Deciphering eukaryotic cis-regulatory logic with 100 million random promoters

[1]  Yang I Li,et al.  Trans Effects on Gene Expression Can Drive Omnigenic Inheritance , 2018, Cell.

[2]  Sarah M. Goggin,et al.  High-resolution genome-wide functional dissection of transcriptional regulatory regions and nucleotides in human , 2018, Nature Communications.

[3]  Łukasz M. Boryń,et al.  Resolving systematic errors in widely-used enhancer activity assays in human cells , 2017, Nature Methods.

[4]  N. Jojic,et al.  Deep learning of the regulatory grammar of yeast 5′ untranslated regions from 500,000 random sequences , 2017, bioRxiv.

[5]  Sarah M. Goggin,et al.  High-resolution genome-wide functional dissection of transcriptional regulatory regions in human , 2017, bioRxiv.

[6]  Yang I Li,et al.  An Expanded View of Complex Traits: From Polygenic to Omnigenic , 2017, Cell.

[7]  J. Gore,et al.  Random sequences rapidly evolve into de novo promoters , 2018, Nature Communications.

[8]  Z. Yakhini,et al.  Systematic Investigation of Transcription Factor Activity in the Context of Chromatin Using Massively Parallel Binding and Expression Assays. , 2017, Molecular cell.

[9]  H. Bussemaker,et al.  Genome-wide mapping of autonomous promoter activity in human cells , 2016, Nature Biotechnology.

[10]  Bongsoo Park,et al.  Genomic Nucleosome Organization Reconstituted with Pure Proteins , 2016, Cell.

[11]  Lin Yang,et al.  DNA Shape Features Improve Transcription Factor Binding Site Predictions In Vivo. , 2016, Cell systems.

[12]  Jianzhi Zhang,et al.  The Genomic Landscape of Position Effects on Protein Expression Level and Noise in Yeast. , 2016, Cell systems.

[13]  Martín Abadi,et al.  TensorFlow: Large-Scale Machine Learning on Heterogeneous Distributed Systems , 2016, ArXiv.

[14]  Timothy Daley,et al.  Applications of species accumulation curves in large-scale biological data analysis , 2015, Quantitative Biology.

[15]  D. Carl,et al.  Model for how poly-dA:dT sites act as nucleosome turnstiles , 2015 .

[16]  D. Carl,et al.  The RSC complex may be the poly-A nucleosome turnstile mechanism , 2015 .

[17]  L. Kruglyak,et al.  The role of regulatory variation in complex traits and disease , 2015, Nature Reviews Genetics.

[18]  Z. Yakhini,et al.  Systematic Dissection of the Sequence Determinants of Gene 3’ End Mediated Expression Control , 2015, PLoS genetics.

[19]  Martha L. Bulyk,et al.  UniPROBE, update 2015: new tools and content for the online database of protein-binding microarray data on protein–DNA interactions , 2014, Nucleic Acids Res..

[20]  Carl G. de Boer,et al.  Poly-dA:dT Tracts Form an In Vivo Nucleosomal Turnstile , 2014, PloS one.

[21]  Kevin Struhl,et al.  Global Analysis of mRNA Isoform Half-Lives Reveals Stabilizing and Destabilizing Elements in Yeast , 2014, Cell.

[22]  Carl G. de Boer,et al.  A unified model for yeast transcript definition , 2014, Genome research.

[23]  Timothy R. Hughes,et al.  Mapping Yeast Transcriptional Networks , 2013, Genetics.

[24]  Vivek K. Mutalik,et al.  Composability of regulatory sequences controlling transcription and translation in Escherichia coli , 2013, Proceedings of the National Academy of Sciences.

[25]  T. Ideker,et al.  Decoupling epigenetic and genetic effects through systematic analysis of gene position. , 2013, Cell reports.

[26]  Juan M. Vaquerizas,et al.  DNA-Binding Specificities of Human Transcription Factors , 2013, Cell.

[27]  Z. Yakhini,et al.  Inferring gene regulatory logic from high-throughput measurements of thousands of systematically designed promoters , 2012, Nature Biotechnology.

[28]  Steven L Salzberg,et al.  Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.

[29]  Edith D. Wong,et al.  Saccharomyces Genome Database: the genomics resource of budding yeast , 2011, Nucleic Acids Res..

[30]  Timothy R. Hughes,et al.  YeTFaSCo: a database of evaluated yeast transcription factor sequence specificities , 2011, Nucleic Acids Res..

[31]  S. Hahn,et al.  Transcriptional Regulation in Saccharomyces cerevisiae: Transcription Factor Regulation and Function, Mechanisms of Initiation, and Roles of Activators and Coactivators , 2011, Genetics.

