Identification and function of enhancers in the human genome
TLDR
The study of gene regulation has rapidly advanced by leveraging next-generation sequencing to identify and characterize the cis and trans elements that are critical for defining cell identity, but currently lagging behind the generation of vast datasets and annotations is ability to examine these putative elements in the dynamic context of a developing organism.Abstract:
The study of gene regulation has rapidly advanced by leveraging next-generation sequencing to identify and characterize the cis and trans elements that are critical for defining cell identity. These advances have paralleled a movement towards whole genome sequencing in clinics. These two tracks have increasingly synergized to underscore the importance of cis-regulatory elements in development as well produce countless studies implicating these elements in human disease. Other studies have emphasized the clinical phenotypes associated with variation or mutations in trans factors, including non-coding RNAs and chromatin regulators. These studies highlight the importance of obtaining a comprehensive understanding of mammalian gene regulation for predicting the impact of genetic variation on patient phenotypes. Currently lagging behind the generation of vast datasets and annotations is our ability to examine these putative elements in the dynamic context of a developing organism.read more
Citations
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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.
A Large Intergenic Noncoding RNA Induced by p53 Mediates Global Gene Repression in the p53 Response
Maite Huarte,Mitchell Guttman,Mitchell Guttman,David M. Feldser,Manuel Garber,Magdalena J. Koziol,Magdalena J. Koziol,Daniela Kenzelmann-Broz,Ahmad M. Khalil,Ahmad M. Khalil,Or Zuk,Ido Amit,Michal Rabani,Laura D. Attardi,Aviv Regev,Aviv Regev,Eric S. Lander,Eric S. Lander,Eric S. Lander,Tyler Jacks,John L. Rinn,John L. Rinn +21 more
TL;DR: In this paper, the identification of lincRNAs (lincRNA-p21) that serve as a repressor in p53-dependent transcriptional responses was reported, and the observed transcriptional repression was mediated through the physical association with hnRNP-K at repressed genes and regulation of p53 mediates apoptosis.
Journal Article
A High-Resolution Map of Human Evolutionary Constraint Using 29 Mammals
Stefan Washietl,Pouya Kheradpour,Jason Ernst,Lucas D. Ward,Irwin Jungreis,Matthew D. Rasmussen,Manolis Kellis +6 more
TL;DR: The comparison of related genomes has emerged as a powerful lens for genome interpretation as mentioned in this paper, which reveals a small number of new coding exons, candidate stop codon readthrough events and over 10,000 regions of overlapping synonymous constraint within protein-coding exons.
Journal ArticleDOI
Epigenetic regulation of ACE2, the receptor of the SARS-CoV-2 virus1.
TL;DR: The chemical and mechanical signal transduction pathways regulating the expression of the ACE2 gene and the epigenetic/chromatin features of the expressed gene are reviewed.
References
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Journal ArticleDOI
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
Multiplex Genome Engineering Using CRISPR/Cas Systems
Le Cong,Le Cong,F. Ann Ran,F. Ann Ran,David M. Cox,David M. Cox,Shuailiang Lin,Shuailiang Lin,Robert P. J. Barretto,Naomi Habib,Patrick D. Hsu,Patrick D. Hsu,Xuebing Wu,Wenyan Jiang,Luciano A. Marraffini,Feng Zhang +15 more
TL;DR: The type II prokaryotic CRISPR (clustered regularly interspaced short palindromic repeats)/Cas adaptive immune system has been shown to facilitate RNA-guided site-specific DNA cleavage as discussed by the authors.
Multiplex Genome Engineering Using CRISPR/Cas Systems
Le Cong,F. A. Ran,David Benjamin Turitz Cox,Shuailiang Lin,Robert P. J. Barretto,Naomi Habib,Patrick D. Hsu,Xuebing Wu,Wenyan Jiang,Luciano A. Marraffini,Feng Zhang +10 more
TL;DR: Two different type II CRISPR/Cas systems are engineered and it is demonstrated that Cas9 nucleases can be directed by short RNAs to induce precise cleavage at endogenous genomic loci in human and mouse cells, demonstrating easy programmability and wide applicability of the RNA-guided nuclease technology.
Journal ArticleDOI
The Human Genome Browser at UCSC
W. James Kent,Charles W. Sugnet,Terrence S. Furey,Krishna M. Roskin,Tom H. Pringle,Alan M. Zahler,and David Haussler +6 more
TL;DR: A mature web tool for rapid and reliable display of any requested portion of the genome at any scale, together with several dozen aligned annotation tracks, is provided at http://genome.ucsc.edu.
Journal ArticleDOI
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.
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