarity
    • Fisher S, Grice EA, Vinton RM, Bessling SL, McCallion AS. (2006). Conservation of RET regulatory function from human to zebrafish without sequence similarity. Science 312: 276-279
    • (2006) Science , vol.312 , pp. 276-279
    • Fisher, S.1    Grice, E.A.2    Vinton, R.M.3    Bessling, S.L.4    McCallion, A.S.5
  • 15
    • 79951528195 scopus 로고    scopus 로고
    • Minor change, major difference: Divergent functions of highly conserved cis-regulatory elements subsequent to whole genome duplication events
    • Goode DK, Callaway HA, Cerda GA, Lewis KE, Elgar G. (2011). Minor change, major difference: Divergent functions of highly conserved cis-regulatory elements subsequent to whole genome duplication events. Development 138: 879-884
    • (2011) Development , vol.138 , pp. 879-884
    • Goode, D.K.1    Callaway, H.A.2    Cerda, G.A.3    Lewis, K.E.4    Elgar, G.5
  • 16
    • 46249134068 scopus 로고    scopus 로고
    • Sepsid evenskipped enhancers are functionally conserved in Drosophila despite lack of sequence conservation
    • Hare EE, Peterson BK, Iyer VN, Meier R, Eisen MB. (2008). Sepsid evenskipped enhancers are functionally conserved in Drosophila despite lack of sequence conservation. PLoS Genet. 4: e1000106
    • (2008) Plos Genet , vol.4 , pp. e1000106
    • Hare, E.E.1    Peterson, B.K.2    Iyer, V.N.3    Meier, R.4    Eisen, M.B.5
  • 18
    • 77952359315 scopus 로고    scopus 로고
    • Contrasts between adaptive coding and noncoding changes during human evolution
    • Haygood R, Babbitt CC, Fedrigo O, Wray GA. (2010). Contrasts between adaptive coding and noncoding changes during human evolution. Proc Natl Acad Sci U S A. 107: 7853-7857
    • (2010) Proc Natl Acad Sci U S A. , vol.107 , pp. 7853-7857
    • Haygood, R.1    Babbitt, C.C.2    Fedrigo, O.3    Wray, G.A.4
  • 19
    • 34548346860 scopus 로고    scopus 로고
    • Promoter regions of many neural-and nutrition-related genes have experienced positive selection during human evolution
    • Haygood R, Fedrigo O, Hanson B, Yokoyama K-D, Wray GA. (2007). Promoter regions of many neural-and nutrition-related genes have experienced positive selection during human evolution. Nat Genet. 39: 1140-1144
    • (2007) Nat Genet , vol.39 , pp. 1140-1144
    • Haygood, R.1    Fedrigo, O.2    Hanson, B.3    Yokoyama, K.-D.4    Wray, G.A.5
  • 20
    • 84871254993 scopus 로고    scopus 로고
    • Hundreds of conserved noncoding genomic regions are independently lost in mammals
    • Hiller M, Schaar BT, Bejerano G. (2012). Hundreds of conserved noncoding genomic regions are independently lost in mammals. Nucleic Acids Res. 40: 11463-11476
    • (2012) Nucleic Acids Res , vol.40 , pp. 11463-11476
    • Hiller, M.1    Schaar, B.T.2    Bejerano, G.3
  • 21
    • 34247493236 scopus 로고    scopus 로고
    • Matplotlib: A 2D graphics environment
    • Hunter JD. (2007). Matplotlib: a 2D graphics environment. Comput Sci Eng. 9: 90-95
    • (2007) Comput Sci Eng , vol.9 , pp. 90-95
    • Hunter, J.D.1
  • 24
    • 78649716038 scopus 로고    scopus 로고
    • Nomadic enhancers: Tissue-specific cis-regulatory elements of yellow have divergent genomic positions among drosophila species
    • Kalay G, Wittkopp PJ. (2010). Nomadic enhancers: Tissue-specific cis-regulatory elements of yellow have divergent genomic positions among Drosophila species. PLoS Genet. 6: e1001222
    • (2010) Plos Genet , vol.6 , pp. e1001222
    • Kalay, G.1    Wittkopp, P.J.2
  • 25
    • 84887497668 scopus 로고    scopus 로고
    • A fast-evolving human NPAS3 enhancer gained reporter expression in the developing forebrain of transgenic mice
    • Kamm GB, López-Leal R, Lorenzo JR, Franchini LF. (2013a). A fast-evolving human NPAS3 enhancer gained reporter expression in the developing forebrain of transgenic mice. Philos Trans R Soc Lond B Biol Sci. 368: 20130019
