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 …

The dynamic broad epigenetic (H3K4me3, H3K27ac) domain as a mark of essential genes

TH Beacon, GP Delcuve, C López, G Nardocci… - Clinical …, 2021 - Springer
Transcriptionally active chromatin is marked by tri-methylation of histone H3 at lysine 4
(H3K4me3) located after first exons and around transcription start sites. This epigenetic mark …

Parallel analysis of transcription, integration, and sequence of single HIV-1 proviruses

KB Einkauf, MR Osborn, C Gao, W Sun, X Sun, X Lian… - Cell, 2022 - cell.com
HIV-1-infected cells that persist despite antiretroviral therapy (ART) are frequently
considered" transcriptionally silent," but active viral gene expression may occur in some …

Evolution of the ancestral mammalian karyotype and syntenic regions

J Damas, M Corbo, J Kim… - Proceedings of the …, 2022 - National Acad Sciences
Decrypting the rearrangements that drive mammalian chromosome evolution is critical to
understanding the molecular bases of speciation, adaptation, and disease susceptibility …

LHX2-and LDB1-mediated trans interactions regulate olfactory receptor choice

K Monahan, A Horta, S Lomvardas - Nature, 2019 - nature.com
The genome is partitioned into topologically associated domains and genomic
compartments with shared chromatin valence. This architecture is constrained by the DNA …

Extrachromosomal DNA: an emerging hallmark in human cancer

S Wu, V Bafna, HY Chang… - Annual Review of …, 2022 - annualreviews.org
Human genes are arranged on 23 pairs of chromosomes, but in cancer, tumor-promoting
genes and regulatory elements can free themselves from chromosomes and relocate to …

Next-generation sequencing in newborn screening: a review of current state

ZI Remec, K Trebusak Podkrajsek… - Frontiers in …, 2021 - frontiersin.org
Newborn screening was first introduced at the beginning of the 1960s with the successful
implementation of the first phenylketonuria screening programs. Early expansion of the …

Gene regulation on extrachromosomal DNA

KL Hung, PS Mischel, HY Chang - Nature structural & molecular …, 2022 - nature.com
Oncogene amplification on extrachromosomal DNA (ecDNA) is prevalent in human cancer
and is associated with poor outcomes. Clonal, megabase-sized circular ecDNAs in cancer …

Multiplexed imaging of nucleome architectures in single cells of mammalian tissue

M Liu, Y Lu, B Yang, Y Chen, JSD Radda, M Hu… - Nature …, 2020 - nature.com
The three-dimensional architecture of the genome affects genomic functions. Multiple
genome architectures at different length scales, including chromatin loops, domains …

Phase separation drives decision making in cell division

X Liu, X Liu, H Wang, Z Dou, K Ruan, DL Hill… - Journal of Biological …, 2020 - ASBMB
Liquid–liquid phase separation (LLPS) of biomolecules drives the formation of subcellular
compartments with distinct physicochemical properties. These compartments, free of lipid …