메뉴 건너뛰기




Volumn 13, Issue 11, 2017, Pages

Genetic circuit characterization and debugging using RNA-seq

Author keywords

biofab; combinatorial logic; omics; synthetic biology; systems biology

Indexed keywords

ANHYDROTETRACYCLINE; ARABINOSE; ISOPROPYL THIOGALACTOSIDE; MESSENGER RNA; NUCLEOTIDE; RNA POLYMERASE; YELLOW FLUORESCENT PROTEIN; AMTR PROTEIN, CORYNEBACTERIUM GLUTAMICUM; BACTERIAL PROTEIN; BM3R1 PROTEIN, BACILLUS MEGATERIUM; PHLF PROTEIN, PSEUDOMONAS FLUORESCENS; REPRESSOR PROTEIN; RNA;

EID: 85035147591     PISSN: None     EISSN: 17444292     Source Type: Journal    
DOI: 10.15252/msb.20167461     Document Type: Article
Times cited : (68)

References (72)
  • 1
    • 84928987900 scopus 로고    scopus 로고
    • HTSeq – a Python framework to work with high-throughput sequencing data
    • Anders S, Pyl PT, Huber W (2015) HTSeq – a Python framework to work with high-throughput sequencing data. Bioinformatics 31: 166–169
    • (2015) Bioinformatics , vol.31 , pp. 166-169
    • Anders, S.1    Pyl, P.T.2    Huber, W.3
  • 2
    • 29144482539 scopus 로고    scopus 로고
    • Environmentally controlled invasion of cancer cells by engineered bacteria
    • Anderson JC, Clarke EJ, Arkin AP, Voigt CA (2006) Environmentally controlled invasion of cancer cells by engineered bacteria. J Mol Biol 355: 619–627
    • (2006) J Mol Biol , vol.355 , pp. 619-627
    • Anderson, J.C.1    Clarke, E.J.2    Arkin, A.P.3    Voigt, C.A.4
  • 3
  • 5
    • 34247099372 scopus 로고    scopus 로고
    • Regulatory mechanisms employed by cis-encoded antisense RNAs
    • Brantl S (2007) Regulatory mechanisms employed by cis-encoded antisense RNAs. Curr Opin Microbiol 10: 102–109
    • (2007) Curr Opin Microbiol , vol.10 , pp. 102-109
    • Brantl, S.1
  • 6
    • 84899694320 scopus 로고    scopus 로고
    • Principles of genetic circuit design
    • Brophy JA, Voigt CA (2014) Principles of genetic circuit design. Nat Methods 11: 508–520
    • (2014) Nat Methods , vol.11 , pp. 508-520
    • Brophy, J.A.1    Voigt, C.A.2
  • 7
    • 84957058205 scopus 로고    scopus 로고
    • Antisense transcription as a tool to tune gene expression
    • Brophy JAN, Voigt CA (2015) Antisense transcription as a tool to tune gene expression. Mol Syst Biol 12: 854
    • (2015) Mol Syst Biol , vol.12 , pp. 854
    • Brophy, J.A.N.1    Voigt, C.A.2
  • 8
    • 46949091517 scopus 로고    scopus 로고
    • Refinement and standardization of synthetic biological parts and devices
    • Canton B, Labno A, Endy D (2008) Refinement and standardization of synthetic biological parts and devices. Nat Biotechnol 26: 787–793
    • (2008) Nat Biotechnol , vol.26 , pp. 787-793
    • Canton, B.1    Labno, A.2    Endy, D.3
  • 9
    • 84880772006 scopus 로고    scopus 로고
    • Effects of genetic variation on the E. coli host-circuit interface
    • Cardinale S, Joachimiak MP, Arkin AP (2013) Effects of genetic variation on the E. coli host-circuit interface. Cell Rep 4: 231–237
    • (2013) Cell Rep , vol.4 , pp. 231-237
    • Cardinale, S.1    Joachimiak, M.P.2    Arkin, A.P.3
  • 10
    • 84928927536 scopus 로고    scopus 로고
    • Quantifying cellular capacity identifies gene expression designs with reduced burden
    • Ceroni F, Algar R, Stan GB, Ellis T (2015) Quantifying cellular capacity identifies gene expression designs with reduced burden. Nat Methods 12: 415–418
    • (2015) Nat Methods , vol.12 , pp. 415-418
    • Ceroni, F.1    Algar, R.2    Stan, G.B.3    Ellis, T.4