    • (2013) Philos Trans R Soc Lond B Biol Sci , vol.368 , pp. 20130019
    • Kamm, G.B.1    López-Leal, R.2    Lorenzo, J.R.3    Franchini, L.F.4
  • 26
    • 84876520556 scopus 로고    scopus 로고
    • The developmental brain gene NPAS3 contains the largest number of accelerated regulatory sequences in the human genome
    • Kamm GB, Pisciottano F, Kliger R, Franchini LF. (2013b). The developmental brain gene NPAS3 contains the largest number of accelerated regulatory sequences in the human genome. Mol Biol Evol. 30: 1088-1102
    • (2013) Mol Biol Evol , vol.30 , pp. 1088-1102
    • Kamm, G.B.1    Pisciottano, F.2    Kliger, R.3    Franchini, L.F.4
  • 29
    • 34848901059 scopus 로고    scopus 로고
    • Adaptive evolution of conserved noncoding elements in mammals
    • Kim SY, Pritchard JK. (2007). Adaptive evolution of conserved noncoding elements in mammals. PLoS Genet. 3: e147
    • (2007) Plos Genet , vol.3 , pp. e147
    • Kim, S.Y.1    Pritchard, J.K.2
  • 30
    • 84867306721 scopus 로고    scopus 로고
    • Snakemake-A scalable bioinformatics workflow engine
    • Köster J, Rahmann S. (2012). Snakemake-A scalable bioinformatics workflow engine. Bioinformatics 28: 2520-2522
    • (2012) Bioinformatics , vol.28 , pp. 2520-2522
    • Köster, J.1    Rahmann, S.2
  • 32
    • 84896735766 scopus 로고    scopus 로고
    • Voom: Precisionweightsunlocklinear model analysis tools for RNA-seq read counts
    • Law C, Chen Y, Shi W, Smyth G. (2014). voom: precisionweightsunlocklinear model analysis tools for RNA-seq read counts. Genome Biol. 15: R29
    • (2014) Genome Biol , vol.15 , pp. R29
    • Law, C.1    Chen, Y.2    Shi, W.3    Smyth, G.4
  • 35
    • 84876569149 scopus 로고    scopus 로고
    • Vertebrate paralogous conserved noncoding sequences may be related to gene expressions in brain
    • Matsunami M, Saitou N. (2013). Vertebrate paralogous conserved noncoding sequences may be related to gene expressions in brain. Genome Biol. Evol. 5: 140-150
    • (2013) Genome Biol. Evol , vol.5 , pp. 140-150
    • Matsunami, M.1    Saitou, N.2
  • 36
    • 62549109118 scopus 로고    scopus 로고
    • Testing significance relative to a foldchange threshold is a treat
    • McCarthy DJ, Smyth GK. (2009). Testing significance relative to a foldchange threshold is a TREAT. Bioinformatics 25: 765-771
    • (2009) Bioinformatics , vol.25 , pp. 765-771
    • McCarthy, D.J.1    Smyth, G.K.2
  • 37
    • 74249085481 scopus 로고    scopus 로고
    • Early evolution of conserved regulatory sequences associated with development in vertebrates
    • McEwen GK, Goode DK, Parker HJ, Woolfe A, Callaway H, Elgar G. (2009). Early evolution of conserved regulatory sequences associated with development in vertebrates. PLoS Genet. 5: e1000762
    • (2009) Plos Genet , vol.5 , pp. e1000762
    • McEwen, G.K.1    Goode, D.K.2    Parker, H.J.3    Woolfe, A.4    Callaway, H.5    Elgar, G.6
  • 40
    • 84875082455 scopus 로고    scopus 로고
    • Conserved non-coding elements and cis regulation: Actions speak louder than words
    • Nelson AC, Wardle FC. (2013). Conserved non-coding elements and cis regulation: Actions speak louder than words. Development 140: 1385-1395
    • (2013) Development , vol.140 , pp. 1385-1395
    • Nelson, A.C.1    Wardle, F.C.2
  • 41
    • 0142084743 scopus 로고    scopus 로고
    • Scanning human gene deserts for long-range enhancers
    • Nobrega MA, Ovcharenko I, Afzal V, Rubin EM. (2003). Scanning human gene deserts for long-range enhancers. Science 302: 413-413
    • (2003) Science , vol.302 , pp. 413
    • Nobrega, M.A.1    Ovcharenko, I.2    Afzal, V.3    Rubin, E.M.4
  • 43
    • 47649125626 scopus 로고    scopus 로고
    • Widespread ultraconservation divergence in primates
