Deciphering the multi-scale, quantitative cis-regulatory code
S Kim, J Wysocka - Molecular cell, 2023 - cell.com
Uncovering the cis-regulatory code that governs when and how much each gene is
transcribed in a given genome and cellular state remains a central goal of biology. Here, we …
transcribed in a given genome and cellular state remains a central goal of biology. Here, we …
Transcriptional control of energy metabolism by nuclear receptors
C Scholtes, V Giguère - Nature reviews Molecular cell biology, 2022 - nature.com
Transcriptional regulation of catabolic pathways is a central mechanism by which cells
respond to physiological cues to generate the energy required for anabolic pathways …
respond to physiological cues to generate the energy required for anabolic pathways …
Joint profiling of chromatin accessibility and gene expression in thousands of single cells
Although we can increasingly measure transcription, chromatin, methylation, and other
aspects of molecular biology at single-cell resolution, most assays survey only one aspect of …
aspects of molecular biology at single-cell resolution, most assays survey only one aspect of …
Towards a comprehensive catalogue of validated and target-linked human enhancers
The human gene catalogue is essentially complete, but we lack an equivalently vetted
inventory of bona fide human enhancers. Hundreds of thousands of candidate enhancers …
inventory of bona fide human enhancers. Hundreds of thousands of candidate enhancers …
Sequence determinants of human gene regulatory elements
DNA can determine where and when genes are expressed, but the full set of sequence
determinants that control gene expression is unknown. Here, we measured the …
determinants that control gene expression is unknown. Here, we measured the …
Adaptive sequence divergence forged new neurodevelopmental enhancers in humans
Searches for the genetic underpinnings of uniquely human traits have focused on human-
specific divergence in conserved genomic regions, which reflects adaptive modifications of …
specific divergence in conserved genomic regions, which reflects adaptive modifications of …
[HTML][HTML] A genetic variant associated with five vascular diseases is a distal regulator of endothelin-1 gene expression
RM Gupta, J Hadaya, A Trehan, SM Zekavat, C Roselli… - Cell, 2017 - cell.com
Genome-wide association studies (GWASs) implicate the PHACTR1 locus (6p24) in risk for
five vascular diseases, including coronary artery disease, migraine headache, cervical …
five vascular diseases, including coronary artery disease, migraine headache, cervical …
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 …
Lisa: inferring transcriptional regulators through integrative modeling of public chromatin accessibility and ChIP-seq data
Abstract We developed Lisa (http://lisa. cistrome. org/) to predict the transcriptional
regulators (TRs) of differentially expressed or co-expressed gene sets. Based on the input …
regulators (TRs) of differentially expressed or co-expressed gene sets. Based on the input …
[HTML][HTML] Mechanisms of interplay between transcription factors and the 3D genome
S Kim, J Shendure - Molecular cell, 2019 - cell.com
Transcription factors (TFs) bind DNA in a sequence-specific manner and thereby serve as
the protein anchors and determinants of 3D genome organization. Conversely, chromatin …
the protein anchors and determinants of 3D genome organization. Conversely, chromatin …