3D enhancer-promoter interactions and multi-connected hubs: Organizational principles and functional roles

CM Uyehara, E Apostolou - Cell reports, 2023 - cell.com
The spatiotemporal control of gene expression is dependent on the activity of cis-acting
regulatory sequences, called enhancers, which regulate target genes over variable genomic …

Structural insights into nuclear transcription by eukaryotic DNA-dependent RNA polymerases

M Girbig, AD Misiaszek, CW Müller - Nature Reviews Molecular Cell …, 2022 - nature.com
The eukaryotic transcription apparatus synthesizes a staggering diversity of RNA molecules.
The labour of nuclear gene transcription is, therefore, divided among multiple DNA …

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 …

SPT5 stabilizes RNA polymerase II, orchestrates transcription cycles, and maintains the enhancer landscape

S Hu, L Peng, C Xu, Z Wang, A Song, FX Chen - Molecular Cell, 2021 - cell.com
Transcription progression is governed by multitasking regulators including SPT5, an
evolutionarily conserved factor implicated in virtually all transcriptional steps from enhancer …

Ancient homomorphy of molluscan sex chromosomes sustained by reversible sex-biased genes and sex determiner translocation

W Han, L Liu, J Wang, H Wei, Y Li, L Zhang… - Nature Ecology & …, 2022 - nature.com
Contrary to classic theory prediction, sex-chromosome homomorphy is prevalent in the
animal kingdom but it is unclear how ancient homomorphic sex chromosomes avoid …

Donafenib and GSK‐J4 synergistically induce ferroptosis in liver cancer by upregulating HMOX1 expression

C Zheng, B Zhang, Y Li, K Liu, W Wei… - Advanced …, 2023 - Wiley Online Library
Hepatocellular carcinoma (HCC) is one of the most lethal cancers worldwide. Donafenib is a
multi‐receptor tyrosine kinase inhibitor approved for the treatment of patients with advanced …

Decoding enhancer complexity with machine learning and high-throughput discovery

GD Smith, WH Ching, P Cornejo-Páramo, ES Wong - Genome biology, 2023 - Springer
Enhancers are genomic DNA elements controlling spatiotemporal gene expression. Their
flexible organization and functional redundancies make deciphering their sequence-function …

Enhancer–promoter specificity in gene transcription: molecular mechanisms and disease associations

MJ Friedman, T Wagner, H Lee… - … & Molecular Medicine, 2024 - nature.com
Although often located at a distance from their target gene promoters, enhancers are the
primary genomic determinants of temporal and spatial transcriptional specificity in …

Analysis of the P. lividus sea urchin genome highlights contrasting trends of genomic and regulatory evolution in deuterostomes

F Marlétaz, A Couloux, J Poulain, K Labadie… - Cell Genomics, 2023 - cell.com
Sea urchins are emblematic models in developmental biology and display several
characteristics that set them apart from other deuterostomes. To uncover the genomic cues …

Enhancers associated with unstable RNAs are rare in plants

BR Mcdonald, CL Picard, IM Brabb, MI Savenkova… - Nature Plants, 2024 - nature.com
Unstable transcripts have emerged as markers of active enhancers in vertebrates and
shown to be involved in many cellular processes and medical disorders. However, their …