Fig. 1: Complexity of RNA transcripts in the placenta. | Nature Communications

Fig. 1: Complexity of RNA transcripts in the placenta.

From: The RNA landscape of the human placenta in health and disease

Fig. 1

After sequencing and alignment to the human reference genome various RNA biotypes were identified in the placenta. The proportions mapped reads to various types of long (a) and small (b) RNAs are shown. In (a), definitions of RNA types were from the biotypes of Ensembl as follows: mRNA (protein-coding messenger RNA), lincRNA, pseudogenes (processed pseudogene, unprocessed pseudogene, transcribed unprocessed pseudogene, transcribed processed pseudogenes, or pseudogenes), Mt rRNA (mitochondrial ribosomal RNA), misc RNA (non-coding RNA that cannot be classified), others (other remaining biotypes such as antisense, snRNA, snoRNA, processed transcripts). In (b), ‘other exonic’ refers to reads mapped to any exonic regions except miRNA, piRNA, tRNA, and sncRNA and ‘remaining’ refers to mapped reads except miRNA, piRNA, tRNA, scRNA, and ‘other exonic’. sncRNAs include the following three types of RNAs: snoRNA (small nucleolar RNA), snRNA (small nuclear RNA), and sRNA (small RNA). RNAs are plotted as the percentage of quantified transcripts against the expression level (c) and the frequency of transcripts (density) against expression level (d). In (cd), the RPKM values have a pseudo-count (0.0001) added to allow plotting on a logarithmic scale. For the density plot (d), the probability density functions were estimated using kernel density estimation, where the area under the curve equals one. e The placental transcriptome is represented as the cumulative percentage of various RNA biotypes in the current study. f The total mRNAs pool is represented as the cumulative percentage of protein-coding transcripts in 50 tissues, including the placenta. In (ef), each point represents a transcript (with RPKM > 0.1) and the dashed line represents the TA50, i.e., the percentage of transcripts required to reach half of the total transcript abundance. To reach TA50 in (f), the following numbers of protein-coding RNAs are needed: 2 (blood), 7 (pancreas), 110 (liver), 135 (muscle – skeletal), 191 (esophagus – mucosa), 232 (minor salivary gland), and 271 (placenta). g For each tissue, the bar chart shows the contribution of the most abundant 1% of mRNAs to the total pool of protein-coding transcripts.

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