In Epstein-Barr virus (EBV) latency III (LTIII) infection, BHRF1 encodes three microRNAs (miRNAs).Herein we report that Drosha cleavage of LTIII BHRF1 RNA and cis-acting splicing effects inhibit splicing and inhibit BHRF1 RNA and protein expression. Evidence shown here supports the view that Drosha cleavage to generate mature miRNAs and cis-acting sequences that prevent mRNA maturation are independent processes that prevent LTIII BHRF1 expression in lymphoblastoid cell lines.Eukaryotic RNA polymerase II (RNAP II) synthesizes premessenger RNAs (pre-mRNAs), which usually contain multiple exons and introns. Pre-mRNAs undergo processing steps, including 5Ј capping, 3Ј polyadenylation, and splicing to remove introns in the nucleus prior to transport to the cytoplasm for translation. These RNA-processing steps are coordinated and coupled to RNAP II transcription (37,40,45).MicroRNAs (miRNAs) are a class of approximately 22-nucleotide (nt) small noncoding RNAs which regulate protein expression in eukaryotes (5,9,20,30). Mature miRNA is processed largely from RNAP II 5Ј-capped and 3Ј-polyadenylated primary RNA (pri-miRNA) (6, 36). The pri-miRNA is cleaved in the nucleus by an RNase III enzyme, Drosha, and other interacting proteins, such as DGCR8 (23,35), to release an approximately 70-nt hairpin pre-miRNA, which is exported into the cytoplasm and processed by the RNase III enzyme Dicer complex (11,25) to produce an approximately 22-nt duplex (16). In addition to canonical pre-mRNA processing in the nucleus, Drosha cleavage occurs on pre-mRNAs that encode miRNA as well as protein. This noncanonical processing occurs on transcripts encoding miRNAs in introns or on the independently transcribed miRNA-coding transcripts (4,19,31,42). However, for RNA transcripts that encode miRNAs in exons, the correlation of Drosha cleavage with canonical premRNA processing steps, mRNA accumulation, and encoded protein expression is not clear.Epstein-Barr virus (EBV), a human gammaherpesvirus, establishes latency III (LTIII) infection in B lymphocytes (29), causing infected cell proliferation into lymphoblastoid cell lines (LCLs) in vitro or lymphoproliferative diseases in vivo (29,50). In LTIII infection, EBV expresses LTIII BHRF1 RNA that encodes three BHRF1 miRNAs (miR-BHRF1-1, miR-BHRF1-2, and miR-BHRF1-3) (7, 47). LTIII BHRF1 RNA is distinct from the EBV replication-associated 1.4-kb BHRF1 mRNA that is fully spliced and initiated by the virus replication-activated BHRF1 promoter (15). LTIII BHRF1 RNA has a long 5Ј-untranslated region (UTR) and is not spliced (3,44,48). Transcripts from the Cp or Wp promoter initiate alternatively spliced EBNA transcripts in LTIII infection and can be polyadenylated after the BHRF1 3Ј-UTR to produce LTIII BHRF1 RNAs (29). miR-BHRF1-1 is in the 5Ј-UTR of the LTIII BHRF1 mRNA and overlaps the TATA box of the EBV replication-activated BHRF1 promoter (15), whereas miR-BHRF1-2 and miR-BHRF1-3 are located in the 3Ј-UTR. While the BHRF1 miRNAs are produced in LTIII infection (57), BHRF1 protein has not been ...