Nucleotide quartets in the vicinity of eukaryotic transcriptional initiation sites: some DNA and chromatin structural implications

Analysis of eukaryotic promoter sequences reveals a systematically occurring CT-signal

A general data study of eukaryotic promoter sequences from widely different species is presented. Mammalian promoters with known transcription initiation sites represented the largest subclass of the data, and for this group neural network algorithms were trained to predict the location of the initiation site in a test set. The prediction accuracy of this local method was higher than what could be expected from the known non-local structure of eukaryotic promoters. Subsequent analysis revealed, besides the consensus of the two known important subregions: the TATA-box TATAAA and the Cap-signal CA, a CT-signal positioned on the average seven nucleotides downstream of the transcription initiation site. The consensus of the CT-signal is CTNCNG. The details of this core promoter element were disclosed using multiple alignment and have earlier only been described in a few isolated examples.

Strong sequence patterns in eukaryotic promoter regions: potential implications for DNA structure

1. Analysis of eukaryotic sequences reveals recurring trends in upstream regions. Oligomers composed of (G/C)n and (A/T)m blocks are preferentially flanked by (G/C)2 doublets on their 3' rather than on their 5' ends, that is (G/C)n(A/T)m(G/C)2 > (G/C)n+2(A/T)m. 2. These trends are stronger for larger n and smaller m. Additional trends are outlined below. 3. The trends are correlated with DNA structural parameters, in particular with twist and roll angles. 4. Generally, the trends hold if the base pair step joining the 5' (G/C)2 doublet to the (G/C)n (A/T)m oligomer is not undertwisted and is not strongly rolled into the major groove. 5. Other DNA parameters crucial for DNA-protein interactions are discussed as well.

DNA sequences at and between the GC and TATA boxes: potential DNA looping and spatial juxtapositioning of the protein factors

Regulation of gene expression in eukaryotes involves a complex assembly of DNA recognition sequence elements and their respective protein factors. The upstream promoter/enhancer sequences are position and orientation independent. Despite their variable distances from the TATA box and transcription start site, interaction between the protein activators and TATA general transcription factors takes place, enabling induced levels of transcription initiation. Here the intervening sequences between the GC and TATA boxes are examined as functions of their lengths. Regardless of the substantial differences in the spacer sizes, similar mono and dinucleotide distributions are noted. Purine-purine base pair steps, except for AA, are more frequent at and near the GC box in the 5' ends of the loops than in their 3' ends. Pyrimidine-pyrimidine base pair steps, except for TT behave similarly. AT and TA (as well as AA and TT) are more frequent in the 3' ends of the loops near the TATA. Examination of these distributions, as well as of the sequences composing the GC and TATA boxes indicates that the DNA in the upstream part of the loop is more rigid, whereas the downstream regions are far more flexible. The flexibility of the general TATA region may afford correct spatial juxtapositioning of the proteins with respect to each other, enabling interactions between the activators and the general transcription factors.

Non-random distribution and co-localization of purine/pyrimidine-encoded information and transcriptional regulatory domains

In order to detect sequence-based information predictive for the location of eukaryotic transcriptional regulatory domains, the frequencies and distributions of the 36 possible purine/pyrimidine reverse complement hexamer pairs was determined for test sets of real and random sequences. The distribution of one of the hexamer pairs (RRYYRR/YYRRYY, referred to as M1) was further examined in a larger set of sequences (> 32 genes, 230 kb). Predominant clusters of M1 and the locations of eukaryotic transcriptional regulatory domains were found to be associated and non-randomly distributed along the DNA consistent with a periodicity of approximately 1.2 kb. In the context of higher ordered chromatin this would align promoters, enhancers and the predominant clusters of M1 longitudinally along one face of a 30 nm fiber. Using only information about the distribution of the M1 motif, 50-70% of a sequence could be eliminated as being unlikely to contain transcriptional regulatory domains with an 87% recovery of the regulatory domains present.

Statistical analysis of nucleotide sequences

In order to scan nucleic acid databases for potentially relevant but as yet unknown signals, we have developed an improved statistical model for pattern analysis of nucleic acid sequences by modifying previous methods based on Markov chains. We demonstrate the importance of selecting the appropriate parameters in order for the method to function at all. The model allows the simultaneous analysis of several short sequences with unequal base frequencies and Markov order k not equal to 0 as is usually the case in databases. As a test of these modifications, we show that in E. coli sequences there is a bias against palindromic hexamers which correspond to known restriction enzyme recognition sites.

