메뉴 건너뛰기




Volumn 51, Issue 1, 2019, Pages 185-197.e6

Characterization of Transcriptional Regulatory Networks that Promote and Restrict Identities and Functions of Intestinal Innate Lymphoid Cells

Author keywords

ATAC seq; gene regulation; Inferelator; lineage commitment; lymphocyte development

Indexed keywords

PROTEIN BCL 6; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR C MAF; BCL6 PROTEIN, MOUSE; TRANSCRIPTOME;

EID: 85068727387     PISSN: 10747613     EISSN: 10974180     Source Type: Journal    
DOI: 10.1016/j.immuni.2019.06.001     Document Type: Article
Times cited : (63)

References (85)
  • 2
    • 84928987900 scopus 로고    scopus 로고
    • HTSeq–a Python framework to work with high-throughput sequencing data
    • Anders, S., Pyl, P.T., Huber, W., HTSeq–a Python framework to work with high-throughput sequencing data. Bioinformatics 31 (2015), 166–169.
    • (2015) Bioinformatics , vol.31 , pp. 166-169
    • Anders, S.1    Pyl, P.T.2    Huber, W.3
  • 4
    • 68949086616 scopus 로고    scopus 로고
    • The expression and function of the NKRP1 receptor family in C57BL/6 mice
    • Aust, J.G., Gays, F., Mickiewicz, K.M., Buchanan, E., Brooks, C.G., The expression and function of the NKRP1 receptor family in C57BL/6 mice. J. Immunol. 183 (2009), 106–116.
    • (2009) J. Immunol. , vol.183 , pp. 106-116
    • Aust, J.G.1    Gays, F.2    Mickiewicz, K.M.3    Buchanan, E.4    Brooks, C.G.5
  • 8
    • 84930224883 scopus 로고    scopus 로고
    • Integrating motif, DNA accessibility and gene expression data to build regulatory maps in an organism
    • Blatti, C., Kazemian, M., Wolfe, S., Brodsky, M., Sinha, S., Integrating motif, DNA accessibility and gene expression data to build regulatory maps in an organism. Nucleic Acids Res. 43 (2015), 3998–4012.
    • (2015) Nucleic Acids Res. , vol.43 , pp. 3998-4012
    • Blatti, C.1    Kazemian, M.2    Wolfe, S.3    Brodsky, M.4    Sinha, S.5
  • 9
    • 33747813561 scopus 로고    scopus 로고
    • The Inferelator: an algorithm for learning parsimonious regulatory networks from systems-biology data sets de novo
    • Bonneau, R., Reiss, D.J., Shannon, P., Facciotti, M., Hood, L., Baliga, N.S., Thorsson, V., The Inferelator: an algorithm for learning parsimonious regulatory networks from systems-biology data sets de novo. Genome Biol., 7, 2006, R36.
    • (2006) Genome Biol. , vol.7 , pp. R36
    • Bonneau, R.1    Reiss, D.J.2    Shannon, P.3    Facciotti, M.4    Hood, L.5    Baliga, N.S.6    Thorsson, V.7
  • 10
    • 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 (2013), 1213–1218.
    • (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
  • 12
    • 0029902260 scopus 로고    scopus 로고
    • BCL-6, a POZ/zinc-finger protein, is a sequence-specific transcriptional repressor
    • Chang, C.C., Ye, B.H., Chaganti, R.S., Dalla-Favera, R., BCL-6, a POZ/zinc-finger protein, is a sequence-specific transcriptional repressor. Proc. Natl. Acad. Sci. USA 93 (1996), 6947–6952.
    • (1996) Proc. Natl. Acad. Sci. USA , vol.93 , pp. 6947-6952
    • Chang, C.C.1    Ye, B.H.2    Chaganti, R.S.3    Dalla-Favera, R.4
  • 13
    • 84862690161 scopus 로고    scopus 로고
    • Development and function of intestinal innate lymphoid cells
    • Cherrier, M., Ohnmacht, C., Cording, S., Eberl, G., Development and function of intestinal innate lymphoid cells. Curr. Opin. Immunol. 24 (2012), 277–283.
    • (2012) Curr. Opin. Immunol. , vol.24 , pp. 277-283
    • Cherrier, M.1    Ohnmacht, C.2    Cording, S.3    Eberl, G.4
  • 17
    • 75649136214 scopus 로고    scopus 로고
    • Effectors and memories: Bcl-6 and Blimp-1 in T and B lymphocyte differentiation
