Long non-coding RNAs: definitions, functions, challenges and recommendations

JS Mattick, PP Amaral, P Carninci… - … reviews Molecular cell …, 2023 - nature.com
Genes specifying long non-coding RNAs (lncRNAs) occupy a large fraction of the genomes
of complex organisms. The term 'lncRNAs' encompasses RNA polymerase I (Pol I), Pol II …

Gene regulation in time and space during X-chromosome inactivation

A Loda, S Collombet, E Heard - Nature Reviews Molecular Cell Biology, 2022 - nature.com
X-chromosome inactivation (XCI) is the epigenetic mechanism that ensures X-linked dosage
compensation between cells of females (XX karyotype) and males (XY). XCI is essential for …

From telomere to telomere: The transcriptional and epigenetic state of human repeat elements

SJ Hoyt, JM Storer, GA Hartley, PGS Grady… - Science, 2022 - science.org
Mobile elements and repetitive genomic regions are sources of lineage-specific genomic
innovation and uniquely fingerprint individual genomes. Comprehensive analyses of such …

Enhancer–promoter interactions can bypass CTCF-mediated boundaries and contribute to phenotypic robustness

S Chakraborty, N Kopitchinski, Z Zuo, A Eraso… - Nature …, 2023 - nature.com
How enhancers activate their distal target promoters remains incompletely understood. Here
we dissect how CTCF-mediated loops facilitate and restrict such regulatory interactions …

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 …

On the existence and functionality of topologically associating domains

JA Beagan, JE Phillips-Cremins - Nature genetics, 2020 - nature.com
Genomes across a wide range of eukaryotic organisms fold into higher-order chromatin
domains. Topologically associating domains (TADs) were originally discovered empirically …

Biological function of long non-coding RNA (LncRNA) Xist

W Wang, L Min, X Qiu, X Wu, C Liu, J Ma… - Frontiers in cell and …, 2021 - frontiersin.org
Long non-coding RNAs (lncRNAs) regulate gene expression in a variety of ways at
epigenetic, chromatin remodeling, transcriptional, and translational levels. Accumulating …

Transcription regulation by long non-coding RNAs: mechanisms and disease relevance

J Ferrer, N Dimitrova - Nature Reviews Molecular Cell Biology, 2024 - nature.com
Long non-coding RNAs (lncRNAs) outnumber protein-coding transcripts, but their functions
remain largely unknown. In this Review, we discuss the emerging roles of lncRNAs in the …

Molecular basis of CTCF binding polarity in genome folding

EP Nora, L Caccianini, G Fudenberg, K So… - Nature …, 2020 - nature.com
Current models propose that boundaries of mammalian topologically associating domains
(TADs) arise from the ability of the CTCF protein to stop extrusion of chromatin loops by …

X inactivation and escape: epigenetic and structural features

H Fang, CM Disteche, JB Berletch - Frontiers in cell and …, 2019 - frontiersin.org
X inactivation represents a complex multi-layer epigenetic mechanism that profoundly
modifies chromatin composition and structure of one X chromosome in females. The …