메뉴 건너뛰기




Volumn 10, Issue 1, 2019, Pages

CUT&Tag for efficient epigenomic profiling of small samples and single cells

Author keywords

[No Author keywords available]

Indexed keywords

BINDING PROTEIN; GENOMIC DNA; HISTONE; MEMBRANE FUSION PROTEIN; PROTEIN A; RNA POLYMERASE II; TRANSCRIPTION FACTOR; TRANSPOSASE; BEVIFIMOD; FUSION PROTEIN; TN5 TRANSPOSASE;

EID: 85065063725     PISSN: None     EISSN: 20411723     Source Type: Journal    
DOI: 10.1038/s41467-019-09982-5     Document Type: Article
Times cited : (1129)

References (33)
  • 1
    • 84926203507 scopus 로고    scopus 로고
    • High-resolution digital profiling of the epigenome
    • COI: 1:CAS:528:DC%2BC2cXhslajurvJ
    • Zentner, G. E. & Henikoff, S. High-resolution digital profiling of the epigenome. Nat. Rev. Genet. 15, 814–827 (2014).
    • (2014) Nat. Rev. Genet. , vol.15 , pp. 814-827
    • Zentner, G.E.1    Henikoff, S.2
  • 2
    • 85045881644 scopus 로고    scopus 로고
    • Enzymatic methods for genome-wide profiling of protein binding sites
    • COI: 1:CAS:528:DC%2BC1MXmt1Sqt7c%3D
    • Policastro, R. A. & Zentner, G. E. Enzymatic methods for genome-wide profiling of protein binding sites. Brief. Funct. Genom. 17, 138–145 (2018).
    • (2018) Brief. Funct. Genom. , vol.17 , pp. 138-145
    • Policastro, R.A.1    Zentner, G.E.2
  • 3
    • 83255164884 scopus 로고    scopus 로고
    • Comprehensive genome-wide protein-DNA interactions detected at single-nucleotide resolution
    • COI: 1:CAS:528:DC%2BC3MXhs1Sgtr3K
    • Rhee, H. S. & Pugh, B. F. Comprehensive genome-wide protein-DNA interactions detected at single-nucleotide resolution. Cell 147, 1408–1419 (2011).
    • (2011) Cell , vol.147 , pp. 1408-1419
    • Rhee, H.S.1    Pugh, B.F.2
  • 4
    • 84933060493 scopus 로고    scopus 로고
    • A simple method for generating high-resolution maps of genome-wide protein binding
    • Skene, P. J. & Henikoff, S. A simple method for generating high-resolution maps of genome-wide protein binding. eLife 4, e09225 (2015).
    • (2015) eLife , vol.4
    • Skene, P.J.1    Henikoff, S.2
  • 5
    • 84895072244 scopus 로고    scopus 로고
    • High-resolution mapping of transcription factor binding sites on native chromatin
    • COI: 1:CAS:528:DC%2BC3sXhvFensb3N
    • Kasinathan, S., Orsi, G. A., Zentner, G. E., Ahmad, K. & Henikoff, S. High-resolution mapping of transcription factor binding sites on native chromatin. Nat. Methods 11, 203–209 (2014).
    • (2014) Nat. Methods , vol.11 , pp. 203-209
    • Kasinathan, S.1    Orsi, G.A.2    Zentner, G.E.3    Ahmad, K.4    Henikoff, S.5
  • 6
    • 84887478181 scopus 로고    scopus 로고
    • Highly expressed loci are vulnerable to misleading ChIP localization of multiple unrelated proteins
    • COI: 1:CAS:528:DC%2BC3sXhvVygsLfJ
    • Teytelman, L., Thurtle, D. M., Rine, J. & van Oudenaarden, A. Highly expressed loci are vulnerable to misleading ChIP localization of multiple unrelated proteins. Proc. Natl Acad. Sci. USA 110, 18602–18607 (2013).
    • (2013) Proc. Natl Acad. Sci. USA , vol.110 , pp. 18602-18607
