Aqsa, Jamia Millia Islamia
A nucleosome is a DNA segment of 147-bp coiled around a histone octamer. Each histone octamer is made up of two copies of each of the histone proteins H2A, H2B, H3, and H4. It is the fundamental subunit of chromatin. Although it seems that the nucleosome has its significance only in DNA packaging, there is much more to it. It is also involved in various regulatory activities. For example, interacting with DNA binding proteins, regulatory factors, chromatin remodelers, histone chaperones, and polymerases
Hence, the need for a database of nucleosome organization is undeniable.
But two major problems follow up: First, nucleosomes occupy a large percentage of the genome which makes it fairly difficult to sequence.
And the second problem lies in the analysis method used. Currently, researchers usually illustrate nucleosome organization by aggregating nucleosome organization profiles on a large number of genomic regions, which ignores the difference between individual genomic regions.
Introduction to NUCOME:
To solve the above-mentioned problems, a comprehensive database of nucleosome organizations called NUCOME (Nucleosome Organization Referenced Landscapes in Mammalian Genomes) is established. This database organizes the qualified data sources and provides nucleosome organization referenced landscapes of various cell and tissue types in humans and mice. This database uses MNase-seq, which is the most widely used technology for generating nucleosome organization maps
Some features of the NUCOME are as follows:
● It efficiently manages and filters MNase-seq data in humans and mice, which exempts the users from redundant data selection.
● It provides reliable and high-quality nucleosome organization referenced landscapes for various human and mouse cell and tissue types.
● It provides a web interface, which contains multiple modules such as processed data download, an analysis module that quantifies informative nucleosome organization features in genomic regions, and search modules.
● It also verifies the reliability and accuracy of quantified nucleosome organization information.
The generation of NUCOME involved: collecting available data sets from the Gene Expression Omnibus and downloading raw data sets from the Sequence Read Archive. The data source comprised 69 kinds of mouse cell or tissue types and 33 kinds of a human cell or tissue types.
All data were then processed and analyzed accompanying with QCs measurements specific for MNase-seq data.
Utility:
NUCOME has three analysis or search modules :
(a) ‘NuP Browser’ (nucleosome positioning browser),
(b) ‘TSS-centered Annotation’, and
(c) ‘DHS-centered Annotation’.
NUCOME also includes a ‘Download’ module, which allows users to access standardized processed files.
The major benefits that this database provides are:
1. It allows users to download files in the ‘download’ module. It also provides users access to visualizing nucleosome organization profiles in the UCSC browser.
2. The ‘NuP Browser’ module allows users to inquire about nucleosome organization in any gene or genomic region. This module quantifies multiple nucleosome organization features describing the local chromatin structure, nucleosome occupancy, nucleosome array score, nucleosome depletion level, and nucleosome profile.
3. The ‘TSS-centered Annotation’ module lets users request multiple nucleosome organization features.
4. The ‘DHS-centered Annotation’ module is similar to the ‘TSS-centered Annotation’ in terms of nucleosome organization features, operation, and result from the exhibition.
Also read: Native State Mass Spectrometry
Source:
NUCOME: A comprehensive database of nucleosome organization referenced landscapes in mammalian genomes –https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-021-04239-9
Very well explained about NUCOME, as the new technology stratigies are being coming , biotechnology play a a very important role , while giving nanotechnology and nanoscience as major development sources.