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Volumn 17, Issue 1, 2016, Pages

Sort-seq under the hood: Implications of design choices on large-scale characterization of sequence-function relations

Author keywords

Fluorescence activated cell sorting; High throughput sequencing; Sequence function relations; Systems biology

Indexed keywords

EXPERIMENTAL MODEL; FLUORESCENCE; MODEL; QUANTITATIVE STUDY; BIOLOGICAL MODEL; COMPUTER SIMULATION; FLOW CYTOMETRY; GENE LIBRARY; HIGH THROUGHPUT SEQUENCING; MUTATION; PROCEDURES; SEQUENCE ANALYSIS; STATISTICAL MODEL;

EID: 84960091824     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/s12864-016-2533-5     Document Type: Article
Times cited : (57)

References (58)
  • 1
    • 84902810053 scopus 로고    scopus 로고
    • In pursuit of design principles of regulatory sequences
    • Levo M, Segal E. In pursuit of design principles of regulatory sequences. Nature Rev Gen. 2014; 15(7):453-68.
    • (2014) Nature Rev Gen , vol.15 , Issue.7 , pp. 453-468
    • Levo, M.1    Segal, E.2
  • 2
    • 84908049845 scopus 로고    scopus 로고
    • Viewing Protein Fitness Landscapes Through a Next-Gen Lens
    • Boucher JI, Cote P, Flynn J, Jiang L, Laban A, Mishra P, et al. Viewing Protein Fitness Landscapes Through a Next-Gen Lens. Genetics. 2014; 198(2):461-471.
    • (2014) Genetics , vol.198 , Issue.2 , pp. 461-471
    • Boucher, J.I.1    Cote, P.2    Flynn, J.3    Jiang, L.4    Laban, A.5    Mishra, P.6
  • 3
    • 84902775598 scopus 로고    scopus 로고
    • Empirical fitness landscapes and the predictability of evolution
    • de Visser JAGM, Krug J. Empirical fitness landscapes and the predictability of evolution. Nature Rev Gen. 2014; 15(7):480-90.
    • (2014) Nature Rev Gen , vol.15 , Issue.7 , pp. 480-490
    • de Visser, J.A.G.M.1    Krug, J.2
  • 4
    • 77952706498 scopus 로고    scopus 로고
    • Using deep sequencing to characterize the biophysical mechanism of a transcriptional regulatory sequence
    • Kinney JB, Murugan A, Callan CG, Cox EC. Using deep sequencing to characterize the biophysical mechanism of a transcriptional regulatory sequence. Proc Natl Acad Sci USA. 2010; 107(20):9158-63.
    • (2010) Proc Natl Acad Sci USA , vol.107 , Issue.20 , pp. 9158-9163
    • Kinney, J.B.1    Murugan, A.2    Callan, C.G.3    Cox, E.C.4
  • 5
    • 84862002321 scopus 로고    scopus 로고
    • Inferring gene regulatory logic from high-throughput measurements of thousands of systematically designed promoters
    • Sharon E, Kalma Y, Sharp A, Raveh-Sadka T, Levo M, Zeevi D, et al. Inferring gene regulatory logic from high-throughput measurements of thousands of systematically designed promoters. Nature Biotechnol. 2012; 30(6):521-30.
    • (2012) Nature Biotechnol , vol.30 , Issue.6 , pp. 521-530
    • Sharon, E.1    Kalma, Y.2    Sharp, A.3    Raveh-Sadka, T.4    Zeevi, D.5
  • 6
    • 84882777421 scopus 로고    scopus 로고
    • Composability of regulatory sequences controlling transcription and translation in Escherichia coli
    • Kosuri S, Goodman DB, Cambray G, Mutalik VK, Gao Y, Arkin AP, et al. Composability of regulatory sequences controlling transcription and translation in Escherichia coli. Proc Natl Acad Sci USA. 2013; 110(34):14024-9.