    • Crotty, S., Johnston, R.J., Schoenberger, S.P., Effectors and memories: Bcl-6 and Blimp-1 in T and B lymphocyte differentiation. Nat. Immunol. 11 (2010), 114–120.
    • (2010) Nat. Immunol. , vol.11 , pp. 114-120
    • Crotty, S.1    Johnston, R.J.2    Schoenberger, S.P.3
  • 19
    • 84929996266 scopus 로고    scopus 로고
    • Innate lymphoid cells. Innate lymphoid cells: a new paradigm in immunology
    • Eberl, G., Colonna, M., Di Santo, J.P., McKenzie, A.N.J., Innate lymphoid cells. Innate lymphoid cells: a new paradigm in immunology. Science, 348, 2015, aaa6566.
    • (2015) Science , vol.348 , pp. aaa6566
    • Eberl, G.1    Colonna, M.2    Di Santo, J.P.3    McKenzie, A.N.J.4
  • 20
    • 85021954469 scopus 로고    scopus 로고
    • Dynamic balance between master transcription factors determines the fates and functions of CD4 T cell and innate lymphoid cell subsets
    • Fang, D., Zhu, J., Dynamic balance between master transcription factors determines the fates and functions of CD4 T cell and innate lymphoid cell subsets. J. Exp. Med. 214 (2017), 1861–1876.
    • (2017) J. Exp. Med. , vol.214 , pp. 1861-1876
    • Fang, D.1    Zhu, J.2
  • 21
    • 84862777436 scopus 로고    scopus 로고
    • The transcription factors T-bet and Eomes control key checkpoints of natural killer cell maturation
    • Gordon, S.M., Chaix, J., Rupp, L.J., Wu, J., Madera, S., Sun, J.C., Lindsten, T., Reiner, S.L., The transcription factors T-bet and Eomes control key checkpoints of natural killer cell maturation. Immunity 36 (2012), 55–67.
    • (2012) Immunity , vol.36 , pp. 55-67
    • Gordon, S.M.1    Chaix, J.2    Rupp, L.J.3    Wu, J.4    Madera, S.5    Sun, J.C.6    Lindsten, T.7    Reiner, S.L.8
  • 22
    • 85012883069 scopus 로고    scopus 로고
    • Intestinal commensal bacteria mediate lung mucosal immunity and promote resistance of newborn mice to infection
    • Gray, J., Oehrle, K., Worthen, G., Alenghat, T., Whitsett, J., Deshmukh, H., Intestinal commensal bacteria mediate lung mucosal immunity and promote resistance of newborn mice to infection. Sci. Transl. Med., 9, 2017, eaaf9412.
    • (2017) Sci. Transl. Med. , vol.9 , pp. eaaf9412
    • Gray, J.1    Oehrle, K.2    Worthen, G.3    Alenghat, T.4    Whitsett, J.5    Deshmukh, H.6
  • 27
    • 0038636078 scopus 로고    scopus 로고
    • Redundant functions of TCF-1 and LEF-1 during T and NK cell development, but unique role of TCF-1 for Ly49 NK cell receptor acquisition
    • Held, W., Clevers, H., Grosschedl, R., Redundant functions of TCF-1 and LEF-1 during T and NK cell development, but unique role of TCF-1 for Ly49 NK cell receptor acquisition. Eur. J. Immunol. 33 (2003), 1393–1398.
    • (2003) Eur. J. Immunol. , vol.33 , pp. 1393-1398
    • Held, W.1    Clevers, H.2    Grosschedl, R.3
  • 31
    • 84885123308 scopus 로고    scopus 로고
    • Insights into the role of Bcl6 in follicular Th cells using a new conditional mutant mouse model
    • Hollister, K., Kusam, S., Wu, H., Clegg, N., Mondal, A., Sawant, D.V., Dent, A.L., Insights into the role of Bcl6 in follicular Th cells using a new conditional mutant mouse model. J. Immunol. 191 (2013), 3705–3711.
    • (2013) J. Immunol. , vol.191 , pp. 3705-3711
    • Hollister, K.1    Kusam, S.2    Wu, H.3    Clegg, N.4    Mondal, A.5    Sawant, D.V.6    Dent, A.L.7
  • 33
    • 33845432928 scopus 로고    scopus 로고
    • Adjusting batch effects in microarray expression data using empirical Bayes methods
    • Johnson, W.E., Li, C., Rabinovic, A., Adjusting batch effects in microarray expression data using empirical Bayes methods. Biostatistics 8 (2007), 118–127.
    • (2007) Biostatistics , vol.8 , pp. 118-127
    • Johnson, W.E.1    Li, C.2    Rabinovic, A.3
  • 34
    • 79951470129 scopus 로고    scopus 로고