  • 11
    • 84879681227 scopus 로고    scopus 로고
    • Characterization of 582 natural and synthetic terminators and quantification of their design constraints
    • Chen YJ, Liu P, Nielsen AAK, Brophy JA, Clancy K, Peterson T, Voigt CA (2013) Characterization of 582 natural and synthetic terminators and quantification of their design constraints. Nat Methods 10: 659–664
    • (2013) Nat Methods , vol.10 , pp. 659-664
    • Chen, Y.J.1    Liu, P.2    Nielsen, A.A.K.3    Brophy, J.A.4    Clancy, K.5    Peterson, T.6    Voigt, C.A.7
  • 12
    • 84922888717 scopus 로고    scopus 로고
    • Genome-wide study of mRNA degradation and transcript elongation in Escherichia coli
    • Chen H, Shiroguchi K, Ge H, Xie XS (2015) Genome-wide study of mRNA degradation and transcript elongation in Escherichia coli. Mol Syst Biol 11: 781
    • (2015) Mol Syst Biol , vol.11 , pp. 781
    • Chen, H.1    Shiroguchi, K.2    Ge, H.3    Xie, X.S.4
  • 14
    • 84878381909 scopus 로고    scopus 로고
    • Synthetic analog computation in living cells
    • Daniel R, Rubens JR, Sarpeshkar R, Lu TK (2013) Synthetic analog computation in living cells. Nature 497: 619–623
    • (2013) Nature , vol.497 , pp. 619-623
    • Daniel, R.1    Rubens, J.R.2    Sarpeshkar, R.3    Lu, T.K.4
  • 16
    • 0034688173 scopus 로고    scopus 로고
    • A synthetic oscillatory network of transcriptional regulators
    • Elowitz MB, Leibler S (2000) A synthetic oscillatory network of transcriptional regulators. Nature 403: 335–338
    • (2000) Nature , vol.403 , pp. 335-338
    • Elowitz, M.B.1    Leibler, S.2
  • 20
    • 84896901420 scopus 로고    scopus 로고
    • Using synthetic biological parts and microbioreactors to explore the protein expression characteristics of Escherichia coli
    • Gorochowski TE, van den Berg E, Kerkman R, Roubos JA, Bovenberg RA (2014) Using synthetic biological parts and microbioreactors to explore the protein expression characteristics of Escherichia coli. ACS Synth Biol 3: 129–139
    • (2014) ACS Synth Biol , vol.3 , pp. 129-139
    • Gorochowski, T.E.1    van den Berg, E.2    Kerkman, R.3    Roubos, J.A.4    Bovenberg, R.A.5
  • 21
    • 84978768039 scopus 로고    scopus 로고
    • A minimal model of ribosome allocation dynamics captures trade-offs in expression between endogenous and synthetic genes
    • Gorochowski TE, Avcilar-Kucukgoze I, Bovenberg RAL, Roubos JA, Ignatova Z (2016) A minimal model of ribosome allocation dynamics captures trade-offs in expression between endogenous and synthetic genes. ACS Synth Biol 5: 710–720
    • (2016) ACS Synth Biol , vol.5 , pp. 710-720
    • Gorochowski, T.E.1    Avcilar-Kucukgoze, I.2    Bovenberg, R.A.L.3    Roubos, J.A.4    Ignatova, Z.5
  • 22
    • 84901831004 scopus 로고    scopus 로고
    • Validation of noise models for single-cell transcriptomics
    • Grün D, Kester L, van Oudenaarden A (2014) Validation of noise models for single-cell transcriptomics. Nat Methods 11: 637–640
    • (2014) Nat Methods , vol.11 , pp. 637-640
    • Grün, D.1    Kester, L.2    van Oudenaarden, A.3
  • 23
    • 85014739781 scopus 로고    scopus 로고
    • Dynamic regulation of metabolic flux in engineered bacteria using a pathway-independent quorum-sensing circuit
    • Gupta A, Reizman IM, Reisch CR, Prather KL (2017) Dynamic regulation of metabolic flux in engineered bacteria using a pathway-independent quorum-sensing circuit. Nat Biotechnol 35: 273–279
