Fig. 3

Baseline characterization of sncRNA landscape of human sperm. (a) Relative abundance of sncRNA subtypes identified during the baseline characterization of the sncRNA landscape of sperm samples collected at the pre-intervention visit. tRFs were the most abundant sncRNAs (mentioned as tRNA by Genboree tool), followed by miRNAs and piRNAs. Small amounts of mitochondrial tRNAs and rRNAs were also present. The misc_RNA included additional small RNA subtypes and fragmented mRNA. ‘Other’ includes small RNAs identified in this study, but not yet annotated in available sncRNA databases. (b) Phenogram showing chromosome-based enrichment analysis of 401 baseline miRNAs. Lighter shade of green represents the miRNA expressed from unique genomic locations, and the darker shade represents the miRNAs that mapped to multiple sites in the genome. *: chromosomes with over-represented miRNA expression (Z-score ≥ 2). #: chromosomes with under-represented miRNA expression (Z-score ≤ -2). (c) Phenogram showing chromosome-based enrichment analysis of 143 baseline tRFs. Lighter shade of blue represents the tRF expressed from unique genomic locations, and the darker shade represents the tRF that mapped to multiple sites in the genome. *: chromosomes with over-represented tRF expression (Z-score ≥ 2). #: chromosomes with under-represented tRF expression (Z-score ≤ -2). (d) Phenogram showing chromosome-based enrichment analysis of 2290 baseline piRNAs. Lighter shade of pink represents the piRNA expressed from unique genomic locations, and the darker shade represents the piRNA that mapped to multiple sites in the genome. *: chromosomes with over-represented piRNA expression (Z-score ≥ 2). #: chromosomes with under-represented piRNA expression (Z-score ≤ -2) (e) Genomic annotation enrichment of the sperm baseline sncRNA. The genomic regions analysed comprised of genes, introns exons, CpG islands, 5’UTRs, 3’UTRs, 2 Kb downstream of transcription termination site (Down) and 2 Kb upstream of transcription start site (Up). To statistically evaluate the associations between the baseline sncRNA and the genomic region sets, permutation tests were used. The z-scores generated indicate the enrichment/depletion of the baseline sncRNA in a particular genomic region and the * indicates p-value of < 0.01.