13 N 6 -methyladenosine (m 6 A) is a ubiquitous RNA post-transcriptional modification found 14 in coding as well as non-coding RNAs. m 6 A has also been found in viral RNAs where it 15 is proposed to modulate host-pathogen interactions. Two m 6 A sites have been reported 16 in the HIV-1 Rev response element (RRE) stem IIB, one of which was shown to 17 enhance binding to the viral protein Rev and viral RNA export. However, because these 18 m 6 A sites have not been observed in other studies mapping m 6 A in HIV-1 RNA, their 19 significance remains to be firmly established. Here, using optical melting experiments, 20 NMR spectroscopy, and in vitro binding assays, we show that m 6 A minimally impacts 21 the stability, structure, and dynamics of RRE stem IIB as well as its binding affinity to 22 the Rev arginine-rich-motif (ARM). Our results indicate that if present in stem IIB, m 6 A 23 is unlikely to modulate RRE-Rev interaction by altering the conformational properties of 24 the RNA. Our results add to a growing view that the impact of m 6 A on RNA depends on 25 sequence context and Mg 2+ .
26 Introduction27 N 6 -methyladenosine (m 6 A) is an abundant reversible epitranscriptomic modification 28 found in coding and non-coding RNAs [1][2][3][4]. It plays important roles in RNA metabolism 29 [5][6][7][8] and is implicated in a growing number of cellular processes [9][10][11][12][13][14][15]. m 6 A has also 30 been found in viral RNAs where it is proposed to modulate host-pathogen interactions 31 [16][17][18][19].
32A number of studies have reported m 6 A in the HIV-1 RNA genome [18,20,21].33 One study examining HIV-1 infected human T cells [20] reported two m 6 A sites (A68 34 and A62, Fig 1) in the Rev response element (RRE) stem IIB. RRE is a ~350 nt cis-35 acting RNA element that is recognized by viral Rev protein to promote the export of 36 unspliced or partially spliced viral RNA to express the structural proteins required for 37 viral replication [22][23][24]. The two m 6 A sites were found in stem IIB (RREIIB), which is 38 the primary binding site for Rev [23,[25][26][27]. Knocking down the methyltransferase 39 complex (METTL3/METTL14) was shown to suppress Rev-RRE mediated RNA export 40 and viral replication, and point substitution mutation of one of the two highly conserved 41 adenines (A68) strongly suppressed viral replication (> 90%) [20]. It was proposed [20] 42 that the methyl group of m 6 A68 may interact with Rev protein to stabilize Rev-RRE 43 binding, and/or that m 6 A68 may alter the conformational properties of stem IIB to 44 facilitate Rev recognition. Another different study employing distinct cell lines and 45 mapping methods did not observe these m 6 A sites on RREIIB [21] while a third study 46 found m 6 A in RRE but did not identify the specific site [18].
47Here, we asked whether methylation of RREIIB with m 6 A leads to changes in its 48 conformational and Rev arginine rich motif (ARM) binding properties. We were driven 4 49 to test this hypothesis because our recent studies showed that t...