Structural wrinkles and the genomic regulatory sites of eukaryotes

Prediction of function in DNA sequence analysis

Recognition of function of newly sequenced DNA fragments is an important area of computational molecular biology. Here we present an extensive review of methods for prediction of functional sites, tRNA, and protein-coding genes and discuss possible further directions of research in this area.

Sequence signals in eukaryotic upstream regions

Two DNA sequence elements are known to recur frequently upstream of eukaryotic polymerase II-transcribed genes. The TATAAA, at position -40, specifies the transcription initiation site. The GGCCAATCT is less frequent around -80. Sequence analysis of upstream regions reveals that the underlined yeast UAS2 consensus sequence, TGATTGGT, is also very frequent at -80 in higher polymerase II-transcribed animal sequences. The underlined CCAAT box and yeast UAS sequences are complementary. Structural analysis suggests some symmetry in their DNA structures. Upstream of the TATAAT-rich region there is an abundance of GC sequences. Analysis of nucleotide tracts indicates that these are preferentially flanked by their complementary nucleotides with a pyrimidine-purine junction, i.e., TTAN, CCGn, CnGG, TnAA. Here, I discuss DNA structural consideration in upstream regions along with protein readout of the major and minor groove information content. These sequence-structure aspects are put in the general context of protein (factors)-DNA (elements) recognition and regulation.

Theoretical molecular biology: prospectives and perspectives

I briefly discuss some aspects of theoretical molecular biology. Specifically, I include the issues of searches for homologies via string matchings, for patterns of specific nucleotide groupings and of sequence-structure relationship. The various approaches developed in order to achieve this end are described, attempting to convey some of the excitement in this quickly growing field.

Asymmetry in the distributions of the four nucleotides at mRNA initiation and 3' termini sites: some geometrical implications

All mammalian and non-mammalian vertebrate sequences in the database have been aligned by their transcription initiation sites, and separately, by their mRNA 3' termini. A simple analysis of the distribution of single nucleotide composition in the 1000 nucleotides around these sites yields surprising results. An asymmetric pattern in the behaviour of complementary nucleotides, i.e., C vs. G and A vs. T, in both these sites is observed. The four nucleotides also behave in an opposite manner around mRNA transcription initiation and 3' termini. This may suggest that these are signals affecting the intrinsic dynamics of the DNA structure and as such facilitate the first stages of the recognition process of the RNA polymerase in the neighbourhood of transcription initiation. These signals may also play a role in transcription termination rather than serve as signals for the mRNA cleavage/processing machinery.

Detection, sequence patterns and function of unusual DNA structures

Unusual DNA structures were detected by an electrophoretic procedure in which DNA fragments were separated according to size on agarose gels and then by shape on polyacrylamide gels. Fragments from yeast centromeres migrated faster in polyacrylamide than predicted from their base composition and size and this property was attributed to a nonrandom distribution of oligomeric A tracts that exhibited minima at 10-11 base intervals. Fragments from seven loci in 107 kb of DNA migrated anomalously slow and these fragments contained blocks of A2-6 in a 10-11 base periodicity which is indicative of bent DNA. The most pronounced bent sequences were found within yeast ARS1 and centered at 245 and 240 bp from the left and right ends of the adenovirus genome. Each sequence is approximately 150 bp away from a replication origin and the adenovirus sequences are within 50 bp of enhancers. Nuclear matrix attachment sites, which are also adjacent to enhancers, contain sequences characteristic of bent DNA. These results suggest that bent structures reside at the base of DNA loops in chromosomes.

Compilation of eukaryotic sequences around transcription initiation sites

All vertebrate and invertebrate sequences present in the GenBank database have been aligned according to their mRNA start sites. For some cases the regions between positions -110 and +110 are presented. Previously, two general transcription initiation signals have been noted, the universal TATA box at position -30 and the CAAT box at -75. Our analysis indicates the presence of other signals, at least as significant as the CAAT. Inspection of the aligned sequences reveals the high concentration of G + C near mRNA initiation sites in non-mammalian vertebrates and in mammalians.

Sequence signals in eukaryotic upstream regions

In eukaryotes, as in prokaryotes, evidence is accumulating showing that transcription factors recognize and bind to certain promoter elements. Sequence and chromatin structure perturbation specify the transcription initiation site and govern its efficiency. Two oligomers have been implicated in these processes: the TATAAATA and CCAAT. In the present work, all mammalian, non-mammalian vertebrate and invertebrate sequences accumulated in the database have been aligned by their mRNA start positions and scanned for recurrences of the 32 complementary triplets. The more significant signals are summarized here. In particular, TAT/ATA recurs very frequently further upstream, at -275, in addition to the 'classical' -40 position. Downstream their level is very low. The CAAT box complementary triplet components are not among the more striking signals. Closer examination of the -275 region indicates that to a large extent the signal is due to both the ATAT and the TATA quartets. Comparison of the frequencies of these quartets at -275 with the CAAT quartet at -80 suggests that the former signal is twice the strength of the latter. The oligomers' distribution charts support notions that several components are involved in recognition, making the regulatory regions more robust and less sensitive to mutations.

Structure and expression of a new murine interferon-alpha gene: MuIFN-alpha I9

A new murine alpha interferon gene, MuIFN-alpha I9, isolated from a BALB/c genomic clone, was characterized. It encodes a mature polypeptide of 167 amino acids (aa), presenting from 77 to 86% homology with the seven other MuIFN-alpha I aa sequences previously described. When compared to the latter, pre-IFN-alpha I9 has 13 distinctive aa, and, remarkably, ten of these occur in pairs. The coding region, fused to the SV40 early promoter and introduced into COS monkey cells, directed the transient secretion of an acid-stable functional IFN of 18-21 kDa. The production in this system reached levels of 300 000 units per 0.15 ml. A comparison of the aa sequence of different murine, rat, bovine, and human alpha and beta IFNs revealed certain common features allowing us to propose a putative secondary structure of the IFN proteins. A detailed analysis of results previously published by us and by others showed that the MuIFN-alpha I9 gene is, together with a least twelve other MuIFN-alpha I genes, located on chromosome 4.