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Deciphering eukaryotic cis -regulatory logic with 100 million random promoters

https://doi.org/10.1101/224907
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1002/jcb.20352openalex-snapshot
Transcriptional enhancers: Intelligent enhanceosomes or flexible billboards?
inferredcites →https://doi.org/10.1006/jmbi.1995.0640openalex-snapshot
Determination of DNA Persistence Length by Cryo-electron Microscopy. Separation of the Static and Dynamic Contributions to the Apparent Persistence Length of DNA
inferredcites →https://doi.org/10.1016/j.cell.2009.02.043openalex-snapshot
Mechanisms that Specify Promoter Nucleosome Location and Identity
inferredcites →https://doi.org/10.1016/j.cell.2012.12.009openalex-snapshot
DNA-Binding Specificities of Human Transcription Factors
inferredcites →https://doi.org/10.1016/j.tig.2009.08.003openalex-snapshot
Different gene regulation strategies revealed by analysis of binding motifs
inferredcites →https://doi.org/10.1016/j.tig.2009.12.002openalex-snapshot
Conserved expression without conserved regulatory sequence: the more things change, the more they stay the same
inferredcites →https://doi.org/10.1016/s0014-5793(99)01654-3openalex-snapshot
The E‐box DNA binding protein Sgc1p suppresses the gcr2 mutation, which is involved in transcriptional activation of glycolytic genes in Saccharomyces cerevisiae
inferredcites →https://doi.org/10.1016/s0092-8674(04)00304-6openalex-snapshot
Predicting Gene Expression from Sequence
inferredcites →https://doi.org/10.1038/msb.2010.112openalex-snapshot
Dynamic transcriptome analysis measures rates of mRNA synthesis and decay in yeast
inferredcites →https://doi.org/10.1038/nature02800openalex-snapshot
Transcriptional regulatory code of a eukaryotic genome
inferredcites →https://doi.org/10.1038/nature07521openalex-snapshot
Analysis of combinatorial cis-regulation in synthetic and genomic promoters
inferredcites →https://doi.org/10.1038/nbt.1882openalex-snapshot
Direct measurement of DNA affinity landscapes on a high-throughput sequencing instrument
inferredcites →https://doi.org/10.1038/nbt.2205openalex-snapshot
Inferring gene regulatory logic from high-throughput measurements of thousands of systematically designed promoters
inferredcites →https://doi.org/10.1038/nbt.3754openalex-snapshot
Genome-wide mapping of autonomous promoter activity in human cells
inferredcites →https://doi.org/10.1038/nmeth.1313openalex-snapshot
Global mapping of protein-DNA interactions in vivo by digital genomic footprinting
inferredcites →https://doi.org/10.1038/nmeth.4534openalex-snapshot
Resolving systematic errors in widely used enhancer activity assays in human cells
inferredcites →https://doi.org/10.1038/nrg2591openalex-snapshot
From DNA sequence to transcriptional behaviour: a quantitative approach
inferredcites →https://doi.org/10.1038/nrg3891openalex-snapshot
The role of regulatory variation in complex traits and disease
inferredcites →https://doi.org/10.1038/s41467-018-04026-wopenalex-snapshot
Random sequences rapidly evolve into de novo promoters
inferredcites →https://doi.org/10.1038/s41467-018-07746-1openalex-snapshot
High-resolution genome-wide functional dissection of transcriptional regulatory regions and nucleotides in human
inferredcites →https://doi.org/10.1073/pnas.0605140103openalex-snapshot
Identifying transcription factor functions and targets by phenotypic activation
inferredcites →https://doi.org/10.1073/pnas.1004290107openalex-snapshot
Using deep sequencing to characterize the biophysical mechanism of a transcriptional regulatory sequence
inferredcites →https://doi.org/10.1073/pnas.1301301110openalex-snapshot
Composability of regulatory sequences controlling transcription and translation in Escherichia coli
inferredcites →https://doi.org/10.1073/pnas.240345197openalex-snapshot
Glucose depletion causes haploid invasive growth in yeast
inferredcites →https://doi.org/10.1073/pnas.83.19.7405openalex-snapshot
Promoters selected from random DNA sequences.
inferredcites →https://doi.org/10.1074/jbc.m008752200openalex-snapshot
The Transcriptional Activator Cat8p Provides a Major Contribution to the Reprogramming of Carbon Metabolism during the Diauxic Shift in Saccharomyces cerevisiae
inferredcites →https://doi.org/10.1093/bioinformatics/btl158openalex-snapshot
Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences
inferredcites →https://doi.org/10.1093/bioinformatics/btm403openalex-snapshot
Exploring the functional landscape of gene expression: directed search of large microarray compendia
inferredcites →https://doi.org/10.1093/nar/gkq1161openalex-snapshot
Extensive role of the general regulatory factors, Abf1 and Rap1, in determining genome-wide chromatin structure in budding yeast
inferredcites →https://doi.org/10.1093/nar/gkr1029openalex-snapshot
Saccharomyces Genome Database: the genomics resource of budding yeast
inferredcites →https://doi.org/10.1093/nar/gkr993openalex-snapshot
YeTFaSCo: a database of evaluated yeast transcription factor sequence specificities
inferredcites →https://doi.org/10.1101/gad.3.8.1166openalex-snapshot
Identification and characterization of HAP4: a third component of the CCAAT-bound HAP2/HAP3 heteromer.
