Mechanisms of lncRNA biogenesis as revealed by nascent transcriptomics

T Nojima, NJ Proudfoot - Nature reviews Molecular cell biology, 2022 - nature.com
Mammalian genomes express two principal gene categories through RNA polymerase II-
mediated transcription: protein-coding transcription units and non-coding RNA transcription …

[LLIBRE][B] RNA, the epicenter of genetic information

J Mattick, P Amaral - 2023 - library.oapen.org
The origin story and emergence of molecular biology is muddled. The early triumphs in
bacterial genetics and the complexity of animal and plant genomes complicate an intricate …

Enhancers are activated by p300/CBP activity-dependent PIC assembly, RNAPII recruitment, and pause release

T Narita, S Ito, Y Higashijima, WK Chu, K Neumann… - Molecular Cell, 2021 - cell.com
The metazoan-specific acetyltransferase p300/CBP is involved in activating signal-induced,
enhancer-mediated transcription of cell-type-specific genes. However, the global kinetics …

MLL-AF4 cooperates with PAF1 and FACT to drive high-density enhancer interactions in leukemia

NT Crump, AL Smith, L Godfrey… - Nature …, 2023 - nature.com
Aberrant enhancer activation is a key mechanism driving oncogene expression in many
cancers. While much is known about the regulation of larger chromosome domains in …

Cohesin couples transcriptional bursting probabilities of inducible enhancers and promoters

I Robles-Rebollo, S Cuartero… - Nature …, 2022 - nature.com
Innate immune responses rely on inducible gene expression programmes which, in contrast
to steady-state transcription, are highly dependent on cohesin. Here we address …

Capture-C: a modular and flexible approach for high-resolution chromosome conformation capture

DJ Downes, AL Smith, MA Karpinska, T Velychko… - Nature protocols, 2022 - nature.com
Chromosome conformation capture (3C) methods measure the spatial proximity between
DNA elements in the cell nucleus. Many methods have been developed to sample 3C …

[HTML][HTML] Loss-of-Function Variants in SUPT5H as Modifying Factors in Beta-Thalassemia

CL Harteveld, A Achour… - International Journal of …, 2024 - mdpi.com
It is well known that modifiers play a role in ameliorating or exacerbating disease
phenotypes in patients and carriers of recessively inherited disorders such as sickle cell …

Differences in transcription initiation directionality underlie distinctions between plants and animals in chromatin modification patterns at genes and cis-regulatory …

BD Silver, CG Willett, KA Maher… - G3: Genes, Genomes …, 2024 - academic.oup.com
Transcriptional initiation is among the first regulated steps controlling eukaryotic gene
expression. High-throughput profiling of fungal and animal genomes has revealed that RNA …

Promoter-proximal RNA polymerase II termination regulates transcription during human cell type transition

K Lysakovskaia, A Devadas, B Schwalb… - Nature Structural & …, 2025 - nature.com
Metazoan gene transcription by RNA polymerase II (Pol II) is regulated in the promoter-
proximal region. Pol II can undergo termination in the promoter-proximal region but whether …

Enhancers are genes that express organizational RNAs

JS Mattick - Frontiers in RNA Research, 2023 - frontiersin.org
A longstanding enigma in molecular biology is the lack of scaling of protein-coding genes
with developmental complexity, referred to as the g-value paradox. On the other hand, a …