[HTML][HTML] The accessible chromatin landscape of the human genome
…, ED Nguyen, H Qu, AP Reynolds, V Roach, A Safi… - Nature, 2012 - nature.com
DNase I hypersensitive sites (DHSs) are markers of regulatory DNA and have underpinned
the discovery of all classes of cis-regulatory elements including enhancers, promoters, …
the discovery of all classes of cis-regulatory elements including enhancers, promoters, …
Highly specific epigenome editing by CRISPR-Cas9 repressors for silencing of distal regulatory elements
PI Thakore, AM D'ippolito, L Song, A Safi… - Nature …, 2015 - nature.com
Epigenome editing with the CRISPR (clustered, regularly interspaced, short palindromic
repeats)-Cas9 platform is a promising technology for modulating gene expression to direct cell …
repeats)-Cas9 platform is a promising technology for modulating gene expression to direct cell …
CRISPR–Cas9 epigenome editing enables high-throughput screening for functional regulatory elements in the human genome
Large genome-mapping consortia and thousands of genome-wide association studies have
identified non-protein-coding elements in the genome as having a central role in various …
identified non-protein-coding elements in the genome as having a central role in various …
Transcriptome-wide association study of schizophrenia and chromatin activity yields mechanistic disease insights
Genome-wide association studies (GWAS) have identified over 100 risk loci for schizophrenia,
but the causal mechanisms remain largely unknown. We performed a transcriptome-wide …
but the causal mechanisms remain largely unknown. We performed a transcriptome-wide …
[PDF][PDF] Distinct properties of cell-type-specific and shared transcription factor binding sites
Most human transcription factors bind a small subset of potential genomic sites and often
use different subsets in different cell types. To identify mechanisms that govern cell-type-…
use different subsets in different cell types. To identify mechanisms that govern cell-type-…
Patterns of regulatory activity across diverse human cell types predict tissue identity, transcription factor binding, and long-range interactions
NC Sheffield, RE Thurman, L Song, A Safi… - Genome …, 2013 - genome.cshlp.org
Regulatory elements recruit transcription factors that modulate gene expression distinctly
across cell types, but the relationships among these remains elusive. To address this, we …
across cell types, but the relationships among these remains elusive. To address this, we …
Transcriptome and epigenome landscape of human cortical development modeled in organoids
INTRODUCTION The human cerebral cortex has undergone an extraordinary increase in
size and complexity during mammalian evolution. Cortical cell lineages are specified in the …
size and complexity during mammalian evolution. Cortical cell lineages are specified in the …
[PDF][PDF] Direct GR binding sites potentiate clusters of TF binding across the human genome
The glucocorticoid receptor (GR) binds the human genome at >10,000 sites but only regulates
the expression of hundreds of genes. To determine the functional effect of each site, we …
the expression of hundreds of genes. To determine the functional effect of each site, we …
Genome-wide specificity of DNA binding, gene regulation, and chromatin remodeling by TALE-and CRISPR/Cas9-based transcriptional activators
…, CM Vockley, P Bledsoe, L Song, A Safi… - Genome …, 2015 - genome.cshlp.org
Genome engineering technologies based on the CRISPR/Cas9 and TALE systems are
enabling new approaches in science and biotechnology. However, the specificity of these tools …
enabling new approaches in science and biotechnology. However, the specificity of these tools …
Regulation of chromatin accessibility and Zic binding at enhancers in the developing cerebellum
To identify chromatin mechanisms of neuronal differentiation, we characterized chromatin
accessibility and gene expression in cerebellar granule neurons (CGNs) of the developing …
accessibility and gene expression in cerebellar granule neurons (CGNs) of the developing …