Three human homologs of a murine gene encoding an inhibitor of stem cell proliferation

The G0S19 genes are members of the "small inducible" family of genes, which have similar exon-intron organizations and encode secreted proteins with similar dispositions of cysteine and proline residues. G0S19-1 mRNA is increased shortly after the addition of lectin or cycloheximide to cultured human blood mononuclear cells. The cDNA sequence is homologous to that of a murine gene encoding an inhibitory cytokine (MIP1 alpha/SCI), which decreases hemopoietic stem cell proliferation. The homology extends to the 3' noncoding region, which contains two conserved elements: (i) GGGACTCTTC, a potential transcription factor NF chi B-binding site, and (ii) TTTTGTAATTTATTTT, which is found in some related genes (e.g., that encoding the immediate early protein ornithine decarboxylase). A similar but complementary sequence is present in human immunodeficiency virus. Two of the three human genes that hybridize to G0S19-1 cDNA were sequenced. G0S19-1 has 5' AP1-like recognition elements as found in some other phorbol ester-responsive genes (e.g., c-fos). G0S19-2 has a 5' Alu sequence, but is likely to be expressed because of the conservation of sections of the gene believed to be important for function. The 5' flanks of both genes contain the nucleotide motifs CK-2 and SRE, indicating cytokine-like genes with the potential to respond to growth factors. G0S19-1 is the main G0S19 gene expressed in adult T lymphocytes and may encode a homeostatic negative regulator of the size of cell populations (or subpopulations) which are derived ultimately from marrow stem cells. As such, it is a potential antioncogene.

Potential genetic functions of tandem repeated DNA sequence blocks in the human genome are based on a highly conserved "chromatin folding code"

This review is based on a thorough description of the structure and sequence organization of tandemly organized repetitive DNA sequence families in the human genome; it is aimed at revealing the locus-specific sequence organization of tandemly repetitive sequence structures as a highly conserved DNA sequence code. These repetitive so-called "super-structures" or "higher-order" structures are able to attract specific nuclear proteins. I shall define this code therefore as a "chromatin folding code". Since locus-specific superstructures of tandemly repetitive sequence units are present not only in the chromosome centromere or telomere region but also on the arms of the chromosomes, I assume that their chromatin folding code may contribute to, or even organize, the folding pathway of the chromatin chain in the nucleus. The "chromatin folding code" is based on its specific "chromatin code", which describes the sequence dependence of the helical pathway of the DNA primary sequence (i.e., secondary structure) entrapping the histone octamers in preferential positions. There is no periodicity in the distribution of the nucleosomes along the DNA chain. The folding pathway of the nucleosomal chromatin chain is however still flexible and determined by e.g., the length of the DNA chain between the nucleosomes. The fixation and stabilization of the chromatin chain in the space of the nucleus (i.e., its "functional state") may be mediated by additionally unique DNA protein interactions that are dictated by the "chromatin folding code". The unique DNA-protein interactions around the centromeres of human chromosomes are revealed for example by their "C-banding". I wish to stress that it is not my aim to relate each block of repetitive DNA sequences to a specific "chromatin folding code", but I shall demonstrate that there is an inherent potential for tandem repeated sequence units to develop a locus-specific repetitive higher order structure; this potential may create a specific chromatin folding code whenever a selection force exists at the position of this repetitive DNA structure in the genome.

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.

Structure of the 5'-external transcribed spacer of the human ribosomal RNA gene

We report the complete nucleotide sequence of the 3627 bp long 5'-external transcribed spacer (ETS) of a human ribosomal RNA gene. This sequence exhibits only very limited homologies with its mouse counterpart, the only other mammalian specimen analyzed so far. It has very peculiar compositional characteristics, with a highly biased base content (very rich in G + C, very poor in A) and also some very strong dinucleotide preferences. Interestingly, these specific features are shared by the mouse sequence, despite the extensive sequence divergence, and also apply to the other transcribed spacers of mammals indicating that a common and strong structural constraint is exerted on all these regions of the ribosomal gene. An outstanding secondary structure can be formed within the human ETS RNA, which could have a significant role in preribosome assembly.