    • Ovcharenko I. (2008). Widespread ultraconservation divergence in primates. Mol Biol Evol. 25: 1668-1676
    • (2008) Mol Biol Evol , vol.25 , pp. 1668-1676
    • Ovcharenko, I.1
  • 45
    • 15244341767 scopus 로고    scopus 로고
    • Enhancer sequence conservation between vertebrates is favoured in developmental regulator genes
    • Plessy C, Dickmeis T, Chalmel F, Strähle U. (2005). Enhancer sequence conservation between vertebrates is favoured in developmental regulator genes. Trends Genet. 21: 207-210
    • (2005) Trends Genet , vol.21 , pp. 207-210
    • Plessy, C.1    Dickmeis, T.2    Chalmel, F.3    Strähle, U.4
  • 49
    • 33750737061 scopus 로고    scopus 로고
    • Acceleratedevolution of conservednoncoding sequences inhumans
    • Prabhakar S, Noonan JP, Pääbo S, Rubin EM. (2006a). Acceleratedevolution of conservednoncoding sequences inhumans. Science 314: 786-786
    • (2006) Science , vol.314 , pp. 786
    • Prabhakar, S.1    Noonan, J.P.2    Pääbo, S.3    Rubin, E.M.4
  • 52
    • 77951770756 scopus 로고    scopus 로고
    • BEDTools: A flexible suite of utilities for comparing genomic features
    • Quinlan AR, Hall IM. (2010). BEDTools: A flexible suite of utilities for comparing genomic features. Bioinformatics 26: 841-842
    • (2010) Bioinformatics , vol.26 , pp. 841-842
    • Quinlan, A.R.1    Hall, I.M.2
  • 53
    • 84975753826 scopus 로고    scopus 로고
    • R Core Team. R Foundation for Statistical Computing, Vienna, Austria. Available from last accessed November 6, 2016
    • R Core Team. (2016). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. Available from: https://www.R-project.org/, last accessed November 6, 2016
    • (2016) R A Language and Environment for Statistical Computing
  • 56
    • 85019092756 scopus 로고    scopus 로고
    • Emergence and evolution of hominidae-specific coding and noncoding genomic sequences
    • Saber MM, Adeyemi Babarinde I, Hettiarachchi N, Saitou N. (2016). Emergence and evolution of Hominidae-specific coding and noncoding genomic sequences. Genome Biol Evol. 8: 2076-2092
    • (2016) Genome Biol Evol , vol.8 , pp. 2076-2092
    • Saber, M.M.1    Adeyemi Babarinde, I.2    Hettiarachchi, N.3    Saitou, N.4
  • 58
    • 84982180013 scopus 로고    scopus 로고
    • Inferring selective constraint from population genomic data suggests recent regulatory turnover in the human brain
    • Schrider DR, Kern AD. (2015). Inferring selective constraint from population genomic data suggests recent regulatory turnover in the human brain. Genome Biol Evol. 7: 3511-3528
    • (2015) Genome Biol Evol , vol.7 , pp. 3511-3528
    • Schrider, D.R.1    Kern, A.D.2
  • 60
    • 84921714149 scopus 로고    scopus 로고
    • From trans to cis: Transcriptional regulatory networks in neocortical development
    • Shibata M, Gulden FO, Sestan N. (2015). From trans to cis: Transcriptional regulatory networks in neocortical development. Trends Genet. 31: 77-87
    • (2015) Trends Genet , vol.31 , pp. 77-87
    • Shibata, M.1    Gulden, F.O.2    Sestan, N.3
  • 61
    • 84861932338 scopus 로고    scopus 로고
    • Cis-regulatory control of corticospinal system development and evolution
    • Shim S, Kwan KY, Li M, Lefebvre V, Sestan N. (2012). Cis-regulatory control of corticospinal system development and evolution. Nature 486: 74-79
    • (2012) Nature , vol.486 , pp. 74-79
    • Shim, S.1    Kwan, K.Y.2    Li, M.3    Lefebvre, V.4    Sestan, N.5
  • 63
    • 84996504468 scopus 로고    scopus 로고
    • The cellular and molecular landscapes of the developing human central nervous system
    • Silbereis JC, Pochareddy S, Zhu Y, Li M, Sestan N. (2016). The cellular and molecular landscapes of the developing human central nervous system. Neuron 89: 248-268
    • (2016) Neuron , vol.89 , pp. 248-268
