Multi-omics annotation of human long non-coding RNAs

LncBook 2.0: integrating human long non-coding RNAs with multi-omics annotations

LncBook, a comprehensive resource of human long non-coding RNAs (lncRNAs), has been used in a wide range of lncRNA studies across various biological contexts. Here, we present LncBook 2.0 (https://ngdc.cncb.ac.cn/lncbook), with significant updates and enhancements as follows: (i) incorporation of 119 722 new transcripts, 9632 new genes, and gene structure update of 21 305 lncRNAs; (ii) characterization of conservation features of human lncRNA genes across 40 vertebrates; (iii) integration of lncRNA-encoded small proteins; (iv) enrichment of expression and DNA methylation profiles with more biological contexts and (v) identification of lncRNA-protein interactions and improved prediction of lncRNA-miRNA interactions. Collectively, LncBook 2.0 accommodates a high-quality collection of 95 243 lncRNA genes and 323 950 transcripts and incorporates their abundant annotations at different omics levels, thereby enabling users to decipher functional significance of lncRNAs in different biological contexts.

KaKs_Calculator 3.0: Calculating Selective Pressure on Coding and Non-coding Sequences

KaKs_Calculator 3.0 is an updated toolkit that is capable of calculating selective pressure on both coding and non-coding sequences. Similar to the nonsynonymous/synonymous substitution rate ratio for coding sequences, selection on non-coding sequences can be quantified as the ratio of non-coding nucleotide substitution rate to synonymous substitution rate of adjacent coding sequences. As testified on empirical data, KaKs_Calculator 3.0 shows effectiveness to detect the strength and mode of selection operated on molecular sequences, accordingly demonstrating its great potential to achieve genome-wide scan of natural selection on diverse sequences and identification of potentially functional elements at a whole-genome scale. The package of KaKs_Calculator 3.0 is freely available for academic use only at https://ngdc.cncb.ac.cn/biocode/tools/BT000001.

LncRNAWiki 2.0: a knowledgebase of human long non-coding RNAs with enhanced curation model and database system

LncRNAWiki, a knowledgebase of human long non-coding RNAs (lncRNAs), has been rapidly expanded by incorporating more experimentally validated lncRNAs. Since it was built based on MediaWiki as its database system, it fails to manage data in a structured way and is ineffective to support systematic exploration of lncRNAs. Here we present LncRNAWiki 2.0 (https://ngdc.cncb.ac.cn/lncrnawiki), which is significantly improved with enhanced database system and curation model. In LncRNAWiki 2.0, all contents are organized in a structured manner powered by MySQL/Java and curators are able to submit/edit annotations based on the curation model that includes a wider range of annotation items. Moreover, it is equipped with popular online tools to help users identify lncRNAs with potentially important functions, and provides more user-friendly web interfaces to facilitate data curation, retrieval and visualization. Consequently, LncRNAWiki 2.0 incorporates a total of 2512 lncRNAs and 106 242 associations for disease, function, drug, interacting partner, molecular signature, experimental sample, CRISPR design, etc., thus providing a comprehensive and up-to-date resource of functionally annotated lncRNAs in human.

LncExpDB: an expression database of human long non-coding RNAs

Expression profiles of long non-coding RNAs (lncRNAs) across diverse biological conditions provide significant insights into their biological functions, interacting targets as well as transcriptional reliability. However, there lacks a comprehensive resource that systematically characterizes the expression landscape of human lncRNAs by integrating their expression profiles across a wide range of biological conditions. Here, we present LncExpDB (https://bigd.big.ac.cn/lncexpdb), an expression database of human lncRNAs that is devoted to providing comprehensive expression profiles of lncRNA genes, exploring their expression features and capacities, identifying featured genes with potentially important functions, and building interactions with protein-coding genes across various biological contexts/conditions. Based on comprehensive integration and stringent curation, LncExpDB currently houses expression profiles of 101 293 high-quality human lncRNA genes derived from 1977 samples of 337 biological conditions across nine biological contexts. Consequently, LncExpDB estimates lncRNA genes' expression reliability and capacities, identifies 25 191 featured genes, and further obtains 28 443 865 lncRNA-mRNA interactions. Moreover, user-friendly web interfaces enable interactive visualization of expression profiles across various conditions and easy exploration of featured lncRNAs and their interacting partners in specific contexts. Collectively, LncExpDB features comprehensive integration and curation of lncRNA expression profiles and thus will serve as a fundamental resource for functional studies on human lncRNAs.

Deciphering LncRNA-protein interactions using docking complexes

Deciphering RNA-protein interactions are important to study principal biological mechanisms including transcription and translation regulation, gene silencing, among others. Predicting RNA molecule interaction with the target protein could allow us to understand important cellular processes and design novel treatment therapies for various diseases. As non-coding RNAs do not have coding potential our knowledge about their functions is still limited. Therefore, RNA-binding proteins of non-coding RNAs regulating functions, viz. including cellular maturation, nuclear export and stability may play a very important role. Keeping in view of the need for refined methods to understand protein-RNA interactions, we have attempted a docking model to infer binding sites between lncRNA NONHSAT02007 and protein KIF13A for a rare disease phenotype that we are studying in our lab.Communicated by Ramaswamy H. Sarma.