메뉴 건너뛰기




Volumn 555, Issue 7697, 2018, Pages 538-542

The cis-regulatory dynamics of embryonic development at single-cell resolution

Author keywords

[No Author keywords available]

Indexed keywords

BIOASSAY; CELL; DIFFERENTIATION; EMBRYONIC DEVELOPMENT; FLY; GENE; GENE EXPRESSION; GENETIC ANALYSIS; GENOME;

EID: 85044334985     PISSN: 00280836     EISSN: 14764687     Source Type: Journal    
DOI: 10.1038/nature25981     Document Type: Article
Times cited : (252)

References (58)
  • 1
    • 84930006926 scopus 로고    scopus 로고
    • Multiplex single cell profiling of chromatin accessibility by combinatorial cellular indexing
    • Cusanovich, D. A. et al. Multiplex single cell profiling of chromatin accessibility by combinatorial cellular indexing. Science 348, 910-914 (2015).
    • (2015) Science , vol.348 , pp. 910-914
    • Cusanovich, D.A.1
  • 2
    • 0035265680 scopus 로고    scopus 로고
    • Restriction of mesendoderm to a single blastomere by the combined action of SKN-1 and a GSK-3β homolog is mediated by MED-1 and-2 in C
    • Maduro, M. F., Meneghini, M. D., Bowerman, B., Broitman-Maduro, G. &Rothman, J. H. Restriction of mesendoderm to a single blastomere by the combined action of SKN-1 and a GSK-3β homolog is mediated by MED-1 and-2 in C. elegans. Mol. Cell 7, 475-485 (2001).
    • (2001) Elegans. Mol. Cell , vol.7 , pp. 475-485
    • Maduro, M.F.1    Meneghini, M.D.2    Bowerman, B.3    Broitman-Maduro, G.4    Rothman, J.H.5
  • 3
    • 84856683088 scopus 로고    scopus 로고
    • Sequential signaling crosstalk regulates endomesoderm segregation in sea urchin embryos
    • Sethi, A. J., Wikramanayake, R. M., Angerer, R. C., Range, R. C. &Angerer, L. M. Sequential signaling crosstalk regulates endomesoderm segregation in sea urchin embryos. Science 335, 590-593 (2012).
    • (2012) Science , vol.335 , pp. 590-593
    • Sethi, A.J.1    Wikramanayake, R.M.2    Angerer, R.C.3    Range, R.C.4    Angerer, L.M.5
  • 5
    • 79955760882 scopus 로고    scopus 로고
    • Dynamic reprogramming of chromatin accessibility during Drosophila embryo development
    • Thomas, S. et al. Dynamic reprogramming of chromatin accessibility during Drosophila embryo development. Genome Biol. 12, R43 (2011).
    • (2011) Genome Biol. , vol.12 , pp. R43
    • Thomas, S.1
  • 6
    • 84856239091 scopus 로고    scopus 로고
    • Tissue-specific analysis of chromatin state identifies temporal signatures of enhancer activity during embryonic development
    • Bonn, S. et al. Tissue-specific analysis of chromatin state identifies temporal signatures of enhancer activity during embryonic development. Nat. Genet. 44, 148-156 (2012).
    • (2012) Nat. Genet. , vol.44 , pp. 148-156
    • Bonn, S.1
  • 7
    • 84905642951 scopus 로고    scopus 로고
    • Genome-scale functional characterization of Drosophila developmental enhancers in vivo
    • Kvon, E. Z. et al. Genome-scale functional characterization of Drosophila developmental enhancers in vivo. Nature 512, 91-95 (2014).
    • (2014) Nature , vol.512 , pp. 91-95
    • Kvon, E.Z.1
  • 8
    • 78651335916 scopus 로고    scopus 로고
    • REDfly v3.0: Toward a comprehensive database of transcriptional regulatory elements in Drosophila
    • Gallo, S. M. et al. REDfly v3.0: toward a comprehensive database of transcriptional regulatory elements in Drosophila. Nucleic Acids Res. 39, D118-D123 (2011).
