The chromosomal positions of selected lncRNAs are depicted. lncRNAs discussed in the text are underlined. The corresponding genomic coordinates for all lncRNAs are provided in the supplementary file …
(A) lncRNA names and sizes are shown in the middle section (blue columns). The distance, size and transcriptional orientation of the neighboring genes, in a 200 kb window centered on lncRNA’s TSS …
LncRNAs are color coded as blue (Intergenic), brown (Overlapping) and green (Divergent/Promoter associated) (see Figure 1—figure supplement 1B). For each lncRNA and its upstream (top) and downstream …
Nine guide RNAs (the first six plus three additional gRNAs around the Transcriptional Termination Site, TTS) were used to generate the gene deletions. Relative positions of genotyping primers are …
Visual representation of the expression level changes for each lncRNA and its neighboring genes in homozygous deletion mutants. Three biological replicates for homozygous mutant and wild-type …
(A) The positions of TSS-deletion allele and gene deletion allele are marked by dashed red lines. Green box represents the conserved element in cyrano which is complementary to miR-7. Solid red …
(A) Position of the TSS-deletion allele in gas5 is marked by dashed red line. Arrows flanking black dotted lines mark the primer binding sites for 5’-qPCR and 3’-qPCR products. (B) Representative in …
(A) The relative position of lnc-setd1ba and the protein-coding gene setd1ba. The gene deletion region is marked by dashed red line. Arrows flanking black dotted line mark the primer-binding sites …
(A) The position of untranslated regions (brown), coding region (green), putative Dorsal Localization Element- DLE (blue) and the gene deletion (red dashed line) in the squint genomic locus. Arrows …
(A) Schematic representation of injected mRNAs. Cap-analog is indicated by in blue circles at the beginning of each mRNA. squint non-protein coding mRNA was generated by adding 8 Adenine-nucleotides …
(A) The red dashed lines depict the respective positions of the lnc-phox2bb TSS and gene deletion. Arrows flanking black dotted line mark the primer binding sites for qRT-PCR product. (B) Homozygous …
lncRNAs were named using the last four digits of their corresponding ENSEMBL Transcript ID or their chromosome number if no transcript ID was available (e.g. lnc-1200 is located on chromosome 12). …
lncRNA mutant, deletion type | Ribosome Profiling, class | lncRNA transcript ID | Deletion size | Percent reduction | Embryonic phenotype | Viability and fertility | Neighboring genes | Selection criteria | |
---|---|---|---|---|---|---|---|---|---|
Up 100 Kb | Down 100 Kb | ||||||||
cyranoa171, TSS-del. | Trailerlike | ENSDART00000139872 | 326 bp | 98% | No | Yes | tmem39b | oip5 | Syntenic and sequence conservation, Reported phenotype |
cyranoa172, gene del. | Trailerlike | ENSDART00000139872 | 4374 bp | 94% | No | Yes | tmem39b | oip5 | Syntenic and sequence conservation, Reported phenotype |
gas5a173, TSS-del. | Leaderlike | ENSDART00000156268 | 296 bp | 100% | No | Yes | osbpl9 | tor3a | Syntenic conservation, well studied lncRNA, host of several snoRNA |
lnc-setd1baa174, gene del. | Leaderlike | ENSDART00000141500 | 3137 bp | 100% | No | Yes | setd1ba | rhoF | Syntenic and sequence conservation, Proximity to developmental regulatory genes |
squinta175, gene del. | Coding | ENSDART0 0000079692 | 1032 bp | 95% | No | Yes | htr1ab | eif4ebp1 | Evolutionary conservation, Reported phenotype, putative cncRNA |
lnc-phox2bba176, TSS-del. | Leaderlike | ENSDART00000158002 | 652 bp | 99% | No | Yes | smntl1 | phox2bb | Syntenic conservation |
lnc-phox2bba177, gene del. | Leaderlike | ENSDART00000158002 | 9361 bp | 87% | Yes | No | smntl1 | phox2bb | Syntenic conservation |
lnc-3852a178, TSS-del. | Leaderlike | ENSDART00000153852 | 447 bp | 100% | No | Yes | lima1a | hoxc1a | Maternal expression, Proximity to developmental regulatory genes |
lnc-1562a179, TSS-del. | Leaderlike | ENSDART00000131562 | 409 bp | 90% | No | Yes | * | fgf10a | Maternal expression, Proximity to developmental regulatory genes |