    • Teytelman, L.1    Thurtle, D.M.2    Rine, J.3    van Oudenaarden, A.4
  • 7
    • 0035093828 scopus 로고    scopus 로고
    • Chromatin profiling using targeted DNA adenine methyltransferase
    • van Steensel, B., Delrow, J. & Henikoff, S. Chromatin profiling using targeted DNA adenine methyltransferase. Nat. Genet. 27, 304–308 (2001).
    • (2001) Nat. Genet. , vol.27 , pp. 304-308
    • van Steensel, B.1    Delrow, J.2    Henikoff, S.3
  • 8
    • 84944937652 scopus 로고    scopus 로고
    • ChEC-seq kinetics discriminates transcription factor binding sites by DNA sequence and shape in vivo
    • COI: 1:CAS:528:DC%2BC2MXhslSmt7zN
    • Zentner, G. E., Kasinathan, S., Xin, B., Rohs, R. & Henikoff, S. ChEC-seq kinetics discriminates transcription factor binding sites by DNA sequence and shape in vivo. Nat. Commun. 6, 8733 (2015).
    • (2015) Nat. Commun. , vol.6
    • Zentner, G.E.1    Kasinathan, S.2    Xin, B.3    Rohs, R.4    Henikoff, S.5
  • 9
    • 85013174100 scopus 로고    scopus 로고
    • An efficient targeted nuclease strategy for high-resolution mapping of DNA binding sites
    • Skene, P. J. & Henikoff, S. An efficient targeted nuclease strategy for high-resolution mapping of DNA binding sites. Elife 6, e21856 (2017).
    • (2017) Elife , vol.6
    • Skene, P.J.1    Henikoff, S.2
  • 10
    • 85046096265 scopus 로고    scopus 로고
    • Targeted in situ genome-wide profiling with high efficiency for low cell numbers
    • COI: 1:CAS:528:DC%2BC1cXnsFCns7c%3D
    • Skene, P. J., Henikoff, J. G. & Henikoff, S. Targeted in situ genome-wide profiling with high efficiency for low cell numbers. Nat. Protoc. 13, 1006–1019 (2018).
    • (2018) Nat. Protoc. , vol.13 , pp. 1006-1019
    • Skene, P.J.1    Henikoff, J.G.2    Henikoff, S.3
  • 11
    • 4944227536 scopus 로고    scopus 로고
    • ChlC and ChEC: genomic mapping of chromatin proteins
    • COI: 1:CAS:528:DC%2BD2cXptVKqtrk%3D, PID: 15469830
    • Schmid, M., Durussel, T. & Laemmli, U. K. ChlC and ChEC: genomic mapping of chromatin proteins. Mol. Cell 16, 147–157 (2004).
    • (2004) Mol. Cell , vol.16 , pp. 147-157
    • Schmid, M.1    Durussel, T.2    Laemmli, U.K.3
  • 12
    • 85052990879 scopus 로고    scopus 로고
    • High-throughput chromatin accessibility profiling at single-cell resolution
    • Mezger, A. et al. High-throughput chromatin accessibility profiling at single-cell resolution. Nat. Commun. 9, 3647 (2018).
    • (2018) Nat. Commun. , vol.9 , pp. 3647
    • Mezger, A.1
  • 13
    • 85009446777 scopus 로고    scopus 로고
    • Massively parallel digital transcriptional profiling of single cells
    • COI: 1:CAS:528:DC%2BC2sXht1WlsLo%3D
    • Zheng, G. X. et al. Massively parallel digital transcriptional profiling of single cells. Nat. Commun. 8, 14049 (2017).
    • (2017) Nat. Commun. , vol.8
    • Zheng, G.X.1
  • 14
    • 0037336665 scopus 로고    scopus 로고
    • Tn5 as a model for understanding DNA transposition
    • COI: 1:CAS:528:DC%2BD3sXitFWrtrs%3D
    • Reznikoff, W. S. Tn5 as a model for understanding DNA transposition. Mol. Microbiol. 47, 1199–1206 (2003).