    • (2011) Nucleic Acids Res. , vol.39 , pp. D118-D123
    • Gallo, S.M.1
  • 9
    • 76149094177 scopus 로고    scopus 로고
    • Systematic image-driven analysis of the spatial Drosophila embryonic expression landscape
    • Frise, E., Hammonds, A. S. &Celniker, S. E. Systematic image-driven analysis of the spatial Drosophila embryonic expression landscape. Mol. Syst. Biol. 6, 345 (2010).
    • (2010) Mol. Syst. Biol. , vol.6 , pp. 345
    • Frise, E.1    Hammonds, A.S.2    Celniker, S.E.3
  • 10
    • 0012252471 scopus 로고    scopus 로고
    • Systematic determination of patterns of gene expression during Drosophila embryogenesis
    • Tomancak, P. et al. Systematic determination of patterns of gene expression during Drosophila embryogenesis. Genome Biol 3, research0088.1 (2002).
    • (2002) Genome Biol , vol.3
    • Tomancak, P.1
  • 11
    • 84872112391 scopus 로고    scopus 로고
    • Cell type-specific chromatin immunoprecipitation from multicellular complex samples using BiTS-ChIP
    • Bonn, S. et al. Cell type-specific chromatin immunoprecipitation from multicellular complex samples using BiTS-ChIP. Nat. Protoc. 7, 978-994 (2012).
    • (2012) Nat. Protoc. , vol.7 , pp. 978-994
    • Bonn, S.1
  • 12
    • 85031019470 scopus 로고    scopus 로고
    • Temporal patterning in the Drosophila CNS
    • Doe, C. Q. Temporal patterning in the Drosophila CNS. Annu. Rev. Cell Dev. Biol. 33, 219-240 (2017).
    • (2017) Annu. Rev. Cell Dev. Biol. , vol.33 , pp. 219-240
    • Doe, C.Q.1
  • 13
    • 70549096299 scopus 로고    scopus 로고
    • Conservation and divergence in developmental networks: A view from Drosophila myogenesis
    • Ciglar, L. &Furlong, E. E. Conservation and divergence in developmental networks: a view from Drosophila myogenesis. Curr. Opin. Cell Biol. 21, 754-760 (2009).
    • (2009) Curr. Opin. Cell Biol. , vol.21 , pp. 754-760
    • Ciglar, L.1    Furlong, E.E.2
  • 14
    • 84892485370 scopus 로고    scopus 로고
    • Multiple regulatory safeguards confine the expression of the GATA factor serpent to the hemocyte primordium within the Drosophila mesoderm
    • Spahn, P. et al. Multiple regulatory safeguards confine the expression of the GATA factor serpent to the hemocyte primordium within the Drosophila mesoderm. Dev. Biol. 386, 272-279 (2014).
    • (2014) Dev. Biol. , vol.386 , pp. 272-279
    • Spahn, P.1
  • 15
    • 0028354289 scopus 로고
    • The gene serpent has homeotic properties and specifies endoderm versus ectoderm within the Drosophila gut
    • Reuter, R. The gene serpent has homeotic properties and specifies endoderm versus ectoderm within the Drosophila gut. Development 120, 1123-1135 (1994).
    • (1994) Development , vol.120 , pp. 1123-1135
    • Reuter, R.1
  • 16
    • 85016685764 scopus 로고    scopus 로고
    • Genetic variants regulating expression levels and isoform diversity during embryogenesis
    • Cannavò, E. et al. Genetic variants regulating expression levels and isoform diversity during embryogenesis. Nature 541, 402-406 (2017).
    • (2017) Nature , vol.541 , pp. 402-406
    • Cannavò, E.1
  • 18
    • 84903289127 scopus 로고    scopus 로고
    • Machine learning Clustering by fast search and find of density peaks
    • Rodriguez, A. &Laio, A. Machine learning. Clustering by fast search and find of density peaks. Science 344, 1492-1496 (2014).
