Drd4
            gene polymorphisms are associated with personality variation in a passerine bird

Polymorphisms in several neurotransmitter-associated genes have been associated with variation in human personality traits. Among the more promising of such associations is that between the human dopamine receptor D4 gene ( Drd4 ) variants and novelty-seeking behaviour. However, genetic epistasis, genotype–environment interactions and confounding environmental factors all act to obscure genotype–personality relationships. Such problems can be addressed by measuring personality under standardized conditions and by selection experiments, with both approaches only feasible with non-human animals. Looking for similar Drd4 genotype–personality associations in a free-living bird, the great tit ( Parus major ), we detected 73 polymorphisms (66 SNPs, 7 indels) in the P. major Drd4 orthologue. Two of the P. major Drd4 gene polymorphisms were investigated for evidence of association with novelty-seeking behaviour: a coding region synonymous single nucleotide polymorphism (SNP830) and a 15 bp indel (ID15) located 5′ to the putative transcription initiation site. Frequencies of the three Drd4 SNP830 genotypes, but not the ID15 genotypes, differed significantly between two P. major lines selected over four generations for divergent levels of ‘early exploratory behaviour’ (EEB). Strong corroborating evidence for the significance of this finding comes from the analysis of free-living, unselected birds where we found a significant association between SNP830 genotypes and differing mean EEB levels. These findings suggest that an association between Drd4 gene polymorphisms and animal personality variation predates the divergence of the avian and mammalian lineages. Furthermore, this work heralds the possibility of following microevolutionary changes in frequencies of behaviourally relevant Drd4 polymorphisms within populations where natural selection acts differentially on different personality types.

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Structure and tissue-specific expression of the Drosophila melanogaster organellar-type Ca2+-ATPase gene

Biochemical Journal ◽

10.1042/bj3100757 ◽

1995 ◽

Vol 310 (3) ◽

pp. 757-763 ◽

Cited By ~ 18

Author(s):

A Magyar ◽

E Bakos ◽

A Váradi

Keyword(s):

Drosophila Melanogaster ◽

Transcription Initiation ◽

Initiation Site ◽

Drosophila Genome ◽

Coding Region ◽

Specific Expression ◽

S1 Nuclease ◽

Protein Coding ◽

Atpase Gene ◽

High Level

A 14 kb genomic clone covering the organellar-type Ca(2+)-ATPase gene of Drosophila melanogaster has been isolated and characterized. The sequence of a 7132 bp region extending from 1.1 kb 5′ upstream of the initiation ATG codon over the polyadenylation signal at the 3′ end has been determined. The gene consists of nine exons including one with an exceptional size of 2172 bp representing 72% of the protein coding region. Introns are relatively small (< 100 bp) except for the 3′ intron which has a size of 2239 bp, an exceptionally large size among Drosophila introns. Five of the introns are in the same positions in Drosophila, Artemia and rabbit SERCA1 Ca(2+)-ATPase genes. There is only one organellar-type Ca(2+)-ATPase gene in the Drosophila genome, as was shown by Southern-blot analysis [Váradi, Gilmore-Hebert and Benz (1989) FEBS Lett. 258, 203-207] and by chromosomal localization [Magyar and Váradi (1990) Biochem. Biophys. Res. Commun. 173, 872-877]. Primer extension and S1-nuclease assays revealed a potential transcription initiation site 876 bp upstream of the translation initiation ATG with a TATA-box 23 bp upstream of this site. Analysis of the 5′ region of the Drosophila organellar-type Ca(2+)-ATPase gene suggests the presence of potential recognition sequences of various muscle-specific transcription factors and shows a region with remarkable similarity to that in the rabbit SERCA2 gene. The tissue distribution of expression of the organellar-type Ca(2+)-ATPase gene has been studied by in situ RNA-RNA hybridization on microscopic sections. A low mRNA abundance can be detected in each tissue of adult flies, suggesting a housekeeping function for the gene. On the other hand a pronounced tissue specificity of expression has also been found as the organellar-type Ca(2+)-ATPase is expressed at a very high level in cell bodies of the central nervous system and in various muscles.