    • (2017) Nat Biotechnol , vol.35 , pp. 273-279
    • Gupta, A.1    Reizman, I.M.2    Reisch, C.R.3    Prather, K.L.4
  • 24
    • 84871599142 scopus 로고    scopus 로고
    • How deep is deep enough for RNA-Seq profiling of bacterial transcriptomes
    • Haas BJ, Chin M, Nusbaum C, Birren BW, Livny J (2012) How deep is deep enough for RNA-Seq profiling of bacterial transcriptomes. BMC Genom 13: 734
    • (2012) BMC Genom , vol.13 , pp. 734
    • Haas, B.J.1    Chin, M.2    Nusbaum, C.3    Birren, B.W.4    Livny, J.5
  • 25
    • 14844358192 scopus 로고    scopus 로고
    • Ultrasensitivity and noise propagation in a synthetic transcriptional cascade
    • Hooshangi S, Thiberge S, Weiss R (2005) Ultrasensitivity and noise propagation in a synthetic transcriptional cascade. Proc Natl Acad Sci USA 102: 3581–3586
    • (2005) Proc Natl Acad Sci USA , vol.102 , pp. 3581-3586
    • Hooshangi, S.1    Thiberge, S.2    Weiss, R.3
  • 27
    • 62549134121 scopus 로고    scopus 로고
    • Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling
    • Ingolia NT, Ghaemmaghami S, Newman JRS, Weissman JS (2009) Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science 324: 218–223
    • (2009) Science , vol.324 , pp. 218-223
    • Ingolia, N.T.1    Ghaemmaghami, S.2    Newman, J.R.S.3    Weissman, J.S.4
  • 28
    • 84894318608 scopus 로고    scopus 로고
    • Ribosome profiling: new views of translation, from single codons to genome scale
    • Ingolia NT (2014) Ribosome profiling: new views of translation, from single codons to genome scale. Nat Rev Genet 15: 205–213
    • (2014) Nat Rev Genet , vol.15 , pp. 205-213
    • Ingolia, N.T.1
  • 29
    • 84882676796 scopus 로고    scopus 로고
    • Retroactivity controls the temporal dynamics of gene transcription
    • Jayanthi S, Nilgiriwala KS, Del Vecchio D (2013) Retroactivity controls the temporal dynamics of gene transcription. ACS Synth Biol 2: 431–441
    • (2013) ACS Synth Biol , vol.2 , pp. 431-441
    • Jayanthi, S.1    Nilgiriwala, K.S.2    Del Vecchio, D.3
  • 31
    • 0035216867 scopus 로고    scopus 로고
    • Homogeneous expression of the PBAD promoter in Escherichia coli by constitutive expression of the low-affinity high-capacity AraE transporter
    • Khlebnikov A, Datsenko KA, Skaug T, Wanner BL, Keasling JD (2001) Homogeneous expression of the PBAD promoter in Escherichia coli by constitutive expression of the low-affinity high-capacity AraE transporter. Microbiology 147: 3241–3247
    • (2001) Microbiology , vol.147 , pp. 3241-3247
    • Khlebnikov, A.1    Datsenko, K.A.2    Skaug, T.3    Wanner, B.L.4    Keasling, J.D.5
  • 33
    • 84857058761 scopus 로고    scopus 로고
    • A systems-level approach for metabolic engineering of yeast cell factories
    • Kim IK, Roldao A, Siewers V, Nielsen J (2012) A systems-level approach for metabolic engineering of yeast cell factories. FEMS Yeast Res 12: 228–248
    • (2012) FEMS Yeast Res , vol.12 , pp. 228-248
    • Kim, I.K.1    Roldao, A.2    Siewers, V.3    Nielsen, J.4
  • 34
    • 84894028698 scopus 로고    scopus 로고
    • Culture volume and vessel affect long-term survival, mutation frequency, and oxidative stress of Escherichia coli
    • Kram KE, Finkel SE (2014) Culture volume and vessel affect long-term survival, mutation frequency, and oxidative stress of Escherichia coli. Appl Environ Microbiol 80: 1732–1738
    • (2014) Appl Environ Microbiol , vol.80 , pp. 1732-1738
    • Kram, K.E.1    Finkel, S.E.2