    • (2014) Science , vol.344 , pp. 1492-1496
    • Rodriguez, A.1    Laio, A.2
  • 19
    • 85031017685 scopus 로고    scopus 로고
    • Reversed graph embedding resolves complex single-cell developmental trajectories
    • Qiu, X. et al. Reversed graph embedding resolves complex single-cell developmental trajectories. Nat. Methods 14, 979-982 (2017).
    • (2017) Nat. Methods , vol.14 , pp. 979-982
    • Qiu, X.1
  • 20
    • 0036228689 scopus 로고    scopus 로고
    • Slam encodes a developmental regulator of polarized membrane growth during cleavage of the Drosophila embryo
    • Lecuit, T., Samanta, R. &Wieschaus, E. slam encodes a developmental regulator of polarized membrane growth during cleavage of the Drosophila embryo. Dev. Cell 2, 425-436 (2002).
    • (2002) Dev. Cell , vol.2 , pp. 425-436
    • Lecuit, T.1    Samanta, R.2    Wieschaus, E.3
  • 21
    • 0029845996 scopus 로고    scopus 로고
    • Heartless, a Drosophila FGF receptor homolog, is essential for cell migration and establishment of several mesodermal lineages
    • Beiman, M., Shilo, B. Z. &Volk, T. Heartless, a Drosophila FGF receptor homolog, is essential for cell migration and establishment of several mesodermal lineages. Genes Dev. 10, 2993-3002 (1996).
    • (1996) Genes Dev. , vol.10 , pp. 2993-3002
    • Beiman, M.1    Shilo, B.Z.2    Volk, T.3
  • 22
    • 12944325779 scopus 로고    scopus 로고
    • An endodermspecific GATA factor gene, dGATAe, is required for the terminal differentiation of the Drosophila endoderm
    • Okumura, T., Matsumoto, A., Tanimura, T. &Murakami, R. An endodermspecific GATA factor gene, dGATAe, is required for the terminal differentiation of the Drosophila endoderm. Dev. Biol. 278, 576-586 (2005).
    • (2005) Dev. Biol. , vol.278 , pp. 576-586
    • Okumura, T.1    Matsumoto, A.2    Tanimura, T.3    Murakami, R.4
  • 23
    • 0029048545 scopus 로고
    • Dachsous encodes a member of the cadherin superfamily that controls imaginal disc morphogenesis in Drosophila
    • Clark, H. F. et al. Dachsous encodes a member of the cadherin superfamily that controls imaginal disc morphogenesis in Drosophila. Genes Dev. 9, 1530-1542 (1995).
    • (1995) Genes Dev. , vol.9 , pp. 1530-1542
    • Clark, H.F.1
  • 24
    • 0020759590 scopus 로고
    • When does determination occur in Drosophila embryos?
    • Simcox, A. A. &Sang, J. H. When does determination occur in Drosophila embryos? Dev. Biol. 97, 212-221 (1983).
    • (1983) Dev. Biol. , vol.97 , pp. 212-221
    • Simcox, A.A.1    Sang, J.H.2
  • 25
    • 0035957424 scopus 로고    scopus 로고
    • The GATA factor serpent is required for the onset of the humoral immune response in Drosophila embryos
    • Tingvall, T. O., Roos, E. &Engström, Y. The GATA factor serpent is required for the onset of the humoral immune response in Drosophila embryos. Proc. Natl Acad. Sci. USA 98, 3884-3888 (2001).
    • (2001) Proc. Natl Acad. Sci. USA , vol.98 , pp. 3884-3888
    • Tingvall, T.O.1    Roos, E.2    Engström, Y.3
  • 26
    • 85028303209 scopus 로고    scopus 로고
    • Comprehensive single-cell transcriptional profiling of a multicellular organism
    • Cao, J. et al. Comprehensive single-cell transcriptional profiling of a multicellular organism. Science 357, 661-667 (2017).
    • (2017) Science , vol.357 , pp. 661-667
    • Cao, J.1
  • 27
    • 84974576984 scopus 로고    scopus 로고
    • Whole-organism lineage tracing by combinatorial and cumulative genome editing
    • McKenna, A. et al. Whole-organism lineage tracing by combinatorial and cumulative genome editing. Science 353, aaf7907 (2016).
