Journal ArticleDOI
Transcriptional enhancers: from properties to genome-wide predictions.
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TLDR
How properties of enhancer sequences and chromatin are used to predict enhancers in genome-wide studies are discussed and recently developed high-throughput methods that allow the direct testing and identification of enhancers on the basis of their activity are covered.Abstract:
Cellular development, morphology and function are governed by precise patterns of gene expression. These are established by the coordinated action of genomic regulatory elements known as enhancers or cis-regulatory modules. More than 30 years after the initial discovery of enhancers, many of their properties have been elucidated; however, despite major efforts, we only have an incomplete picture of enhancers in animal genomes. In this Review, we discuss how properties of enhancer sequences and chromatin are used to predict enhancers in genome-wide studies. We also cover recently developed high-throughput methods that allow the direct testing and identification of enhancers on the basis of their activity. Finally, we discuss recent technological advances and current challenges in the field of regulatory genomics.read more
Citations
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Journal ArticleDOI
Unique features of long non-coding RNA biogenesis and function
Jeffrey J. Quinn,Howard Y. Chang +1 more
TL;DR: This Review describes special events in the lifetimes of lncRNAs — before, during and after transcription — and discusses how these events ultimately shape the unique characteristics and functional roles of lNCRNAs.
Journal ArticleDOI
Identification of common genetic risk variants for autism spectrum disorder
TL;DR: A genome-wide association meta-analysis of 18,381 austim spectrum disorder cases and 27,969 controls identifies five risk loci and the authors find quantitative and qualitative polygenic heterogeneity across ASD subtypes.
Journal ArticleDOI
Environment Drives Selection and Function of Enhancers Controlling Tissue-Specific Macrophage Identities
David Gosselin,Verena M. Link,Casey E. Romanoski,Gregory J. Fonseca,Dawn Z Eichenfield,Nathanael J. Spann,Joshua D. Stender,Hyun B. Chun,Hannah Garner,Frederic Geissmann,Christopher K. Glass +10 more
TL;DR: It is found that distinct tissue environments drive divergent programs of gene expression by differentially activating a common enhancer repertoire and by inducing the expression of divergent secondary transcription factors that collaborate with PU.1 to establish tissue-specific enhancers.
Journal ArticleDOI
GeneHancer: genome-wide integration of enhancers and target genes in GeneCards
Simon Fishilevich,Ron Nudel,Noa Rappaport,Rotem Hadar,Inbar Plaschkes,Tsippi Iny Stein,Naomi Rosen,Asher Kohn,Michal Twik,Marilyn Safran,Doron Lancet,Dana Cohen +11 more
TL;DR: GeneHancer is presented, a novel database of human enhancers and their inferred target genes, in the framework of GeneCards, which assists in the mapping of non-coding variants to enhancers, and via the linked genes, forms a basis for variant–phenotype interpretation of whole-genome sequences in health and disease.
Journal ArticleDOI
Mechanisms and consequences of Jak–STAT signaling in the immune system
TL;DR: Recent advances in Jak–STAT biology are reviewed, focusing on immune cell function, disease etiology and therapeutic intervention, as well as broader principles of gene regulation and signal-dependent TFs.
References
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TL;DR: The Encyclopedia of DNA Elements project provides new insights into the organization and regulation of the authors' genes and genome, and is an expansive resource of functional annotations for biomedical research.
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A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity.
Martin Jinek,Krzysztof Chylinski,Krzysztof Chylinski,Ines Fonfara,Michael H. Hauer,Jennifer A. Doudna,Emmanuelle Charpentier +6 more
TL;DR: This study reveals a family of endonucleases that use dual-RNAs for site-specific DNA cleavage and highlights the potential to exploit the system for RNA-programmable genome editing.
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Chromatin Modifications and Their Function
TL;DR: The surface of nucleosomes is studded with a multiplicity of modifications that can dictate the higher-order chromatin structure in which DNA is packaged and can orchestrate the ordered recruitment of enzyme complexes to manipulate DNA.
Journal ArticleDOI
Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase
Craig Tuerk,Larry Gold +1 more
TL;DR: High-affinity nucleic acid ligands for a protein were isolated by a procedure that depends on alternate cycles of ligand selection from pools of variant sequences and amplification of the bound species.
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RNA-Guided Human Genome Engineering via Cas9
Prashant Mali,Luhan Yang,Kevin M. Esvelt,John Aach,Marc Güell,James E. DiCarlo,Julie E. Norville,George M. Church,George M. Church +8 more
TL;DR: The type II bacterial CRISPR system is engineer to function with custom guide RNA (gRNA) in human cells to establish an RNA-guided editing tool for facile, robust, and multiplexable human genome engineering.