Determinants of enhancer and promoter activities of regulatory elements
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Title
Determinants of enhancer and promoter activities of regulatory elements
Authors
Keywords
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Journal
NATURE REVIEWS GENETICS
Volume -, Issue -, Pages -
Publisher
Springer Science and Business Media LLC
Online
2019-10-12
DOI
10.1038/s41576-019-0173-8
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Note: Only part of the references are listed.- Systematic interrogation of human promoters
- (2019) Shira Weingarten-Gabbay et al. GENOME RESEARCH
- Chromatin accessibility and the regulatory epigenome
- (2019) Sandy L. Klemm et al. NATURE REVIEWS GENETICS
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- (2019) Kaia Mattioli et al. GENOME RESEARCH
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- (2019) Laura L. Colbran et al. GENETICS
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- (2019) Leighton Core et al. GENES & DEVELOPMENT
- Transcriptional cofactors display specificity for distinct types of core promoters
- (2019) Vanja Haberle et al. NATURE
- Long-range enhancer–promoter contacts in gene expression control
- (2019) Stefan Schoenfelder et al. NATURE REVIEWS GENETICS
- Regulatory Landscaping: How Enhancer-Promoter Communication Is Sculpted in 3D
- (2019) Michael I. Robson et al. MOLECULAR CELL
- Ultraconserved Enhancers Are Required for Normal Development
- (2018) Diane E. Dickel et al. CELL
- Assessing sufficiency and necessity of enhancer activities for gene expression and the mechanisms of transcription activation
- (2018) Rui R. Catarino et al. GENES & DEVELOPMENT
- Widespread transcriptional pausing and elongation control at enhancers
- (2018) Telmo Henriques et al. GENES & DEVELOPMENT
- The degree of enhancer or promoter activity is reflected by the levels and directionality of eRNA transcription
- (2018) Olga Mikhaylichenko et al. GENES & DEVELOPMENT
- Local sequence features that influence AP-1cis-regulatory activity
- (2018) Hemangi G. Chaudhari et al. GENOME RESEARCH
- Eukaryotic core promoters and the functional basis of transcription initiation
- (2018) Vanja Haberle et al. NATURE REVIEWS MOLECULAR CELL BIOLOGY
- Transcription start site analysis reveals widespread divergent transcription in D. melanogaster and core promoter-encoded enhancer activities
- (2018) Sarah Rennie et al. NUCLEIC ACIDS RESEARCH
- A Single-Cell Atlas of In Vivo Mammalian Chromatin Accessibility
- (2018) Darren A. Cusanovich et al. CELL
- Repurposing of promoters and enhancers during mammalian evolution
- (2018) Francesco N. Carelli et al. Nature Communications
- Identifying cis Elements for Spatiotemporal Control of Mammalian DNA Replication
- (2018) Jiao Sima et al. CELL
- The Human Transcription Factors
- (2018) Samuel A. Lambert et al. CELL
- CRISPR-mediated activation of a promoter or enhancer rescues obesity caused by haploinsufficiency
- (2018) Navneet Matharu et al. SCIENCE
- Studying Transcriptional Enhancers: The Founder Fallacy, Validation Creep, and Other Biases
- (2018) Marc S. Halfon TRENDS IN GENETICS
- Determinants of Histone H3K4 Methylation Patterns
- (2017) Luis M. Soares et al. MOLECULAR CELL
- Discovery of stimulation-responsive immune enhancers with CRISPR activation
- (2017) Dimitre R. Simeonov et al. NATURE
- CRISPR–Cas9 epigenome editing enables high-throughput screening for functional regulatory elements in the human genome
- (2017) Tyler S Klann et al. NATURE BIOTECHNOLOGY
- SMARCB1 is required for widespread BAF complex–mediated activation of enhancers and bivalent promoters
- (2017) Robert T Nakayama et al. NATURE GENETICS
- Genome-wide characterization of mammalian promoters with distal enhancer functions
- (2017) Lan T M Dao et al. NATURE GENETICS
- A tiling-deletion-based genetic screen for cis-regulatory element identification in mammalian cells
- (2017) Yarui Diao et al. NATURE METHODS
- Resolving systematic errors in widely used enhancer activity assays in human cells
- (2017) Felix Muerdter et al. NATURE METHODS
- Systematic dissection of genomic features determining transcription factor binding and enhancer function
- (2017) Sharon R. Grossman et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Multiplex Enhancer Interference Reveals Collaborative Control of Gene Regulation by Estrogen Receptor α-Bound Enhancers
- (2017) Julia B. Carleton et al. Cell Systems
- Gene activation by metazoan enhancers: Diverse mechanisms stimulate distinct steps of transcription
