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Yeast As a Chassis for Developing Functional Assays to Study Human P53

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piRBase: a web resource assisting piRNA functional study.

Peng Zhang¹, Xiaohui Si², Geir Skogerbø¹

¹Key Laboratory of the Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China, University of Chinese Academy of Science, Beijing 100049, China, Laboratory of Bioinformatics and Noncoding RNA, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China, College of Life Sciences, Hebei University, Baoding 071002, Hebei, China and College of Plant Protection, Shandong Agricultural University, Tai'an 271018, Shandong, China.

Database : the Journal of Biological Databases and Curation

|November 27, 2014

Summary

This summary is machine-generated.

piRNA databases are crucial for understanding small RNA functions in the animal germ line. The piRBase platform offers the largest collection of piRNA sequences and integrated data for functional analysis.

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Area of Science:

* Molecular Biology
* Genomics
* Bioinformatics

Background:

* PIWI-interacting RNAs (piRNAs) are key small RNAs regulating transposons and genes, primarily in the animal germ line.
* Understanding piRNA functions requires integrating diverse high-throughput data, including epigenetic and post-transcriptional regulatory information.
* Existing piRNA databases lack comprehensive data integration for functional analysis.

Purpose of the Study:

* To develop piRBase, a comprehensive database for collecting, annotating, and structuring piRNA-related data.
* To provide the largest collection of piRNA sequences and associated epigenetic and target data for functional studies.
* To facilitate a deeper understanding of piRNA functions in epigenetic and post-transcriptional regulation.

Main Methods:

* Aggregated and annotated 77 million piRNA sequences from nine species using high-throughput sequencing data.
* Integrated epigenetic data and experimentally validated piRNA targets.
* Developed the piRBase platform for data organization and accessibility.

Main Results:

* piRBase is the most extensive piRNA database currently available, housing 77 million sequences from nine organisms.
* The database systematically integrates repeat-derived and gene-derived piRNAs, alongside epigenetic and post-transcriptional target data.
* This integrated approach supports comprehensive piRNA functional analysis.

Conclusions:

* piRBase represents a significant advancement in piRNA research by providing a centralized, integrated data resource.
* The platform facilitates the systematic analysis of piRNA functions in epigenetic and post-transcriptional gene regulation.
* piRBase is expected to accelerate discoveries in germ line biology and small RNA research.