Methylated blocked 5' terminal sequences of sea urchin embryo messenger RNA classes containing and lacking poly(A)

The formation of internal 6-methyladenine residues in eucaryotic messenger RNA

1. The formation of internal 6-methyladenine (m6A) residues in eucaryotic messenger RNA (mRNA) is a postsynthetic modification in which S-adenosyl-L-methionine (SAM) serves as the methyl donor. 2. Of the methyl groups incorporated into mature mRNA 30-50% occur in m6A residues. 3. Although most cellular and certain viral mRNAs contain at least one m6A residue, some transcripts such as those coding for histone and globin are completely lacking in this modification. 4. 6-Methyladenine residues have also been localized to heterogeneous nuclear RNA (HnRNA), and for the most part these residues are conserved during mRNA processing. 5. In all known cases, the m6A residues are also found in a strict consensus sequence, Gm6AC or Am6AC, within the transcript. 6. Although the biological significance of internal adenine methylation in eucaryotic mRNA remains unclear, a great deal of research has indicated that this modification may be required for mRNA transport to the cytoplasm, the selection of splice sites or other RNA processing reactions.

The role of cap methylation in the translational activation of stored maternal histone mRNA in sea urchin embryos

Cap methylation was examined in the early sea urchin embryo. Nucleotide analyses of 3H-methyl methionine-labeled RNA in two-cell embryos and in unfertilized eggs show that fertilization activates the cap methylation of about 10(7) RNA molecules. Greater than 37% of methyl-labeled RNAs following fertilization hybridize with so-called early histone genes H1, H4, and H2B, which encode a subpopulation of the maternal mRNA molecules. Activation of RNA cap methylation is inhibited by aphidicolin, but not by actinomycin D, suggesting that this process is temporally coordinated with DNA replication, but independent of RNA transcription. These results indicate that the translational activation of maternal early histone mRNA during fertilization is a consequence of cap methylation of mRNAs incompletely formed during oogenesis.

In vivo splicing products of the rabbit beta-globin pre-mRNA

Analysis of the rabbit beta-globin transcripts present in the steady-state RNA population of fetal liver reveals that there is no strict order in the removal of the two introns from the pre-mRNA, though IVS1 seems to be preferentially eliminated first. The population of RNA molecules contains, among other splicing products, two forms of full-length IVS2 (and presumably of IVS1), released from exon sequences. One of these forms is linear, while the other has a lariat structure (circle with tail), which results from looping of the intron sequence to itself and formation of a covalent bond between the 5' end and an internal IVS2 position at a distance of 31 bases from the 3' splice site. This branching point maps at the penultimate position of the heptamer TGCTAAC. Branched Y-forms of IVS2, presumably resulting from nicking of the lariat loop (in vivo or during purification) are also detected. Comparison of in vivo RNA with in vitro splicing products reveals corresponding lariat forms. However, the in vivo linear intron species are absent from the in vitro products, which, in contrast, contain more than one intron conformer.

Mapping of N6-methyladenosine residues in bovine prolactin mRNA

N6-Methyladenosine (m6A) residues, which are found internally in viral and cellular mRNA populations at the sequences Apm6ApC and Gpm6ApC, have been proposed to play a role in mRNA processing and transport. We have developed a sensitive approach to analyze the level and location of m6A in specific purified cellular mRNAs in an attempt to correlate m6A location with function. Polyadenylylated mRNA is hybridized to cDNA clones representing the full size mRNA under study or fragments of it, and the protected RNA is digested and labeled with polynucleotide kinase in vitro. After enrichment for m6A with anti-m6A antibody, the [32P]-pm6A is separated on TLC plates, and compared with the total amount of radiolabeled nucleotides. Using this combination of in vitro RNA labeling and antibody selection, we were able to detect m6A in purified stable mRNAs that cannot be readily labeled in cells with greater sensitivity than was possible by previous techniques. We applied this technique to bovine prolactin mRNA and showed that this mRNA contains m6A. Moreover, all of the m6A residues in this message are found within the 3' two-thirds of the molecule and are highly concentrated (61%) within a sequence of 108 nucleotides at the 3' noncoding region of the message. The nonrandom distribution of m6A in a specific cellular mRNA, as demonstrated for bovine prolactin, will have to be taken into account when designing a model for m6A function.