Conserved signals around the 5' splice sites in eukaryotic nuclear precursor mRNAs: G-runs are frequent in the introns and C in the exons near both 5' and 3' splice sites

It is known that the GT doublet is well conserved at the 5' exon/intron splice junction and is frequently embedded in the AGGT quartet. Although only the underlined G is invariable, splicing and ligation are accurately executed. In this work we search for additional conserved potential signals which may aid in 5' splice site recognition. Extensive searches which are not limited to a preconceived consensus sequence are carried out. We investigate the distributions of the 256 quartets in a 1000 nucleotide span around the 5' splice sites in approximately 1700 eukaryotic nuclear precursor mRNAs. Several potential signals are noted. Of particular interest are quartets containing runs of G, e.g., G4, G3T, G3C, G3A and AG3 in the intron immediately downstream and some C-containing quartets in the exon upstream of the 5' splice site. In an analogous calculation, (A)GGG(A) has also been found to be frequent in the intron, 60 nucleotides upstream and (A)CCC(A) in the exon downstream of the 3' splice site. These results are consistent with the recent indications that exon sequences may play a role in efficient splicing. Some models are proposed.

Conserved quartets near 5' intron junctions in primate nuclear pre-mRNA

Analysis of a 1000 nucleotide span around 664 primate 5' exon/intron junctions revealed frequent recurrences of G-rich runs downstream of the 5' splice sites. In particular, AGGG, GGGA, GGGG, GGGT and TGGG are frequent at this site. Some C-rich quarters are frequent upstream of the 5' splice site. Similar behaviour of these G- and C-rich quartets is indicated for the 587 rodent introns and for a combined eukaryotic file containing 1688 introns. (A)GGG(A) is also frequent in the introns 60 nucleotides upstream of the 3' splice site, and (A)CCC(A) is frequently found in the exons downstream of the 3' site. The same consistent behaviour of the 3' splice sites is obtained as for the 5' sites, for the primates, rodents and combined eukaryotic file. These results suggest that in addition to the well-conserved 5' and 3' splice sequences, exon as well as intron sequences may play a role in nuclear pre-mRNA splicing.

Structural and functional analysis of the promoter region of the nerve growth factor gene

Molecular clones containing the NGF gene promoter regions and exons I were isolated from mouse and rat genomic libraries with synthetic oligonucleotide hybridization probes that corresponded to the 5' end of mouse submandibular gland NGF mRNA. The nucleotide sequences of the 5' flanking regions and exons I were determined and compared. There was 95% similarity in exons I and the adjacent promoter regions between mouse and rat sequences. Further upstream, the similarity decreased to 76%. Both mouse and rat promoter regions were only 33% similar to the presumptive human NGF gene promoter region. Upstream from the capsite of submandibular gland NGF mRNA as determined by an S1-nuclease protection assay, two promoter-like TATA-boxes were found at positions -28 and -49, resp., and two CAAT-like boxes at -379 and -546, resp. Both promoter regions contained a cluster of conserved CpG dinucleotide sequences in a GC-rich island whereas less conserved upstream regions contained only one CpG sequence. The promoter regions were fused to the human growth hormone gene reporter function. Transient expression in L929 cells yielded appropriate fusion mRNAs and secretion of hGH, demonstrating that the cloned promoters are functional.

Low molecular weight human pulmonary surfactant protein (SP5): isolation, characterization, and cDNA and amino acid sequences

Pulmonary surfactant is a lipid-protein complex that promotes alveolar stability by lowering the surface tension at the air-fluid interface in the peripheral air spaces. A group of hydrophobic surfactant-associated proteins has been shown to be essential for rapid surface film formation by surfactant phospholipids. We have purified a hydrophobic surfactant protein of approximately 5 kDa that we term SP5 from bronchopulmonary lavage fluid from a patient with alveolar proteinosis and shown that it promotes rapid surface film formation by simple mixtures of phospholipids. We have derived the full amino acid sequence of human SP5 from the nucleotide sequence of cDNAs identified with oligonucleotide probes based on the NH2-terminal sequence of SP5. SP5 isolated from surfactant is a fragment of a much larger precursor protein (21 kDa). The precursor contains an extremely hydrophobic region of 34 amino acids that comprises most of the mature SP5. This hydrophobicity explains the unusual solubility characteristics of SP5 and the fact that it is lipid-associated when isolated from lung.