    • (2016) Science , vol.353 , pp. aaf7907
    • McKenna, A.1
  • 29
    • 85028864573 scopus 로고    scopus 로고
    • The Drosophila embryo at single-cell transcriptome resolution
    • Karaiskos, N. et al. The Drosophila embryo at single-cell transcriptome resolution. Science 358, 194-199 (2017).
    • (2017) Science , vol.358 , pp. 194-199
    • Karaiskos, N.1
  • 30
    • 85016160400 scopus 로고    scopus 로고
    • Synthetic recording and in situ readout of lineage information in single cells
    • Frieda, K. L. et al. Synthetic recording and in situ readout of lineage information in single cells. Nature 541, 107-111 (2017).
    • (2017) Nature , vol.541 , pp. 107-111
    • Frieda, K.L.1
  • 31
    • 38349127974 scopus 로고    scopus 로고
    • Global analysis of patterns of gene expression during Drosophila embryogenesis
    • Tomancak, P. et al. Global analysis of patterns of gene expression during Drosophila embryogenesis. Genome Biol. 8, R145 (2007).
    • (2007) Genome Biol. , vol.8 , pp. R145
    • Tomancak, P.1
  • 32
    • 84890492742 scopus 로고    scopus 로고
    • Spatial expression of transcription factors in Drosophila embryonic organ development
    • Hammonds, A. S. et al. Spatial expression of transcription factors in Drosophila embryonic organ development. Genome Biol. 14, R140 (2013).
    • (2013) Genome Biol. , vol.14 , pp. R140
    • Hammonds, A.S.1
  • 33
    • 34548855933 scopus 로고    scopus 로고
    • ChIP-on-chip protocol for genome-wide analysis of transcription factor binding in Drosophila melanogaster embryos
    • Sandmann, T., Jakobsen, J. S. &Furlong, E. E. ChIP-on-chip protocol for genome-wide analysis of transcription factor binding in Drosophila melanogaster embryos. Nat. Protoc. 1, 2839-2855 (2006).
    • (2006) Nat. Protoc. , vol.1 , pp. 2839-2855
    • Sandmann, T.1    Jakobsen, J.S.2    Furlong, E.E.3
  • 34
    • 84888877924 scopus 로고    scopus 로고
    • Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position
    • Buenrostro, J. D., Giresi, P. G., Zaba, L. C., Chang, H. Y. &Greenleaf, W. J. Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. Nat. Methods 10, 1213-1218 (2013).
    • (2013) Nat. Methods , vol.10 , pp. 1213-1218
    • Buenrostro, J.D.1    Giresi, P.G.2    Zaba, L.C.3    Chang, H.Y.4    Greenleaf, W.J.5
  • 35
    • 84922537404 scopus 로고    scopus 로고
    • Haplotype-resolved whole-genome sequencing by contiguitypreserving transposition and combinatorial indexing
    • Amini, S. et al. Haplotype-resolved whole-genome sequencing by contiguitypreserving transposition and combinatorial indexing. Nat. Genet. 46, 1343-1349 (2014).
    • (2014) Nat. Genet. , vol.46 , pp. 1343-1349
    • Amini, S.1
  • 36
    • 84859210032 scopus 로고    scopus 로고
    • Fast gapped-read alignment with Bowtie 2
    • Langmead, B. &Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357-359 (2012).
    • (2012) Nat. Methods , vol.9 , pp. 357-359
    • Langmead, B.1    Salzberg, S.L.2
  • 37
    • 0035998835 scopus 로고    scopus 로고
    • Model-based clustering, discriminant analysis and density estimation
    • Fraley, C. &Raftery, A. E. Model-based clustering, discriminant analysis and density estimation. J. Am. Stat. Assoc. 97, 611-631 (2002).