    • (2013) Proc Natl Acad Sci USA , vol.110 , Issue.34 , pp. 14024-14029
    • Kosuri, S.1    Goodman, D.B.2    Cambray, G.3    Mutalik, V.K.4    Gao, Y.5    Arkin, A.P.6
  • 8
    • 84907527856 scopus 로고    scopus 로고
    • Probing the effect of promoters on noise in gene expression using thousands of designed sequences
    • Sharon E, Dijk Dv, Kalma Y, Keren L, Manor O, Yakhini Z, et al. Probing the effect of promoters on noise in gene expression using thousands of designed sequences. Genome Res. 2014; 24(10):1698-706.
    • (2014) Genome Res , vol.24 , Issue.10 , pp. 1698-1706
    • Sharon, E.1    Dijk, D.2    Kalma, Y.3    Keren, L.4    Manor, O.5    Yakhini, Z.6
  • 9
    • 84925283037 scopus 로고    scopus 로고
    • Large-scale mapping of sequence-function relations in small regulatory RNAs reveals plasticity and modularity
    • Peterman N, Lavi-Itzkovitz A, Levine E. Large-scale mapping of sequence-function relations in small regulatory RNAs reveals plasticity and modularity. Nucleic Acids Res. 2014; 42(19):12177-88.
    • (2014) Nucleic Acids Res , vol.42 , Issue.19 , pp. 12177-12188
    • Peterman, N.1    Lavi-Itzkovitz, A.2    Levine, E.3
  • 11
    • 79956357160 scopus 로고    scopus 로고
    • Experimental illumination of a fitness landscape
    • Hietpas RT, Jensen JD, Bolon DNA. Experimental illumination of a fitness landscape. Proc Natl Acad Sci. 2011; 108(19):201016024.
    • (2011) Proc Natl Acad Sci , vol.108 , Issue.19 , pp. 201016024
    • Hietpas, R.T.1    Jensen, J.D.2    Bolon, D.N.A.3
  • 12
    • 84906217475 scopus 로고    scopus 로고
    • Comprehensive mutational scanning of a kinase in vivo reveals substrate-dependent fitness landscapes
    • Melnikov A, Rogov P, Wang L, Gnirke A, Mikkelsen TS. Comprehensive mutational scanning of a kinase in vivo reveals substrate-dependent fitness landscapes. Nucl Acids Res. 2014; 42(14):e112.
    • (2014) Nucl Acids Res , vol.42 , Issue.14 , pp. e112
    • Melnikov, A.1    Rogov, P.2    Wang, L.3    Gnirke, A.4    Mikkelsen, T.S.5
  • 13
    • 84922384542 scopus 로고    scopus 로고
    • A Systematic Survey of an Intragenic Epistatic Landscape
    • Bank C, Hietpas RT, Jensen JD, Bolon DNA. A Systematic Survey of an Intragenic Epistatic Landscape. Mol Biol Evol. 2015; 32(1):229-38.
    • (2015) Mol Biol Evol , vol.32 , Issue.1 , pp. 229-238
    • Bank, C.1    Hietpas, R.T.2    Jensen, J.D.3    Bolon, D.N.A.4
  • 14
    • 84923321398 scopus 로고    scopus 로고
    • Evolvability as a Function of Purifying Selection in TEM-1 β-Lactamase
    • Stiffler M, Hekstra D, Ranganathan R. Evolvability as a Function of Purifying Selection in TEM-1 β-Lactamase. Cell. 2015; 160(5):882-92.
    • (2015) Cell , vol.160 , Issue.5 , pp. 882-892
    • Stiffler, M.1    Hekstra, D.2    Ranganathan, R.3
  • 17
    • 77957963240 scopus 로고    scopus 로고
    • Rapid Construction of Empirical RNA Fitness Landscapes
    • Pitt JN, Ferré-D'Amaré AR. Rapid Construction of Empirical RNA Fitness Landscapes. Science. 2010; 330(6002):376-9.
    • (2010) Science , vol.330 , Issue.6002 , pp. 376-379
    • Pitt, J.N.1    Ferré-D'Amaré, A.R.2
  • 18
    • 84867644046 scopus 로고    scopus 로고
    • A fundamental protein property, thermodynamic stability, revealed solely from large-scale measurements of protein function
    • Araya CL, Fowler DM, Chen W, Muniez I, Kelly JW, Fields S. A fundamental protein property, thermodynamic stability, revealed solely from large-scale measurements of protein function. Proc Natl Acad Sci. 2012; 109(42):16858-63.