[32]  Ionas Erb,et al.  Transcription Factor Binding Site Positioning in Yeast: Proximal Promoter Motifs Characterize TATA-Less Promoters , 2011, PloS one.

[33]  S. Luo,et al.  Direct measurement of DNA affinity landscapes on a high-throughput sequencing instrument , 2011, Nature Biotechnology.

[34]  E. O’Shea,et al.  Integrated approaches reveal determinants of genome-wide binding and function of the transcription factor Pho4. , 2011, Molecular cell.

[35]  Zhenhai Zhang,et al.  A Packing Mechanism for Nucleosome Organization Reconstituted Across a Eukaryotic Genome , 2011, Science.

[36]  Achim Tresch,et al.  Dynamic transcriptome analysis measures rates of mRNA synthesis and decay in yeast , 2011, Molecular systems biology.

[37]  M. Palumbo,et al.  Extensive role of the general regulatory factors, Abf1 and Rap1, in determining genome-wide chromatin structure in budding yeast , 2010, Nucleic acids research.

[38]  J. Kinney,et al.  Using deep sequencing to characterize the biophysical mechanism of a transcriptional regulatory sequence , 2010, Proceedings of the National Academy of Sciences.

[39]  Timothy R Hughes,et al.  Conserved expression without conserved regulatory sequence: the more things change, the more they stay the same. , 2010, Trends in genetics : TIG.

[40]  L. Mirny,et al.  Different gene regulation strategies revealed by analysis of binding motifs. , 2009, Trends in genetics : TIG.

[41]  R. Mann,et al.  The role of DNA shape in protein-DNA recognition , 2009, Nature.

[42]  Eran Segal,et al.  From DNA sequence to transcriptional behaviour: a quantitative approach , 2009, Nature Reviews Genetics.

[43]  S. Letovsky,et al.  Quantification of the yeast transcriptome by single-molecule sequencing , 2009, Nature Biotechnology.

[44]  D. G. Gibson,et al.  Enzymatic assembly of DNA molecules up to several hundred kilobases , 2009, Nature Methods.

[45]  H. Madhani,et al.  Mechanisms that Specify Promoter Nucleosome Location and Identity , 2009, Cell.

[46]  Daniel E. Newburger,et al.  High-resolution DNA-binding specificity analysis of yeast transcription factors. , 2009, Genome research.

[47]  William Stafford Noble,et al.  Global mapping of protein-DNA interactions in vivo by digital genomic footprinting , 2009, Nature Methods.

[48]  E. Siggia,et al.  Analysis of Combinatorial cis-Regulation in Synthetic and Genomic Promoters , 2008, Nature.

[49]  Christopher L. Warren,et al.  A library of yeast transcription factor motifs reveals a widespread function for Rsc3 in targeting nucleosome exclusion at promoters. , 2008, Molecular cell.

[50]  Lei Guo,et al.  Predicting Gene Expression from Sequence: A Reexamination , 2007, PLoS Comput. Biol..

[51]  J. Lieb,et al.  Forkhead proteins control the outcome of transcription factor binding by antiactivation , 2007, The EMBO journal.

[52]  Kai Li,et al.  Exploring the functional landscape of gene expression: directed search of large microarray compendia , 2007, Bioinform..

[53]  S. Petruk,et al.  Transcriptional interference: an unexpected layer of complexity in gene regulation , 2007, Journal of Cell Science.

[54]  Barrett C. Foat,et al.  Predictive modeling of genome-wide mRNA expression: from modules to molecules. , 2007, Annual review of biophysics and biomolecular structure.

[55]  Neil D Clarke,et al.  Whole-genome comparison of Leu3 binding in vitro and in vivo reveals the importance of nucleosome occupancy in target site selection. , 2006, Genome research.

[56]  Charles Boone,et al.  Identifying transcription factor functions and targets by phenotypic activation , 2006, Proceedings of the National Academy of Sciences.

[57]  Amos Tanay,et al.  Extensive low-affinity transcriptional interactions in the yeast genome. , 2006, Genome research.

[58]  Adam Godzik,et al.  Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences , 2006, Bioinform..

[59]  George G. Roberts,et al.  Transcriptome profiling of Saccharomyces cerevisiae during a transition from fermentative to glycerol-based respiratory growth reveals extensive metabolic and structural remodeling , 2006, Molecular Genetics and Genomics.

[60]  A. Tong,et al.  Synthetic genetic array analysis in Saccharomyces cerevisiae. , 2006, Methods in molecular biology.

[61]  N. D. Clarke,et al.  Explicit equilibrium modeling of transcription-factor binding and gene regulation , 2005, Genome Biology.

[62]  David N Arnosti,et al.  Transcriptional enhancers: Intelligent enhanceosomes or flexible billboards? , 2005, Journal of cellular biochemistry.

