High-resolution interrogation of functional elements in the noncoding genome
Neville E. Sanjana,Neville E. Sanjana,Jason Wright,Jason Wright,Kaijie Zheng,Kaijie Zheng,Ophir Shalem,Ophir Shalem,Pierre Fontanillas,Julia Joung,Julia Joung,Christine S. Cheng,Christine S. Cheng,Aviv Regev,Aviv Regev,Feng Zhang,Feng Zhang +16 more
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TLDR
A CRISPR screen using ~18,000 single guide RNAs targeting >700 kilobases surrounding the genes NF1, NF2, and CUL3, which are involved in BRAF inhibitor resistance in melanoma, finds that noncoding locations that modulate drug resistance also harbor predictive hallmarks ofnoncoding function.Abstract:
The noncoding genome affects gene regulation and disease, yet we lack tools for rapid identification and manipulation of noncoding elements. We developed a CRISPR screen using ~18,000 single guide RNAs targeting >700 kilobases surrounding the genes NF1, NF2, and CUL3, which are involved in BRAF inhibitor resistance in melanoma. We find that noncoding locations that modulate drug resistance also harbor predictive hallmarks of noncoding function. With a subset of regions at the CUL3 locus, we demonstrate that engineered mutations alter transcription factor occupancy and long-range and local epigenetic environments, implicating these sites in gene regulation and chemotherapeutic resistance. Through our expansion of the potential of pooled CRISPR screens, we provide tools for genomic discovery and for elucidating biologically relevant mechanisms of gene regulation.read more
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Integrative analysis of 111 reference human epigenomes
Anshul Kundaje,Wouter Meuleman,Jason Ernst,Angela Yen,Pouya Kheradpour,Zhizhuo Zhang,Jianrong Wang,Lucas D. Ward,Abhishek Sarkar,Gerald Quon,Matthew L. Eaton,Yi-Chieh Wu,Andreas R. Pfenning,Xinchen Wang,Melina Claussnitzer,Yaping Liu,Mukul S. Bansal,Soheil Feizi-Khankandi,Ah Ram Kim,Richard C Sallari,Nicholas A Sinnott-Armstrong,Laurie A. Boyer,Elizabeta Gjoneska,Li-Huei Tsai,Manolis Kellis +24 more
TL;DR: In this article, the authors describe the integrative analysis of 111 reference human epigenomes generated as part of the NIH Roadmap Epigenomics Consortium, profiled for histone modification patterns, DNA accessibility, DNA methylation and RNA expression.
Journal Article
Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes
Adrian L. Sanborn,Suhas S.P. Rao,Su-Chen Huang,Neva C. Durand,Miriam H. Huntley,Andrew I. Jewett,Ivan D. Bochkov,Dharmaraj Chinnappan,Ashok Cutkosky,Jian Li,Kristopher Geeting,Doug McKenna,Elena K. Stamenova,Andreas Gnirke,Alexandre Melnikov,Eric S. Lander,Erez Lieberman Aiden +16 more
TL;DR: In this article, high-resolution spatial proximity maps are consistent with a model in which a complex, including the proteins CCCTC-binding factor (CTCF) and cohesin, mediates the formation of loops by a process of extrusion.
Journal ArticleDOI
Genome-scale CRISPR-Cas9 knockout and transcriptional activation screening
Julia Joung,Silvana Konermann,Jonathan S. Gootenberg,Omar O. Abudayyeh,Randall Jeffrey Platt,Mark D. Brigham,Mark D. Brigham,Mark D. Brigham,Neville E. Sanjana,Feng Zhang +9 more
TL;DR: In this article, a protocol for genome-scale knockout and transcriptional activation screening using the CRISPR-Cas9 system is described, where custom or ready-made guide RNA libraries are constructed and packaged into lentiviral vectors for delivery into cells for screening.
Journal ArticleDOI
Long-range enhancer-promoter contacts in gene expression control.
TL;DR: The latest understanding of long-range enhancer–promoter crosstalk is discussed, including target-gene specificity, interaction dynamics, protein and RNA architects of interactions, roles of 3D genome organization and the pathological consequences of regulatory rewiring.
Journal ArticleDOI
Activity-by-contact model of enhancer-promoter regulation from thousands of CRISPR perturbations.
Charles P. Fulco,Charles P. Fulco,Joseph Nasser,Thouis R. Jones,Glen Munson,Drew T. Bergman,Vidya Subramanian,Sharon R. Grossman,Sharon R. Grossman,Rockwell Anyoha,Benjamin R. Doughty,Tejal A. Patwardhan,Tung T. Nguyen,Michael Kane,Elizabeth M. Perez,Neva C. Durand,Caleb A. Lareau,Elena K. Stamenova,Erez Lieberman Aiden,Eric S. Lander,Eric S. Lander,Eric S. Lander,Jesse M. Engreitz,Jesse M. Engreitz +23 more
TL;DR: A simple activity-by-contact model substantially outperformed previous methods at predicting the complex connections in the CRISPR dataset and allows systematic mapping of enhancer–gene connections in a given cell type, on the basis of chromatin-state measurements.
References
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An integrated encyclopedia of DNA elements in the human genome.
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.
Journal ArticleDOI
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