    • (2002) J. Am. Stat. Assoc. , vol.97 , pp. 611-631
    • Fraley, C.1    Raftery, A.E.2
  • 39
    • 53849146020 scopus 로고    scopus 로고
    • Model-based analysis of ChIP-seq (MACS)
    • Zhang, Y. et al. Model-based analysis of ChIP-seq (MACS). Genome Biol. 9, R137 (2008).
    • (2008) Genome Biol. , vol.9 , pp. R137
    • Zhang, Y.1
  • 40
    • 77951770756 scopus 로고    scopus 로고
    • BEDTools: A flexible suite of utilities for comparing genomic features
    • Quinlan, A. R. &Hall, I. M. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841-842 (2010).
    • (2010) Bioinformatics , vol.26 , pp. 841-842
    • Quinlan, A.R.1    Hall, I.M.2
  • 41
    • 84900873950 scopus 로고    scopus 로고
    • The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells
    • Trapnell, C. et al. The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells. Nat. Biotechnol. 32, 381-386 (2014).
    • (2014) Nat. Biotechnol. , vol.32 , pp. 381-386
    • Trapnell, C.1
  • 42
    • 84930607386 scopus 로고    scopus 로고
    • SeqGL identifies context-dependent binding signals in genome-wide regulatory element maps
    • Setty, M. &Leslie, C. S. SeqGL identifies context-dependent binding signals in genome-wide regulatory element maps. PLOS Comput. Biol. 11, e1004271 (2015).
    • (2015) PLOS Comput. Biol. , vol.11 , pp. e1004271
    • Setty, M.1    Leslie, C.S.2
  • 43
    • 84905484602 scopus 로고    scopus 로고
    • Enhanced regulatory sequence prediction using gapped k-mer features
    • Ghandi, M., Lee, D., Mohammad-Noori, M. &Beer, M. A. Enhanced regulatory sequence prediction using gapped k-mer features. PLOS Comput. Biol. 10, e1003711 (2014).
    • (2014) PLOS Comput. Biol. , vol.10 , pp. e1003711
    • Ghandi, M.1    Lee, D.2    Mohammad-Noori, M.3    Beer, M.A.4
  • 44
    • 79953300078 scopus 로고    scopus 로고
    • FIMO: Scanning for occurrences of a given motif
    • Grant, C. E., Bailey, T. L. &Noble, W. S. FIMO: scanning for occurrences of a given motif. Bioinformatics 27, 1017-1018 (2011).
    • (2011) Bioinformatics , vol.27 , pp. 1017-1018
    • Grant, C.E.1    Bailey, T.L.2    Noble, W.S.3
  • 45
    • 84919775831 scopus 로고    scopus 로고
    • Accelerating t-SNE using tree-based algorithms
    • Van Der Maaten, L. Accelerating t-SNE using tree-based algorithms. J. Mach. Learn. Res. 15, 3221-3245 (2014).
    • (2014) J. Mach. Learn. Res. , vol.15 , pp. 3221-3245
    • Van Der Maaten, L.1
  • 46
    • 34548855933 scopus 로고    scopus 로고
    • ChIP-on-chip protocol for genome-wide analysis of transcription factor binding in Drosophila melanogaster embryos
    • Sandmann, T., Jakobsen, J. S. &Furlong, E. E. ChIP-on-chip protocol for genome-wide analysis of transcription factor binding in Drosophila melanogaster embryos. Nat. Protoc. 1, 2839-2855 (2006).
    • (2006) Nat. Protoc. , vol.1 , pp. 2839-2855
    • Sandmann, T.1    Jakobsen, J.S.2    Furlong, E.E.3
  • 47
    • 84888877924 scopus 로고    scopus 로고
    • Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position
    • Buenrostro, J. D., Giresi, P. G., Zaba, L. C., Chang, H. Y. &Greenleaf, W. J. Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. Nat. Methods 10, 1213-1218 (2013).