    • (2003) Mol. Microbiol. , vol.47 , pp. 1199-1206
    • Reznikoff, W.S.1
  • 15
    • 84913593681 scopus 로고    scopus 로고
    • Tn5 transposase and tagmentation procedures for massively scaled sequencing projects
    • COI: 1:CAS:528:DC%2BC2cXitVOls7%2FF
    • Picelli, S. et al. Tn5 transposase and tagmentation procedures for massively scaled sequencing projects. Genome Res. 24, 2033–2040 (2014).
    • (2014) Genome Res. , vol.24 , pp. 2033-2040
    • Picelli, S.1
  • 16
    • 33744824117 scopus 로고    scopus 로고
    • Defining characteristics of Tn5 transposase non-specific DNA binding
    • COI: 1:CAS:528:DC%2BD28XmsVeisLs%3D
    • Steiniger, M., Adams, C. D., Marko, J. F. & Reznikoff, W. S. Defining characteristics of Tn5 transposase non-specific DNA binding. Nucleic Acids Res. 34, 2820–2832 (2006).
    • (2006) Nucleic Acids Res. , vol.34 , pp. 2820-2832
    • Steiniger, M.1    Adams, C.D.2    Marko, J.F.3    Reznikoff, W.S.4
  • 17
    • 84888877924 scopus 로고    scopus 로고
    • Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position
    • COI: 1:CAS:528:DC%2BC3sXhsFOiu7jO
    • 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(2013).
    • (2013) Nat. Methods , vol.10 , pp. 1213
    • Buenrostro, J.D.1    Giresi, P.G.2    Zaba, L.C.3    Chang, H.Y.4    Greenleaf, W.J.5
  • 18
    • 85058906901 scopus 로고    scopus 로고
    • Automated in situ profiling of chromatin modifications resolves cell types and gene regulatory programs
    • Janssens, D. H. et al. Automated in situ profiling of chromatin modifications resolves cell types and gene regulatory programs. Epigenetics Chromatin 11, 74 (2018).
    • (2018) Epigenetics Chromatin , vol.11 , pp. 74
    • Janssens, D.H.1
  • 19
    • 84865777819 scopus 로고    scopus 로고
    • ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia
    • COI: 1:CAS:528:DC%2BC38XhtlentLvJ
    • Landt, S. G. et al. ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome Res. 22, 1813–1831 (2012).
    • (2012) Genome Res. , vol.22 , pp. 1813-1831
    • Landt, S.G.1
  • 20
    • 84986877616 scopus 로고    scopus 로고
    • The pol II CTD: new twists in the tail
    • COI: 1:CAS:528:DC%2BC28XhsV2jurjM
    • Zaborowska, J., Egloff, S. & Murphy, S. The pol II CTD: new twists in the tail. Nat. Struct. Mol. Biol. 23, 771–777 (2016).
    • (2016) Nat. Struct. Mol. Biol. , vol.23 , pp. 771-777
    • Zaborowska, J.1    Egloff, S.2    Murphy, S.3
  • 21
    • 84865790047 scopus 로고    scopus 로고
    • An integrated encyclopedia of DNA elements in the human genome
    • Consortium, E. P. An integrated encyclopedia of DNA elements in the human genome. Nature 489, 57–74 (2012).
    • (2012) Nature , vol.489 , pp. 57-74
    • Consortium, E.P.1
  • 22
    • 84927559450 scopus 로고    scopus 로고
    • Analysis of nascent RNA identifies a unified architecture of initiation regions at mammalian promoters and enhancers
    • COI: 1:CAS:528:DC%2BC2cXhvFKmtbbI
    • Core, L. J. et al. Analysis of nascent RNA identifies a unified architecture of initiation regions at mammalian promoters and enhancers. Nat. Genet. 46, 1311–1320 (2014).