Chromatin assembled in the presence of cytosine arabinoside has a short nucleosome repeat

Incubation of MSB cells with cytosine arabinoside (1-beta-D-arabinofuranosylcytosine, ara-C) inhibits 3H-thymidine incorporation into nascent DNA while nucleosome core histone synthesis proceeds in molar stoichiometry at about 20% of control rates. The excess nascent histone is incorporated into chromatin and nucleosome cores are assembled normally on the small amount of DNA which is synthesized at submaximal levels of ara-C. This DNA becomes packaged into a shortened nucleosome repeat, however. These results indicate that the nucleosome core is a strongly conserved unit of chromatin replication and suggest that the stoichiometry of nascent histone to DNA may be one factor influencing the establishment of the nucleosome repeat length. It cannot be the only factor, however, since the closely packed nucleosomes made in the presence of ara-C begin to return to their normal spacing within six hours after reversal.

Effect of aminonucleoside on transcription, methylation, and maturation of ribosomal RNA in SV40-transformed human lung fibroblasts

The effects of puromycin aminonucleoside (AMS) have been studied in the nucleoli of SV40-transformed human lung fibroblasts with attention to the relationship between transcription, methylation, and maturation of ribosomal RNA (rRNA). Inhibition of the transcription of pre-rRNA became evident between 1 and 2 hr of exposure to AMS, and the degree of inhibition remained approximately constant throughout the remainder of the 18-hr period of study. Methylation of the ribose units of pre-rRNA was inhibited by AMS approximately as much as RNA transcription, but later, suggesting that the inhibition of methylation is a consequence of the lowered rate of RNA transcription. It was also noted that ribose methylation of nucleolar RNA occurs in the absence of concurrent RNA transcription, indicating that rRNA may be methylated post-transcriptionally. Exposure of the fibroblasts to fresh serum had the capacity to increase the rate of nucleolar RNA transcription if the fibroblasts were treated with AMS for periods of less than 2 hr but was ineffective thereafter, confirming that the inhibitory effect of AMS on pre-rRNA transcription is established in approximately 2 hr. On the other hand, processing of the primary transcript (45 S RNA) to the mature rRNA species (28 and 18 S) was inhibited more gradually, with a complete inhibition of rRNA maturation being noted after 18 hr of AMS treatment. These data are consistent with the view that the primary effect of AMS is on the rate of rRNA transcription, with a later effect on its maturation, while RNA methylation is reduced only because of the diminished availability of the RNA substrate.

The modified nucleotide constituents of human prostatic cancer cell (MA-160) poly(A)-containing RNA

Cytoplasmic poly A(+) RNA from human prostatic cancer cells grown in the presence of 32P was isolated by affinity chromatography on columns of oligo(dT)-cellulose. The RNA was digested with RNAase T2 and the products of digestion were fractionated by two-dimensional electrophoresis. The resulting autoradiograms revealed the presence of many different cap groups as well as two internal modified nucleotide components. 19 different type 1 and type 2 'cap' groups were identified. The internal modified nucleotides were N6-methyl adenosine and a 2'-O-methyl nucleotide possessing an unusual modified base.

Sea urchin histone mRNA termini are located in gene regions downstream from putative regulatory sequences

S1 nuclease mapping of the Psammechinus miliaris embryonic histone mRNAs locates the 5' termini in or adjacent to a short sequence homology (5'pyCATTCpu3') downstream from the putative RNA polymerase II regulatory sequence (5'TATAAATA3') or related sequences. The 3' termini map just after a sequence containing GC-rich hyphenated dyad symmetry, a feature of most known terminator sequences.

