Chromatin Hubs: A biological and computational outlook
This review discusses our current understanding of chromatin biology and bioinformatics under the unifying concept of “chromatin hubs.” The first part reviews the biology of chromatin hubs, including chromatin–chromatin interaction hubs, chromatin hubs at the nuclear periphery, hubs around macromole...
| Main Authors: | , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Elsevier
2022-01-01
|
| Series: | Computational and Structural Biotechnology Journal |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2001037022002823 |
| _version_ | 1797978249362407424 |
|---|---|
| author | Antonio Mora Xiaowei Huang Shaurya Jauhari Qin Jiang Xuri Li |
| author_facet | Antonio Mora Xiaowei Huang Shaurya Jauhari Qin Jiang Xuri Li |
| author_sort | Antonio Mora |
| collection | DOAJ |
| description | This review discusses our current understanding of chromatin biology and bioinformatics under the unifying concept of “chromatin hubs.” The first part reviews the biology of chromatin hubs, including chromatin–chromatin interaction hubs, chromatin hubs at the nuclear periphery, hubs around macromolecules such as RNA polymerase or lncRNAs, and hubs around nuclear bodies such as the nucleolus or nuclear speckles. The second part reviews existing computational methods, including enhancer–promoter interaction prediction, network analysis, chromatin domain callers, transcription factory predictors, and multi-way interaction analysis. We introduce an integrated model that makes sense of the existing evidence. Understanding chromatin hubs may allow us (i) to explain long-unsolved biological questions such as interaction specificity and redundancy of mechanisms, (ii) to develop more realistic kinetic and functional predictions, and (iii) to explain the etiology of genomic disease. |
| first_indexed | 2024-04-11T05:19:59Z |
| format | Article |
| id | doaj.art-ddc804228bc44bd6bb27f2f1d8282102 |
| institution | Directory Open Access Journal |
| issn | 2001-0370 |
| language | English |
| last_indexed | 2024-04-11T05:19:59Z |
| publishDate | 2022-01-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Computational and Structural Biotechnology Journal |
| spelling | doaj.art-ddc804228bc44bd6bb27f2f1d82821022022-12-24T04:53:19ZengElsevierComputational and Structural Biotechnology Journal2001-03702022-01-012037963813Chromatin Hubs: A biological and computational outlookAntonio Mora0Xiaowei Huang1Shaurya Jauhari2Qin Jiang3Xuri Li4Joint School of Life Sciences, Guangzhou Medical University and Guangzhou Institutes of Biomedicine and Health (Chinese Academy of Sciences), Guangzhou 511436, PR China; Corresponding authors.Joint School of Life Sciences, Guangzhou Medical University and Guangzhou Institutes of Biomedicine and Health (Chinese Academy of Sciences), Guangzhou 511436, PR ChinaJoint School of Life Sciences, Guangzhou Medical University and Guangzhou Institutes of Biomedicine and Health (Chinese Academy of Sciences), Guangzhou 511436, PR ChinaAffiliated Eye Hospital of Nanjing Medical University, Nanjing 210000, PR ChinaState Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, and Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, PR China; Corresponding authors.This review discusses our current understanding of chromatin biology and bioinformatics under the unifying concept of “chromatin hubs.” The first part reviews the biology of chromatin hubs, including chromatin–chromatin interaction hubs, chromatin hubs at the nuclear periphery, hubs around macromolecules such as RNA polymerase or lncRNAs, and hubs around nuclear bodies such as the nucleolus or nuclear speckles. The second part reviews existing computational methods, including enhancer–promoter interaction prediction, network analysis, chromatin domain callers, transcription factory predictors, and multi-way interaction analysis. We introduce an integrated model that makes sense of the existing evidence. Understanding chromatin hubs may allow us (i) to explain long-unsolved biological questions such as interaction specificity and redundancy of mechanisms, (ii) to develop more realistic kinetic and functional predictions, and (iii) to explain the etiology of genomic disease.http://www.sciencedirect.com/science/article/pii/S2001037022002823Chromatin interactionChromatin hubHi-CTranscription factoryNuclear specklesTAD |
| spellingShingle | Antonio Mora Xiaowei Huang Shaurya Jauhari Qin Jiang Xuri Li Chromatin Hubs: A biological and computational outlook Computational and Structural Biotechnology Journal Chromatin interaction Chromatin hub Hi-C Transcription factory Nuclear speckles TAD |
| title | Chromatin Hubs: A biological and computational outlook |
| title_full | Chromatin Hubs: A biological and computational outlook |
| title_fullStr | Chromatin Hubs: A biological and computational outlook |
| title_full_unstemmed | Chromatin Hubs: A biological and computational outlook |
| title_short | Chromatin Hubs: A biological and computational outlook |
| title_sort | chromatin hubs a biological and computational outlook |
| topic | Chromatin interaction Chromatin hub Hi-C Transcription factory Nuclear speckles TAD |
| url | http://www.sciencedirect.com/science/article/pii/S2001037022002823 |
| work_keys_str_mv | AT antoniomora chromatinhubsabiologicalandcomputationaloutlook AT xiaoweihuang chromatinhubsabiologicalandcomputationaloutlook AT shauryajauhari chromatinhubsabiologicalandcomputationaloutlook AT qinjiang chromatinhubsabiologicalandcomputationaloutlook AT xurili chromatinhubsabiologicalandcomputationaloutlook |