[63]  Jin Ho Yoon,et al.  Recruitment of the Swi/Snf Complex by Ste12-Tec1 Promotes Flo8-Mss11-Mediated Activation of STA1 Expression , 2004, Molecular and Cellular Biology.

[64]  Nicola J. Rinaldi,et al.  Transcriptional regulatory code of a eukaryotic genome , 2004, Nature.

[65]  S. Schreiber,et al.  Global nucleosome occupancy in yeast , 2004, Genome Biology.

[66]  J. Mellor,et al.  Cbf1p Is Required for Chromatin Remodeling at Promoter-proximal CACGTG Motifs in Yeast* , 2004, Journal of Biological Chemistry.

[67]  Michael A. Beer,et al.  Predicting Gene Expression from Sequence , 2004, Cell.

[68]  D. Arnosti,et al.  Information display by transcriptional enhancers , 2003, Development.

[69]  Craig D. Kaplan,et al.  Transcription Elongation Factors Repress Transcription Initiation from Cryptic Sites , 2003, Science.

[70]  Jun S. Liu,et al.  Integrating regulatory motif discovery and genome-wide expression analysis , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[71]  J. Workman,et al.  Transcription Activator Interactions with Multiple SWI/SNF Subunits , 2002, Molecular and Cellular Biology.

[72]  B. Akache,et al.  Phenotypic analysis of genes encoding yeast zinc cluster proteins. , 2001, Nucleic acids research.

[73]  H. Bussemaker,et al.  Regulatory element detection using correlation with expression , 2001, Nature Genetics.

[74]  M. Perrot,et al.  The Transcriptional Activator Cat8p Provides a Major Contribution to the Reprogramming of Carbon Metabolism during the Diauxic Shift inSaccharomyces cerevisiae * , 2001, The Journal of Biological Chemistry.

[75]  P J Cullen,et al.  Glucose depletion causes haploid invasive growth in yeast. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[76]  B. Rønnow,et al.  Carbon source-dependent transcriptional regulation of the mitochondrial glycerol-3-phosphate dehydrogenase gene, GUT2, from Saccharomyces cerevisiae. , 2000, Canadian journal of microbiology.

[77]  Y Jigami,et al.  The E‐box DNA binding protein Sgc1p suppresses the gcr2 mutation, which is involved in transcriptional activation of glycolytic genes in Saccharomyces cerevisiae , 1999, FEBS letters.

[78]  R. Morse,et al.  Chromatin Opening and Transactivator Potentiation by RAP1 in Saccharomyces cerevisiae , 1999, Molecular and Cellular Biology.

[79]  A. Andrianopoulos,et al.  Evolution of a fungal regulatory gene family: the Zn(II)2Cys6 binuclear cluster DNA binding motif. , 1997, Fungal genetics and biology : FG & B.

[80]  G. Fink,et al.  Combinatorial Control Required for the Specificity of Yeast MAPK Signaling , 1997, Science.

[81]  C. J. Gimeno,et al.  Saccharomyces cerevisiae TEC1 is required for pseudohyphal growth , 1996, Molecular microbiology.

[82]  J. Dubochet,et al.  Determination of DNA persistence length by cryo-electron microscopy. Separation of the static and dynamic contributions to the apparent persistence length of DNA. , 1995, Journal of molecular biology.

[83]  V. Iyer,et al.  Poly(dA:dT), a ubiquitous promoter element that stimulates transcription via its intrinsic DNA structure. , 1995, The EMBO journal.

[84]  K. Entian,et al.  CAT8, a new zinc cluster-encoding gene necessary for derepression of gluconeogenic enzymes in the yeast Saccharomyces cerevisiae , 1995, Molecular and cellular biology.

[85]  G. Winter,et al.  Making antibodies by phage display technology. , 1994, Annual review of immunology.

[86]  R. Morse.  Nucleosome disruption by transcription factor binding in yeast. , 1993, Science.

[87]  J. Axelrod,et al.  GAL4 disrupts a repressing nucleosome during activation of GAL1 transcription in vivo. , 1993, Genes & development.

[88]  L. Guarente,et al.  HAP1 positive control mutants specific for one of two binding sites. , 1992, Genes & development.

[89]  L. Guarente,et al.  Identification and characterization of HAP4: a third component of the CCAAT-bound HAP2/HAP3 heteromer. , 1989, Genes & development.

[90]  K. Struhl,et al.  Defining the sequence specificity of DNA-binding proteins by selecting binding sites from random-sequence oligonucleotides: analysis of yeast GCN4 protein , 1989, Molecular and cellular biology.

[91]  L. Loeb,et al.  Promoters selected from random DNA sequences. , 1986, Proceedings of the National Academy of Sciences of the United States of America.