Ubiquitous and gene-specific regulatory 5' sequences in a sea urchin histone DNA clone coding for histone protein variants

The DNA sequences of the entire structural H4, H3, H2A and H2B genes and of their 5' flanking regions have been determined in the histone DNA clone h19 of the sea urchin Psammechinus miliaris. In clone h19 the polarity of transcription and the relative arrangement of the histone genes is identical to that in clone h22 of the same species. The histone proteins encoded by h19 DNA differ in their primary structure from those encoded by clone h22 and have been compared to histone protein sequences of other sea urchin species as well as other eukaryotes. A comparative analysis of the 5' flanking DNA sequences of the structural histone genes in both clones revealed four ubiquitous sequence motifs; a pentameric element GATCC, followed at short distance by the Hogness box GTATAAATAG, a conserved sequence PyCATTCPu, in or near which the 5' ends of the mRNAs map in h22 DNA and lastly a sequence A, containing the initiation codon. These sequences are also found, sometimes in modified version, in front of other eukaryotic genes transcribed by polymerase II. When prelude sequences of isocoding histone genes in clone h19 and h22 are compared areas of homology are seen to extend beyond the ubiquitous sequence motifs towards the divergent AT-rich spacer and terminate between approximately 140 and 240 nucleotides away from the structural gene. These prelude regions contain quite large conservative sequence blocks which are specific for each type of histone genes.

Identification of regulatory sequences in the prelude sequences of an H2A histone gene by the study of specific deletion mutants in vivo

Conserved DNA sequence elements of putative regulatory functions were deleted from the prelude region of a sea urchin H2A histone gene. For this, the wild-type H2A gene of the 6-kilobase histone DNA repeat unit was replaced by various mutant H2A genes by cloning. The effects of the manipulation on H2A mRNA synthesis were studied by injection of the mutant DNAs into centrifuged Xenopus oocytes. The unmanipulated H2B gene residing within the same repeat unit provided a suitable internal control for these studies. Deletion of the T-A-T-A-A-A-T-A motif, once thought to be the functional equivalent of the bacterial Pribnow box, did not abolish transcription of the gene; instead, a number of novel mRNA 5' termini were generated. We argue that the T-A-T-A-A-A-T-A motif is a specificity element, a selector of eukaryotic gene transcription. Deletion of the "cap-sequence," 5' pyrimidine-C-A-T-T-C-purine 3' and most of the mRNA leader sequence did not abolish transcription but created yet another mRNA 5' terminus. In contrast to these deletions, which are both down-mutations, deletion of H2A gene-specific conserved DNA sequences upstream from the T-A-T-A-A-A-T-A motif enhanced mRNA synthesis. A hypothesis for the function of these DNA sequences as eukaryotic promoter elements is discussed.

Leader sequences of Strongylocentrotus purpuratus histone mRNAs start at a unique heptanucleotide common to all five histone genes

We have determined the sequence of the untranslated leader nucleotides of all five histone mRNAs from Strongylocentrotus purpuratus by the dideoxy chain termination method. Total polysomal RNA from sea urchin embryos was used as a substrate for cDNA synthesis primed by specific DNA restriction fragments. Each of the primers was derived from the 5'-terminal part of the coding region for a different histone protein. The five histone mRNA leader sequences are different in length and primary structure. The 5' termini of all five histone mRNAs coincide with the unique heptanucleotide Py-Py-A-T-T-C-Pu in genomic DNA. This sequence, which defines the start of the individual histone mRNAs, is preceded by the A+T-rich octanucleotide identified in front of all eukaryotic structural genes where sequences have been determined to date.

