메뉴 건너뛰기




Volumn 362, Issue 6420, 2018, Pages

Transcriptome and epigenome landscape of human cortical development modeled in organoids

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTOME;

EID: 85058398161     PISSN: 00368075     EISSN: 10959203     Source Type: Journal    
DOI: 10.1126/science.aat6720     Document Type: Article
Times cited : (209)

References (49)
  • 1
    • 0029132983 scopus 로고
    • A small step for the cell, a giant leap for mankind: A hypothesis of neocortical expansion during evolution
    • pmid: 7482803
    • P. Rakic, A small step for the cell, a giant leap for mankind: A hypothesis of neocortical expansion during evolution. Trends Neurosci. 18, 383-388 (1995). doi: 10.1016/0166-2236(95)93934-P; pmid: 7482803
    • (1995) Trends Neurosci. , vol.18 , pp. 383-388
    • Rakic, P.1
  • 2
    • 0027938146 scopus 로고
    • The embryonic vertebrate forebrain: The prosomeric model
    • pmid: 7939711
    • J. L. R. Rubenstein, S. Martinez, K. Shimamura, L. Puelles, The embryonic vertebrate forebrain: The prosomeric model. Science 266, 578-580 (1994). doi: 10.1126/science.7939711; pmid: 7939711
    • (1994) Science , vol.266 , pp. 578-580
    • Rubenstein, J.L.R.1    Martinez, S.2    Shimamura, K.3    Puelles, L.4
  • 3
    • 84874118170 scopus 로고    scopus 로고
    • A high-resolution enhancer atlas of the developing telencephalon
    • pmid: 23375746
    • A. Visel et al., A high-resolution enhancer atlas of the developing telencephalon. Cell 152, 895-908 (2013). doi: 10.1016/j.cell.2012.12.041; pmid: 23375746
    • (2013) Cell , vol.152 , pp. 895-908
    • Visel, A.1
  • 4
    • 84889561601 scopus 로고    scopus 로고
    • Integrative functional genomic analyses implicate specific molecular pathways and circuits in autism
    • pmid: 24267887
    • N. N. Parikshak et al., Integrative functional genomic analyses implicate specific molecular pathways and circuits in autism. Cell 155, 1008-1021 (2013). doi: 10.1016/j.cell.2013.10.031; pmid: 24267887
    • (2013) Cell , vol.155 , pp. 1008-1021
    • Parikshak, N.N.1
  • 5
    • 84889583293 scopus 로고    scopus 로고
    • Coexpression networks implicate human midfetal deep cortical projection neurons in the pathogenesis of autism
    • pmid: 24267886
    • A. J. Willsey et al., Coexpression networks implicate human midfetal deep cortical projection neurons in the pathogenesis of autism. Cell 155, 997-1007 (2013). doi: 10.1016/ j.cell.2013.10.020; pmid: 24267886
    • (2013) Cell , vol.155 , pp. 997-1007
    • Willsey, A.J.1
  • 6
    • 84937212591 scopus 로고    scopus 로고
    • FOXG1-dependent dysregulation of GABA/glutamate neuron differentiation in autism spectrum disorders
    • pmid: 26186191
    • J. Mariani et al., FOXG1-Dependent Dysregulation of GABA/ Glutamate Neuron Differentiation in Autism Spectrum Disorders. Cell 162, 375-390 (2015). doi: 10.1016/ j.cell.2015.06.034; pmid: 26186191
    • (2015) Cell , vol.162 , pp. 375-390
    • Mariani, J.1
  • 7
    • 84881193129 scopus 로고    scopus 로고
    • Spatial and temporal mapping of de novo mutations in schizophrenia to a fetal prefrontal cortical network
    • pmid: 23911319
    • S. Gulsuner et al., Spatial and temporal mapping of de novo mutations in schizophrenia to a fetal prefrontal cortical network. Cell 154, 518-529 (2013). doi: 10.1016/ j.cell.2013.06.049; pmid: 23911319
    • (2013) Cell , vol.154 , pp. 518-529
    • Gulsuner, S.1
  • 8
    • 85058412077 scopus 로고    scopus 로고
    • See supplementary materials
    • See supplementary materials.