- (2016) Robert A. Beagrie et al. BIOESSAYS
- Lineage-Specific Genome Architecture Links Enhancers and Non-coding Disease Variants to Target Gene Promoters
- (2016) Biola M. Javierre et al. CELL
- High-throughput functional comparison of promoter and enhancer activities
- (2016) Thomas A. Nguyen et al. GENOME RESEARCH
- A systematic comparison reveals substantial differences in chromosomal versus episomal encoding of enhancer activity
- (2016) Fumitaka Inoue et al. GENOME RESEARCH
- Local regulation of gene expression by lncRNA promoters, transcription and splicing
- (2016) Jesse M. Engreitz et al. NATURE
- Genome-wide mapping of autonomous promoter activity in human cells
- (2016) Joris van Arensbergen et al. NATURE BIOTECHNOLOGY
- Genome-wide assessment of sequence-intrinsic enhancer responsiveness at single-base-pair resolution
- (2016) Cosmas D Arnold et al. NATURE BIOTECHNOLOGY
- High-throughput mapping of regulatory DNA
- (2016) Nisha Rajagopal et al. NATURE BIOTECHNOLOGY
- Functional genetic screens for enhancer elements in the human genome using CRISPR-Cas9
- (2016) Gozde Korkmaz et al. NATURE BIOTECHNOLOGY
- Principles for RNA metabolism and alternative transcription initiation within closely spaced promoters
- (2016) Yun Chen et al. NATURE GENETICS
- Histone H3 globular domain acetylation identifies a new class of enhancers
- (2016) Madapura M Pradeepa et al. NATURE GENETICS
- Applying CRISPR–Cas9 tools to identify and characterize transcriptional enhancers
- (2016) Rui Lopes et al. NATURE REVIEWS MOLECULAR CELL BIOLOGY
- Syntax compensates for poor binding sites to encode tissue specificity of developmental enhancers
- (2016) Emma K. Farley et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- High-resolution interrogation of functional elements in the noncoding genome
- (2016) N. E. Sanjana et al. SCIENCE
- Systematic mapping of functional enhancer–promoter connections with CRISPR interference
- (2016) Charles P. Fulco et al. SCIENCE
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- (2015) Walter Schaffner BIOLOGICAL CHEMISTRY
- Native Elongating Transcript Sequencing Reveals Human Transcriptional Activity at Nucleotide Resolution
- (2015) Andreas Mayer et al. CELL
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- (2015) Takayuki Nojima et al. CELL
- Architectural and Functional Commonalities between Enhancers and Promoters
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- Transcriptional enhancers: functional insights and role in human disease
- (2015) Irene Miguel-Escalada et al. CURRENT OPINION IN GENETICS & DEVELOPMENT
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- (2015) Susan Q. Shen et al. GENOME RESEARCH
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- (2015) Anshul Kundaje et al. NATURE
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- (2015) Matthew C. Canver et al. NATURE
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- (2015) Borbala Mifsud et al. NATURE GENETICS
- Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells
- (2015) Erik Arner et al. SCIENCE
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- (2015) E. K. Farley et al. SCIENCE
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- (2014) Christopher M. Weber et al. MOLECULAR CELL
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- (2014) Muhammad A. Zabidi et al. NATURE
- An atlas of active enhancers across human cell types and tissues
- (2014) Robin Andersson et al. NATURE
- Principles of regulatory information conservation between mouse and human
- (2014) Yong Cheng et al. NATURE
- A promoter-level mammalian expression atlas
- (2014) NATURE
- Analysis of nascent RNA identifies a unified architecture of initiation regions at mammalian promoters and enhancers
- (2014) Leighton J Core et al. NATURE GENETICS
- Transcriptional enhancers: from properties to genome-wide predictions
- (2014) Daria Shlyueva et al. NATURE REVIEWS GENETICS
- Nuclear stability and transcriptional directionality separate functionally distinct RNA species
- (2014) Robin Andersson et al. Nature Communications
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- (2014) Nisha Rajagopal et al. G3-Genes Genomes Genetics
- Tissue-Specific RNA Expression Marks Distant-Acting Developmental Enhancers
- (2014) Han Wu et al. PLoS Genetics
- Repurposing CRISPR as an RNA-Guided Platform for Sequence-Specific Control of Gene Expression
- (2013) Lei S. Qi et al. CELL
- Divergent Transcription: A Driving Force for New Gene Origination?
