HPV16 and HPV18 Genome Structure, Expression, and Post-Transcriptional Regulation

Abstract

Human papillomaviruses (HPV) are a group of small non-enveloped DNA viruses whose infection causes benign tumors or cancers. HPV16 and HPV18, the two most common high-risk HPVs, are responsible for ~70% of all HPV-related cervical cancers and head and neck cancers. The expression of the HPV genome is highly dependent on cell differentiation and is strictly regulated at the transcriptional and post-transcriptional levels. Both HPV early and late transcripts differentially expressed in the infected cells are intron-containing bicistronic or polycistronic RNAs bearing more than one open reading frame (ORF), because of usage of alternative viral promoters and two alternative viral RNA polyadenylation signals. Papillomaviruses proficiently engage alternative RNA splicing to express individual ORFs from the bicistronic or polycistronic RNA transcripts. In this review, we discuss the genome structures and the updated transcription maps of HPV16 and HPV18, and the latest research advances in understanding RNA cis-elements, intron branch point sequences, and RNA-binding proteins in the regulation of viral RNA processing. Moreover, we briefly discuss the epigenetic modifications, including DNA methylation and possible APOBEC-mediated genome editing in HPV infections and carcinogenesis.

Keywords: RNA polyadenylation; RNA splicing; epigenetic modification; genome structure; papillomaviruses.

Figure 1

Papillomavirus genome structure, annotated ORFs, and conserved ACS in the origin of replication (Ori). (a) HPV16 genome and annotated ORFs. The non-structural proteins from the early region of the genome, including E1, E2, E1^E4, E5, E6, E7, and E8^E2, are shown in purple. The viral capsid proteins, L1 and L2, from the late region of the genome are shown in blue. URR (yellow), upstream regulatory region. P_E and P_L mark the early and late promoters, and pA_E and pA_L stand for the early and late polyadenylation sites. (b) Conservation of the mammalian ARS consensus sequence (ACS) [16] in the Ori of selected papillomavirus genomes. Shown in this panel are conserved bases with position weight matrix (sequence logo bits) of the 167 predicted ACS elements [16] in comparison with the viral Ori sequences from the selected viral URR tail (red)-head (black) regions. Adapted with permission from Ref. [16]. Copyright 2018 Springer Nature. ARS—autonomously replicating sequence.

Figure 2

Translation modes of HPV proteins from polycistronic viral transcripts. (a) Diagram of a polycistronic mRNA harboring multiple ORFs (ORF A–D), of which only the first ORF A is translated by eukaryotic ribosomes (in grey) into a functional protein. (b–d) Strategies utilized by papillomaviruses to express viral proteins from polycistronic transcripts by possible ribosome leaking scanning (b), alternative splicing (c), or usage of alternative frames created by RNA splicing (d).

Figure 3

The transcription map of HPV16 updated from Ref. [44]. The HPV16 genome in a linear form diagramed as a bracket line consists of the upstream regulatory region (URR, dark grey box), early region (white box) and late region (light grey box) with nucleotide positions of viral promoters (P), early (pA_E) and late (pA_L) polyadenylation signals, and polyadenylation cleavage sites (Cs). The diagram is not to scale. The predicted viral ORFs with nucleotide positions in the viral genome and the corresponding frame used for their translation are shown above. Below the linearized genome are the mapped viral transcripts with identified exons (thick lines) and introns (thin lines). The numbers represent the nucleotide positions of splicing donor sites (5′ splice site) and splicing acceptor sites (3′ splice site). On the right are coding potentials for each transcript, with the most abundant (>60%) transcripts labeled in red color, and less abundant, but detectable ones (<5%), being underlined.

Figure 4

The transcription map of HPV18 updated from Ref. [56]. See the HPV16 transcription map for other description details.

Figure 5

Regulation of E6 and E7 translation from HPV16 and HPV18 polycistronic E6E7 transcripts by alternative RNA splicing. (a) Diagrams showing E6 translation from the unspliced E6E7 RNA and (b) E7 translation from the spliced E6*I RNA by translation re-initiation.

Figure 6

Regulation of HPV18 and HPV16 RNA splicing and polyadenylation by RNA cis-elements and host RBPs. (a) Diagrams (not to scale) showing the exonic (colored boxes) and intronic (thick lines) regions of HPV18 and HPV16 transcripts. The major alternative splicing events are depicted by dashed lines with the nucleotide positions of splicing sites shown below. Exonic splicing enhancers (ESE), exonic splicing silencers (ESS), intronic splicing enhancers (ISE), and negative regulatory elements (NRE) are shown in green for positive (+) and in red (−) for negative regulation. The black arrows show the host RBPs binding to individual cis-elements. The mapped branch site A in the intron branch point sequence is indicated by its genome position in the viral early transcript. (b) Depiction of HPV-infected epithelium with productive HPV infection (on the left) or with HPV-transformed cells invasive of the basement membrane (on the right). HPV-infected cells expressing viral early proteins are shown in red and the cells expressing HPV late proteins in light green. The changes in the expression of viral proteins and host splicing factors (SR proteins) are on the right of each diagram.