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PubMed1999

Highly diverse intergenic regions of the paramyxovirus simian virus 5 cooperate with the gene end U tract in viral transcription termination and can influence reinitiation at a downstream gene.

A dicistronic minigenome containing the M-F gene junction was used to determine the role of the simian virus 5 (SV5) intergenic regions in transcription. The M-F junction differs from the other SV5 junctions by having a short M gene end U tract of only four residues (U4 tract) and a 22-base M-F intergenic sequence between the M gene end and F gene start site. Replacing the 22-base M-F intergenic region with nonviral sequences resulted in a minigenome template (Rep 22) that was defective in termination at the end of the M gene. Efficient M gene termination could be restored to the mutant Rep 22 template in either of two ways: by increasing the U tract length from four to six residues or by restoring a G residue immediately downstream of the wild-type (WT) U4 tract. In a dicistronic SH-HN minigenome, a U4-G combination was functionally equivalent to the naturally occurring SH U6-A gene end in directing SH transcription termination. In addition to affecting termination, the M-F intergenic region also influenced polymerase reinitiation. In the context of the WT U4-G M gene end, substituting nonviral sequences into the M-F intergenic region had a differential effect on F gene reinitiation, where some but not all nonviral sequences inhibited reinitiation. The inhibition of F gene reinitiation correlated with foreign sequences having a high C content. Deleting 6 bases or inserting 18 additional nucleotides into the middle of the 22-base M-F intergenic segment did not influence M gene termination or F gene reinitiation, indicating that M-F intergenic length per se is not a important factor modulating the SV5 polymerase activity. Our results suggest that the sequence diversity at an SV5 gene junction reflects specific combinations which may differentially affect SV5 gene expression and provide an additional level of transcriptional control beyond that which results from the distance of a gene from the 3' end promoter.

3' Untranslated Regions↗

PubMed2003

Sequences in the (A)gamma-delta intergenic region are not required for stage-specific regulation of the human beta-globin gene locus.

The human beta-globin locus has been extensively studied as a model of tissue and developmental stage-specific gene expression. Structural mapping of naturally occurring mutations, including transfection and transgenic studies, and the recent finding of intergenic transcripts have suggested that there are cis-acting sequence elements in the (A)gamma-delta intergenic region involved in regulating gamma- and beta-globin gene expression. To determine whether previously identified sequences in the (A)gamma-delta intergenic region are required for appropriate developmental expression of the human beta-globin gene cluster, transgenic mice were generated by transfer of yeast artificial chromosomes containing the entire human beta-globin locus. Three different deletions of the (A)gamma-delta intergenic region were introduced, including (i) deletion of the 750-bp (A)gamma 3' regulatory element ((A)gammae), (ii) deletion of 3.2 kb upstream of the delta-globin gene encompassing pyrimidine-rich sequences and the recently described intergenic transcript initiation site, and (iii) deletion of a 12.5-kb fragment encompassing most of the (A)gamma-delta globin intergenic region. Analysis of multiple transgenic lines carrying these deletion constructs demonstrated that the normal stage-specific sequential expression of the epsilon -, gamma-, and beta-globin genes was preserved, despite deletion of these putative regulatory sequences. These studies suggest that regulatory sequences required for activation and silencing of the human beta-globin gene family during ontogeny reside proximally to the genes and immediately 5' to the human gamma- and beta-globin genes.

Animals↗

PubMed2006

The UGA3-GLT1 intergenic region constitutes a promoter whose bidirectional nature is determined by chromatin organization in Saccharomyces cerevisiae.

Transcription of an important number of divergent genes of Saccharomyces cerevisiae is controlled by intergenic regions, which constitute factual bidirectional promoters. However, few of such promoters have been characterized in detail. The analysis of the UGA3-GLT1 intergenic region has provided an interesting model to study the joint action of two global transcriptional activators that had been considered to act independently. Our results show that Gln3p and Gcn4p exert their effect upon cis-acting elements, which are shared in a bidirectional promoter. Accordingly, when yeast is grown on a low-quality nitrogen source, or under amino acid deprivation, the expression of both UGA3 and GLT1 is induced through the action of both these global transcriptional modulators that bind to a region of the bidirectional promoter. In addition, we demonstrate that chromatin organization plays a major role in the bidirectional properties of the UGA3-GLT1 promoter, through the action of an upstream Abf1p-binding consensus sequence and a polydAdT(tract). Mutations in these cis-elements differentially affect transcription of UGA3 and GLT1, and thus alter the overall relative expression. This is the first example of an intergenic region constituting a promoter whose bidirectional character is determined by chromatin organization.