  • 36
    • 84886993480 scopus 로고    scopus 로고
    • CRISPR interference (CRISPRi) for sequence-specific control of gene expression
    • Larson MH, Gilbert LA, Wang X, Lim WA, Weissman JS, Qi LS (2013) CRISPR interference (CRISPRi) for sequence-specific control of gene expression. Nat Protoc 8: 2180–2196
    • (2013) Nat Protoc , vol.8 , pp. 2180-2196
    • Larson, M.H.1    Gilbert, L.A.2    Wang, X.3    Lim, W.A.4    Weissman, J.S.5    Qi, L.S.6
  • 37
    • 84906317195 scopus 로고    scopus 로고
    • Recent advances in genomic DNA sequencing of microbial species from single cells
    • Lasken RS, McLean JS (2014) Recent advances in genomic DNA sequencing of microbial species from single cells. Nat Rev Genet 15: 577–584
    • (2014) Nat Rev Genet , vol.15 , pp. 577-584
    • Lasken, R.S.1    McLean, J.S.2
  • 38
    • 67649884743 scopus 로고    scopus 로고
    • Fast and accurate short read alignment with Burrows-Wheeler transform
    • Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25: 1754–1760
    • (2009) Bioinformatics , vol.25 , pp. 1754-1760
    • Li, H.1    Durbin, R.2
  • 40
    • 84899550455 scopus 로고    scopus 로고
    • Quantifying absolute protein synthesis rates reveals principles underlying allocation of cellular resources
    • Li GW, Burkhardt D, Gross C, Weissman JS (2014) Quantifying absolute protein synthesis rates reveals principles underlying allocation of cellular resources. Cell 157: 624–635
    • (2014) Cell , vol.157 , pp. 624-635
    • Li, G.W.1    Burkhardt, D.2    Gross, C.3    Weissman, J.S.4
  • 41
    • 84947019500 scopus 로고    scopus 로고
    • Genome-wide identification and evaluation of constitutive promoters in streptomycetes
    • Li S, Wang J, Li X, Yin S, Wang W, Yang K (2015) Genome-wide identification and evaluation of constitutive promoters in streptomycetes. Microb Cell Fact 14: 172
    • (2015) Microb Cell Fact , vol.14 , pp. 172
    • Li, S.1    Wang, J.2    Li, X.3    Yin, S.4    Wang, W.5    Yang, K.6
  • 42
    • 84869476328 scopus 로고    scopus 로고
    • Ribozyme-based insulator parts buffer synthetic circuits from genetic context
    • Lou C, Stanton B, Chen YJ, Munsky B, Voigt CA (2012) Ribozyme-based insulator parts buffer synthetic circuits from genetic context. Nat Biotechnol 30: 1137–1142
    • (2012) Nat Biotechnol , vol.30 , pp. 1137-1142
    • Lou, C.1    Stanton, B.2    Chen, Y.J.3    Munsky, B.4    Voigt, C.A.5
  • 43
    • 84868619337 scopus 로고    scopus 로고
    • Genetic programs constructed from layered logic gates in single cells
    • Moon TS, Lou C, Tamsir A, Stanton BC, Voigt CA (2012) Genetic programs constructed from layered logic gates in single cells. Nature 491: 249–253
    • (2012) Nature , vol.491 , pp. 249-253
    • Moon, T.S.1    Lou, C.2    Tamsir, A.3    Stanton, B.C.4    Voigt, C.A.5
  • 47
  • 49
    • 84934936070 scopus 로고    scopus 로고
    • Multi-input CRISPR/Cas genetic circuits that interface host regulatory networks
    • Nielsen AAK, Voigt CA (2014) Multi-input CRISPR/Cas genetic circuits that interface host regulatory networks. Mol Syst Biol 10: 763
    • (2014) Mol Syst Biol , vol.10 , pp. 763
    • Nielsen, A.A.K.1    Voigt, C.A.2
  • 51
    • 84867389802 scopus 로고    scopus 로고
    • RNA processing enables predictable programming of gene expression
    • Qi L, Haurwitz RE, Shao W, Doudna JA, Arkin AP (2012) RNA processing enables predictable programming of gene expression. Nat Biotechnol 30: 1002–1006