  • 9
    • 85058377382 scopus 로고    scopus 로고
    • Integrative functional genomic analysis of human brain development and neuropsychiatric risks
    • M. Li et al., Integrative functional genomic analysis of human brain development and neuropsychiatric risks. Science 362, eaat7615 (2018).
    • (2018) Science , vol.362 , pp. eaat7615
    • Li, M.1
  • 10
    • 84948741313 scopus 로고    scopus 로고
    • The PsychENCODE project
    • pmid: 26605881
    • S. Akbarian et al., The PsychENCODE project. Nat. Neurosci. 18, 1707-1712 (2015). doi: 10.1038/nn.4156; pmid: 26605881
    • (2015) Nat. Neurosci. , vol.18 , pp. 1707-1712
    • Akbarian, S.1
  • 11
    • 84923362619 scopus 로고    scopus 로고
    • Integrative analysis of 111 reference human epigenomes
    • pmid: 25693563
    • A. Kundaje et al., Integrative analysis of 111 reference human epigenomes. Nature 518, 317-330 (2015). doi: 10.1038/ nature14248; pmid: 25693563
    • (2015) Nature , vol.518 , pp. 317-330
    • Kundaje, A.1
  • 12
    • 80055015161 scopus 로고    scopus 로고
    • Temporal dynamics and genetic control of transcription in the human prefrontal cortex
    • pmid: 22031444
    • C. Colantuoni et al., Temporal dynamics and genetic control of transcription in the human prefrontal cortex. Nature 478, 519-523 (2011). doi: 10.1038/nature10524; pmid: 22031444
    • (2011) Nature , vol.478 , pp. 519-523
    • Colantuoni, C.1
  • 13
    • 84896393703 scopus 로고    scopus 로고
    • The developmental transcriptome of the human brain: Implications for neurodevelopmental disorders
    • pmid: 24565942
    • A. T. Tebbenkamp, A. J. Willsey, M. W. State, N. Sestan, The developmental transcriptome of the human brain: Implications for neurodevelopmental disorders. Curr. Opin. Neurol. 27, 149-156 (2014). doi: 10.1097/WCO.0000000000000069; pmid: 24565942
    • (2014) Curr. Opin. Neurol. , vol.27 , pp. 149-156
    • Tebbenkamp, A.T.1    Willsey, A.J.2    State, M.W.3    Sestan, N.4
  • 14
    • 84963544829 scopus 로고    scopus 로고
    • Single-cell analysis of long non-coding RNAs in the developing human neocortex
    • pmid: 27081004
    • S. J. Liu et al., Single-cell analysis of long non-coding RNAs in the developing human neocortex. Genome Biol. 17, 67 (2016). doi: 10.1186/s13059-016-0932-1; pmid: 27081004
    • (2016) Genome Biol. , vol.17 , pp. 67
    • Liu, S.J.1
  • 15
    • 85037631415 scopus 로고    scopus 로고
    • Spatiotemporal gene expression trajectories reveal developmental hierarchies of the human cortex
    • pmid: 29217575
    • T. J. Nowakowski et al., Spatiotemporal gene expression trajectories reveal developmental hierarchies of the human cortex. Science 358, 1318-1323 (2017). doi: 10.1126/science. aap8809; pmid: 29217575
    • (2017) Science , vol.358 , pp. 1318-1323
    • Nowakowski, T.J.1
  • 16
    • 84993993658 scopus 로고    scopus 로고
    • Chromosome conformation elucidates regulatory relationships in developing human brain
    • pmid: 27760116
    • H. Won et al., Chromosome conformation elucidates regulatory relationships in developing human brain. Nature 538, 523-527 (2016). doi: 10.1038/nature19847; pmid: 27760116
    • (2016) Nature , vol.538 , pp. 523-527
    • Won, H.1
  • 17
    • 84865760395 scopus 로고    scopus 로고
    • GENCODE: The reference human genome annotation for the ENCODE Project
    • pmid: 22955987