    • (2013) Nat. Methods , vol.10 , pp. 1213-1218
    • Buenrostro, J.D.1    Giresi, P.G.2    Zaba, L.C.3    Chang, H.Y.4    Greenleaf, W.J.5
  • 48
    • 84922537404 scopus 로고    scopus 로고
    • Haplotype-resolved whole-genome sequencing by contiguitypreserving transposition and combinatorial indexing
    • Amini, S. et al. Haplotype-resolved whole-genome sequencing by contiguitypreserving transposition and combinatorial indexing. Nat. Genet. 46, 1343-1349 (2014).
    • (2014) Nat. Genet. , vol.46 , pp. 1343-1349
    • Amini, S.1
  • 49
    • 84859210032 scopus 로고    scopus 로고
    • Fast gapped-read alignment with Bowtie 2
    • Langmead, B. &Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357-359 (2012).
    • (2012) Nat. Methods , vol.9 , pp. 357-359
    • Langmead, B.1    Salzberg, S.L.2
  • 50
    • 0035998835 scopus 로고    scopus 로고
    • Model-based clustering, discriminant analysis and density estimation
    • Fraley, C. &Raftery, A. E. Model-based clustering, discriminant analysis and density estimation. J. Am. Stat. Assoc. 97, 611-631 (2002).
    • (2002) J. Am. Stat. Assoc. , vol.97 , pp. 611-631
    • Fraley, C.1    Raftery, A.E.2
  • 52
    • 53849146020 scopus 로고    scopus 로고
    • Model-based analysis of ChIP-seq (MACS)
    • Zhang, Y. et al. Model-based analysis of ChIP-seq (MACS). Genome Biol. 9, R137 (2008).
    • (2008) Genome Biol. , vol.9 , pp. R137
    • Zhang, Y.1
  • 53
    • 77951770756 scopus 로고    scopus 로고
    • BEDTools: A flexible suite of utilities for comparing genomic features
    • Quinlan, A. R. &Hall, I. M. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841-842 (2010).
    • (2010) Bioinformatics , vol.26 , pp. 841-842
    • Quinlan, A.R.1    Hall, I.M.2
  • 54
    • 84900873950 scopus 로고    scopus 로고
    • The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells
    • Trapnell, C. et al. The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells. Nat. Biotechnol. 32, 381-386 (2014).
    • (2014) Nat. Biotechnol. , vol.32 , pp. 381-386
    • Trapnell, C.1
  • 55
    • 84930607386 scopus 로고    scopus 로고
    • SeqGL identifies context-dependent binding signals in genome-wide regulatory element maps
    • Setty, M. &Leslie, C. S. SeqGL identifies context-dependent binding signals in genome-wide regulatory element maps. PLOS Comput. Biol. 11, e1004271 (2015).
    • (2015) PLOS Comput. Biol. , vol.11 , pp. e1004271
    • Setty, M.1    Leslie, C.S.2
  • 56
    • 84905484602 scopus 로고    scopus 로고
    • Enhanced regulatory sequence prediction using gapped k-mer features
    • Ghandi, M., Lee, D., Mohammad-Noori, M. &Beer, M. A. Enhanced regulatory sequence prediction using gapped k-mer features. PLOS Comput. Biol. 10, e1003711 (2014).
    • (2014) PLOS Comput. Biol. , vol.10 , pp. e1003711
    • Ghandi, M.1    Lee, D.2    Mohammad-Noori, M.3    Beer, M.A.4
  • 57
    • 79953300078 scopus 로고    scopus 로고
    • FIMO: Scanning for occurrences of a given motif
    • Grant, C. E., Bailey, T. L. &Noble, W. S. FIMO: scanning for occurrences of a given motif. Bioinformatics 27, 1017-1018 (2011).
    • (2011) Bioinformatics , vol.27 , pp. 1017-1018
    • Grant, C.E.1    Bailey, T.L.2    Noble, W.S.3
  • 58
    • 84919775831 scopus 로고    scopus 로고
    • Accelerating t-SNE using tree-based algorithms
    • Van Der Maaten, L. Accelerating t-SNE using tree-based algorithms. J. Mach. Learn. Res. 15, 3221-3245 (2014).
    • (2014) J. Mach. Learn. Res. , vol.15 , pp. 3221-3245
    • Van Der Maaten, L.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.