TY - JOUR
T1 - Genome modeling
T2 - From chromatin fibers to genes
AU - Portillo-Ledesma, Stephanie
AU - Li, Zilong
AU - Schlick, Tamar
N1 - Publisher Copyright:
© 2022 Elsevier Ltd
PY - 2023/2
Y1 - 2023/2
N2 - The intricacies of the 3D hierarchical organization of the genome have been approached by many creative modeling studies. The specific model/simulation technique combination defines and restricts the system and phenomena that can be investigated. We present the latest modeling developments and studies of the genome, involving models ranging from nucleosome systems and small polynucleosome arrays to chromatin fibers in the kb-range, chromosomes, and whole genomes, while emphasizing gene folding from first principles. Clever combinations allow the exploration of many interesting phenomena involved in gene regulation, such as nucleosome structure and dynamics, nucleosome-nucleosome stacking, polynucleosome array folding, protein regulation of chromatin architecture, mechanisms of gene folding, loop formation, compartmentalization, and structural transitions at the chromosome and genome levels. Gene-level modeling with full details on nucleosome positions, epigenetic factors, and protein binding, in particular, can in principle be scaled up to model chromosomes and cells to study fundamental biological regulation.
AB - The intricacies of the 3D hierarchical organization of the genome have been approached by many creative modeling studies. The specific model/simulation technique combination defines and restricts the system and phenomena that can be investigated. We present the latest modeling developments and studies of the genome, involving models ranging from nucleosome systems and small polynucleosome arrays to chromatin fibers in the kb-range, chromosomes, and whole genomes, while emphasizing gene folding from first principles. Clever combinations allow the exploration of many interesting phenomena involved in gene regulation, such as nucleosome structure and dynamics, nucleosome-nucleosome stacking, polynucleosome array folding, protein regulation of chromatin architecture, mechanisms of gene folding, loop formation, compartmentalization, and structural transitions at the chromosome and genome levels. Gene-level modeling with full details on nucleosome positions, epigenetic factors, and protein binding, in particular, can in principle be scaled up to model chromosomes and cells to study fundamental biological regulation.
KW - Chromatin folding
KW - Epigenetic regulation
KW - Gene regulation
KW - Gene structure
KW - Genome organization
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U2 - 10.1016/j.sbi.2022.102506
DO - 10.1016/j.sbi.2022.102506
M3 - Review article
C2 - 36577295
AN - SCOPUS:85144620586
SN - 0959-440X
VL - 78
JO - Current Opinion in Structural Biology
JF - Current Opinion in Structural Biology
M1 - 102506
ER -