Integrative studies of 3D genome organization and chromatin structure
The structural organization of the genome is emerging as a crucial regulator of the cell state,
affecting gene transcription, DNA replication, and repair. Over the last twenty years …
affecting gene transcription, DNA replication, and repair. Over the last twenty years …
Loop-extrusion and polymer phase-separation can co-exist at the single-molecule level to shape chromatin folding
Loop-extrusion and phase-separation have been proposed as mechanisms that shape
chromosome spatial organization. It is unclear, however, how they perform relative to each …
chromosome spatial organization. It is unclear, however, how they perform relative to each …
Computational approaches from polymer physics to investigate chromatin folding
Microscopy and sequencing-based technologies are providing increasing insights into
chromatin architecture. Nevertheless, a full comprehension of chromosome folding and its …
chromatin architecture. Nevertheless, a full comprehension of chromosome folding and its …
Comparison of the Hi-C, GAM and SPRITE methods using polymer models of chromatin
Hi-C, split-pool recognition of interactions by tag extension (SPRITE) and genome
architecture map** (GAM) are powerful technologies utilized to probe chromatin …
architecture map** (GAM) are powerful technologies utilized to probe chromatin …
Extracting multi-way chromatin contacts from Hi-C data
There is a growing realization that multi-way chromatin contacts formed in chromosome
structures are fundamental units of gene regulation. However, due to the paucity and …
structures are fundamental units of gene regulation. However, due to the paucity and …
Polymer physics reveals a combinatorial code linking 3D chromatin architecture to 1D chromatin states
The mammalian genome has a complex, functional 3D organization. However, it remains
largely unknown how DNA contacts are orchestrated by chromatin organizers. Here, we …
largely unknown how DNA contacts are orchestrated by chromatin organizers. Here, we …
A modern challenge of polymer physics: novel ways to study, interpret, and reconstruct chromatin structure
The constant development of sophisticated technologies is allowing to dissect three‐
dimensional chromatin structure at high resolution level. The tremendous amount of …
dimensional chromatin structure at high resolution level. The tremendous amount of …
3D genomics and its applications in precision medicine
M Chen, X Liu, Q Liu, D Shi, H Li - Cellular & Molecular Biology Letters, 2023 - Springer
Abstract Three-dimensional (3D) genomics is an emerging discipline that studies the three-
dimensional structure of chromatin and the three-dimensional and functions of genomes. It …
dimensional structure of chromatin and the three-dimensional and functions of genomes. It …
Polymer models are a versatile tool to study chromatin 3D organization
The development of new experimental technologies is opening the way to a deeper
investigation of the three-dimensional organization of chromosomes inside the cell nucleus …
investigation of the three-dimensional organization of chromosomes inside the cell nucleus …
The physics of DNA folding: polymer models and phase-separation
Within cell nuclei, several biophysical processes occur in order to allow the correct activities
of the genome such as transcription and gene regulation. To quantitatively investigate such …
of the genome such as transcription and gene regulation. To quantitatively investigate such …