    • A role for Blimp1 in the transcriptional network controlling natural killer cell maturation
    • Kallies, A., Carotta, S., Huntington, N.D., Bernard, N.J., Tarlinton, D.M., Smyth, M.J., Nutt, S.L., A role for Blimp1 in the transcriptional network controlling natural killer cell maturation. Blood 117 (2011), 1869–1879.
    • (2011) Blood , vol.117 , pp. 1869-1879
    • Kallies, A.1    Carotta, S.2    Huntington, N.D.3    Bernard, N.J.4    Tarlinton, D.M.5    Smyth, M.J.6    Nutt, S.L.7
  • 36
    • 84898985349 scopus 로고    scopus 로고
    • Systematic discovery and characterization of regulatory motifs in ENCODE TF binding experiments
    • Kheradpour, P., Kellis, M., Systematic discovery and characterization of regulatory motifs in ENCODE TF binding experiments. Nucleic Acids Res. 42 (2014), 2976–2987.
    • (2014) Nucleic Acids Res. , vol.42 , pp. 2976-2987
    • Kheradpour, P.1    Kellis, M.2
  • 40
    • 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 (2012), 357–359.
    • (2012) Nat. Methods , vol.9 , pp. 357-359
    • Langmead, B.1    Salzberg, S.L.2
  • 43
  • 44
    • 85162067025 scopus 로고    scopus 로고
    • Stability approach to regularization selection (StARS) for high dimensional graphical models
    • J.D. Lafferty C.K.I. Williams J. Shawe-Taylor R.S. Zemel A. Culotta Curran Associates
    • Liu, H., Roeder, K., Wasserman, L., Stability approach to regularization selection (StARS) for high dimensional graphical models. Lafferty, J.D., Williams, C.K.I., Shawe-Taylor, J., Zemel, R.S., Culotta, A., (eds.) Advances in Neural Information Processing Systems 23, 2010, Curran Associates, 1432–1440.
    • (2010) Advances in Neural Information Processing Systems 23 , pp. 1432-1440
    • Liu, H.1    Roeder, K.2    Wasserman, L.3
  • 45
    • 84924629414 scopus 로고    scopus 로고
    • Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
    • Love, M.I., Huber, W., Anders, S., Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol., 15, 2014, 550.
    • (2014) Genome Biol. , vol.15 , pp. 550
    • Love, M.I.1    Huber, W.2    Anders, S.3
  • 47
    • 84899519120 scopus 로고    scopus 로고
    • PeaKDEck: a kernel density estimator-based peak calling program for DNaseI-seq data
    • McCarthy, M.T., O'Callaghan, C.A., PeaKDEck: a kernel density estimator-based peak calling program for DNaseI-seq data. Bioinformatics 30 (2014), 1302–1304.
    • (2014) Bioinformatics , vol.30 , pp. 1302-1304
    • McCarthy, M.T.1    O'Callaghan, C.A.2
  • 48
    • 85007529996 scopus 로고    scopus 로고
    • Functional and phenotypic heterogeneity of group 3 innate lymphoid cells
    • Melo-Gonzalez, F., Hepworth, M.R., Functional and phenotypic heterogeneity of group 3 innate lymphoid cells. Immunology 150 (2017), 265–275.
    • (2017) Immunology , vol.150 , pp. 265-275
    • Melo-Gonzalez, F.1    Hepworth, M.R.2
  • 53
    • 84954214965 scopus 로고    scopus 로고
    • Differentiation and function of group 3 innate lymphoid cells, from embryo to adult
    • van de Pavert, S.A., Vivier, E., Differentiation and function of group 3 innate lymphoid cells, from embryo to adult. Int. Immunol. 28 (2016), 35–42.
    • (2016) Int. Immunol. , vol.28 , pp. 35-42
    • van de Pavert, S.A.1    Vivier, E.2
  • 54
    • 84958568281 scopus 로고    scopus 로고
    • Cutting edge: eomesodermin is sufficient to direct type 1 innate lymphocyte development into the conventional NK lineage
    • Pikovskaya, O., Chaix, J., Rothman, N.J., Collins, A., Chen, Y.-H., Scipioni, A.M., Vivier, E., Reiner, S.L., Cutting edge: eomesodermin is sufficient to direct type 1 innate lymphocyte development into the conventional NK lineage. J. Immunol. 196 (2016), 1449–1454.
