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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 …
Enhancer selectivity in space and time: from enhancer–promoter interactions to promoter activation
The primary regulators of metazoan gene expression are enhancers, originally functionally
defined as DNA sequences that can activate transcription at promoters in an orientation …
defined as DNA sequences that can activate transcription at promoters in an orientation …
Increased enhancer–promoter interactions during developmental enhancer activation in mammals
Remote enhancers are thought to interact with their target promoters via physical proximity,
yet the importance of this proximity for enhancer function remains unclear. Here we …
yet the importance of this proximity for enhancer function remains unclear. Here we …
Current sequence-based models capture gene expression determinants in promoters but mostly ignore distal enhancers
Background The largest sequence-based models of transcription control to date are
obtained by predicting genome-wide gene regulatory assays across the human genome …
obtained by predicting genome-wide gene regulatory assays across the human genome …
Integrated single-cell chromatin and transcriptomic analyses of human scalp identify gene-regulatory programs and critical cell types for hair and skin diseases
Genome-wide association studies have identified many loci associated with hair and skin
disease, but identification of causal variants requires deciphering of gene-regulatory …
disease, but identification of causal variants requires deciphering of gene-regulatory …
H3K18 lactylation marks tissue-specific active enhancers
Background Histone lactylation has been recently described as a novel histone post-
translational modification linking cellular metabolism to epigenetic regulation. Results Given …
translational modification linking cellular metabolism to epigenetic regulation. Results Given …
Current challenges in understanding the role of enhancers in disease
Enhancers play a central role in the spatiotemporal control of gene expression and tend to
work in a cell-type-specific manner. In addition, they are suggested to be major contributors …
work in a cell-type-specific manner. In addition, they are suggested to be major contributors …
Deciphering the impact of genomic variation on function
Code of Conduct Committee (alphabetical by last name … - Nature, 2024 - nature.com
Our genomes influence nearly every aspect of human biology—from molecular and cellular
functions to phenotypes in health and disease. Studying the differences in DNA sequence …
functions to phenotypes in health and disease. Studying the differences in DNA sequence …
3D Enhancer–promoter networks provide predictive features for gene expression and coregulation in early embryonic lineages
Mammalian embryogenesis commences with two pivotal and binary cell fate decisions that
give rise to three essential lineages: the trophectoderm, the epiblast and the primitive …
give rise to three essential lineages: the trophectoderm, the epiblast and the primitive …
[HTML][HTML] Systematic analysis of intrinsic enhancer-promoter compatibility in the mouse genome
Gene expression is in part controlled by cis-regulatory elements (CREs) such as enhancers
and repressive elements. Anecdotal evidence has indicated that a CRE and a promoter …
and repressive elements. Anecdotal evidence has indicated that a CRE and a promoter …