    • (2012) Proc Natl Acad Sci , vol.109 , Issue.42 , pp. 16858-16863
    • Araya, C.L.1    Fowler, D.M.2    Chen, W.3    Muniez, I.4    Kelly, J.W.5    Fields, S.6
  • 19
    • 84901804745 scopus 로고    scopus 로고
    • Quantitative analysis of RNA-protein interactions on a massively parallel array reveals biophysical and evolutionary landscapes
    • Buenrostro JD, Araya CL, Chircus LM, Layton CJ, Chang HY, Snyder MP, et al. Quantitative analysis of RNA-protein interactions on a massively parallel array reveals biophysical and evolutionary landscapes. Nature Biotechnol. 2014; 32(6):562-8.
    • (2014) Nature Biotechnol , vol.32 , Issue.6 , pp. 562-568
    • Buenrostro, J.D.1    Araya, C.L.2    Chircus, L.M.3    Layton, C.J.4    Chang, H.Y.5    Snyder, M.P.6
  • 20
    • 84905217368 scopus 로고    scopus 로고
    • Deep mutational scanning: a new style of protein science
    • Fowler DM, Fields S. Deep mutational scanning: a new style of protein science. Nature Methods. 2014; 11(8):801-7.
    • (2014) Nature Methods , vol.11 , Issue.8 , pp. 801-807
    • Fowler, D.M.1    Fields, S.2
  • 21
    • 71849118573 scopus 로고    scopus 로고
    • High-resolution analysis of DNA regulatory elements by synthetic saturation mutagenesis
    • Patwardhan RP, Lee C, Litvin O, Young DL, Pe'er D, Shendure J. High-resolution analysis of DNA regulatory elements by synthetic saturation mutagenesis. 27. 2009; 12:1173-75.
    • (2009) 27 , vol.12 , pp. 1173-1175
    • Patwardhan, R.P.1    Lee, C.2    Litvin, O.3    Young, D.L.4    Pe'er, D.5    Shendure, J.6
  • 23
    • 84863229330 scopus 로고    scopus 로고
    • Systematic dissection and optimization of inducible enhancers in human cells using a massively parallel reporter assay
    • Melnikov A, Murugan A, Zhang X, Tesileanu T, Wang L, Rogov P, et al. Systematic dissection and optimization of inducible enhancers in human cells using a massively parallel reporter assay. Nature Biotechnol. 2012; 30(3):271-7.
    • (2012) Nature Biotechnol , vol.30 , Issue.3 , pp. 271-277
    • Melnikov, A.1    Murugan, A.2    Zhang, X.3    Tesileanu, T.4    Wang, L.5    Rogov, P.6
  • 24
    • 84869853147 scopus 로고    scopus 로고
    • Complex effects of nucleotide variants in a mammalian cis-regulatory element
    • Kwasnieski JC, Mogno I, Myers CA, Corbo JC, Cohen BA. Complex effects of nucleotide variants in a mammalian cis-regulatory element. Proc Natl Acad Sci. 2012; 109(47):19498-503.
    • (2012) Proc Natl Acad Sci , vol.109 , Issue.47 , pp. 19498-19503
    • Kwasnieski, J.C.1    Mogno, I.2    Myers, C.A.3    Corbo, J.C.4    Cohen, B.A.5
  • 25
    • 84874381107 scopus 로고    scopus 로고
    • Genome-Wide Quantitative Enhancer Activity Maps Identified by STARR-seq
    • Arnold CD, Gerlach D, Stelzer C, Boryń LM, Rath M, Stark A. Genome-Wide Quantitative Enhancer Activity Maps Identified by STARR-seq. Science. 2013; 339(6123):1074-77.
