Antisense RNA occurs naturally. They are small RNA molecule representing a unique type of DNA transcript that comprises 19–23 nucleotides. They pair to target a specific complementary region to control their biological function hence regulating gene expression. They therefore play a crucial role in regulating gene expression at multiple levels, such as at replication, transcription, and translation. In addition, artificial antisense RNAs can effectively regulate the express.
Analyzing thousands of small RNAseq samples, it was also possible to identify antisense RNA. Raw antisense RNA information derived from the expression analysis is now loosely termed as NepSeq-AS. These consisted of NepSeq-AS+, which are antisense also found in the human genome as complementary sequence and NepSeq-AS- which are pure antisense RNA which does not occured in human genome as complementary strand.
Fig. 1. Heatmap of raw expression value of a putative antisense to SLC30A7 (Solute Carrier Family 30 Member 7) with sequence “TTGTGGGTTATTGTTAAAA” was observed in 19 samples. The sequence is complementary with a mismatch on the intron of SLC30A7.
Zinc functions as a cofactor for numerous enzymes, nuclear factors, and hormones and as an intra- and intercellular signal ion. Members of the zinc transporter (ZNT)/SLC30 subfamily of the cation diffusion facilitator family, such as SLC30A7, permit cellular efflux of zinc (Seve et al., 2004).
The closest miRNA is MIMAT0011913, which is mi-RNA from Bos taurus.
Treatment of 4 ug/ml ActinomycinD on human hodgkin’s lymphoma cell line, increase the express of the antisense RNA. It is expressed in various types of cells including different cancer cells.
Raw NepSeq-AS data contains more putative antisense RNA, which is not yet analyzed. However if you are interested it further analysis can be done.
| Human Genomic Region | NepSeqVar | NepSeq-AS + | NepSeq-AS– |
|---|---|---|---|
| region | 388224 | 230309 | 39147 |
| gene | 291524 | 138656 | 23507 |
| exon | 212864 | 22095 | 3467 |
| mRNA | 133058 | 110508 | 18713 |
| match | 120015 | 66763 | 11552 |
| lnc_RNA | 75580 | 34784 | 5971 |
| primary_transcript | 65024 | 29 | 4 |
| miRNA | 64659 | 18 | 4 |
| rRNA | 63915 | 102 | 1 |
| transcript | 35105 | 27971 | 4831 |
| tRNA | 29539 | 3 | 0 |
| biological_region | 22195 | 8685 | 1473 |
| sequence_feature | 21447 | 4317 | 640 |
| enhancer | 19303 | 8076 | 1428 |
| pseudogene | 14947 | 2161 | 325 |
| CDS | 13980 | 7712 | 1270 |
| snoRNA | 11830 | 9 | 1 |
| snRNA | 2226 | 3 | 1 |
| silencer | 2093 | 330 | 27 |
| Y_RNA | 869 | 0 | 0 |
| centromere | 845 | 181 | 21 |
| transcriptional_cis_regulatory_region | 713 | 100 | 9 |
| cDNA_match | 534 | 188 | 37 |
| ncRNA | 441 | 1 | 0 |
| vault_RNA | 330 | 0 | 0 |
| scRNA | 257 | 0 | 0 |
| RNase_P_RNA | 191 | 0 | 0 |
| origin_of_replication | 157 | 4 | 0 |
| RNase_MRP_RNA | 144 | 0 | 0 |
| D_loop | 82 | 0 | 0 |
| antisense_RNA | 73 | 52 | 5 |
| promoter | 61 | 76 | 8 |
| non_allelic_homologous_recombination_region | 54 | 44 | 5 |
| sequence_alteration_artifact | 38 | 72 | 15 |
| meiotic_recombination_region | 26 | 30 | 0 |
| mitotic_recombination_region | 15 | 32 | 0 |
| DNaseI_hypersensitive_site | 13 | 23 | 3 |
| locus_control_region | 12 | 19 | 4 |
| telomerase_RNA | 10 | 0 | 0 |
| protein_binding_site | 3 | 6 | 2 |
| repeat_instability_region | 3 | 6 | 0 |
| tandem_repeat | 3 | 6 | 2 |
| V_gene_segment | 3 | 2 | 2 |
| CAGE_cluster | 2 | 1 | 0 |
| replication_regulatory_region | 2 | 0 | 0 |
| conserved_region | 1 | 4 | 0 |
| enhancer_blocking_element | 1 | 5 | 1 |
| microsatellite | 1 | 0 | 0 |
| mobile_genetic_element | 1 | 5 | 0 |
| nucleotide_motif | 1 | 1 | 0 |
| direct_repeat | 0 | 1 | 0 |
| imprinting_control_region | 0 | 1 | 0 |
| insulator | 0 | 3 | 1 |
| matrix_attachment_site | 0 | 1 | 0 |
| recombination_feature | 0 | 2 | 1 |
Table 1: Total number of NepSeq-AS variants observed in human genomic regions