    • J. Harrow et al., GENCODE: The reference human genome annotation for The ENCODE Project. Genome Res. 22, 1760-1774 (2012). doi: 10.1101/gr.135350.111; pmid: 22955987
    • (2012) Genome Res. , vol.22 , pp. 1760-1774
    • Harrow, J.1
  • 18
    • 84865790047 scopus 로고    scopus 로고
    • An integrated encyclopedia of DNA elements in the human genome
    • The ENCODE Project Consortium, pmid: 22955616
    • The ENCODE Project Consortium, An integrated encyclopedia of DNA elements in the human genome. Nature 489, 57-74 (2012). doi: 10.1038/nature11247; pmid: 22955616
    • (2012) Nature , vol.489 , pp. 57-74
  • 19
    • 84875085989 scopus 로고    scopus 로고
    • The patterns of histone modifications in the vicinity of transcription factor binding sites in human lymphoblastoid cell lines
    • pmid: 23527292
    • Y. Nie, H. Liu, X. Sun, The patterns of histone modifications in the vicinity of transcription factor binding sites in human lymphoblastoid cell lines. PLOS ONE 8, e60002 (2013). doi: 10.1371/journal.pone.0060002; pmid: 23527292
    • (2013) PLOS ONE , vol.8 , pp. e60002
    • Nie, Y.1    Liu, H.2    Sun, X.3
  • 20
    • 18744400798 scopus 로고    scopus 로고
    • Beta-catenin directly displaces Groucho/TLE repressors from Tcf/Lef in Wnt-mediated transcription activation
    • pmid: 15768032
    • D. L. Daniels, W. I. Weis, Beta-catenin directly displaces Groucho/TLE repressors from Tcf/Lef in Wnt-mediated transcription activation. Nat. Struct. Mol. Biol. 12, 364-371 (2005). doi: 10.1038/nsmb912; pmid: 15768032
    • (2005) Nat. Struct. Mol. Biol. , vol.12 , pp. 364-371
    • Daniels, D.L.1    Weis, W.I.2
  • 21
    • 60549111634 scopus 로고    scopus 로고
    • WGCNA: An R package for weighted correlation network analysis
    • pmid: 19114008
    • P. Langfelder, S. Horvath, WGCNA: An R package for weighted correlation network analysis. BMC Bioinformatics 9, 559 (2008). doi: 10.1186/1471-2105-9-559; pmid: 19114008
    • (2008) BMC Bioinformatics , vol.9 , pp. 559
    • Langfelder, P.1    Horvath, S.2
  • 22
    • 84992147507 scopus 로고    scopus 로고
    • A systematic variant annotation approach for ranking genes associated with autism spectrum disorders
    • pmid: 27790361
    • E. Larsen et al., A systematic variant annotation approach for ranking genes associated with autism spectrum disorders. Mol. Autism 7, 44 (2016). doi: 10.1186/s13229-016-0103-y; pmid: 27790361
    • (2016) Mol. Autism , vol.7 , pp. 44
    • Larsen, E.1
  • 23
    • 84952674076 scopus 로고    scopus 로고
    • Human cerebral organoids recapitulate gene expression programs of fetal neocortex development
    • pmid: 26644564
    • J. G. Camp et al., Human cerebral organoids recapitulate gene expression programs of fetal neocortex development. Proc. Natl. Acad. Sci. U.S.A. 112, 15672-15677 (2015). pmid: 26644564
    • (2015) Proc. Natl. Acad. Sci. U.S.A. , vol.112 , pp. 15672-15677
    • Camp, J.G.1
  • 24
    • 85039917750 scopus 로고    scopus 로고
    • The Dynamic Landscape of Open Chromatin during Human Cortical Neurogenesis
    • pmid: 29307494
    • L. de la Torre-Ubieta et al., The Dynamic Landscape of Open Chromatin during Human Cortical Neurogenesis. Cell 172, 289-304.e18 (2018). doi: 10.1016/j.cell.2017.12.014; pmid: 29307494
    • (2018) Cell , vol.172 , pp. 289-289e18
    • De La Torre-Ubieta, L.1
