Large-scale analysis of structural, sequence and thermodynamic characteristics of A-to-I RNA editing sites in human Alu repeats

Abstract

Background: Alu repeats in the human transcriptome undergo massive adenosine to inosine RNA editing. This process is selective, as editing efficiency varies greatly among different adenosines. Several studies have identified weak sequence motifs characterizing the editing sites, but these alone do not account for the large diversity observed.

Results: Here we build a dataset of 29,971 editing sites and use it to characterize editing preferences. We focus on structural aspects, studying the double-stranded RNA structure of the Alu repeats, and show the editing frequency of a given site to depend strongly on the micro-structure it resides in. Surprisingly, we find that interior loops, and especially the nucleotides at their edges, are more likely to be edited than helices. In addition, the sequence motifs characterizing editing sites vary with the micro-structure. Finally, we show that thermodynamic stability of the site is important for its editing.

Conclusions: Analysis of a large dataset of editing events reveals more information on sequence and structural motifs characterizing the A-to-I editing process.

Figure 1

Secondary structure substructures. Bold lines indicate those nucleotides formally included in a given substructure.

Figure 2

E¹ frequency vs. helix length.

Figure 3

E¹ frequency vs. interior-loop strand length.

Figure 4

E¹ frequency decreases with asymmetry. Editing frequency is presented for sites within interior-loop strands of lengths 1 (circles), 2 (squares), 3 (diamonds), 4 (triangles), as a function of the asymmetry of the loop. Asymmetry is defined as the difference between the length of the strand opposing the editing site and the edited strand length. Frequencies are normalized by the averaged editing frequency for sites having same strand length, regardless of opposite strand length.

Figure 5

E¹ frequency vs. cePos for helices.

Figure 6

E¹ frequency vs. cePos for interior loops.

Figure 7

Enrichment factors for upstream nucleotide in helices and interior loops.

Figure 8

Enrichment factors for downstream nucleotide in helices and interior loops.

Figure 9

Enrichment factors for joint upstream, downstream nucleotides in helices and interior loops.

Figure 10

E¹ frequency vs. structural entropy for ground state helix.

Figure 11

E¹ frequency vs. structural entropy for ground state interior-loop.