Computational Methods for Assessing Chromatin Hierarchy
| Autor: | Pao-Yang Chen, Ming-Ren Yen, Moloya Gohain, Pearl Chang |
|---|---|
| Rok vydání: | 2017 |
| Předmět: |
0301 basic medicine
Computer science lcsh:Biotechnology Biophysics Cellular functions ATAC-seq Computational biology Biochemistry Chromosome conformation capture 03 medical and health sciences 0302 clinical medicine Structural Biology Chromosome architecture Hi-C lcsh:TP248.13-248.65 Genetics Hierarchical organization Profiling (information science) Computational analysis Chromatin accessibility 3C-technologies 3D genome Computer Science Applications Chromatin 030104 developmental biology Short Survey 030217 neurology & neurosurgery Biotechnology |
| Zdroj: | Computational and Structural Biotechnology Journal Computational and Structural Biotechnology Journal, Vol 16, Iss, Pp 43-53 (2018) |
| ISSN: | 2001-0370 |
| Popis: | The hierarchical organization of chromatin is known to associate with diverse cellular functions; however, the precise mechanisms and the 3D structure remain to be determined. With recent advances in high-throughput next generation sequencing (NGS) techniques, genome-wide profiling of chromatin structures is made possible. Here, we provide a comprehensive overview of NGS-based methods for profiling “higher-order” and “primary-order” chromatin structures from both experimental and computational aspects. Experimental requirements and considerations specific for each method were highlighted. For computational analysis, we summarized a common analysis strategy for both levels of chromatin assessment, focusing on the characteristic computing steps and the tools. The recently developed single-cell level techniques based on Hi-C and ATAC-seq present great potential to reveal cell-to-cell variability in chromosome architecture. A brief discussion on these methods in terms of experimental and data analysis features is included. We also touch upon the biological relevance of chromatin organization and how the combination with other techniques uncovers the underlying mechanisms. We conclude with a summary and our prospects on necessary improvements of currently available methods in order to advance understanding of chromatin hierarchy. Our review brings together the analyses of both higher- and primary-order chromatin structures, and serves as a roadmap when choosing appropriate experimental and computational methods for assessing chromatin hierarchy. Keywords: 3D genome, Chromatin accessibility, Chromosome conformation capture, 3C-technologies, Hi-C, ATAC-seq |
| Databáze: | OpenAIRE |
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