Amino Acids↗

PubMed1997

Characterization of the intergenic region which regulates the MspI restriction-modification system.

The 110-bp intergenic region between mspIM and mspIR, the genes encoding the MspI modification (M.MspI) and restriction (R.MspI) enzymes, respectively, was fused, in both orientations, with lacZ. Expression of a single-copy mspIM-lacZ fusion is more than 400-fold stronger than expression of an mspIR-lacZ fusion. M.MspI in trans represses expression of the mspIM-lacZ fusion by binding to the DNA but does not affect expression of the mspIR-lacZ fusion. Transcription start sites of the genes were identified, and a set of nonoverlapping promoters was assigned. DNase I footprinting showed that M.MspI binds to a site within the intergenic region that includes only the mspIM regulatory elements.

DNA Footprinting↗

PubMed1987

Nucleotide sequence of the 18-25 S ribosomal RNA intergenic region from a thermophile, Thermomyces lanuginosus.

To identify important structural features in the intergenic sequences of ribosomal DNAs, the nucleotide sequence of the 18-25 S rRNA intergene region was determined in a thermophilic fungus, Thermomyces lanuginosus, and compared to that of common yeasts. While a striking sequence homology was observed in the mature ribosomal sequences, the two internal transcribed spacer regions were found to be unusually G + C rich and significantly shorter than any other organism. An extensive secondary structure could be predicted but estimates of the secondary structure did not reveal a minimum structure which is common to other species; rather, in all rDNA transcripts the intergenic regions appear organized into a secondary structure in which all of the mature rRNA junctions are localized within one domain. This suggests that a role of the internal transcribed spacer in ribosome maturation may be that of a "biological spring" which maintains processed sites in close proximity.

Base Sequence↗

PubMed1991

Comparative studies of the quinic acid (qa) cluster in several Neurospora species with special emphasis on the qa-x-qa-2 intergenic region.

The organization of the quinic acid (qa) genes in Neurospora crassa has been compared to that in several other Neurospora species. This gene cluster was found to be highly conserved in all species examined. However, there are numberous restriction fragment length polymorphisms that distinguish the heterothallic and homothallic species. Catabolic dehydroquinase assays indicated that qa-2 gene expression in the homothallic species is subject to induction by quinic acid, as is the case in N. crassa. The qa-x-qa-2 intergenic region of the homothallic species N. africana was cloned and sequenced. Conserved qa activator (qa-1F) binding sites have been identified in this region. When the qa-x-qa-2 intergenic region of N. crassa was replaced with its N. africana counterpart, qa-2 gene expression was reduced; however repression by glucose appeared normal. Furthermore, the N. africana start site for qa-2 transcription (which differs from the N. crassa start site) was utilized in the transformant. The overall evidence suggests that a weakening of the -120 activator binding site in the qa-x-qa-2 intergenic region may be responsible for these differences.

Base Sequence↗

PubMed1994

Intramolecular recombination in polyomavirus DNA is a nonconservative process directed from the viral intergenic region.

Previously, we have studied intramolecular homologous recombination in polyomavirus replicons under conditions allowing only one amplifiable recombination product to be generated from a single precursor molecule. In order to detect putative reciprocal product(s), we have now constructed precursor polyomavirus replicons which contain two copies, instead of one copy, of the viral intergenic region, including the origin of replication as well as both promoters. Upon transfection of mouse cells, constructs containing directly repeated intergenic regions yielded distinct amplifiable products, in number depending upon the functional integrity of both intergenic regions. Our data indicate that of two possible reciprocal products, a given precursor molecule would yield either one or the other but never both at the same time. Most striking, however, is the observation that promoter function is required for recombination, while the origin of replication function may be needed only for amplification of the recombination product once it has been formed. The data reported here confirm and extend previous data suggesting that (i) transcription is instrumental in recombination between direct repeats and (ii) nonconservative recombination involving direct repeats relies upon two promoters of opposing polarities.

DNA, Viral↗

PubMed1998

The length and sequence composition of vesicular stomatitis virus intergenic regions affect mRNA levels and the site of transcript initiation.