    • (2014) Nat. Genet. , vol.46 , pp. 1311-1320
    • Core, L.J.1
  • 23
    • 85028389163 scopus 로고    scopus 로고
    • In situ capture of chromatin interactions by biotinylated dCas9
    • COI: 1:CAS:528:DC%2BC2sXhtlyltLzJ
    • Liu, X. et al. In situ capture of chromatin interactions by biotinylated dCas9. Cell 170, 1028–1043 e1019 (2017).
    • (2017) Cell , vol.170 , pp. 1028-1043 e1019
    • Liu, X.1
  • 24
    • 0036429193 scopus 로고    scopus 로고
    • The human and mouse replication-dependent histone genes
    • COI: 1:CAS:528:DC%2BD38XotVyqu7s%3D
    • Marzluff, W. F., Gongidi, P., Woods, K. R., Jin, J. P. & Maltais, L. J. The human and mouse replication-dependent histone genes. Genomics 80, 487–498 (2002).
    • (2002) Genomics , vol.80 , pp. 487-498
    • Marzluff, W.F.1    Gongidi, P.2    Woods, K.R.3    Jin, J.P.4    Maltais, L.J.5
  • 26
    • 84922537404 scopus 로고    scopus 로고
    • Haplotype-resolved whole-genome sequencing by contiguity-preserving transposition and combinatorial indexing
    • COI: 1:CAS:528:DC%2BC2cXhslOisrnN
    • Amini, S. et al. Haplotype-resolved whole-genome sequencing by contiguity-preserving transposition and combinatorial indexing. Nat. Genet. 46, 1343–1349 (2014).
    • (2014) Nat. Genet. , vol.46 , pp. 1343-1349
    • Amini, S.1
  • 27
    • 85044252958 scopus 로고    scopus 로고
    • Exponential scaling of single-cell RNA-seq in the past decade
    • COI: 1:CAS:528:DC%2BC1cXjs1agu74%3D
    • Svensson, V., Vento-Tormo, R. & Teichmann, S. A. Exponential scaling of single-cell RNA-seq in the past decade. Nat. Protoc. 13, 599–604 (2018).
    • (2018) Nat. Protoc. , vol.13 , pp. 599-604
    • Svensson, V.1    Vento-Tormo, R.2    Teichmann, S.A.3
  • 29
    • 85065097786 scopus 로고    scopus 로고
    • 10xgenomics. https://www.10xgenomics.com/solutions/single-cell-atac.
  • 30
    • 84946545109 scopus 로고    scopus 로고
    • Single-cell ChIP-seq reveals cell subpopulations defined by chromatin state
    • COI: 1:CAS:528:DC%2BC2MXhs1ChurfK
    • Rotem, A. et al. Single-cell ChIP-seq reveals cell subpopulations defined by chromatin state. Nat. Biotechnol. 33, 1165–1172 (2015).
    • (2015) Nat. Biotechnol. , vol.33 , pp. 1165-1172
    • Rotem, A.1
  • 31
    • 85049621520 scopus 로고    scopus 로고
    • Single-cell multi-omics: an engine for new quantitative models of gene regulation
    • COI: 1:CAS:528:DC%2BC1cXht1Cjt7fL
    • Packer, J. & Trapnell, C. Single-cell multi-omics: an engine for new quantitative models of gene regulation. Trends Genet. 34, 653–665 (2018).
    • (2018) Trends Genet. , vol.34 , pp. 653-665
    • Packer, J.1    Trapnell, C.2
  • 33
    • 84937857359 scopus 로고    scopus 로고
    • Single-cell chromatin accessibility reveals principles of regulatory variation
    • COI: 1:CAS:528:DC%2BC2MXhtFyltLrN
    • Buenrostro, J. D. et al. Single-cell chromatin accessibility reveals principles of regulatory variation. Nature 523, 486–U264 (2015).
    • (2015) Nature , vol.523 , pp. 264-486
    • Buenrostro, J.D.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.