Intertwining roles of R-loops and G-quadruplexes in DNA repair, transcription and genome organization

P Wulfridge, K Sarma - Nature Cell Biology, 2024 - nature.com
R-loops are three-stranded nucleic acid structures that are abundant and widespread across
the genome and that have important physiological roles in many nuclear processes. Their …

When you come to a fork in the road, take it: wnt signaling activates multiple pathways through the APC/Axin/GSK-3 complex

C Li, EE Furth, AK Rustgi, PS Klein - Cells, 2023 - mdpi.com
The Wnt signaling pathway is a highly conserved regulator of metazoan development and
stem cell maintenance. Activation of Wnt signaling is an early step in diverse malignancies …

High-throughput image processing software for the study of nuclear architecture and gene expression

A Keikhosravi, F Almansour, CH Bohrer, NA Fursova… - Scientific Reports, 2024 - nature.com
High-throughput imaging (HTI) generates complex imaging datasets from a large number of
experimental perturbations. Commercial HTI software programs for image analysis …

Image-based 3D genomics through chromatin tracing

T Yang, S Wang - Nature Reviews Methods Primers, 2024 - nature.com
Correct organization of higher-order genome folding is essential for the regulation of gene
expression, DNA replication and other genomic functions. Technological advances in high …

Technological advances in probing 4D genome organization

J Soroczynski, VI Risca - Current Opinion in Cell Biology, 2023 - Elsevier
The last two decades of work on chromosome conformation in eukaryotic nuclei have
revealed a complex and highly regulated hierarchy of architectural features, from self …

A nuclear architecture screen in Drosophila identifies Stonewall as a link between chromatin position at the nuclear periphery and germline stem cell fate

A Chavan, R Isenhart, SC Nguyen… - Genes & …, 2024 - genesdev.cshlp.org
The association of genomic loci to the nuclear periphery is proposed to facilitate cell type-
specific gene repression and influence cell fate decisions. However, the interplay between …

Co-depletion of NIPBL and WAPL balance cohesin activity to correct gene misexpression

JM Luppino, A Field, SC Nguyen, DS Park… - PLoS …, 2022 - journals.plos.org
The relationship between cohesin-mediated chromatin loo** and gene expression
remains unclear. NIPBL and WAPL are two opposing regulators of cohesin activity; …

Dynamics of nuclear architecture during early embryonic development and lessons from liveimaging

F Pecori, ME Torres-Padilla - Developmental cell, 2023 - cell.com
Nuclear organization has emerged as a potential key regulator of genome function. During
development, the deployment of transcriptional programs must be tightly coordinated with …

Inter-chromosomal contacts demarcate genome topology along a spatial gradient

M Mokhtaridoost, JJ Chalmers, M Soleimanpoor… - Nature …, 2024 - nature.com
Non-homologous chromosomal contacts (NHCCs) between different chromosomes
participate considerably in gene and genome regulation. Due to analytical challenges …

From feulgen to modern methods: marking a century of DNA imaging advances

M Lakadamyali - Histochemistry and Cell Biology, 2024 - Springer
The mystery of how human DNA is compactly packaged into a nucleus—a space a hundred
thousand times smaller—while still allowing for the regulation of gene function, has long …