Genome-wide analysis of lncRNA stability in human

Abstract

Transcript stability is associated with many biological processes, and the factors affecting mRNA stability have been extensively studied. However, little is known about the features related to human long noncoding RNA (lncRNA) stability. By inhibiting transcription and collecting samples in 10 time points, genome-wide RNA-seq studies was performed in human lung adenocarcinoma cells (A549) and RNA half-life datasets were constructed. The following observations were obtained. First, the half-life distributions of both lncRNAs and messanger RNAs (mRNAs) with one exon (lnc-human1 and m-human1) were significantly different from those of both lncRNAs and mRNAs with more than one exon (lnc-human2 and m-human2). Furthermore, some factors such as full-length transcript secondary structures played a contrary role in lnc-human1 and m-human2. Second, through the half-life comparisons of nucleus- and cytoplasm-specific and common lncRNAs and mRNAs, lncRNAs (mRNAs) in the nucleus were found to be less stable than those in the cytoplasm, which was derived from transcripts themselves rather than cellular location. Third, kmers-based protein-RNA or RNA-RNA interactions promoted lncRNA stability from lnc-human1 and decreased mRNA stability from m-human2 with high probability. Finally, through applying deep learning-based regression, a non-linear relationship was found to exist between the half-lives of lncRNAs (mRNAs) and related factors. The present study established lncRNA and mRNA half-life regulation networks in the A549 cell line and shed new light on the degradation behaviors of both lncRNAs and mRNAs.

Fig 1. Flowchat for the whole experiments and data analysis.

Fig 2. Half-life cumulative distributions for both lncRNAs and mRNAs (h).

Fig 3. Half-life cumulative distributions for lnc-human1, lnc-human2, m-human1, and m-human2 (h).

Fig 4. Half-life cumulative distributions for class sense, intergenic, intronic and antisense lncRNAs (h).

Fig 5. Spearman correlation between the half-lives of transcripts and their lengths, GC contents, or secondary structures (RNA2D) were displayed for lnc-human1, lnc-human2, lnc-human, m-human1, m-human2, and m-human, respectively.

For lncRNA, the full, 5UTR, and 3UTR stand for full lengths, 5’ UTR and 3’ UTR local fragments. For mRNAs, the cDNA, CDS, 5UTR and 3UTR stands for cDNAs, CDSs, 5’ UTR fragments, and 3’ UTR fragments, in which the 5UTR and 3UTR represent the regions with the most significant P value. The signs “×” and “na” stand for no statistical significance at P = 0.01 and missing value, respectively, and the sizes of round dots stand for the correlation coefficients.

Fig 6. Relationship between the number of lncRNAs sampled from lnc-human1 and the number of times with their P > 0.1 in 1000 simulations, in which P was calculated from the Spearman correlation analysis between the half-lives of lncRNAs and their lengths.

Fig 7

The Half-life cumulative distributions and the related Kolmogorov-Smirnor test for nucleus- and cytoplasm-specific lncRNAs and mRNAs (A), and nucleus and cytoplasm-common lncRNAs and mRNAs (B), in which the lnc-nuc., lnc-cyt., m-nuc., and m-cyt. stands for lncRNAs in the nucleus, lncRNAs in the cytoplasm, mRNAs in the nucleus, and mRNAs in the cytoplasm, respectively.

Fig 8. Spearman correlation coefficients between the half-lives of mRNAs and their codon contents are displayed, in which the red bars stand for the positive correlation of the 21 codons with their FDR values less than 1.00E-2 and the green bars stand for the negative correlation of the 16 codons with their FDR values less than 1.00E-2.

Fig 9. Half-life regulation networks for lnc-human1 and m-human2; red lines stand for positive correlation and black lines for negative correlation.

The thick, medium, and thin lines represent the strong (P < 1.0E−33), medium (p∈[1.0E−33, 1.0E−26]), and weak (p∈(1.0E−26, 1.0E−5)) correlation, respectively. The meaning of the words Half-life, Length (_length), GC (_GC), and RNA2D (_RNA2D) in the lncRNA (mRNA) regulation network are lncRNA (mRNA) half-lives, length, GC contents, and RNA secondary structures. PRRM and miRNAsites are the total number of protein recognition motifs and miRNA-binding sites, respectively, in lncRNAs or mRNAs.

Fig 10. Five categories of lncRNAs.