An unexpected ending: noncanonical 3' end processing mechanisms

Abstract

Proper 3' end processing of a nascent transcript is critical for the functionality of the mature RNA. Although it has long been thought that virtually all long RNA polymerase II transcripts terminate in a poly(A) tail that is generated by endonucleolytic cleavage followed by polyadenylation, noncanonical 3' end processing mechanisms have recently been identified at several gene loci. Unexpectedly, enzymes with well-characterized roles in other RNA processing events, such as tRNA biogenesis and pre-mRNA splicing, cleave these nascent transcripts to generate their mature 3' ends despite the presence of nearby polyadenylation signals. In fact, the presence of multiple potential 3' end cleavage sites is the norm at many human genes, and recent work suggests that the choice among sites is regulated during development and in response to cellular cues. It is, therefore, becoming increasing clear that the selection of a proper 3' end cleavage site represents an important step in the regulation of gene expression and that the mature 3' ends of RNA polymerase II transcripts can be generated via multiple mechanisms.

FIGURE 1.

MALAT1 is processed at its 3′ end by the tRNA processing machinery. (A) Although there is a canonical polyadenylation signal at the 3′ end of the mouse MALAT1 locus, MALAT1 is primarily processed via an upstream cleavage mechanism, which yields a mature ∼6.7-kb transcript with a short poly(A) tail-like moiety at its 3′ end (Wilusz et al. 2008). Endonucleolytic cleavage by RNase P simultaneously generates the mature 3′ end of MALAT1 and the 5′ end of mascRNA. The small RNA is subsequently cleaved by RNase Z and subjected to CCA addition to generate the mature 61-nt tRNA-like transcript. (B) The MALAT1 poly(A) tail-like moiety (shaded in blue) is highly conserved and encoded in the genome. Further upstream are two nearly perfectly conserved U-rich motifs (shaded in green and orange) separated by a conserved predicted stem–loop.

FIGURE 2.

Incomplete splicing generates the functional S. pombe TER1 transcript. A short intron, with canonical 5′ and 3′ splice sites (denoted 5′ ss and 3′ ss, respectively) and branch point sequences, is located upstream of a canonical polyadenylation signal at the 3′ end of the S. pombe TER1 locus. Although the two transesterification steps of splicing are normally tightly coupled, they somehow become uncoupled at the TER1 locus such that only the first step is normally completed. The 5′ exon is released and subsequently functions as the active RNA component of telomerase (Box et al. 2008). If both splicing steps are completed or if the mature 3′ end of TER1 is generated by cleavage/polyadenylation, the resulting TER1 transcripts are inactive and fail to support telomere maintenance.