Table 2.
Differentially regulated lncRNAs in the ventral midbrain of cocaine abusers
| lncRNA | ENSEMBL gene ID | Gene location | Average fold difference | Relative abundance | Polyadenylation consensus sequence and conservation | Splice site consensus sequence and conservation | Detected brain expression | Remarks |
|---|---|---|---|---|---|---|---|---|
| Up‐regulated lncRNAs | ||||||||
| RP11‐309G3.3 | ENSG00000272198 | chr1q25.3 | 2.35 | 16.2 | No | No | B, S | Intergenic. Adjacent to IER5 (same strand) |
| RP1‐212P9.2 | ENSG00000226852 | chr1p35.3 | 2.03 | 74.1 | Yes: conserved | Yes: conserved | B, F, S | Intergenic. Adjacent to OPRD1 (same strand) |
| LOC101929176 | ENSG00000250579 | chr5p15.32 | 1.77 | 30.1 | Yes: primate | Yes: mixed | S | Intergenic. Adjacent to ADAMTS16 (same strand) |
| LOC100507534 | ENSG00000261325 | chr16q12.1 | 1.67 | 117.2 | Yes: primate | Yes: conserved | B, F, S | Intergenic. Within a cluster of lncRNAs (both strands) |
| RP11‐109G23.3 | ENSG00000260278 | chr4q21.21 | 1.61 | 8.9 | Yes: conserved | Yes: mixed | S | Intergenic. Adjacent to BMP2K (opposite strand) |
| HOTAIRM1 | ENSG00000233429 | chr7p15.2 | 1.53 | 293.5 | Yes: conserved | Yes: conserved | F, S | Antisense. Regulates transcription of HOXA1 and HOXA2 genes |
| RPPH1 | ENSG00000259001 | chr14q11.2 | 1.49 | 22.4 | No | No | B, F, S | Antisense. Component of RNAse P involved in tRNA maturation |
| TRAF3IP2‐AS1 | ENSG00000231889 | chr6q21 | 1.45 | 477.4 | Yes: conserved | Yes: conserved | A, B, F, S | Antisense to TRAF3IP2 |
| RP11‐552F3.9 | ENSG00000267801 | chr17q25.1 | 1.40 | 5.9 | No | No | F, S | Antisense to TRIM47 |
| RP11‐49I11.1 | ENSG00000260552 | chr18q12.2 | 1.37 | 4.4 | Yes: primate | Yes: conserved | F, S | Antisense to MOCOS |
| RP4‐809F18.2 | ENSG00000257061 | chr12q24.32 | 1.37 | 8.0 | No | Yes: mixed | B, S | Intergenic. Adjacent to LINC RP4‐809F18.1 (same strand) |
| AC083843.1 | ENSG00000259820 | chr8q24.22 | 1.33 | 60.4 | Yes: conserved | No | B, S | Intergenic. Adjacent to MIR30B and MIR30D (same strand) |
| WDR11‐AS1 | ENSG00000227165 | chr10q26.12 | 1.33 | 36.9 | No | Yes: conserved | B, F, S | Antisense to WDR11 |
| RP11‐521016.2 | ENSG00000260163 | chr2q14.3 | 1.31 | 56.9 | Yes: primate | Yes: mixed | B, F, S | Antisense to LINC RP11‐521016.1 |
| Down‐regulated lncRNAs | ||||||||
| RNF219‐AS1 | ENSG00000234377 | chr13q22.3 | −1.31 | 87.8 | Yes: conserved | Yes: mixed | B, F, S | Antisense to RNF219 |
| RP11‐553L6.5 | ENSG00000259976 | chr3q13.31 | −1.31 | 3471.8 | Yes: conserved | No | B | Sense overlapping with ZBTB20 |
| PRKCQ‐AS1 | ENSG00000237943 | chr10p14 | −1.33 | 149.2 | Yes: primate | Yes: conserved | B, F, S | Antisense to (shared 5′ region with) PRKCQ |
| RP11‐388C12.1 | ENSG00000263063 | chr17q25.3 | −1.33 | 34.4 | No | No | S | Intergenic. Adjacent to FN3KRP (opposite strand) |
| STX18‐AS1 | ENSG00000247708 | chr4p16.2 | −1.35 | 5.1 | Yes: conserved | No | B, F, S | Antisense to STX18 |
| LINC00540 | NA | chr13q12.11 | −1.36 | 10.1 | No | Yes: conserved | S | Intergenic. Nearest neighbors are clusters of lncRNAs |
| LOC100507140 | ENSG00000237166 | chr2q33.1 | −1.37 | 196.1 | No | Yes: conserved | B, F, S | Antisense to AOX2P |
| LINC00403 | ENSG00000224243 | chr13q34 | −1.39 | 865.9 | No | Yes: mixed | A, B, F, S | Sense overlapping with SOX1, SNORD441, and RP11‐450H6.3 |
| RP11‐539L10.3 | ENSG00000251580 | chr4p16.1 | −1.42 | 985.1 | Yes: conserved | Yes: primate | B, F, S | Antisense to lncRNAs LOC93622 and AC093323.3 |
| AP001505.9 | ENSG00000261706 | chr21q22.3 | −1.43 | 47.3 | Yes: conserved | No | F, S | Intergenic. Adjacent to lncRNAs LINC00163 and LINC00162 |
| LOC400548 | ENSG00000278214 | chr16q24.1 | −1.44 | 17.0 | No | Yes: mixed | B, F, S | Intergenic. Nearest genes FAM92B and CTC‐786C10.1 |
| LOC643763 | ENSG00000274956 | chr8q12.3 | −1.46 | 1569.0 | Yes: conserved | No | A, B, F | Sense intronic within single exon of NKAIN3 |
| LINC01314 | ENSG00000259417 | chr15q25.1 | −1.49 | 543.8 | Yes: primate | Yes: conserved | A, B, F, S | Intergenic. Adjacent to LINC00927 and FAH (opposite strand) |
| RP11‐23P13.6 | ENSG00000174171 | chr15q15.1 | −1.50 | 6.1 | No | No | B, F, S | Antisense to SPTBN5 |
| AFAP1‐AS1 | ENSG00000272620 | chr4p16.1 | −1.62 | 7.1 | Yes: conserved | Yes: mixed | A, B, F, S | Antisense AFAP1 |
| LINC00645 | ENSG00000258548 | chr14q12 | −1.69 | 87.1 | Yes: conserved | Yes: mixed | S | Antisense intronic to lncRNA BC148262 |
| LINC00162 | ENSG00000224930 | chr21q22.3 | −1.74 | 65.1 | No | Yes: mixed | A, B, F, S | Intergenic. Adjacent to LINC000163, and lncRNA AP001505.9 |
| LINC01010 | ENSG00000236700 | chr6q23.2 | −1.99 | 36.9 | Yes: conserved | Yes: mixed | B, F, S | Antisense to lncRNAs LH15.4OC101928231 and RP11‐557H15.3 |
Relative abundance is overall fluorescence signal/background. In addition to expression data from UCSC Genome Browser, Dec 2009 hg19 chr assembly, transcript detection: A, in substantia nigra by Allen Brain Atlas microarray (Hawrylycz et al. 2012); B, in Burge brain RNA‐Seq (Wang et al. 2008); S, in Sestan brain microarray (Johnson et al., 2009); F in substantia nigra by FANTOM5 CAGE database (Andersson et al. 2014). A gene feature found in primates as well as at least one non‐primate species is denoted as conserved. Primate‐specific gene features, and mixtures of conserved and primate‐specific features, are also indicated.