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Predicting chromosomal compartments directly from the nucleotide sequence with DNA-DDA
Three-dimensional (3D) genome architecture is characterized by multi-scale patterns and plays an essential role in gene regulation. Chromatin conformation capturing experiments have revealed many properties underlying 3D genome architecture, such as the compartmentalization of chromatin based on tra...
Autores principales: | , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10359093/ https://www.ncbi.nlm.nih.gov/pubmed/37264486 http://dx.doi.org/10.1093/bib/bbad198 |
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author | Lainscsek, Xenia Taher, Leila |
author_facet | Lainscsek, Xenia Taher, Leila |
author_sort | Lainscsek, Xenia |
collection | PubMed |
description | Three-dimensional (3D) genome architecture is characterized by multi-scale patterns and plays an essential role in gene regulation. Chromatin conformation capturing experiments have revealed many properties underlying 3D genome architecture, such as the compartmentalization of chromatin based on transcriptional states. However, they are complex, costly and time consuming, and therefore only a limited number of cell types have been examined using these techniques. Increasing effort is being directed towards deriving computational methods that can predict chromatin conformation and associated structures. Here we present DNA-delay differential analysis (DDA), a purely sequence-based method based on chaos theory to predict genome-wide A and B compartments. We show that DNA-DDA models derived from a 20 Mb sequence are sufficient to predict genome wide compartmentalization at the scale of 100 kb in four different cell types. Although this is a proof-of-concept study, our method shows promise in elucidating the mechanisms responsible for genome folding as well as modeling the impact of genetic variation on 3D genome architecture and the processes regulated thereby. |
format | Online Article Text |
id | pubmed-10359093 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-103590932023-07-21 Predicting chromosomal compartments directly from the nucleotide sequence with DNA-DDA Lainscsek, Xenia Taher, Leila Brief Bioinform Problem Solving Protocol Three-dimensional (3D) genome architecture is characterized by multi-scale patterns and plays an essential role in gene regulation. Chromatin conformation capturing experiments have revealed many properties underlying 3D genome architecture, such as the compartmentalization of chromatin based on transcriptional states. However, they are complex, costly and time consuming, and therefore only a limited number of cell types have been examined using these techniques. Increasing effort is being directed towards deriving computational methods that can predict chromatin conformation and associated structures. Here we present DNA-delay differential analysis (DDA), a purely sequence-based method based on chaos theory to predict genome-wide A and B compartments. We show that DNA-DDA models derived from a 20 Mb sequence are sufficient to predict genome wide compartmentalization at the scale of 100 kb in four different cell types. Although this is a proof-of-concept study, our method shows promise in elucidating the mechanisms responsible for genome folding as well as modeling the impact of genetic variation on 3D genome architecture and the processes regulated thereby. Oxford University Press 2023-06-01 /pmc/articles/PMC10359093/ /pubmed/37264486 http://dx.doi.org/10.1093/bib/bbad198 Text en © The Author(s) 2023. Published by Oxford University Press. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Problem Solving Protocol Lainscsek, Xenia Taher, Leila Predicting chromosomal compartments directly from the nucleotide sequence with DNA-DDA |
title | Predicting chromosomal compartments directly from the nucleotide sequence with DNA-DDA |
title_full | Predicting chromosomal compartments directly from the nucleotide sequence with DNA-DDA |
title_fullStr | Predicting chromosomal compartments directly from the nucleotide sequence with DNA-DDA |
title_full_unstemmed | Predicting chromosomal compartments directly from the nucleotide sequence with DNA-DDA |
title_short | Predicting chromosomal compartments directly from the nucleotide sequence with DNA-DDA |
title_sort | predicting chromosomal compartments directly from the nucleotide sequence with dna-dda |
topic | Problem Solving Protocol |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10359093/ https://www.ncbi.nlm.nih.gov/pubmed/37264486 http://dx.doi.org/10.1093/bib/bbad198 |
work_keys_str_mv | AT lainscsekxenia predictingchromosomalcompartmentsdirectlyfromthenucleotidesequencewithdnadda AT taherleila predictingchromosomalcompartmentsdirectlyfromthenucleotidesequencewithdnadda |