NucMap 2.0: An Updated Database of Genome-wide Nucleosome Positioning Maps Across Species

IF 4.7 2区生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY

Journal of Molecular Biology Pub Date : 2024-09-01 DOI:10.1016/j.jmb.2024.168655

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引用次数: 0

Abstract

Nucleosome dynamics plays important roles in many biological processes, such as DNA replication and gene expression. NucMap (https://ngdc.cncb.ac.cn/nucmap) is the first database of genome-wide nucleosome positioning maps across species. Here, we present an updated version, NucMap 2.0, by incorporating more species and MNase-seq samples. In addition, we integrate other related omics data for each MNase-seq sample to provide a comprehensive view of nucleosome positioning, such as gene expression, transcription factor binding sites, histone modifications and DNA methylation. In particular, NucMap 2.0 integrates and pre-analyzes RNA-seq data and ChIP-seq data of human-related samples, which facilitates the interpretation of nucleosome positioning in humans. All processed data are integrated into an in-built genome browser, and users can make comprehensive side-by-side analyses. In addition, more online analytical functions are developed, which allows researchers to identify differential nucleosome regions and explore potential gene regulatory regions. All resources are open access with a user-friendly web interface.

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NucMap 2.0：跨物种全基因组核糖体定位图最新数据库。

核小体动力学在 DNA 复制和基因表达等许多生物过程中发挥着重要作用。NucMap (https://ngdc.cncb.ac.cn/nucmap) 是第一个跨物种的全基因组核糖体定位图数据库。在此，我们将纳入更多物种和 MNase-seq 样本，推出更新版 NucMap 2.0。此外，我们还为每个MNase-seq样本整合了其他相关的omics数据，以提供一个全面的核小体定位视图，如基因表达、转录因子结合位点、组蛋白修饰和DNA甲基化。特别是，NucMap 2.0 整合并预分析了人类相关样本的 RNA-seq 数据和 ChIP-seq 数据，这有助于解读人类的核小体定位。所有处理过的数据都集成到内置的基因组浏览器中，用户可以进行全面的并排分析。此外，还开发了更多在线分析功能，使研究人员能够识别差异核糖体区域并探索潜在的基因调控区域。所有资源都是开放式的，具有用户友好的网络界面。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Journal of Molecular Biology 生物-生化与分子生物学

CiteScore

11.30

自引率

1.80%

发文量

412

审稿时长

28 days

期刊介绍： Journal of Molecular Biology (JMB) provides high quality, comprehensive and broad coverage in all areas of molecular biology. The journal publishes original scientific research papers that provide mechanistic and functional insights and report a significant advance to the field. The journal encourages the submission of multidisciplinary studies that use complementary experimental and computational approaches to address challenging biological questions. Research areas include but are not limited to: Biomolecular interactions, signaling networks, systems biology; Cell cycle, cell growth, cell differentiation; Cell death, autophagy; Cell signaling and regulation; Chemical biology; Computational biology, in combination with experimental studies; DNA replication, repair, and recombination; Development, regenerative biology, mechanistic and functional studies of stem cells; Epigenetics, chromatin structure and function; Gene expression; Membrane processes, cell surface proteins and cell-cell interactions; Methodological advances, both experimental and theoretical, including databases; Microbiology, virology, and interactions with the host or environment; Microbiota mechanistic and functional studies; Nuclear organization; Post-translational modifications, proteomics; Processing and function of biologically important macromolecules and complexes; Molecular basis of disease; RNA processing, structure and functions of non-coding RNAs, transcription; Sorting, spatiotemporal organization, trafficking; Structural biology; Synthetic biology; Translation, protein folding, chaperones, protein degradation and quality control.