Superstructure detection in nucleosome distribution shows common pattern within a chromosome and within the genome
Nucleosome positioning plays an important role in crucial biological processes such as replication, transcription, and gene regulation. It has been widely used to predict the genome’s function and chromatin organisation. So far, the studies of patterns in nucleosome positioning have been limited to...
Saved in:
| Main Authors: | , , , , , |
|---|---|
| Format: | Article (Journal) |
| Language: | English |
| Published: |
6 April 2022
|
| In: |
Life
Year: 2022, Volume: 12, Issue: 4, Pages: 1-11 |
| ISSN: | 2075-1729 |
| DOI: | 10.3390/life12040541 |
| Online Access: | Verlag, lizenzpflichtig, Volltext: https://doi.org/10.3390/life12040541 Verlag, lizenzpflichtig, Volltext: https://www.mdpi.com/2075-1729/12/4/541 
|
| Author Notes: | Sujeet Kumar Mishra, Kunhe Li, Simon Brauburger, Arnab Bhattacherjee, Nestor Norio Oiwa and Dieter W. Heermann |
| Summary: | Nucleosome positioning plays an important role in crucial biological processes such as replication, transcription, and gene regulation. It has been widely used to predict the genome’s function and chromatin organisation. So far, the studies of patterns in nucleosome positioning have been limited to transcription start sites, CTCFs binding sites, and some promoter and loci regions. The genome-wide organisational pattern remains unknown. We have developed a theoretical model to coarse-grain nucleosome positioning data in order to obtain patterns in their distribution. Using hierarchical clustering on the auto-correlation function of this coarse-grained nucleosome positioning data, a genome-wide clustering is obtained for Candida albicans. The clustering shows the existence beyond hetero- and eu-chromatin inside the chromosomes. These non-trivial clusterings correspond to different nucleosome distributions and gene densities governing differential gene expression patterns. Moreover, these distribution patterns inside the chromosome appeared to be conserved throughout the genome and within species. The pipeline of the coarse grain nucleosome positioning sequence to identify underlying genomic organisation used in our study is novel, and the classifications obtained are unique and consistent. |
|---|---|
| Item Description: | This article belongs to the Special issue Epigenetics and Nuclear Architecture Gesehen am 23.06.2022 |
| Physical Description: | Online Resource |
| ISSN: | 2075-1729 |
| DOI: | 10.3390/life12040541 |