    • (2013) Science , vol.339 , Issue.6123 , pp. 1074-1077
    • Arnold, C.D.1    Gerlach, D.2    Stelzer, C.3    Rath, M.4    Stark, A.5    Boryń, LM6
  • 26
    • 84907257107 scopus 로고    scopus 로고
    • Saturation editing of genomic regions by multiplex homology-directed repair
    • Findlay GM, Boyle EA, Hause RJ, Klein JC, Shendure J. Saturation editing of genomic regions by multiplex homology-directed repair. Nature. 2014; 513(7516):120-3.
    • (2014) Nature , vol.513 , Issue.7516 , pp. 120-123
    • Findlay, G.M.1    Boyle, E.A.2    Hause, R.J.3    Klein, J.C.4    Shendure, J.5
  • 27
    • 84923119852 scopus 로고    scopus 로고
    • High-throughput engineering of a mammalian genome reveals building principles of methylation states at CG rich regions
    • Krebs AR, Dessus-Babus S, Burger L, Schübeler D. High-throughput engineering of a mammalian genome reveals building principles of methylation states at CG rich regions. eLife. 2014; 3:e04094.
    • (2014) eLife , vol.3 , pp. e04094
    • Krebs, A.R.1    Dessus-Babus, S.2    Burger, L.3    Schübeler, D.4
  • 28
    • 84897481674 scopus 로고    scopus 로고
    • Comparison of the theoretical and real-world evolutionary potential of a genetic circuit
    • Razo-Mejia M, Boedicker JQ, Jones D, DeLuna A, Kinney JB, Phillips R. Comparison of the theoretical and real-world evolutionary potential of a genetic circuit. Physical biol. 2014; 11(2):026005.
    • (2014) Physical biol , vol.11 , Issue.2 , pp. 026005
    • Razo-Mejia, M.1    Boedicker, J.Q.2    Jones, D.3    DeLuna, A.4    Kinney, J.B.5    Phillips, R.6
  • 29
    • 84899692444 scopus 로고    scopus 로고
    • Function-based identification of mammalian enhancers using site-specific integration
    • Dickel DE, Zhu Y, Nord AS, Wylie JN, Akiyama JA, Afzal V, et al. Function-based identification of mammalian enhancers using site-specific integration. Nature Methods. 2014; 11(5):566-71.
    • (2014) Nature Methods , vol.11 , Issue.5 , pp. 566-571
    • Dickel, D.E.1    Zhu, Y.2    Nord, A.S.3    Wylie, J.N.4    Akiyama, J.A.5    Afzal, V.6
  • 30
    • 84899670369 scopus 로고    scopus 로고
    • FIREWACh: high-throughput functional detection of transcriptional regulatory modules in mammalian cells
    • Murtha M, Tokcaer-Keskin Z, Tang Z, Strino F, Chen X, Wang Y, et al. FIREWACh: high-throughput functional detection of transcriptional regulatory modules in mammalian cells. Nature Methods. 2014; 11(5):559-65.
    • (2014) Nature Methods , vol.11 , Issue.5 , pp. 559-565
    • Murtha, M.1    Tokcaer-Keskin, Z.2    Tang, Z.3    Strino, F.4    Chen, X.5    Wang, Y.6
  • 31
    • 84880652281 scopus 로고    scopus 로고
    • Deciphering the rules by which 5'-UTR sequences affect protein expression in yeast
    • Dvir S, Velten L, Sharon E, Zeevi D, Carey LB, Weinberger A, et al. Deciphering the rules by which 5'-UTR sequences affect protein expression in yeast. Proc Natl Acad Sci USA. 2013; 110(30):E2792-2801.
    • (2013) Proc Natl Acad Sci USA , vol.110 , Issue.30 , pp. E2792-2801
    • Dvir, S.1    Velten, L.2    Sharon, E.3    Zeevi, D.4    Carey, L.B.5    Weinberger, A.6
  • 32
    • 84898048208 scopus 로고    scopus 로고
    • Systematic identification of regulatory elements in conserved 3' UTRs of human transcripts
    • Oikonomou P, Goodarzi H, Tavazoie S. Systematic identification of regulatory elements in conserved 3' UTRs of human transcripts. Cell Reports. 2014; 7(1):281-92.