  • 25
    • 85016140982 scopus 로고    scopus 로고
    • Genome-wide changes in lncRNA, splicing, and regional gene expression patterns in autism
    • pmid: 27919067
    • N. N. Parikshak et al., Genome-wide changes in lncRNA, splicing, and regional gene expression patterns in autism. Nature 540, 423-427 (2016). doi: 10.1038/nature20612; pmid: 27919067
    • (2016) Nature , vol.540 , pp. 423-427
    • Parikshak, N.N.1
  • 26
    • 84924561748 scopus 로고    scopus 로고
    • Evolutionary changes in promoter and enhancer activity during human corticogenesis
    • pmid: 25745175
    • S. K. Reilly et al., Evolutionary changes in promoter and enhancer activity during human corticogenesis. Science 347, 1155-1159 (2015). doi: 10.1126/science.1260943; pmid: 25745175
    • (2015) Science , vol.347 , pp. 1155-1159
    • Reilly, S.K.1
  • 27
    • 85058394301 scopus 로고    scopus 로고
    • Spatiotemporal transcriptomic divergence across human and macaque brain development
    • Y. Zhu et al., Spatiotemporal transcriptomic divergence across human and macaque brain development. Science 362, eaat8077 (2018).
    • (2018) Science , vol.362 , pp. eaat8077
    • Zhu, Y.1
  • 28
    • 84991263060 scopus 로고    scopus 로고
    • Transformation of the radial glia scaffold demarcates two stages of human cerebral cortex development
    • pmid: 27657449
    • T. J. Nowakowski, A. A. Pollen, C. Sandoval-Espinosa, A. R. Kriegstein, Transformation of the Radial Glia Scaffold Demarcates Two Stages of Human Cerebral Cortex Development. Neuron 91, 1219-1227 (2016). doi: 10.1016/ j.neuron.2016.09.005; pmid: 27657449
    • (2016) Neuron , vol.91 , pp. 1219-1227
    • Nowakowski, T.J.1    Pollen, A.A.2    Sandoval-Espinosa, C.3    Kriegstein, A.R.4
  • 29
    • 84867829870 scopus 로고    scopus 로고
    • Individual common variants exert weak effects on the risk for autism spectrum disorders
    • pmid: 22843504
    • R. Anney et al., Individual common variants exert weak effects on the risk for autism spectrum disorders. Hum. Mol. Genet. 21, 4781-4792 (2012). doi: 10.1093/hmg/dds301; pmid: 22843504
    • (2012) Hum. Mol. Genet. , vol.21 , pp. 4781-4792
    • Anney, R.1
  • 30
    • 84905582433 scopus 로고    scopus 로고
    • Most genetic risk for autism resides with common variation
    • pmid: 25038753
    • T. Gaugler et al., Most genetic risk for autism resides with common variation. Nat. Genet. 46, 881-885 (2014). doi: 10.1038/ng.3039; pmid: 25038753
    • (2014) Nat. Genet. , vol.46 , pp. 881-885
    • Gaugler, T.1
  • 31
    • 84871298155 scopus 로고    scopus 로고
    • Common genetic variants, acting additively, are a major source of risk for autism
    • pmid: 23067556
    • L. Klei et al., Common genetic variants, acting additively, are a major source of risk for autism. Mol. Autism 3, 9 (2012). doi: 10.1186/2040-2392-3-9; pmid: 23067556
    • (2012) Mol. Autism , vol.3 , pp. 9
    • Klei, L.1
  • 32
    • 85021757773 scopus 로고    scopus 로고
    • Polygenic transmission disequilibrium confirms that common and rare variation act additively to create risk for autism spectrum disorders
    • pmid: 28504703
    • D. J. Weiner et al., Polygenic transmission disequilibrium confirms that common and rare variation act additively to create risk for autism spectrum disorders. Nat. Genet. 49, 978-985 (2017). doi: 10.1038/ng.3863; pmid: 28504703