lnc-3982a180, TSS-del. | Leaderlike | ENSDART00000153982 | 352 bp | 97% | No | Yes | * | bmp2b | Maternal expression, Proximity to developmental regulatory genes |
lnc-6269a181, TSS-del. | Leaderlike | ENSDART00000156269 | 535 bp | 99% | No | Yes | tbx1 | * | Maternal expression, Proximity to developmental regulatory genes |
lnc-2154a182, TSS-del. | Trailerlike | ENSDART00000132154 | 546 bp | 100% | No | Yes | rpz | nr2f5 | Maternal expression, Proximity to developmental regulatory genes |
lnc-1200a183, TSS-del. | Leaderlike | Chr12:1708389-1925779:1 | 590 bp | 95% | No | Yes | * | zip11 | Maternal expression, Longest selected lncRNA |
lnc-1200a184, gene del. | Leaderlike | Chr12:1708389-1925779:1 | 203.8 kb | 84% | No | Yes | * | zip11 | Maternal expression, Longest selected lncRNA |
lnc-2646a185, TSS-del. | Leaderlike | ENSDART00 000152646 | 240 bp | 97% | No | Yes | * | dkk1b | Proximity to developmental regulatory genes |
lnc-4468a186, TSS-del. | Leaderlike | ENSDART00000154468 | 306 bp | 100% | No | Yes | fam169ab | lhx5 | Proximity to developmental regulatory genes, Low expression level |
lnc-0600a187, TSS-del. | Trailerlike | Chr6:59414652-59443141:1 | 244 bp | 95% | No | Yes | * | gli1 | Proximity to developmental regulatory genes, Low expression level |
lnc-0900a188, TSS-del. | Leaderlike | Chr9:6684669-6691350:1 | 377 bp | 83% | No | Yes | pou3f3a | * | Syntenic conservation, Low expression level |
lnc-8507a189, mTSS-del. | Leaderlike | ENSDART00000158507 | 323 bp | 81% | No | Yes | npvf | hoxa1a | Proximity to Hox genes, Maternal and Zygotic promoters |
lnc-8507a190, mzTSS-del. | Leaderlike | ENSDART00000158507 | 9773 bp | 95% | No | Yes | npvf | hoxa1a | Proximity to Hox genes, Maternal and Zygotic promoters |
lnc-7620a191, TSS-del. | Trailerlike | ENSDART00000137620 | 668 bp | 99% | No | Yes | gal3st1b | srsf9 | Syntenic and sequence conservation, Implicated in adult fish and mouse behavior. Bitetti, A., et al. (2018) |
lnc-1300a192, TSS-del. | Leaderlike | Chr13:4535992-4538275:1 | 367 bp | 92% | No | Yes | c1d | pla2g12b | Syntenic and sequence conservation, High expression level |
lnc-7118a193, TSS-del. | Trailerlike | ENSDART00000157118 | 438 bp | 82% | No | Yes | mrps9 | pou3f3b | Syntenic conservation |
lnc-5888a194, TSS-del. | Leaderlike | ENSDART00000155888 | 606 bp | 96% | No | Yes | glrx5 | zgc:100997 | Syntenic conservation, scaRNA13 host gene, shortest selected lncRNA |
lnc-6913a195, TSS-del. | Leaderlike | ENSDART00000156913 | 333 bp | 72% | No | Yes | usp20 | ptges | Proximity to developmental regulatory genes |
lnc-6913a196, gene del. | Leaderlike | ENSDART00000156913 | 5568 bp | 93% | No | Yes | usp20 | ptges | Proximity to developmental regulatory genes |
lnc-1666a197, TSS-del. | Leaderlike | ENSDART00000141666 | 544 bp | 96% | No | Yes | ptf1a | * | Proximity to developmental regulatory genes, Restricted late expression |
lnc-6490a198, TSS-del. | Leaderlike | ENSDART00000146490 | 607 bp | 99% | No | Yes | nr2f2 | * | Syntenic conservation, Restricted late expression |
lnc-6490a199, gene del. | Leaderlike | ENSDART00000146490 | 8378 bp | 100% | No | Yes | nr2f2 | * | Syntenic conservation, Restricted late expression |
lnc-0464a200, TSS-del. | Trailerlike | ENSDART00000140464 | 597 bp | 96% | No | Yes | nr2f1a | * | Restricted late expression pattern |
lnc-4149a201, TSS-del. | Leaderlike | ENSDART00000154149 | 491 bp | 98% | No | Yes | bhlhe22 | * | Proximity to developmental regulatory genes |
lnc-4149a202, gene del. | Leaderlike | ENSDART00000154149 | 35.11 kb | 100% | No | Yes | bhlhe22 | * | Proximity to developmental regulatory genes |
This compressed folder contains three Excel files for the sequences of gRNAs, genotyping and qRT-PCR primers (for lncRNAs and their neighboring genes) and also the annotated sequence files (.ape) for each lncRNA and their deleted segments.
This genome-browser-compatible file is in the bed formant, containing the coordinates for all the lncRNAs investigated in this manuscript based on the GRCz11 (GCA_000002035.4).