    • (2014) Cell Reports , vol.7 , Issue.1 , pp. 281-292
    • Oikonomou, P.1    Goodarzi, H.2    Tavazoie, S.3
  • 33
    • 84930350341 scopus 로고    scopus 로고
    • Systematic Dissection of the Sequence Determinants of Gene 3' End Mediated Expression Control
    • Shalem O, Sharon E, Lubliner S, Regev I, Lotan-Pompan M, Yakhini Z, et al. Systematic Dissection of the Sequence Determinants of Gene 3' End Mediated Expression Control. PLoS Genet. 2015; 11(4):e1005147.
    • (2015) PLoS Genet , vol.11 , Issue.4 , pp. e1005147
    • Shalem, O.1    Sharon, E.2    Lubliner, S.3    Regev, I.4    Lotan-Pompan, M.5    Yakhini, Z.6
  • 35
    • 84877983042 scopus 로고    scopus 로고
    • Massive functional mapping of a 5'UTR by saturation mutagenesis, phenotypic sorting and deep sequencing
    • Holmqvist E, Reimegård J, Wagner EGH. Massive functional mapping of a 5'UTR by saturation mutagenesis, phenotypic sorting and deep sequencing. Nucleic Acids Res. 2013; 41(12):e122.
    • (2013) Nucleic Acids Res , vol.41 , Issue.12 , pp. e122
    • Holmqvist, E.1    Reimegård, J.2    Wagner, E.G.H.3
  • 37
    • 84862025262 scopus 로고    scopus 로고
    • Optimization of affinity, specificity and function of designed influenza inhibitors using deep sequencing
    • Whitehead TA, Chevalier A, Song Y, Dreyfus C, Fleishman SJ, De Mattos C, et al. Optimization of affinity, specificity and function of designed influenza inhibitors using deep sequencing. Nature Biotechnol. 2012; 30(6):543-8.
    • (2012) Nature Biotechnol , vol.30 , Issue.6 , pp. 543-548
    • Whitehead, T.A.1    Chevalier, A.2    Song, Y.3    Dreyfus, C.4    Fleishman, S.J.5    De Mattos, C.6
  • 38
    • 84886302057 scopus 로고    scopus 로고
    • Causes and effects of N-terminal codon bias in bacterial genes
    • Goodman DB, Church GM, Kosuri S. Causes and effects of N-terminal codon bias in bacterial genes. Science New York, NY. 2013; 342(6157):475-9.
    • (2013) Science New York, NY , vol.342 , Issue.6157 , pp. 475-479
    • Goodman, D.B.1    Church, G.M.2    Kosuri, S.3
  • 39
    • 84922439802 scopus 로고    scopus 로고
    • Pervasive degeneracy and epistasis in a protein-protein interface
    • Podgornaia AI, Laub MT. Pervasive degeneracy and epistasis in a protein-protein interface. Science. 2015; 347(6222):673-7.
    • (2015) Science , vol.347 , Issue.6222 , pp. 673-677
    • Podgornaia, A.I.1    Laub, M.T.2
  • 42
    • 84860595791 scopus 로고    scopus 로고
    • Cost-effective, high-throughput DNA sequencing libraries for multiplexed target capture
    • Rohland N, Reich D. Cost-effective, high-throughput DNA sequencing libraries for multiplexed target capture. Genome Res. 2012; 22(5):939-46.
    • (2012) Genome Res , vol.22 , Issue.5 , pp. 939-946
    • Rohland, N.1    Reich, D.2
  • 43
    • 84899696363 scopus 로고    scopus 로고
    • Large-scale de novo DNA synthesis: technologies and applications
    • Kosuri S, Church GM. Large-scale de novo DNA synthesis: technologies and applications. Nature Methods. 2014; 11(5):499-507.
    • (2014) Nature Methods , vol.11 , Issue.5 , pp. 499-507
    • Kosuri, S.1    Church, G.M.2
  • 47
    • 0037119587 scopus 로고    scopus 로고
    • Stochastic Gene Expression in a Single Cell
    • Elowitz MB, Levine AJ, Siggia ED, Swain PS. Stochastic Gene Expression in a Single Cell. Science. 2002; 297(5584):1183-86.