    • (2017) Nat. Genet. , vol.49 , pp. 978-985
    • Weiner, D.J.1
  • 33
    • 85046026156 scopus 로고    scopus 로고
    • An analytical framework for whole-genome sequence association studies and its implications for autism spectrum disorder
    • pmid: 29700473
    • D. M. Werling et al., An analytical framework for whole-genome sequence association studies and its implications for autism spectrum disorder. Nat. Genet. 50, 727-736 (2018). doi: 10.1038/s41588-018-0107-y; pmid: 29700473
    • (2018) Nat. Genet. , vol.50 , pp. 727-736
    • Werling, D.M.1
  • 34
    • 85016156181 scopus 로고    scopus 로고
    • The GeneCards suite: From gene data mining to disease genome sequence analyses
    • pmid: 27322403
    • G. Stelzer et al., The GeneCards Suite: From Gene Data Mining to Disease Genome Sequence Analyses. Curr. Protoc. Bioinformatics 54, 1.30.1-1.30.33 (2016). pmid: 27322403
    • (2016) Curr. Protoc. Bioinformatics , vol.54 , pp. 1301-13033
    • Stelzer, G.1
  • 35
    • 85003972512 scopus 로고    scopus 로고
    • Rare inherited and de Novo CNVs reveal complex contributions to ASD risk in multiplex families
    • pmid: 27569545
    • V. M. Leppa et al., Rare Inherited and De Novo CNVs Reveal Complex Contributions to ASD Risk in Multiplex Families. Am. J. Hum. Genet. 99, 540-554 (2016). doi: 10.1016/ j.ajhg.2016.06.036; pmid: 27569545
    • (2016) Am. J. Hum. Genet. , vol.99 , pp. 540-554
    • Leppa, V.M.1
  • 36
    • 85030709217 scopus 로고    scopus 로고
    • Genomic patterns of de novo mutation in simplex autism
    • pmid: 28965761
    • T. N. Turner et al., Genomic Patterns of De Novo Mutation in Simplex Autism. Cell 171, 710-722.e12 (2017). doi: 10.1016/ j.cell.2017.08.047; pmid: 28965761
    • (2017) Cell , vol.171 , pp. 710-710e12
    • Turner, T.N.1
  • 37
    • 85042546549 scopus 로고    scopus 로고
    • Common schizophrenia alleles are enriched in mutation-intolerant genes and in regions under strong background selection
    • pmid: 29483656
    • A. F. Pardiñas et al., Common schizophrenia alleles are enriched in mutation-intolerant genes and in regions under strong background selection. Nat. Genet. 50, 381-389 (2018). doi: 10.1038/s41588-018-0059-2; pmid: 29483656
    • (2018) Nat. Genet. , vol.50 , pp. 381-389
    • Pardiñas, A.F.1
  • 38
    • 85041117222 scopus 로고    scopus 로고
    • The rise of three-dimensional human brain cultures
    • pmid: 29364288
    • S. P. Paşca, The rise of three-dimensional human brain cultures. Nature 553, 437-445 (2018). pmid: 29364288
    • (2018) Nature , vol.553 , pp. 437-445
    • Paşca, S.P.1
  • 39
    • 84934442315 scopus 로고    scopus 로고
    • Functional cortical neurons and astrocytes from human pluripotent stem cells in 3D culture
    • pmid: 26005811
    • A. M. Paşca et al., Functional cortical neurons and astrocytes from human pluripotent stem cells in 3D culture. Nat. Methods 12, 671-678 (2015). doi: 10.1038/nmeth.3415; pmid: 26005811
    • (2015) Nat. Methods , vol.12 , pp. 671-678
    • Paşca, A.M.1
  • 40
    • 84964619895 scopus 로고    scopus 로고
    • Brain-region-specific organoids using minibioreactors for modeling ZIKV exposure
    • pmid: 27118425
    • X. Qian et al., Brain-Region-Specific Organoids Using Minibioreactors for Modeling ZIKV Exposure. Cell 165, 1238-1254 (2016). doi: 10.1016/j.cell.2016.04.032; pmid: 27118425
