TY - JOUR
T1 - Techniques for and challenges in reconstructing 3D genome structures from 2D chromosome conformation capture data
AU - Li, Zilong
AU - Portillo-Ledesma, Stephanie
AU - Schlick, Tamar
N1 - Funding Information:
We are grateful to Fangzhen Li, Binguang Ma, Oluwatosin Oluwadare, and Jianrong Wang for computing the 3D structures reconstructed from the contact maps as shown in Figure 3 and providing supporting information. This work was supported by the National Institutes of Health, National Institutes of General Medical Sciences Award R35-GM122562 , the National Science Foundation RAPID Award ( 2030377 ) from the Division of Mathematical Sciences and Chemistry and Award 2151777 from the Division of Mathematical Sciences, and Philip–Morris International to T.S. We gratefully acknowledge support from the Simons Foundation through the NYU Simons Center for Computational Physical Chemistry. This work was supported in part through the NYU IT High Performance Computing group, which provided resources, services, and expert advice.
Publisher Copyright:
© 2023 Elsevier Ltd
PY - 2023/8
Y1 - 2023/8
N2 - Chromosome conformation capture technologies that provide frequency information for contacts between genomic regions have been crucial for increasing our understanding of genome folding and regulation. However, such data do not provide direct evidence of the spatial 3D organization of chromatin. In this opinion article, we discuss the development and application of computational methods to reconstruct chromatin 3D structures from experimental 2D contact data, highlighting how such modeling provides biological insights and can suggest mechanisms anchored to experimental data. By applying different reconstruction methods to the same contact data, we illustrate some state-of-the-art of these techniques and discuss our gene resolution approach based on Brownian dynamics and Monte Carlo sampling.
AB - Chromosome conformation capture technologies that provide frequency information for contacts between genomic regions have been crucial for increasing our understanding of genome folding and regulation. However, such data do not provide direct evidence of the spatial 3D organization of chromatin. In this opinion article, we discuss the development and application of computational methods to reconstruct chromatin 3D structures from experimental 2D contact data, highlighting how such modeling provides biological insights and can suggest mechanisms anchored to experimental data. By applying different reconstruction methods to the same contact data, we illustrate some state-of-the-art of these techniques and discuss our gene resolution approach based on Brownian dynamics and Monte Carlo sampling.
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U2 - 10.1016/j.ceb.2023.102209
DO - 10.1016/j.ceb.2023.102209
M3 - Review article
C2 - 37506571
AN - SCOPUS:85165955027
SN - 0955-0674
VL - 83
JO - Current Opinion in Cell Biology
JF - Current Opinion in Cell Biology
M1 - 102209
ER -