- Title
-
Computational prediction and experimental validation identify functionally conserved lncRNAs from zebrafish to human
- Authors
- Huang, W., Xiong, T., Zhao, Y., Heng, J., Han, G., Wang, P., Zhao, Z., Shi, M., Li, J., Wang, J., Wu, Y., Liu, F., Xi, J.J., Wang, Y., Zhang, Q.C.
- Source
- Full text @ Nat. Genet.
Fig. 1: Identification of coPARSE-lncRNA and their homologs across vertebrates.. A simplified workflow for lncHOME analysis of vertebrate lncRNAs. The phylogenetic tree shows the evolutionary descent of eight vertebrates, with the number of annotated lncRNAs in each species. The heatmap shows the Jaccard index of lncRNAs and protein-coding genes identified by sequence similarity across eight vertebrates (top). lncHOME defines coPARSE-lncRNAs by combining the alignment of homologous protein-coding genes and corresponding genomic anchors (bottom left) and analysis of similar motif distribution patterns (bottom right). |
Fig. 2: The coPARSE-lncRNAs and their predicted homologs share similar evolutionary and functional features., The distribution of average conservation scores (PhastCons) for coPARSE-lncRNA homolog pairs with sequence similarity (homolog_ss, |
Fig. 3: CRISPR–Cas12a screening and validation of coPARSE-lncRNA functions., The crRNA library was delivered into cells stably expressing Cas12a by lentiviral infection. Infected cells were collected by fluorescence-activated cell sorting (FACS; green fluorescence). For screening, cells were cultured for 15–45 d before genome DNA extraction and high-throughput sequencing analysis of the barcoded crRNA regions. Each DNA oligonucleotide sequence encodes two crRNAs (represented in red and blue), which will be transcribed and processed to generate individual mature crRNAs by Cas12a; these mature crRNAs will guide Cas12a to cut target genome regions. DR (19 nt). |
Fig. 4: Functional validation of coPARSE-lncRNAs.KO-rescue lentivirus plasmid construction. The plasmid contains three functional cassettes for U6 promoter-driven expression of crRNAs, Dox-inducible ectopic expression of homologs and GFP labeling for infected cells. |
Fig. 5: Identification and functional analysis of the RBP interactome for two coPARSE-lncRNAs., PCA of MS data for HeLa cell lysates pulled down for the indicated human coPARSE-lncRNAs and the predicted mouse and zebrafish homologs. The control samples are based on luciferase transcript segments. |