CTCF shapes chromatin structure and gene expression in health and disease

B Dehingia, M Milewska, M Janowski, A Pękowska - EMBO reports, 2022 - embopress.org
CCCTC‐binding factor (CTCF) is an eleven zinc finger (ZF), multivalent transcriptional
regulator, that recognizes numerous motifs thanks to the deployment of distinct combinations …

Epigenetic regulatory layers in the 3D nucleus

A Willemin, D Szabó, A Pombo - Molecular Cell, 2024 - cell.com
Nearly 7 decades have elapsed since Francis Crick introduced the central dogma of
molecular biology, as part of his ideas on protein synthesis, setting the fundamental rules of …

Sequential in cis mutagenesis in vivo reveals various functions for CTCF sites at the mouse HoxD cluster

AR Amândio, L Beccari, L Lopez-Delisle… - Genes & …, 2021 - genesdev.cshlp.org
Mammalian Hox gene clusters contain a range of CTCF binding sites. In addition to their
importance in organizing a TAD border, which isolates the most posterior genes from the …

An integrative TAD catalog in lymphoblastoid cell lines discloses the functional impact of deletions and insertions in human genomes

C Li, MJ Bonder, S Syed, M Jensen… - Genome …, 2024 - genome.cshlp.org
The human genome is packaged within a three-dimensional (3D) nucleus and organized
into structural units known as compartments, topologically associating domains (TADs), and …

Structural variation at a disease mutation hotspot: Strategies to investigate gene regulation and the 3D genome

A Boyling, G Perez-Siles, ML Kennerson - Frontiers in Genetics, 2022 - frontiersin.org
A rare form of X-linked Charcot-Marie-Tooth neuropathy, CMTX3, is caused by an
interchromosomal insertion occurring at chromosome Xq27. 1. Interestingly, eight other …

Beyond modular enhancers: new questions in cis-regulatory evolution

JMC McDonald, RD Reed - Trends in Ecology & Evolution, 2024 - cell.com
Our understanding of how cis-regulatory elements work has advanced rapidly, outpacing
our evolutionary models. In this review, we consider the implications of new mechanistic …

Duplications disrupt chromatin architecture and rewire GPR101-enhancer communication in X-linked acrogigantism

M Franke, AF Daly, L Palmeira, A Tirosh… - The American Journal of …, 2022 - cell.com
Abstract X-linked acrogigantism (X-LAG) is the most severe form of pituitary gigantism and is
characterized by aggressive growth hormone (GH)-secreting pituitary tumors that occur in …

3D chromatin remodeling potentiates transcriptional programs driving cell invasion

B Lebeau, M Jangal, T Zhao… - Proceedings of the …, 2022 - National Acad Sciences
The contribution of deregulated chromatin architecture, including topologically associated
domains (TADs), to cancer progression remains ambiguous. CCCTC-binding factor (CTCF) …

Enhancer Function in the 3D Genome

SV Razin, SV Ulianov, OV Iarovaia - Genes, 2023 - mdpi.com
In this review, we consider various aspects of enhancer functioning in the context of the 3D
genome. Particular attention is paid to the mechanisms of enhancer-promoter …

3D genome alterations and editing in pathology

EA Tiukacheva, SV Ulianov, A Karpukhina, SV Razin… - Molecular Therapy, 2023 - cell.com
The human genome is folded into a multi-level 3D structure that controls many nuclear
functions including gene expression. Recently, alterations in 3D genome organization were …