Human endogenous unannotated lncRNA (ulncRNA) network

(beta version)

This ulncRNA network was generated from our recent study " Distinctive functional regime of endogenous lncRNAs in dark regions of human genome"

Anyou Wang, Rong Hai

Eukaryotic genomes gradually gain noncoding regions when advancing evolution and human genome actively transcribes >90% of its noncoding regions, suggesting their criticality in evolutionary human genome. Yet <1% of them have been functionally characterized, leaving most human genome in dark. Here we systematically decode endogenous lncRNAs located in unannotated regions of human genome and decipher a distinctive functional regime of lncRNAs hidden in massive RNAseq data. LncRNAs divergently distribute across chromosomes, independent on protein-coding regions. Their transcriptions barely initiate on promoters through polymerase II, but mostly on enhancers. Yet conventional enhancer activators(e.g. H3K4me1) only account for a small proportion of lncRNA activation, suggesting alternatively unknown mechanisms initiating the majority of lncRNAs. Meanwhile, lncRNA-self regulation also notably contributes lncRNA activation. LncRNAs trans-regulate broad bioprocesses, including transcription and RNA processing, cell cycle, respiration, response to stress, chromatin organization, post-translational modification, and development. Overall lncRNAs govern their owned regime distinctive from protein’s.

To search ulncRNAs and their regulatory network, please enter frequency score, absolute coef, max node number and genomic coordinate based on GRCh38.p10.V27.

Genomic coordinate format: chr:start-end. For example, chr3:36642256-36642555.For best network illustration, the max_length is limited to 10,000bp from start to end.

For clear illustration purposes, please also limit the max_node number (e.g. 50 to show top 50 most important nodes)

Network annotation: 1) Node color denotes gene category, lightGreen, blue, red respectively denotes protein_coding, annotated noncoding, uRNA. 2) Edge color represents regulation strength: red, pink, blue, lightSkyBlue, and lightGray respectively represents strong positive, middle positive, strong negative, middle negative and week regulation(positive or negative). 3)Edge thickness denotes confidence, thicker, more confident.

References