In this study, we used a dicistronic vesicular stomatitis virus (VSV) minigenome to investigate the effects of either single or multiple nucleotide insertions placed immediately after the nontranscribed intergenic dinucleotide of the M gene on VSV transcription. Both Northern blot and primer extension analysis showed that the polymerase responded to the inserted nucleotides in a sequence-specific manner such that some insertions had no effect on mRNA synthesis from the downstream G gene, nor on the site of transcript initiation, whereas other insertions resulted in dramatic reductions in transcript accumulation. Some of these transcripts were initiated at the wild-type site, while others initiated within the inserted sequence. We also examined the transcriptional events that occurred when a natural, 21-nucleotide intergenic region located between the G and L genes from the New Jersey (NJ) serotype of VSV was inserted into the minigenome gene junction. In contrast to the normal 25 to 30% attenuation observed for downstream transcription at gene junctions containing the typical dinucleotide (3'-GA-5') intergenic region, the NJ variant showed greater than 75% attenuation at the gene junction. In addition, the polymerase initiated transcription at two major start sites, one of which was located within the intergenic sequence. Collectively, these data suggest that the polymerase "samples" the intergenic sequences following polyadenylation and termination of the upstream transcript by scanning until an appropriate start site is found. One implication of a scanning polymerase is that the polymerase presumably switches states from a processive elongation mode to a stuttering mode for polyadenylation to one in which no transcription occurs, before it reinitiates at the downstream gene. Our data support the hypothesis that sequences surrounding the intergenic region modulate these events such that appropriate amounts of each mRNA are synthesized.

Base Composition↗

PubMed1988

Structure and evolution of the intergenic region in a ribosomal DNA repeat unit of wheat.

The complete nucleotide sequence of the intergenic region between the 25 S and 18 S wheat ribosomal RNA genes has been determined from a 4.6 kb EcoRI-BamHI fragment (1 kb = 10(3) bases or base-pairs) subcloned from the plasmid pTa71. Within this subclone the intergenic DNA is flanked by the 3' end of the 25 S and the 5' end of the 18 S ribosomal RNA sequences. Four repeat families are present within the intergenic region. The major repeat family A, consists of 12 direct repeat units of 135 or 136 base-pairs (bp) flanked by diverged truncated copies. Within each A repeat a subrepeat structure has been revealed. Family B, which is localized to the 5' side of the A repeats, contains three repeat units, one of 152 bp, the second of 150 bp and a truncated unit of 107 bp. Family C, which is localized in the transcribed rRNA precursor, consists of two direct repeat units of 172 and 174 bp and possesses some short subrepeat motifs. The C repeats may have evolved by and diverged from one another by the insertion of short transposable sequences. Family D consists of two direct repeat units of 30 bp located 5' to the start of transcription. Statistical analysis of repeat family A showed that there is a significant association between the similarity of any two repeat units and their distance apart in the array. The near identity of members of the A family is maintained presumably by processes such as unequal crossing over and gene conversion, but the members at each end of the array show more divergence. Sequence motifs in the A and C repeat families and in other regions including the 5' end of 18 S RNA are related, implying that much of the intergenic DNA may have evolved from a few short ancestral sequences. The B and D repeats or their equivalent are not found in a maize ribosomal DNA repeat unit. The DNA in the external transcribed spacer DNA 5' to the 18 S RNA sequence is longer in wheat than in maize. This is due principally to two duplications and insertion of a sequence with dyad symmetry in the wheat gene.

Base Sequence↗

PubMed2004

Sequence periodicity of Escherichia coli is concentrated in intergenic regions.

BACKGROUND: Sequence periodicity with a period close to the DNA helical repeat is a very basic genomic property. This genomic feature was demonstrated for many prokaryotic genomes. The Escherichia coli sequences display the period close to 11 base pairs. RESULTS: Here we demonstrate that practically only ApA/TpT dinucleotides contribute to overall dinucleotide periodicity in Escherichia coli. The noncoding sequences reveal this periodicity much more prominently compared to protein-coding sequences. The sequence periodicity of ApC/GpT, ApT and GpC dinucleotides along the Escherichia coli K-12 is found to be located as well mainly within the intergenic regions. CONCLUSIONS: The observed concentration of the dinucleotide sequence periodicity in the intergenic regions of E. coli suggests that the periodicity is a typical property of prokaryotic intergenic regions. We suppose that this preferential distribution of dinucleotide periodicity serves many biological functions; first of all, the regulation of transcription.

