Nuclear precursor molecules of the two beta-globin mRNAs in Friend erythroleukemia cells

Nuclear non-polyadenylated RNAs containing the first intervening sequence of the major late premessenger RNA from adenovirus-2: characterization and distribution in ribonucleoproteins

The nuclear non-polyadenylated RNA from HeLa cells infected with adenovirus-2 was examined for the presence of molecules containing the first intervening sequence (IVS1) of the major late premessenger RNA. Four molecules with the approximate size of free IVS1 in sucrose gradients (1021 nucleotides) were separated by polyacrylamide gel electrophoresis and characterized by complementary methods: S1 nuclease mapping, susceptibility to debranching enzyme, RNAase-H-directed cleavage. The results indicate that the most abundant RNA form is the excised lariat IVS1. We also find linear IVS1 and a randomly nicked lariat, the latter probably being made during RNA isolation. The fourth RNA is a leader 1-IVS1 molecule. No truncated IVS1 which might indicate that IVS1 is excised by several cycle of cleavage-ligation was detected. A study of the distribution of the four RNAs in hnRNP shows that they are part of RNPs of about 70 S. However, each RNP has distinct sedimentation characteristics and sensitivity to salt dissociation. Together, the results suggest that the excised lariat IVS1 is released from the large late premRNP under the form of a 70 S RNP, where it is linearized.

Splicing of the E2A premessenger RNA of adenovirus serotype 2. Multiple pathways in spite of excision of the entire large intron

During the early period of infection, the 4.9 kb (kb = 10(3) bases) E2A premRNA of adenovirus serotype 2 is matured mainly into a 2.0 kb mRNA by excision of introns of 2233 and 626 nucleotides. In order to define all the possible steps of splicing occurring in vivo, we characterized splicing intermediates present after a limiting treatment of cells with cycloheximide. Three complementary methods of analysis were used: RNA transfer analysis, S1 nuclease mapping and complementary DNA-RNase assay. Our principal conclusions concerning the poly(A)+ species are as follows. The RNA intermediate family detected is more complex than expected, since two major RNA intermediates of 4.6 kb and 4.3 kb, two minor intermediates of 2.9 kb and 2.6 kb, and a 2.3 kb RNA, which represents a minor alternative mRNA form, are revealed. Despite its large size and the presence of multiple internal donor and acceptor signals, intron 1 is exclusively excised as a whole. Intron 2 is either primarily excised as a whole, removing the standard 626-nucleotide sequence, or a smaller sequence of 337 nucleotides is removed, generating the 2.3 kb alternative mRNA. Kinetics of the ligation reaction demonstrate that the minimal time for excision of intron 2 is no more than two minutes, indicating a high level of co-ordination of the multiple individual reactions occurring during excision of an intron. Besides the major pathway for E2A premRNA splicing, namely the excision first of intron 2, followed by the excision of intron 1 after a lag time of five minutes, a minor pathway (used with a frequency of 10%) can be detected where the order of intron excision was inverted. With the alternative variant of excision of intron 2, at least three different pathways are therefore used to mature the E2A premRNA. RNA intermediates resulting from the cleavage at the 5' end of introns and branching can be detected by S1 mapping experiments, but their low accumulative level (1% relatively to the initial premRNA) precluded their direction by RNA transfer experiments and their complete characterization.

RNA splice site selection: evidence for a 5' leads to 3' scanning model

Human G gamma-globin genes containing tandem duplications of the donor (5') or acceptor (3') RNA splice sites of the second intervening sequence were constructed in order to ascertain the directionality of RNA splice site selection. These genes were introduced into cultured monkey cells, and their transcripts were analyzed. Transcripts of these duplication variants were spliced only at the proximal copy of the duplicated splice sites. These data are consistent with a 5' leads to 3' model of splice site selection.

Induction of globin gene expression during erythroid cell differentiation

We can provide increasing insight, albeit still incomplete, into the changes in MELC that accompany globin gene expression induced by polar chemicals, such as DMSO, and other agents. These transformed, CFUe-like erythroid precursor cells exhibit in their uninduced state, a DNA methylation pattern and globin gene (formula; see text) chromatin configuration (DNase I sensitivity) that is compatible with actual or potential gene transcription. Such features may reflect alterations in chromatin configuration that have occurred at a stage prior to leukemic transformation, during the differentiation of earlier erythroid precursor cells and associated with the restriction in developmental potential characteristic of progression to the CFUe (or MELC) stage of erythropoiesis. Uninduced MELC display a low level of globin gene transcription, producing globin mRNA or mRNA precursors whose processing or stabilization is the target of action of hemin. The major increase in MELC globin gene transcription that is initiated by DMSO, HMBA, or butyric acid, is accompanied by, and perhaps preceded by, an increase in DNase I hypersensitivity in the regions 5' to the active globin genes. This suggests that reorganization of chromatin structure in the globin gene domains is associated with accelerated globin gene transcription and may be characteristic of a developmental transition during terminal differentiation in the erythroid cell lineage.

RNA encoded by the IR1-U2 region of Epstein-Barr virus DNA in latently infected, growth-transformed cells

The IR1-U2 region of Epstein-Barr virus DNA consists of multiple copies of a 3.1-kilobase (kb) repeat sequence, IR1, which maps to the left of a 3.3-kb unique region, U2. Although hybridizations of cytoplasmic polyadenylated RNA from latently infected cells to viral DNA indicate that the IR1-U2 region encodes a substantial fraction of the viral RNA in these cells, only a single low-abundance 3-kb cytoplasmic polyadenylated RNA has been identified on Northern blots. Further analysis of the cytoplasmic polyadenylated RNA encoded by the IR1-U2 region indicates that (i) the RNA is transcribed from left to right; (ii) there are only three copies of the 3-kb RNA per cell; and (iii) the RNA is spliced. The RNA hybridizes to possibly contiguous 0.56- and 1.3-kb U2 domains. These domains and part of IR1 hybridize to the 3-kb cytoplasmic RNA. DNA between IR1 and the 0.56-kb U2 domain does not hybridize to the 3-kb RNA. The CCAAT-34 nucleotide-TATAA sequence in IR1 may be part of the promotor for the 3-kb cytoplasmic polyadenylated RNA since (i) it enables left-to-right transcription of IR1 by a HeLa cell extract, and (ii) latently infected cells contain giant polyadenylated nuclear RNAs which differ in size by 3 kb, as would be expected if transcription initiates in any copy of IR1 and continues through the rightward remaining copies into U2.