The Next, Next-Generation of Sequencing, Promising to Boost Research and Clinical Practice

KR Kumar, MJ Cowley, RL Davis - Seminars in Thrombosis …, 2024 - thieme-connect.com
Five years on from our award-winning review on Nextgeneration sequencing and emerging
technologies, 1 a rapid pace of fundamental advances has markedly altered the landscape …

[HTML][HTML] Exploring the interplay between enhancer–promoter interactions and transcription

RH Kittle, M Levo - Current Opinion in Genetics & Development, 2025 - Elsevier
Enhancers in metazoan genomes are known to activate their target genes across both short
and long genomic distances. Recent advances in chromosome conformation capture assays …

Enhancer contacts during embryonic development show diverse interaction modes and modest yet significant increases upon gene activation

DM Ibrahim - Nature Genetics, 2024 - nature.com
The exact relationship between 3D chromatin interactions and enhancer function is unclear.
By probing three-dimensional enhancer interactions in developing embryos, two studies …

A 3D genome view of colon cancer initiation

A Danieli-Mackay, A Papantonis - Nature Cancer, 2024 - nature.com
The early molecular events driving cancer initiation remain elusive, hampering prognostic
accuracy. A comparative analysis of 3D genomics data from all stages of colon malignant …

Single-cell analysis of bidirectional reprogramming between early embryonic states identify mechanisms of differential lineage plasticities in mice

V Garg, Y Yang, S Nowotschin, M Setty, E Salataj… - Developmental Cell, 2024 - cell.com
Two distinct lineages, pluripotent epiblast (EPI) and primitive (extra-embryonic) endoderm
(PrE), arise from common inner cell mass (ICM) progenitors in mammalian embryos. To …

Transient promoter interactions modulate developmental gene activation

S Mahara, S Prüssing, V Smialkovska, S Krall… - Molecular cell, 2024 - cell.com
Transcriptional induction coincides with the formation of various chromatin topologies.
Strong evidence supports that gene activation is accompanied by a general increase in …

De novo genome assemblies of two cryptodiran turtles with ZZ/ZW and XX/XY sex chromosomes provide insights into patterns of genome reshuffling and uncover …

B Bista, L González-Rodelas… - Genome …, 2024 - genome.cshlp.org
Understanding the evolution of chromatin conformation among species is fundamental to
elucidate the architecture and plasticity of genomes. Nonrandom interactions of linearly …

Synergy between cis-regulatory elements can render cohesin dispensable for distal enhancer function

KL Hansen, AS Adachi, L Braccioli, S Kadvani… - bioRxiv, 2024 - biorxiv.org
Enhancers are critical genetic elements controlling transcription from promoters, but the
mechanisms by which they convey regulatory information across large genomic distances …

Predictive Prioritization of Enhancers Associated with Pancreas Disease Risk

L Wang, S Baek, G Prasad, J Wildenthal, K Guo… - …, 2024 - pmc.ncbi.nlm.nih.gov
Genetic and epigenetic variations in regulatory enhancer elements increase susceptibility to
a range of pathologies. Despite recent advances, linking enhancer elements to target genes …

Three-dimensional regulatory hubs support oncogenic programs in glioblastoma

SL Breves, D Campigli Di Giammartino, J Nicholson… - bioRxiv, 2024 - biorxiv.org
Dysregulation of enhancer-promoter communication in the context of the three-dimensional
(3D) nucleus is increasingly recognized as a potential driver of oncogenic programs. Here …