Untranscribed Region Research Articles

Sites hypersensitive to, and protected from, nuclease digestion in the regulatory region of wild-type and mutant polyoma chromatin.

It has been shown that the untranscribed regulatory region of polyoma virus (Py) is hypersensitive (Hs) to DNase I treatment, and that this hypersensitivity is located in two areas which correspond to the A and B domains of the enhancer. We mapped the DNase I hypersensitive sites in the Py regulatory region of wild-type (PyA2) and of mutants, selected in neuroblastoma cells (PyNB), which are characterized by an extensive duplication involving the A domain, with or without deletion of the B domain. The experiments were performed in both a permissive host (3T6 mouse fibroblasts) and in a restrictive host (41A3 mouse neuroblasts). No significant differences were observed between the two hosts. Our results show that four sites, in addition to the ones already described, can be identified in the wild-type A2 strain. These newly identified sites coincide with the domains of the enhancer region as they have recently been established. In PyNB mutants duplications and deletions are generally correlated to the gain or loss of the corresponding hypersensitive sites. However, a new site is formed in one of the duplicated sequences, even if no corresponding hypersensitive site is present in the other identical sequence. A region protected from DNase I digestion occurs in the PyNB mutants which corresponds to the junction of the duplication which is absent in the wild-type strain. In this region, as a consequence of the rearrangement, a GGCGGG motif which is very similar to the one (GGGCGG) present at the binding sites of the cellular regulatory protein SP1, is found.(ABSTRACT TRUNCATED AT 250 WORDS)

Selection of mouse neuroblastoma cell-specific polyoma virus mutants with stage differentiative advantages of replication.

Two mouse neuroblastoma cell lines were analyzed for their permissivity for polyoma virus growth. One (N18) is fully permissive for polyoma replication, the other (41A3) shows limited permissivity and the viral genome persists, without noticeable cell death. Virus persistence does not seem to alter the cells' ability to differentiate in vitro and leads to selection of viral mutants altered in the untranscribed regulatory region of the genome. The mutant types obtained appear to be related to the degree of host cell differentiation. Nucleotide sequence analysis of the restriction fragment covering the regulatory region shows that duplications are present in all mutants, while deletions in the non-duplicated segment are only present in mutants selected from less differentiated cells. These alterations involve both domains of the regulatory region that are considered to be essential for DNA replication and for enhancer activity. Mixed infections with polyoma wild type show that the selected mutants have cis-advantage in replication in neuroblastoma cells and not in 3T6 cells. Mutants carrying the deletion in the non-duplicated segment of the enhancer show a selective advantage in replication over the undeleted one in mixed infection. This advantage is much stronger in neuroblastoma cells in suspension (less-differentiated stage) than in monolayer cells (more-differentiated stage). An interpretation of the overall structure of the regulatory enhancer region, based on the observed differences between the mutants selected at different stages of differentiation in neuroblastoma and previously described mutants selected in undifferentiated cells, is discussed.

THE NATURE OF NUCLEOTIDE SEQUENCE DIVERGENCE BETWEEN BARLEY AND MAIZE CHLOROPLAST DNA

Analysis of a 2175-base pair (bp) SmaI-HindIII fragment of barley chloroplast DNA revealed that rbcL (the gene for the large subunit of ribulose 1,5-bisphosphate carboxylase) and atpB (the gene for the beta subunit of ATPase) are transcribed divergently and are separated by an untranscribed region of 155-166 bp. The rbcL mRNA has a 320-residue untranslated leader region, whereas the atpB mRNA has a 296- to 309-residue leader region. The sequence of these regions, together with the initial 113 bp of the atpB-coding region and the initial 1279 bp of the rbcL-coding region, is compared with the analogous maize chloroplast DNA sequences. Two classes of nucleotide differences are present, substitutions and insertions/deletions. Nucleotide substitutions show a 1.9-fold bias toward transitions in the rbcL-coding region and a 1.5-fold bias toward transitions in the noncoding region. The level of nucleotide substitutions between the barley and maize sequences is about 0.065/bp. Seventy-one percent of the substitutions in the rbcL-coding region are at the third codon position, and 95% of these are synonymous changes. Insertion/deletion events, which are confined to the noncoding regions, are not randomly distributed in these regions and are often associated with short repeated sequences. The extent of change for the noncoding regions (about 0.093 events/bp) is less than the extent of change at the third codon positions in the rbcL-coding region (about 0.135 events/bp), including insertion/delection events. Limited sequence analysis of the analogous DNA from a wild line ( Hordeum spontaneum) and a primitive Iranian barley (H. vulgare) suggested a low rate of chloroplast DNA evolution. Compared to spinach chloroplast DNA, the barley rbcL-atpB untranslated region is extremely diverged, with only the putative rbcL promoters and ribosome-binding site being extensively conserved.