Post-transcriptional modifications of oat coleoptile ribonucleic acids. 5'-Terminal capping and methylation of internal nucleosides in poly(A)-rich RNA

Evidence is presented for the occurrence of 5'-terminal capping structures in poly(A)-rich RNAs from oat coleoptile tissue. Similar to the cap structures in mRNA from other eukaryotic organisms, the 5' terminus of these oat coleoptile RNA molecules consists of 7-methylguanosine joined 5' to 5' with the adjacent (penultimate) nucleoside by means of three phosphate groups in two pyrophosphate linkages. The penultimate nucleoside contains primarily purine bases, but small amounts of pyrimidines (cytidine) are also detectable. Some monophosphorylated 5'-termini were also detected, however, they appear to occur as a result of RNA degradation. In addition to the 5 cap, oat RNA molecules are also post-transcriptionally modified with a low frequency of N6-methylations of internal adenosines.

Complex population of nonpolyadenylated messenger RNA in mouse brain

The complexity of nonadenylated mRNA [poly(A)-mRNA] has been determined by hybridization with single-copy DNA (scDNA) and cDNA. Our results show that poly(A)- and poly(A)+ mRNA are essentially nonoverlapping (nonhomologous) sequence populations of similar complexity. The sum of the complexities of poly(A)+ mRNA and poly(A)- mRNA is equal to that of total polysomal RNA or total mRNA, or the equivalent of approximately 1.7 x 10(5) different sequences 1.5 kb in length. Poly(A)- mRNA, isolated from polysomal RNA by benzoylated cellulose chromatography, hybridized with 3.6% of the scDNA, corresponding to a complexity of 7.8 x 10(4) different 1.5 kb sequences. The equivalent of only one adenosine tract of approximately 20 nucleotides per 100 poly(A)- mRNA molecules 1.5 kb in size was observed by hybridization with poly(U). cDNA was transcribed from poly(A)- mRNA using random oligonucleotides as primers. Only 1-2% of the single-copy fraction of this cDNA was hybridized using poly(A)+ mRNA as a driver. These results show that poly(A)- mRNA shares few sequences with poly(A)+ mRNA and thus constitutes a separate, complex class of messenger RNA. These measurements preclude the presence of a complex class of bimorphic mRNAs [that is, species present in both poly(A)+ and poly(A)- forms] in brain polysomes.

Metabolism of low molecular weight ribonucleic acids in early sea urchin embryos

There are three major low molecular weight RNAs (150-300 nucleotides) larger than 5S rRNA present in sea urchin embryos. Two of these are localized in the nucleus and one is localized in the cytoplasm. The nuclear species contain "capped" 5' termini, with a cap I structure. These RNAs are synthesized starting in late cleavage and continuing through pluteus. Relative to 5S RNA there is a 10-fold change in the rate of synthesis of these RNAs, due primarily to a decrease in their rate of transcription after blastula. The RNAs are metabolically stable and the nuclear RNA genes are reiterated 50--100 times in the genome. Significant amounts of these RNAs are present in sea urchin eggs, enough to supply the embryo during early cleavage, prior to initiation of their synthesis.

Histone messenger RNA from HeLa cells: evidence for modified 5' termini

The distribution of [3H]methyl radioactivity in cytoplasmic histone mRNA, isolated during the DNA synthetic (S) phase of the HeLa S3 cell cycle, has been investigated. Evidence is presented that approximately 30% of the radioactivity is in m7GpppXmpYp oligonucleotides, where Xm represents 2'-O-methylated adenosine and guanosine with a molar ratio of 4:1, respectively. The remainder of the radioactivity is present as m7GpppCmpYmpZp oligonucleotides, where Xm is again 2'-O-methylated adenosine and guanosine (4:1) and where ym represents 2'-O-methylated adenosine, guanosine, cytidine, and uridine with ratios of 2:1:1:1, respectively. While 48.6% of the [3H]methyl radioactivity was present as N6-methyladenosine in poly(adenylic acid)-terminated mRNA from S-phase cells, no evidence for N6-methyladenosine was found in histone mRNA. It thus appears that histone mRNA which lacks 3'-terminal poly(adenylic acid) sequences and functions on cytoplasmic polyribosomes during a limited protion of the cell cycle is capped but lacks internal-modified nucleosides.