An overview of methods for reconstructing 3-D chromosome and genome structures from Hi-C data

O Oluwadare, M Highsmith, J Cheng - Biological procedures online, 2019 - Springer
Over the past decade, methods for predicting three-dimensional (3-D) chromosome and
genome structures have proliferated. This has been primarily due to the development of high …

From integrative structural biology to cell biology

A Sali - Journal of Biological Chemistry, 2021 - ASBMB
Integrative modeling is an increasingly important tool in structural biology, providing
structures by combining data from varied experimental methods and prior information. As a …

Automatic analysis and 3D-modelling of Hi-C data using TADbit reveals structural features of the fly chromatin colors

F Serra, D Baù, M Goodstadt, D Castillo… - PLoS computational …, 2017 - journals.plos.org
The sequence of a genome is insufficient to understand all genomic processes carried out in
the cell nucleus. To achieve this, the knowledge of its three-dimensional architecture is …

Walking along chromosomes with super-resolution imaging, contact maps, and integrative modeling

G Nir, I Farabella, C Pérez Estrada, CG Ebeling… - PLoS …, 2018 - journals.plos.org
Chromosome organization is crucial for genome function. Here, we present a method for
visualizing chromosomal DNA at super-resolution and then integrating Hi-C data to produce …

Simulated binding of transcription factors to active and inactive regions folds human chromosomes into loops, rosettes and topological domains

CA Brackley, J Johnson, S Kelly, PR Cook… - Nucleic acids …, 2016 - academic.oup.com
Biophysicists are modeling conformations of interphase chromosomes, often basing the
strengths of interactions between segments distant on the genetic map on contact …

Dynamics of genome architecture and chromatin function during human B cell differentiation and neoplastic transformation

R Vilarrasa-Blasi, P Soler-Vila, N Verdaguer-Dot… - Nature …, 2021 - nature.com
To investigate the three-dimensional (3D) genome architecture across normal B cell
differentiation and in neoplastic cells from different subtypes of chronic lymphocytic leukemia …

Development of a prototype system for archiving integrative/hybrid structure models of biological macromolecules

B Vallat, B Webb, JD Westbrook, A Sali, HM Berman - Structure, 2018 - cell.com
Essential processes in biology are carried out by large macromolecular assemblies, whose
structures are often difficult to determine by traditional methods. Increasingly, researchers …

Defined chromosome structure in the genome-reduced bacterium Mycoplasma pneumoniae

M Trussart, E Yus, S Martinez, D Bau… - Nature …, 2017 - nature.com
DNA-binding proteins are central regulators of chromosome organization; however, in
genome-reduced bacteria their diversity is largely diminished. Whether the chromosomes of …

Techniques for and challenges in reconstructing 3D genome structures from 2D chromosome conformation capture data

Z Li, S Portillo-Ledesma, T Schlick - Current Opinion in Cell Biology, 2023 - Elsevier
Chromosome conformation capture technologies that provide frequency information for
contacts between genomic regions have been crucial for increasing our understanding of …

[HTML][HTML] Restraint-based three-dimensional modeling of genomes and genomic domains

F Serra, M Di Stefano, YG Spill, Y Cuartero… - FEBS letters, 2015 - Elsevier
Chromosomes are large polymer molecules composed of nucleotides. In some species,
such as humans, this polymer can sum up to meters long and still be properly folded within …