    • (2016) J. Immunol. , vol.196 , pp. 1449-1454
    • Pikovskaya, O.1    Chaix, J.2    Rothman, N.J.3    Collins, A.4    Chen, Y.-H.5    Scipioni, A.M.6    Vivier, E.7    Reiner, S.L.8
  • 55
    • 79952266465 scopus 로고    scopus 로고
    • Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data
    • Pique-Regi, R., Degner, J.F., Pai, A.A., Gaffney, D.J., Gilad, Y., Pritchard, J.K., Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data. Genome Res. 21 (2011), 447–455.
    • (2011) Genome Res. , vol.21 , pp. 447-455
    • Pique-Regi, R.1    Degner, J.F.2    Pai, A.A.3    Gaffney, D.J.4    Gilad, Y.5    Pritchard, J.K.6
  • 56
    • 85050291252 scopus 로고    scopus 로고
    • Emerging principles of gene expression programs and their regulation
    • Pope, S.D., Medzhitov, R., Emerging principles of gene expression programs and their regulation. Mol. Cell 71 (2018), 389–397.
    • (2018) Mol. Cell , vol.71 , pp. 389-397
    • Pope, S.D.1    Medzhitov, R.2
  • 58
    • 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 (2010), 841–842.
    • (2010) Bioinformatics , vol.26 , pp. 841-842
    • Quinlan, A.R.1    Hall, I.M.2
  • 60
    • 84923436228 scopus 로고    scopus 로고
    • Transcriptional programs define molecular characteristics of innate lymphoid cell classes and subsets
    • Robinette, M.L., Fuchs, A., Cortez, V.S., Lee, J.S., Wang, Y., Durum, S.K., Gilfillan, S., Colonna, M., Immunological Genome Consortium. Transcriptional programs define molecular characteristics of innate lymphoid cell classes and subsets. Nat. Immunol. 16 (2015), 306–317.
    • (2015) Nat. Immunol. , vol.16 , pp. 306-317
    • Robinette, M.L.1    Fuchs, A.2    Cortez, V.S.3    Lee, J.S.4    Wang, Y.5    Durum, S.K.6    Gilfillan, S.7    Colonna, M.8
  • 69
    • 84936892270 scopus 로고    scopus 로고
    • Innate lymphoid cells in the initiation, regulation and resolution of inflammation
    • Sonnenberg, G.F., Artis, D., Innate lymphoid cells in the initiation, regulation and resolution of inflammation. Nat. Med. 21 (2015), 698–708.
    • (2015) Nat. Med. , vol.21 , pp. 698-708
    • Sonnenberg, G.F.1    Artis, D.2
  • 70
    • 84859384082 scopus 로고    scopus 로고
    • Innate lymphoid cells: emerging insights in development, lineage relationships, and function
    • Spits, H., Cupedo, T., Innate lymphoid cells: emerging insights in development, lineage relationships, and function. Annu. Rev. Immunol. 30 (2012), 647–675.
    • (2012) Annu. Rev. Immunol. , vol.30 , pp. 647-675
    • Spits, H.1    Cupedo, T.2
  • 73
    • 84867636023 scopus 로고    scopus 로고
    • Innate lymphoid cells: balancing immunity, inflammation, and tissue repair in the intestine
    • Tait Wojno, E.D., Artis, D., Innate lymphoid cells: balancing immunity, inflammation, and tissue repair in the intestine. Cell Host Microbe 12 (2012), 445–457.
    • (2012) Cell Host Microbe , vol.12 , pp. 445-457
    • Tait Wojno, E.D.1    Artis, D.2
  • 74
    • 85017167191 scopus 로고    scopus 로고
    • Emerging concepts and future challenges in innate lymphoid cell biology
    • Tait Wojno, E.D., Artis, D., Emerging concepts and future challenges in innate lymphoid cell biology. J. Exp. Med. 213 (2016), 2229–2248.
    • (2016) J. Exp. Med. , vol.213 , pp. 2229-2248
    • Tait Wojno, E.D.1    Artis, D.2
  • 76
  • 84
    • 84888428219 scopus 로고    scopus 로고
    • Location and cellular stages of natural killer cell development
    • Yu, J., Freud, A.G., Caligiuri, M.A., Location and cellular stages of natural killer cell development. Trends Immunol. 34 (2013), 573–582.
    • (2013) Trends Immunol. , vol.34 , pp. 573-582
    • Yu, J.1    Freud, A.G.2    Caligiuri, M.A.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.