- (2013) Xuebing Wu et al. CELL
- Systematic dissection of regulatory motifs in 2000 predicted human enhancers using a massively parallel reporter assay
- (2013) P. Kheradpour et al. GENOME RESEARCH
- Dealing with Pervasive Transcription
- (2013) Torben Heick Jensen et al. MOLECULAR CELL
- Rev-Erbs repress macrophage gene expression by inhibiting enhancer-directed transcription
- (2013) Michael T. Y. Lam et al. NATURE
- Promoter directionality is controlled by U1 snRNP and polyadenylation signals
- (2013) Albert E. Almada et al. NATURE
- Massively parallel decoding of mammalian regulatory sequences supports a flexible organizational model
- (2013) Robin P Smith et al. NATURE GENETICS
- Polyadenylation site–induced decay of upstream transcripts enforces promoter directionality
- (2013) Evgenia Ntini et al. NATURE STRUCTURAL & MOLECULAR BIOLOGY
- Precise Maps of RNA Polymerase Reveal How Promoters Direct Initiation and Pausing
- (2013) H. Kwak et al. SCIENCE
- Genome-Wide Quantitative Enhancer Activity Maps Identified by STARR-seq
- (2013) C. D. Arnold et al. SCIENCE
- Condensin controls recruitment of RNA polymerase II to achieve nematode X-chromosome dosage compensation
- (2013) William S Kruesi et al. eLife
- CpG islands and GC content dictate nucleosome depletion in a transcription-independent manner at mammalian promoters
- (2012) R. Fenouil et al. GENOME RESEARCH
- The accessible chromatin landscape of the human genome
- (2012) Robert E. Thurman et al. NATURE
- Systematic dissection and optimization of inducible enhancers in human cells using a massively parallel reporter assay
- (2012) Alexandre Melnikov et al. NATURE BIOTECHNOLOGY
- Massively parallel functional dissection of mammalian enhancers in vivo
- (2012) Rupali P Patwardhan et al. NATURE BIOTECHNOLOGY
- Unsupervised pattern discovery in human chromatin structure through genomic segmentation
- (2012) Michael M Hoffman et al. NATURE METHODS
- ChromHMM: automating chromatin-state discovery and characterization
- (2012) Jason Ernst et al. NATURE METHODS
- 5′ end–centered expression profiling using cap-analysis gene expression and next-generation sequencing
- (2012) Hazuki Takahashi et al. Nature Protocols
- Metazoan promoters: emerging characteristics and insights into transcriptional regulation
- (2012) Boris Lenhard et al. NATURE REVIEWS GENETICS
- ChIP–seq and beyond: new and improved methodologies to detect and characterize protein–DNA interactions
- (2012) Terrence S. Furey NATURE REVIEWS GENETICS
- Transcription factors: from enhancer binding to developmental control
- (2012) François Spitz et al. NATURE REVIEWS GENETICS
- Complex effects of nucleotide variants in a mammalian cis-regulatory element
- (2012) J. C. Kwasnieski et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- A Programmable Dual-RNA-Guided DNA Endonuclease in Adaptive Bacterial Immunity
- (2012) M. Jinek et al. SCIENCE
- Systematic Localization of Common Disease-Associated Variation in Regulatory DNA
- (2012) M. T. Maurano et al. SCIENCE
- Enhancers and silencers: an integrated and simple model for their function
- (2012) Petros Kolovos et al. Epigenetics & Chromatin
- Divergent transcription: A new feature of active promoters
- (2011) Amy C. Seila et al. CELL CYCLE
- H3K4 tri-methylation provides an epigenetic signature of active enhancers
- (2011) Aleksandra Pekowska et al. EMBO JOURNAL
