Autocatalytic RNA cleavage in the human β-globin pre-mRNA promotes transcription termination

Abstract

New evidence indicates that termination of transcription is an important regulatory step, closely related to transcriptional interference and even transcriptional initiation. However, how this occurs is poorly understood. Recently, in vivo analysis of transcriptional termination for the human beta-globin gene revealed a new phenomenon--co-transcriptional cleavage (CoTC). This primary cleavage event within beta-globin pre-messenger RNA, downstream of the poly(A) site, is critical for efficient transcriptional termination by RNA polymerase II. Here we show that the CoTC process in the human beta-globin gene involves an RNA self-cleaving activity. We characterize the autocatalytic core of the CoTC ribozyme and show its functional role in efficient termination in vivo. The identified core CoTC is highly conserved in the 3' flanking regions of other primate beta-globin genes. Functionally, it resembles the 3' processive, self-cleaving ribozymes described for the protein-encoding genes from the myxomycetes Didymium iridis and Physarum polycephalum, indicating evolutionary conservation of this molecular process. We predict that regulated autocatalytic cleavage elements within pre-mRNAs may be a general phenomenon and that functionally it may provide the entry point for exonucleases involved in mRNA maturation, turnover and, in particular, transcriptional termination.

Compilation of mRNA Polyadenylation Signals in Arabidopsis Revealed a New Signal Element and Potential Secondary Structures

“…However, the validity of the mFold program has been proven, e.g. in a recent publication by Teixeira et al (2004). The stem observed in both group I and group II is produced by A-and U-rich residues.…”

Transcription termination by nuclear RNA polymerases

“…Indeed, the b-globin gene contains a specific CoTC element, ;1 kb downstream from the poly(A) site, that is required for termination Proudfoot 1999, 2001). The CoTC sequence undergoes a rapid cleavage event that exposes a free 59 monophosphorylated downstream RNA that serves as a substrate for Xrn2 (Teixeira et al 2004;West et al 2004). It is important to note that CoTC appears to be a specific termination signal for some globin genes (it is also found in the e-globin 39 flanking region) (Dye and Proudfoot 2001) that has not yet been identified in other genes.…”

Ribozymes, riboswitches and beyond: regulation of gene expression without proteins

“…Other self-cleaving ribozymes, such as the CPEB3 and CoTC ribozymes, which seem to be involved in splicing 13 and transcription 14 , respectively, might have a direct impact on gene expression. These ribozymes have been identified in only some mammalian species, and further study is needed to determine whether similar RNA elements exist, providing a more generally applicable mechanism for their function.…”

“…1f) has been identified downstream of the protein-coding sequences and poly(A) sites of primate β-globin genes, suggesting that CoTC has a role in transcription termination and RNA processing 14 . Indeed, CoTC integrity was found to be crucial for efficient termination of transcription of these genes by RNA polymerase II 15 , and CoTC RNA can be targeted by several proteins that have been implicated in RNA processing and degradation (A. Akoulitchev, personal communication).…”

“…Nevertheless, they have different catalytic pockets and use different cleavage mechanisms, which are still being debated 16 . The CoTC ribozyme catalyses a different reaction 14 , producing 3′-hydroxyl (3′-OH) and 5′-phosphate (5′-P) ends, and apparently carries out autolytic cleavage in the same way as RNase P.…”