Base Composition↗

PubMed1986

Walking along the rabies genome: is the large G-L intergenic region a remnant gene?

Rabies cDNA clones, obtained by "walking along the genome" using two successive DNA primers, have allowed the sequence determination of the genes encoding the N, M1, M2, G, and the beginning of the L protein as well as the rabies intergenic regions. Start and stop transcription signals located at the border of each gene encoding a protein have been identified and are similar to the corresponding signals from vesicular stomatitis virus (VSV) and Sendai virus. Except for limited stretches of the nucleoprotein, there is no homology between corresponding structural proteins of these three viruses. Rabies intergenic regions are variable both in length and sequence. Evidence for the existence of a remnant protein gene in the 423 nucleotide long G-L intergenic region is presented. This finding is discussed in terms of the evolution of unsegmented negative-strand RNA viruses.

Amino Acid Sequence↗

PubMed1985

The nucleotide sequence of the nitrogen regulation gene ntrB and the glnA-ntrBC intergenic region of Klebsiella pneumoniae.

The nucleotide sequence of the Klebsiella pneumoniae ntrB gene and the glnA-ntrBC intergenic region has been determined. NtrB encodes a 38,409 Dalton polypeptide with a potential DNA-binding domain between residues 67 and 86. This N-terminal domain may play a role in the co-operative control of ntr-regulated promoters by the ntrB and ntrC products. Mapping of in vivo transcripts with S1 nuclease identified three transcripts in the glnA-ntrBC intergenic region. Two transcripts originate upstream of glnA; one reading through into ntrBC and one terminating at a sequence resembling a rho-independent terminator between glnA and ntrBC. A third transcript originates from the ntrBC promoter which has a consensus binding site for the ntrC product in the -10 region. Comparison of the glnA-ntrBC intergenic sequences from K. pneumoniae, Escherichia coli and Salmonella typhimurium has identified a number of conserved features and some significant differences.

Cloning, Molecular↗

PubMed2000

Identification and characterization of a bidirectional promoter from the intergenic region between the human DDX13 and RD genes.

The human DDX13 gene encodes a putative RNA helicase of the DExH-box family. In an earlier report we showed that the human DDX13 and RD genes were arranged head-to-head in the class III MHC complex and their ATG start codons were separated by 745 base pairs. We have now analyzed the common 745 bp intergenic region in detail and characterized their promoters. Northern blot analysis revealed that DDX13 and RD exhibit distinct patterns of steady-state expression among multiple human tissues. The promoter regions for DDX13 and RD genes were identified by deletion analysis from 740 bp to 176 bp of the intergenic region fused to a chloramphenicol acetyltransferase (CAT) reporter gene using transient transfection assays. Results indicated that a promoter sequence as small as 176 bp is sufficient for basal expression of both genes in HeLa and HepG2 cells. Functional analysis using a bidirectional reporter system demonstrates that the sequence 262 bp proximal to the DDX13 gene is sufficient for concurrent expression in both directions. However, the common 740 bp intergenic region showed promoter activity in DDX13 only, suggesting the presence of a negatively acting region for the RD gene within the region -267 to -744. It appears that RD expression is controlled by a complex system of positively and negatively acting elements present on distant portions of both genes.

Blotting, Northern↗

PubMed2005

Insertion/deletion and nucleotide polymorphism data reveal constraints in Drosophila melanogaster introns and intergenic regions.

Our study of nucleotide sequence and insertion/deletion polymorphism in Drosophila melanogaster noncoding DNA provides evidence for selective pressures in both intergenic regions and introns (of the large size class). Intronic and intergenic sequences show a similar polymorphic deletion bias. Insertions have smaller sizes and higher frequencies than deletions, supporting the hypothesis that insertions are selected to compensate for the loss of DNA caused by deletion bias. Analysis of a simple model of selective constraints suggests that the blocks of functional elements located in intergenic sequences are on average larger than those in introns, while the length distribution of relatively unconstrained sequences interspaced between these blocks is similar in intronic and intergenic regions.

Animals↗

PubMed1995

Use of the Escherichia coli uidA gene as a reporter in Methanococcus voltae for the analysis of the regulatory function of the intergenic region between the operons encoding selenium-free hydrogenases.