inferredcites →https://doi.org/10.1101/gad.7.5.857openalex-snapshot
GAL4 disrupts a repressing nucleosome during activation of GAL1 transcription in vivo.
inferredcites →https://doi.org/10.1101/gr.224964.117openalex-snapshot
Deep learning of the regulatory grammar of yeast 5′ untranslated regions from 500,000 random sequences
inferredcites →https://doi.org/10.1101/gr.5113606openalex-snapshot
Extensive low-affinity transcriptional interactions in the yeast genome
inferredcites →https://doi.org/10.1101/gr.5655606openalex-snapshot
Whole-genome comparison of Leu3 binding in vitro and in vivo reveals the importance of nucleosome occupancy in target site selection
inferredcites →https://doi.org/10.1111/j.1365-2958.1996.tb02470.xopenalex-snapshot
Saccharomyces cerevisiae TEC1 is required for pseudohyphal growth
inferredcites →https://doi.org/10.1126/science.1200508openalex-snapshot
A Packing Mechanism for Nucleosome Organization Reconstituted Across a Eukaryotic Genome
inferredcites →https://doi.org/10.1126/science.275.5304.1314openalex-snapshot
Combinatorial Control Required for the Specificity of Yeast MAPK Signaling
inferredcites →https://doi.org/10.1126/science.8248805openalex-snapshot
Nucleosome Disruption by Transcription Factor Binding in Yeast
inferredcites →https://doi.org/10.1128/mcb.15.4.1915openalex-snapshot
CAT8 , a New Zinc Cluster-Encoding Gene Necessary for Derepression of Gluconeogenic Enzymes in the Yeast Saccharomyces cerevisiae
inferredcites →https://doi.org/10.1128/mcb.9.7.2944openalex-snapshot
Defining the Sequence Specificity of DNA-Binding Proteins by Selecting Binding Sites from Random-Sequence Oligonucleotides: Analysis of Yeast GCN4 Protein
inferredcites →https://doi.org/10.1139/cjm-46-12-1096openalex-snapshot
Carbon source-dependent transcriptional regulation of the mitochondrial glycerol-3-phosphate dehydrogenase gene, GUT2, from Saccharomyces cerevisiae
inferredcites →https://doi.org/10.1186/gb-2004-5-9-r62openalex-snapshot
Global nucleosome occupancy in yeast
inferredcites →https://doi.org/10.1186/gb-2005-6-10-r87openalex-snapshot
Explicit equilibrium modeling of transcription-factor binding and gene regulation
inferredcites →https://doi.org/10.1242/dev.00890openalex-snapshot
Information display by transcriptional enhancers
inferredcites →https://doi.org/10.1371/journal.pcbi.0030243openalex-snapshot
Predicting Gene Expression from Sequence: A Reexamination
inferredcites →https://doi.org/10.1371/journal.pgen.1005147openalex-snapshot
Systematic Dissection of the Sequence Determinants of Gene 3’ End Mediated Expression Control
inferredcites →https://doi.org/10.1385/1-59259-958-3:171openalex-snapshot
Synthetic Genetic Array Analysis in Saccharomyces cerevisiae
inferredcites →https://doi.org/10.1534/genetics.113.153262openalex-snapshot
Mapping Yeast Transcriptional Networks
inferredcites →https://doi.org/10.17504/protocols.io.j4tcqwnopenalex-snapshot
High-efficiency S. cerevisiae lithium acetate transformation v1

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1101/289330openalex-snapshot
Differences between the de novo proteome and its non-functional precursor can result from neutral constraints on its birth process, not necessarily from natural selection alone
inferred← citeshttps://doi.org/10.1146/annurev-genom-083118-014845openalex-snapshot
Massively Parallel Assays and Quantitative Sequence–Function Relationships
inferred← citeshttps://doi.org/10.11606/d.17.2018.tde-17072024-095057openalex-snapshot
A multiscale approach for exploring bacterial transcriptional systems
inferred← citeshttps://doi.org/10.1371/journal.pone.0218073openalex-snapshot
Deciphering regulatory DNA sequences and noncoding genetic variants using neural network models of massively parallel reporter assays
inferred← citeshttps://doi.org/10.1534/genetics.119.302187openalex-snapshot
Differences Between the Raw Material and the Products ofde NovoGene Birth Can Result from Mutational Biases
inferred← citeshttps://doi.org/10.7554/elife.103774openalex-snapshot
The adaptive landscapes of three global Escherichia coli transcriptional regulators
inferred← citeshttps://doi.org/10.7554/elife.103774.1openalex-snapshot
The adaptive landscapes of three global Escherichia coli transcriptional regulators
inferred← citeshttps://doi.org/10.7554/elife.103774.3openalex-snapshot
The adaptive landscapes of three global Escherichia coli transcriptional regulators
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