    • (2016) Cell , vol.165 , pp. 1238-1254
    • Qian, X.1
  • 41
    • 75249087100 scopus 로고    scopus 로고
    • EdgeR: A Bioconductor package for differential expression analysis of digital gene expression data
    • pmid: 19910308
    • M. D. Robinson, D. J. McCarthy, G. K. Smyth, edgeR: A Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26, 139-140 (2010). doi: 10.1093/bioinformatics/btp616; pmid: 19910308
    • (2010) Bioinformatics , vol.26 , pp. 139-140
    • Robinson, M.D.1    McCarthy, D.J.2    Smyth, G.K.3
  • 42
    • 85046298440 scopus 로고    scopus 로고
    • Integrating single-cell transcriptomic data across different conditions, technologies, and species
    • pmid: 29608179
    • A. Butler, P. Hoffman, P. Smibert, E. Papalexi, R. Satija, Integrating single-cell transcriptomic data across different conditions, technologies, and species. Nat. Biotechnol. 36, 411-420 (2018). doi: 10.1038/nbt.4096; pmid: 29608179
    • (2018) Nat. Biotechnol. , vol.36 , pp. 411-420
    • Butler, A.1    Hoffman, P.2    Smibert, P.3    Papalexi, E.4    Satija, R.5
  • 43
    • 84900873950 scopus 로고    scopus 로고
    • The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells
    • pmid: 24658644
    • C. Trapnell et al., The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells. Nat. Biotechnol. 32, 381-386 (2014). doi: 10.1038/ nbt.2859; pmid: 24658644
    • (2014) Nat. Biotechnol. , vol.32 , pp. 381-386
    • Trapnell, C.1
  • 44
    • 85058418230 scopus 로고    scopus 로고
    • https://www.doi.org/10.1093/nar/gkn698
  • 45
    • 67849130563 scopus 로고    scopus 로고
    • ToppGene Suite for gene list enrichment analysis and candidate gene prioritization
    • pmid: 19465376
    • J. Chen, E. E. Bardes, B. J. Aronow, A. G. Jegga, ToppGene Suite for gene list enrichment analysis and candidate gene prioritization. Nucleic Acids Res. 37, W305-W311 (2009). doi: 10.1093/nar/gkp427; pmid: 19465376
    • (2009) Nucleic Acids Res. , vol.37 , pp. W305-W311
    • Chen, J.1    Bardes, E.E.2    Aronow, B.J.3    Jegga, A.G.4
  • 46
    • 53849146020 scopus 로고    scopus 로고
    • Model-based analysis of ChIP-Seq (MACS)
    • pmid: 18798982
    • Y. Zhang et al., Model-based analysis of ChIP-Seq (MACS). Genome Biol. 9, R137 (2008). doi: 10.1186/gb-2008-9-9-r137; pmid: 18798982
    • (2008) Genome Biol. , vol.9 , pp. R137
    • Zhang, Y.1
  • 47
    • 84857707318 scopus 로고    scopus 로고
    • ChromHMM: Automating chromatin-state discovery and characterization
    • pmid: 22373907
    • J. Ernst, M. Kellis, ChromHMM: Automating chromatin-state discovery and characterization. Nat. Methods 9, 215-216 (2012). doi: 10.1038/nmeth.1906; pmid: 22373907
    • (2012) Nat. Methods , vol.9 , pp. 215-216
    • Ernst, J.1    Kellis, M.2
  • 48
    • 85040936337 scopus 로고    scopus 로고
    • JASPAR 2018: Update of the open-access database of transcription factor binding profiles and its web framework
    • pmid: 29140473
    • A. Khan et al., JASPAR 2018: Update of the open-access database of transcription factor binding profiles and its web framework. Nucleic Acids Res. 46 (D1), D260-D266 (2018). doi: 10.1093/nar/gkx1126; pmid: 29140473
    • (2018) Nucleic Acids Res. , vol.46 , Issue.D1 , pp. D260-D266
    • Khan, A.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.