    • (2002) Science , vol.297 , Issue.5584 , pp. 1183-1186
    • Elowitz, M.B.1    Levine, A.J.2    Siggia, E.D.3    Swain, P.S.4
  • 48
    • 25444489027 scopus 로고    scopus 로고
    • Phenotypic Diversity, Population Growth, and Information in Fluctuating Environments
    • Kussell E, Leibler S. Phenotypic Diversity, Population Growth, and Information in Fluctuating Environments. Science. 2005; 309(5743):2075-2078.
    • (2005) Science , vol.309 , Issue.5743 , pp. 2075-2078
    • Kussell, E.1    Leibler, S.2
  • 50
    • 33645293152 scopus 로고    scopus 로고
    • An excitable gene regulatory circuit induces transient cellular differentiation
    • Süel GM, Garcia-Ojalvo J, Liberman LM, Elowitz MB. An excitable gene regulatory circuit induces transient cellular differentiation. Nature. 2006; 440(7083):545-50.
    • (2006) Nature , vol.440 , Issue.7083 , pp. 545-550
    • Süel, G.M.1    Garcia-Ojalvo, J.2    Liberman, L.M.3    Elowitz, M.B.4
  • 51
    • 78649838304 scopus 로고    scopus 로고
    • Lysogen stability is determined by the frequency of activity bursts from the fate-determining gene
    • Zong C, So Lh, Sepulveda LA, Skinner SO, Golding I. Lysogen stability is determined by the frequency of activity bursts from the fate-determining gene. Mol Syst Biol. 2010; 6:440.
    • (2010) Mol Syst Biol , vol.6 , pp. 440
    • Zong, C.1    So, L.2    Sepulveda, L.A.3    Skinner, S.O.4    Golding, I.5
  • 53
    • 84877080561 scopus 로고    scopus 로고
    • Genotype to Phenotype Mapping and the Fitness Landscape of the E. coli lac Promoter
    • Otwinowski J, Nemenman I. Genotype to Phenotype Mapping and the Fitness Landscape of the E. coli lac Promoter. PLoS ONE. 2013; 8(5):e61570.
    • (2013) PLoS ONE , vol.8 , Issue.5 , pp. e61570
    • Otwinowski, J.1    Nemenman, I.2
  • 54
    • 85026972246 scopus 로고    scopus 로고
    • Learning Quantitative Sequence-Function Relationships from Massively Parallel Experiments.
    • Atwal GS, Kinney JB. Learning Quantitative Sequence-Function Relationships from Massively Parallel Experiments. J Stat Phys. 2015:1-41.
    • (2015) J Stat Phys. , pp. 1-41
    • Atwal, G.S.1    Kinney, J.B.2
  • 55
    • 33846351302 scopus 로고    scopus 로고
    • Precise physical models of protein-DNA interaction from high-throughput data
    • Kinney JB, Tkačik G, Callan CG. Precise physical models of protein-DNA interaction from high-throughput data. Proc Natl Acad Sci. 2007; 104(2):501-6.
    • (2007) Proc Natl Acad Sci , vol.104 , Issue.2 , pp. 501-506
    • Kinney, J.B.1    Tkačik, G.2    Callan, C.G.3
  • 57
    • 84896855185 scopus 로고    scopus 로고
    • Parametric Inference in the Large Data Limit Using Maximally Informative Models
    • Kinney JB, Atwal GS. Parametric Inference in the Large Data Limit Using Maximally Informative Models. Neural Comput. 2014; 26(4):637-53.
    • (2014) Neural Comput , vol.26 , Issue.4 , pp. 637-653
    • Kinney, J.B.1    Atwal, G.S.2
  • 58
    • 84901847160 scopus 로고    scopus 로고
    • Inferring fitness landscapes by regression produces biased estimates of epistasis
    • Otwinowski J, Plotkin JB. Inferring fitness landscapes by regression produces biased estimates of epistasis. Proc Natl Acad Sci. 2014; 111(22):E2301-E2309.
    • (2014) Proc Natl Acad Sci , vol.111 , Issue.22 , pp. E2301-E2309
    • Otwinowski, J.1    Plotkin, J.B.2


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