    • Silbereis, J.C.1    Pochareddy, S.2    Zhu, Y.3    Li, M.4    Sestan, N.5
  • 64
    • 4544341015 scopus 로고    scopus 로고
    • Linear models and empirical bayes methods for assessing differential expression in microarray experiments
    • Smyth GK. (2004). Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol. 3: 1-25
    • (2004) Stat Appl Genet Mol Biol , vol.3 , pp. 1-25
    • Smyth, G.K.1
  • 65
    • 84954389263 scopus 로고    scopus 로고
    • Stan Development Team. Available from last accessed March 18, 2015
    • Stan Development Team. (2015). Stan: A C++ library for probability and sampling. Available from: http://mc-stan.org/, last accessed March 18, 2015
    • (2015) Stan: A C++ Library for Probability and Sampling
  • 66
    • 80155192425 scopus 로고    scopus 로고
    • Loss-of-function mutation in a repressor module of human-specifically activated enhancer HACNS1
    • Sumiyama K, Saitou N. (2011). Loss-of-function mutation in a repressor module of human-specifically activated enhancer HACNS1. Mol Biol Evol. 28: 3005-3007
    • (2011) Mol Biol Evol , vol.28 , pp. 3005-3007
    • Sumiyama, K.1    Saitou, N.2
  • 67
    • 61449212191 scopus 로고    scopus 로고
    • Variable locus length in the human genome leads to ascertainment bias in functional inference for non-coding elements
    • Taher L, Ovcharenko I. (2009). Variable locus length in the human genome leads to ascertainment bias in functional inference for non-coding elements. Bioinformatics 25: 578-584
    • (2009) Bioinformatics , vol.25 , pp. 578-584
    • Taher, L.1    Ovcharenko, I.2
  • 68
    • 84929001104 scopus 로고    scopus 로고
    • The genotype-tissue expression (GTEx) pilot analysis: Multitissue gene regulation in humans
    • The GTEx Consortium
    • The GTEx Consortium. (2015). The genotype-tissue expression (GTEx) pilot analysis: Multitissue gene regulation in humans. Science 348: 648-660
    • (2015) Science , vol.348 , pp. 648-660
  • 70
    • 84899453734 scopus 로고    scopus 로고
    • Evolution of transcription factor binding in metazoans-Mechanisms and functional implications
    • Villar D, Flicek P, Odom DT. (2014). Evolution of transcription factor binding in metazoans-Mechanisms and functional implications. Nat Rev Genet. 15: 221-233
    • (2014) Nat Rev Genet , vol.15 , pp. 221-233
    • Villar, D.1    Flicek, P.2    Odom, D.T.3
  • 73
    • 78650862532 scopus 로고    scopus 로고
    • Fast stable restricted maximum likelihood and marginal likelihood estimation of semiparametric generalized linear models
    • Wood SN. (2011). Fast stable restricted maximum likelihood and marginal likelihood estimation of semiparametric generalized linear models. J R Stat Soc B. 73: 3-36
    • (2011) J R Stat Soc B. , vol.73 , pp. 3-36
    • Wood, S.N.1
  • 75
    • 33847057226 scopus 로고    scopus 로고
    • The evolutionary significance of cis-regulatory mutations
    • Wray GA. (2007). The evolutionary significance of cis-regulatory mutations. Nat Rev Genet. 8: 206-216
    • (2007) Nat Rev Genet , vol.8 , pp. 206-216
    • Wray, G.A.1
  • 76
    • 0342635450 scopus 로고    scopus 로고
    • A highly conserved enhancer in the Dlx5/Dlx6 intergenic region is the site of crossregulatory interactions between Dlx genes in the embryonic forebrain
    • Zerucha T, Stühmer T, Hatch G, Park BK, Long Q, Yu G, Gambarotta A, Schultz JR, Rubenstein JLR, Ekker M. (2000). A highly conserved enhancer in the Dlx5/Dlx6 intergenic region is the site of crossregulatory interactions between Dlx genes in the embryonic forebrain. J Neurosci. 20: 709-721
    • (2000) J Neurosci , vol.20 , pp. 709-721
    • Zerucha, T.1    Stühmer, T.2    Hatch, G.3    Park, B.K.4    Long, Q.5    Yu, G.6    Gambarotta, A.7    Schultz, J.R.8    Rubenstein, J.L.R.9    Ekker, M.10


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