The Escherichia coli beta-glucuronidase gene uidA was linked to a region of the Methanococcus voltae genome containing the putative promoter of a gene for a DNA-binding protein and introduced into the M. voltae chromosome. It was found that the enzyme was expressed in the cells in easily measurable amounts. The reporter gene was then placed under the control of the intergenic region found between two divergently transcribed gene groups encoding selenium-free hydrogenases, which are measurably transcribed only after selenium depletion. This region is supposed not only to contain the divergent promoters governing the transcription of the hydrogenase genes but also cis regulatory elements necessary for the negative transcriptional regulation in which selenium is involved. It was shown that the intergenic region functioned as a promoter region for the reporter gene in either orientation. The additional finding that beta-glucuronidase expression was dependent on selenium depletion localizes the cis regulatory elements to the intergenic region between the two hydrogenase operons.

Base Sequence↗

PubMed1990

A novel repeated DNA sequence located in the intergenic regions of bacterial chromosomes.

We report the discovery of a novel group of highly conserved DNA sequences located within the intergenic regions of the chromosomes of Escherichia coli, Salmonella typhimurium and other bacteria. These intergenic repeat units (IRUs) are 124-127 nucleotides long and have the potential to form stable stem-loop structures. The location of these sequences within the intergenic regions is variable with respect to known or putative signals for transcription and translation of the flanking genes. Some of the IRU sequences are transcribed, others are probably not. The structure and possible functions of these sequences are discussed in relation to palindromic units and other repeated DNA sequences in bacteria.

Base Sequence↗

PubMed1994

An operator associated with autoregulation of the repressor gene in actinophage phiC31 is found in highly conserved copies in intergenic regions in the phage genome.

Previous reports have suggested that the repressor gene, c, of phiC31 is autoregulated and that likely operators are conserved inverted repeat sequences (CIRs1&2) located just upstream of the promoters, cp1 and cp2. Evidence is now presented that the CIRs 1&2 are indeed binding sites for one of the three inframe, N-terminally different protein isoforms of 42, 54 and 74 kDa produced by the c gene. A cp1-aphII fusion was repressed in a Streptomyces coelicolor A3(2) phiC31 lysogen and characterisation of an operator-constitutive (Oc) mutant showed a single mutation in CIR-1. CIR-1 containing fragments were retarded in electrophoresis gels by the 42 kDa repressor protein isoform and this retardation was inhibited by the addition of competing DNA fragments containing either CIR-1 or CIR-2. Using a combination of Southern blotting and analysis of available DNA sequence we also show that at least 18 copies of the CIRs are present throughout the phiC31 genome. Alignment of 9 CIR sequences showed that 8 contained a perfectly conserved 17 bp core whilst the exception had a single mismatch. The core includes a 16 bp inverted repeat (IR), and is usually part of a more extensive and less highly conserved palindrome. When superimposed on a previously derived transcription map of the early region, the CIRs lie in intergenic regions associated with transcription initiation and/or termination.

Bacteriophages↗

PubMed2001

Comparative genomics of the SOX9 region in human and Fugu rubripes: conservation of short regulatory sequence elements within large intergenic regions.

Campomelic dysplasia (CD), a human skeletal malformation syndrome with XY sex reversal, is caused by heterozygous mutations in and around the gene SOX9. SOX9 has an extended 5' control region, as indicated by CD translocation breakpoints scattered over 1 Mb proximal to SOX9 and by expression data from mice transgenic for human SOX9-spanning yeast artificial chromosomes. To identify long-range regulatory elements within the SOX9 5' control region, we compared approximately 3.7 Mb and 195 kb of sequence around human and Fugu rubripes SOX9, respectively. We identified only seven and five protein-coding genes in the human and F. rubripes sequences, respectively. Four of the F. rubripes genes have been mapped in humans; all reside on chromosome 17 but show extensive intrachromosomal gene shuffling compared with the gene order in F. rubripes. In both species, very large intergenic distances separate SOX9 from its directly flanking genes: 2 Mb and 500 kb on either side of SOX9 in humans, and 68 and 97 kb on either side of SOX9 in F. rubripes. Comparative sequence analysis of the intergenic regions revealed five conserved elements, E1-E5, up to 290 kb 5' to human SOX9 and up to 18 kb 5' to F. rubripes SOX9, and three such elements, E6-E8, 3' to SOX9. Where available, mouse sequences confirm conservation of the elements. From the yeast artificial chromosome transgenic data, elements E3-E5 are candidate enhancers for SOX9 expression in limb and vertebral column, and 8 of 10 CD translocation breakpoints separate these elements from SOX9.

5' Flanking Region↗