Structure and Function of Pre-mRNA 5′-End Capping Quality Control and 3′-End Processing

Abstract

Messenger RNA precursors (pre-mRNAs) are produced as the nascent transcripts of RNA polymerase II (Pol II) in eukaryotes and must undergo extensive maturational processing, including 5′-end capping, splicing, and 3′-end cleavage and polyadenylation. This review will summarize the structural and functional information reported over the past few years on the large machinery required for the 3′-end processing of most pre-mRNAs, as well as the distinct machinery for the 3′-end processing of replication-dependent histone pre-mRNAs, which have provided great insights into the proteins and their subcomplexes in these machineries. Structural and biochemical studies have also led to the identification of a new class of enzymes (the DXO family enzymes) with activity toward intermediates of the 5′-end capping pathway. Functional studies demonstrate that these enzymes are part of a novel quality surveillance mechanism for pre-mRNA 5′-end capping. Incompletely capped pre-mRNAs are produced in yeast and human cells, in contrast to the general belief in the field that capping always proceeds to completion, and incomplete capping leads to defects in splicing and 3′-end cleavage in human cells. The DXO family enzymes are required for the detection and degradation of these defective RNAs.

Invited Review: Decoding the pathophysiological mechanisms that underlieRNAdysregulation in neurodegenerative disorders: a review of the current state of the art

“…RNA‐polymerase II transcribes pre‐mRNAs from the genomic DNA [23]. Nascent mRNA transcripts are co‐transcriptionally capped at their 5′‐end [24]. The spliceosome removes introns and stitches together coding exons in a process called splicing [25].…”

Arsenic Induces Polyadenylation of Canonical Histone mRNA by Down-regulating Stem-Loop-binding Protein Gene Expression

“…After nuclear levels of SLBP have been depleted, the stem-loop structure is unbound and via an unknown mechanism is degraded, allowing the formation of the poly(A) tail. Normally, there are two proteins attached directly to the stem-loop structure, SLBP and 3ЈhExo, a 3Ј-5Ј exoribonuclease, both of which bind cooperatively (52,53). When one binds, the stem-loop conformation is changed, and there is an increased affinity for the other to bind.…”

“…When one binds, the stem-loop conformation is changed, and there is an increased affinity for the other to bind. There are large conformational differences between the stem-loop in the complex versus that in free solution (52,53). Future studies should investigate the possible role of 3ЈhExo in the degradation of the stem-loop structure prior to polyadenylation.…”

Intergenic RNA mainly derives from nascent transcripts of known genes

“…The modest CAGE signal for UoGs (detected for 48 out of 98 UoGs) suggest that they are not efficiently capped, in contrast to mRNAs initiating at annotated start sites of protein-coding genes ( Figure 3B). This indicates that the majority of intergenic TUs might be designated as substrates for exonucleases and prone to degradation [38,39] . Figure 3C (and S3A) shows prominent Pol II occupancies at the start sites of UoGs, albeit at lower levels than at the TSS' of associated genes.…”