- Genome-wide characterization of transcriptional start sites in humans by integrative transcriptome analysis
- (2011) R. Yamashita et al. GENOME RESEARCH
- Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity
- (2011) L. Song et al. GENOME RESEARCH
- Transcription Factor AP1 Potentiates Chromatin Accessibility and Glucocorticoid Receptor Binding
- (2011) Simon C. Biddie et al. MOLECULAR CELL
- Mapping and analysis of chromatin state dynamics in nine human cell types
- (2011) Jason Ernst et al. NATURE
- Large-scale discovery of enhancers from human heart tissue
- (2011) Dalit May et al. NATURE GENETICS
- Mapping of INS promoter interactions reveals its role in long-range regulation of SYT8 transcription
- (2011) Zhixiong Xu et al. NATURE STRUCTURAL & MOLECULAR BIOLOGY
- Transcription initiation platforms and GTF recruitment at tissue-specific enhancers and promoters
- (2011) Frederic Koch et al. NATURE STRUCTURAL & MOLECULAR BIOLOGY
- Discovery of active enhancers through bidirectional expression of short transcripts
- (2011) Michael F Melgar et al. GENOME BIOLOGY
- Perspectives on the RNA polymerase II core promoter
- (2011) James T. Kadonaga Wiley Interdisciplinary Reviews-Developmental Biology
- Multiple faces of the SAGA complex
- (2010) Evangelia Koutelou et al. CURRENT OPINION IN CELL BIOLOGY
- Sequence features that drive human promoter function and tissue specificity
- (2010) J. M. Landolin et al. GENOME RESEARCH
- Widespread transcription at neuronal activity-regulated enhancers
- (2010) Tae-Kyung Kim et al. NATURE
- Histone H3K27ac separates active from poised enhancers and predicts developmental state
- (2010) M. P. Creyghton et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- A Large Fraction of Extragenic RNA Pol II Transcription Sites Overlap Enhancers
- (2010) Francesca De Santa et al. PLOS BIOLOGY
- A Unifying Model for the Selective Regulation of Inducible Transcription by CpG Islands and Nucleosome Remodeling
- (2009) Vladimir R. Ramirez-Carrozzi et al. CELL
- ChIP-seq accurately predicts tissue-specific activity of enhancers
- (2009) Axel Visel et al. NATURE
- High-resolution analysis of DNA regulatory elements by synthetic saturation mutagenesis
- (2009) Rupali P Patwardhan et al. NATURE BIOTECHNOLOGY
- A census of human transcription factors: function, expression and evolution
- (2009) Juan M. Vaquerizas et al. NATURE REVIEWS GENETICS
- Global Analysis of Short RNAs Reveals Widespread Promoter-Proximal Stalling and Arrest of Pol II in Drosophila
- (2009) S. Nechaev et al. SCIENCE
- Genome-wide relationship between histone H3 lysine 4 mono- and tri-methylation and transcription factor binding
- (2008) A. G. Robertson et al. GENOME RESEARCH
- Genome-wide detection and analysis of hippocampus core promoters using DeepCAGE
- (2008) E. Valen et al. GENOME RESEARCH
- Combinatorial patterns of histone acetylations and methylations in the human genome
- (2008) Zhibin Wang et al. NATURE GENETICS
- Divergent Transcription from Active Promoters
- (2008) Amy C. Seila et al. SCIENCE
- RNA Exosome Depletion Reveals Transcription Upstream of Active Human Promoters
- (2008) Pascal Preker et al. SCIENCE
- Nascent RNA Sequencing Reveals Widespread Pausing and Divergent Initiation at Human Promoters
- (2008) Leighton J. Core et al. SCIENCE
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