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 …

Current challenges in understanding the role of enhancers in disease

JB Zaugg, P Sahlén, R Andersson… - Nature structural & …, 2022 - nature.com
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 …

Current sequence-based models capture gene expression determinants in promoters but mostly ignore distal enhancers

A Karollus, T Mauermeier, J Gagneur - Genome biology, 2023 - Springer
Background The largest sequence-based models of transcription control to date are
obtained by predicting genome-wide gene regulatory assays across the human genome …

H3K18 lactylation marks tissue-specific active enhancers

E Galle, CW Wong, A Ghosh, T Desgeorges, K Melrose… - Genome biology, 2022 - Springer
Background Histone lactylation has been recently described as a novel histone post-
translational modification linking cellular metabolism to epigenetic regulation. Results Given …

Enhancer selectivity in space and time: from enhancer–promoter interactions to promoter activation

JH Yang, AS Hansen - Nature Reviews Molecular Cell Biology, 2024 - nature.com
The primary regulators of metazoan gene expression are enhancers, originally functionally
defined as DNA sequences that can activate transcription at promoters in an orientation …

Integrated single-cell chromatin and transcriptomic analyses of human scalp identify gene-regulatory programs and critical cell types for hair and skin diseases

B Ober-Reynolds, C Wang, JM Ko, EJ Rios, SZ Aasi… - Nature Genetics, 2023 - nature.com
Genome-wide association studies have identified many loci associated with hair and skin
disease, but identification of causal variants requires deciphering of gene-regulatory …

Systematic analysis of intrinsic enhancer-promoter compatibility in the mouse genome

M Martinez-Ara, F Comoglio, J van Arensbergen… - Molecular cell, 2022 - cell.com
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 …

Cancer lineage-specific regulation of YAP responsive elements revealed through large-scale functional epigenomic screens

IAM Barbosa, R Gopalakrishnan, S Mercan… - Nature …, 2023 - nature.com
YAP is a key transcriptional co-activator of TEADs, it regulates cell growth and is frequently
activated in cancer. In Malignant Pleural Mesothelioma (MPM), YAP is activated by loss-of …

Repression and 3D-restructuring resolves regulatory conflicts in evolutionarily rearranged genomes

AR Ringel, Q Szabo, AM Chiariello, K Chudzik… - Cell, 2022 - cell.com
Regulatory landscapes drive complex developmental gene expression, but it remains
unclear how their integrity is maintained when incorporating novel genes and functions …

3D Enhancer–promoter networks provide predictive features for gene expression and coregulation in early embryonic lineages

D Murphy, E Salataj, DC Di Giammartino… - Nature Structural & …, 2024 - nature.com
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 …