The complete nucleotide sequence of a legumin gene from pea (Pisum sativum L.).

One of several genes coding for the major pea storage protein, legumin, has been completely sequenced. The sequence covers the whole of the transcribed region, plus 5' and 3' untranscribed sequences. The predicted protein sequence starts with a signal peptide and is followed by the legumin alpha polypeptide sequence of 36. 44kd and the beta polypeptide sequence of 20. 19kd . Compared to other legume storage proteins, the alpha and beta polypeptide sequences encoded by this legumin gene, which contain 3 met and 5 cys residues, are relatively rich in the sulphur amino acids. The coding sequence is interrupted by three introns which show boundary sequences typical of higher plant genes. The 5' end of the gene sequence contains a 'TATA box', a ' CAAT box' and a sequence showing some homology to an ' AGGA box'. An extra sequence, identical to the normal polyadenylation signal of the legumin message is seen in the 3' untranscribed region. The structure of the gene and the possible significance of secondary structures in the nascent RNA transcript in affecting the choice of polyadenylation site is discussed.

Characterization of the TRs/IRS origin of DNA replication of herpes simplex virus Type 1

In previous experiments, an origin of viral DNA replication was localized within a 995-bp DNA fragment that mapped entirely within the TRs/IRs repeated region of the herpes simplex virus type 1 genome (N. D. Stow, EMBO J. 1, 863–867, 1982) . In this paper, this origin is now shown to reside within a 535-bp segment subcloned from the above fragment. Deletions extending various distances into each end of the 535-bp segment were generated using nuclease BAL 31, and the resulting plasmids screened for their ability to replicate in cells superinfected with wild-type HSV-1 helper virus. This analysis indicated that the cis-acting sequences essential for DNA replication were present within a 90-bp region, and a 100-bp viral DNA fragment containing all the signals necessary for origin function was identified. The origin lies within an untranscribed region located between the 5′-ends of two divergently transcribed immediate-early mRNAs. A prominant feature of the origin region is an almost perfect palindromic sequence 45 by long containing 18 consecutive A or T residues at its center.

Mapping functional domains in the promoter region of the herpes thymidine kinase gene.

The cloned herpes simplex virus type 1 (HSV-1) thymidine kinase (TK; ATP:thymidine 5'-phosphotransferase, EC 2.7.1.21) gene can be used to transform TK- cells to a TK+ phenotype. Transformants generated in this way express TK at a basal constitutive level that is inducible to a higher level by infection with TK- herpes virus. We have studied the effect of mutations generated in vitro on both the constitutive and virus-induced expression of TK in transformants. Four Xho I linker insertions and two deletions in the 5' untranscribed region of the cloned HSV-1 TK gene were generated in vitro. A deletion that removed all but nine base pairs of the 5' untranscribed region virtually eliminated constitutive expression and completely prevented induction by herpes virus infection. Two of the insertions have particularly interesting properties. One, nine base pairs upstream from the cap site, inactivates constitutive expression without stopping induction. The other, 50 base pairs upstream from the cap site has the opposite effect (i.e., normal constitutive expression but no induction). Analysis of these results leads us to propose that the 5' untranscribed region of the HSV-1 TK gene is quite complex with several functional domains having differential roles in the constitutive and herpes-induced expression of the TK gene.