H igh-risk human papillomaviruses (HPVs) are the causative agents of cervical and most other anogenital malignancies. Infection by HPVs occurs in the basal layers of stratified epithelia that become exposed due to microabrasions. Following entry, viral genomes are established as low-copy nuclear episomes at approximately 10 to 100 copies per cell (1, 2). In differentiated suprabasal layers, high levels of late gene expression are induced along with genome amplification and virion assembly (3). Two major viral promoters, designated early and late, control transcription during differentiation, but additional regulation also occurs through alternative splicing and other posttranscriptional mechanisms (1, 2, 4). One important mechanism of posttranscriptional control is mediated by small RNAs that are 22 nucleotides in size, referred to as microRNAs (miRNAs). miRNAs bind to partially complementary target sites in mRNA that are often located in the 3=UTR (untranslated regions) but can also be found in coding sequences and the 5=UTR (5). Binding by miRNAs to target sequences results in either the degradation of the target mRNAs or translational repression of the encoded protein (6). A single miRNA can repress the expression of over 100 genes, and a single gene can be repressed by multiple miRNAs. miRNAs often target multiple genes in a pathway and can act cooperatively with other miRNAs (7). Many miRNAs target developmental (8-10) and differentiation pathways (11)(12)(13)(14), as well as cell proliferation and transformation pathways (15-17). Herpesviruses and other small DNA viruses encode their own miRNAs (18); however, this is not the case for HPVs (19). Instead, HPVs modulate expression of host miRNAs to control various aspects of their viral life cycle (20, 21).Several miRNAs have been shown to be modulated by HPV proteins and to play key roles in the viral life cycle. miRNA 203 (miR-203) is a key regulator of epithelial differentiation and is downregulated in HPV-positive cells upon differentiation. This repression allows for the maintenance of high levels of p63, which is normally repressed by miR-203 in differentiating, infected suprabasal cells and is important for maintaining cells in an active state in the cell cycle (21). Additional studies demonstrated miR-218 to be downregulated by HPV E6, which correlates with increased levels of LAMB3, a translational target of this miRNA (22). A number of reports have documented changes in levels of cellular microRNAs in HPV-positive cells using microarray analyses, but only a limited number of studies has examined the significance of these changes in the viral life cycle (23-25).Since HPVs modulate the expression of cellular microRNAs to regulate aspects of their differentiation-dependent life cycle, we sought to identify cellular miRNAs that were altered by HPV proteins in a more physiological context than that reflected in monolayer cultures alone. For this analysis, we performed deep sequencing using organotypic raft cultures of a matched set of normal (viv) and H...