    • (2012) Nat Biotechnol , vol.30 , pp. 1002-1006
    • Qi, L.1    Haurwitz, R.E.2    Shao, W.3    Doudna, J.A.4    Arkin, A.P.5
  • 52
    • 84874687019 scopus 로고    scopus 로고
    • Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression
    • Qi LS, Larson MH, Gilbert LA, Doudna JA, Weissman JS, Arkin AP, Lim WA (2013) Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression. Cell 152: 1173–1183
    • (2013) Cell , vol.152 , pp. 1173-1183
    • Qi, L.S.1    Larson, M.H.2    Gilbert, L.A.3    Doudna, J.A.4    Weissman, J.S.5    Arkin, A.P.6    Lim, W.A.7
  • 53
    • 75249087100 scopus 로고    scopus 로고
    • edgeR: a Bioconductor package for differential expression analysis of digital gene expression data
    • Robinson MD, McCarthy DJ, Smyth GK (2010) edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26: 139–140
    • (2010) Bioinformatics , vol.26 , pp. 139-140
    • Robinson, M.D.1    McCarthy, D.J.2    Smyth, G.K.3
  • 54
    • 77953176036 scopus 로고    scopus 로고
    • A scaling normalization method for differential expression analysis of RNA-seq data
    • Robinson MD, Oshlack A (2010) A scaling normalization method for differential expression analysis of RNA-seq data. Genome Biol 11: R25
    • (2010) Genome Biol , vol.11 , pp. R25
    • Robinson, M.D.1    Oshlack, A.2
  • 56
    • 0037337551 scopus 로고    scopus 로고
    • AraC protein: a love-hate relationship
    • Schleif R (2003) AraC protein: a love-hate relationship. BioEssays 25: 274–282
    • (2003) BioEssays , vol.25 , pp. 274-282
    • Schleif, R.1
  • 58
    • 84882455458 scopus 로고    scopus 로고
    • Single-cell sequencing-based technologies will revolutionize whole-organism science
    • Shapiro E, Biezuner T, Linnarsson S (2013) Single-cell sequencing-based technologies will revolutionize whole-organism science. Nat Rev Genet 14: 618–630
    • (2013) Nat Rev Genet , vol.14 , pp. 618-630
    • Shapiro, E.1    Biezuner, T.2    Linnarsson, S.3
  • 59
    • 19444377759 scopus 로고    scopus 로고
    • Transcriptional interference – a crash course
    • Shearwin KE, Callen BP, Egan JB (2005) Transcriptional interference – a crash course. Trends Genet 21: 339–345
    • (2005) Trends Genet , vol.21 , pp. 339-345
    • Shearwin, K.E.1    Callen, B.P.2    Egan, J.B.3
  • 61
    • 84875230351 scopus 로고    scopus 로고
    • Synthetic circuits integrating logic and memory in living cells
    • Siuti P, Yazbek J, Lu TK (2013) Synthetic circuits integrating logic and memory in living cells. Nat Biotechnol 31: 448–452
    • (2013) Nat Biotechnol , vol.31 , pp. 448-452
    • Siuti, P.1    Yazbek, J.2    Lu, T.K.3
  • 71
    • 84859633048 scopus 로고    scopus 로고
    • Design of a dynamic sensor-regulator system for production of chemicals and fuels derived from fatty acids
    • Zhang F, Carothers JM, Keasling JD (2012) Design of a dynamic sensor-regulator system for production of chemicals and fuels derived from fatty acids. Nat Biotechnol 30: 354–359
    • (2012) Nat Biotechnol , vol.30 , pp. 354-359
    • Zhang, F.1    Carothers, J.M.2    Keasling, J.D.3
  • 72
    • 57749195712 scopus 로고    scopus 로고
    • RNA-Seq: a revolutionary tool for transcriptomics
    • Zhong W, Gerstein M, Snyder M (2009) RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 10: 57–63
    • (2009) Nat Rev Genet , vol.10 , pp. 57-63
    • Zhong, W.1    Gerstein, M.2    Snyder, M.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.