Mutations downstream of the polyadenylation site of a Xenopus beta-globin mRNA affect the position but not the efficiency of 3' processing

Effects of intron length on differential processing of mouse mu heavy-chain mRNA

Production of membrane-bound and secreted forms of mouse mu heavy-chain mRNA is controlled by differential processing in a developmental-stage-specific manner. We have analyzed the effects of various deletions and insertions in the C4-M1 intron of the mouse mu gene on the differential processing of mu mRNA. We show that there is a correlation between the length of the C4-M1 intron and the molar ratio of membrane-bound to secreted mu mRNAs, i.e., the shorter the C4-M1 intron, the higher the ratio. Since the poly(A) addition signal in the C4-M1 intron seems to be intact in the mutant mu genes, it is likely that the efficiency of splicing of the C4-M1 intron is affected by changes in the intron length.

Position-dependent sequence elements downstream of AAUAAA are required for efficient rabbit beta-globin mRNA 3' end formation

We previously demonstrated that a critical 35 bp region 3' of the AAUAAA is required for rabbit beta-globin mRNA 3' end formation. Recently, we synthesized and tested sequence elements derived from this region. Here, we report that a GU-rich and a U-rich sequence element are both required for efficient rabbit beta-globin mRNA 3' end formation. The efficiency of processing is restored to the wild-type level when the two elements are placed together and is greatly diminished when only one element is present. The level of 3' end formation is also decreased when the distance between the two elements is expanded. These results demonstrate that the GU-rich and U-rich elements function synergistically to restore efficient mRNA 3' end formation and that they most likely form a single requisite sequence 3' of the AAUAAA. Furthermore, we show that the effect of the GU-rich and U-rich sequence elements is position-dependent.

A novel endoribonuclease cleaves at a priming site of mouse mitochondrial DNA replication

Priming at the mouse mitochondrial origin of heavy-strand DNA replication is effected by transcripts from the light-strand promoter. The transition from RNA synthesis to DNA synthesis occurs at specific locations between 75 and 165 nucleotides downstream from the transcriptional initiation site. We have identified and partially purified an endonucleolytic activity that cleaves RNA accurately near one of these transition sites; this finding implies a role of specific RNA processing in DNA replication. Cleavage products possess 5'-phosphoryl and 3'-hydroxyl termini. Heterologous assays using mouse or human mitochondrial endoribonuclease with substrates containing the sequences of the human or mouse mitochondrial origins of heavy-strand DNA replication suggest that selection of the cleavage site is guided by sequences adjacent to the actual position of cleavage.

Sequence homologies among the three yolk polypeptide (Yp) genes in Drosophila melanogaster

To identify candidates for cis-acting sequences that regulate the sex-, stage-, and cell-specific expression of three coordinately regulated yolk polypeptide genes (Yp) in Drosophila melanogaster, we have mapped the Yp3 transcript, sequenced a 4278 bp DNA fragment containing the Yp3 gene, compared Yp3 region sequences to corresponding parts of Yp1 and Yp2, and compared the predicted amino acid sequence of YP3 to YP1 and YP2. The results showed that the Yps are largely homologous in translated regions, especially in the 3' half of the genes. Untranscribed flanking regions had little homology. A conserved inverted repeat (the H-box) has homology both to vertebrate steroid hormone receptor binding sites and to the ecdysone control region of Drosophila's hsp23. These results identify sequences to mutate in order to define elements that regulate Yp gene expression and govern YP polypeptide function.

Conserved 12-bp element downstream from mRNA polyadenylation sites

Sequences downstream from the AATAAA motif in a number of cellular and viral transcription units have been compared. A 12-bp conserved element was identified in approximately half of the cases studied, and a consensus sequence TTGANNNTTTTTT was derived from a comparison of 74 such sequences. This element is located immediately (5-20 bp) downstream from the poly(A)-addition site in every case where this is known, and it is suggested that this element may be involved in the cleavage/polyadenylation reaction. This proposal is consistent with published studies on deletion mutants of downstream regions.

Formation of the 3' end of U1 snRNA requires compatible snRNA promoter elements

U1 and U2 snRNAs are thought to be transcribed by RNA polymerase II. A conserved sequence known as the 3' box is located just downstream from the snRNA coding region and directs formation of the 3' end of pre-U1 and pre-U2 snRNA. We show here that a U1 or U2 promoter containing an intact snRNA enhancer is required for the U1 3' box to function efficiently. Promoters for genes encoding mRNAs cannot substitute for the snRNA promoter. Thus snRNAs must be transcribed by a specialized transcription complex that differs from transcription complexes synthesizing mRNAs. Moreover, in contrast to polyadenylated and nonpolyadenylated mRNAs, the 3' ends of pre-snRNAs must be generated either by termination of transcription, or by an RNA processing event intimately coupled to transcription.