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The Genes Encoding Formamidopyrimidine and MutY DNA Glycosylases in Escherichia coli Are Transcribed as Part of Complex Operons

Journal of Bacteriology ◽

10.1128/jb.181.14.4223-4236.1999 ◽

1999 ◽

Vol 181 (14) ◽

pp. 4223-4236 ◽

Cited By ~ 12

Author(s):

Christine M. Gifford ◽

Susan S. Wallace

Keyword(s):

Escherichia Coli ◽

Gene Order ◽

Intergenic Region ◽

Transcription Initiation ◽

Excision Repair ◽

Initiation Site ◽

Dna Glycosylase ◽

Rnase E ◽

Coding Region ◽

Genes Encoding

ABSTRACT Escherichia coli formamidopyrimidine (Fpg) DNA glycosylase and MutY DNA glycosylase are base excision repair proteins that work together to protect cells from the mutagenic effects of the commonly oxidized guanine product 7,8-dihydro-8-oxoguanine. The genes encoding these proteins, fpg and mutY, are both cotranscribed as part of complex operons. fpg is the terminal gene in an operon with the gene order radC,rpmB, rpmG, and fpg. This operon has transcription initiation sites upstream of radC, in theradC coding region, and immediately upstream offpg. There is a strong attenuator in therpmG-fpg intergenic region and three transcription termination sites downstream of fpg. There is an additional site, in the radC-rpmB intergenic region, that corresponds either to a transcription initiation site or to an RNase E or RNase III cleavage site. mutY is the first gene in an operon with the gene order mutY, yggX, mltC, andnupG. This operon has transcription initiation sites upstream of mutY, in the mutY coding region, and immediately upstream of nupG. There also appear to be attenuators in the yggX-mltC and mltC-nupGintergenic regions. The order of genes in these operons has been conserved or partially conserved only in other closely related gram-negative bacteria, although it is not known whether the genes are cotranscribed in these other organisms.

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Genomic footprinting of a yeast tRNA gene reveals stable complexes over the 5'-flanking region.

Molecular and Cellular Biology ◽

10.1128/mcb.9.8.3244 ◽

1989 ◽

Vol 9 (8) ◽

pp. 3244-3252 ◽

Cited By ~ 37

Author(s):

J M Huibregtse ◽

D R Engelke

Keyword(s):

Stationary Phase ◽

Transcription Initiation ◽

Initiation Site ◽

Dnase I ◽

Transcription Initiation Site ◽

Upstream Region ◽

Stable Complex ◽

Coding Region ◽

Flanking Region ◽

Genomic Footprinting

We have shown by genomic footprinting that the 5'-flanking region of the Saccharomyces cerevisiae tRNASUP53 gene is protected from DNase I digestion. The protected region has a 5' boundary at -40 (relative to the transcription initiation site) and extends into the coding region of the gene, with a 3' boundary at approximately +15. Although the DNase I protection over this region was much greater than at the A- and B-box internal promoters, point mutations within the A or B box that reduced transcription in vitro eliminated the upstream DNase I protection. This implies that formation of a stable complex over the 5'-flanking region is dependent on interaction of the gene with transcription factor IIIC but that stability of the complex may not require continued interaction with this factor. The DNase I protection under varied growth conditions further suggested that the upstream complex is composed of two or more components. The region over the transcription initiation site (approximately +15 to -10) was less protected in stationary-phase cultures, whereas the more upstream region (approximately -10 to -40) was protected in both exponential- and stationary-phase cultures.

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Regulatory sequences for the amplification and replication of the ribosomal DNA minichromosome in Tetrahymena thermophila.

Molecular and Cellular Biology ◽

10.1128/mcb.17.12.7237 ◽

1997 ◽

Vol 17 (12) ◽

pp. 7237-7247 ◽

Cited By ~ 21

Author(s):

P Blomberg ◽

C Randolph ◽

C H Yao ◽

M C Yao

Keyword(s):

Transcription Initiation ◽

Tetrahymena Thermophila ◽

Initiation Site ◽

Core Region ◽

Rrna Gene ◽

Regulatory Sequences ◽

Coding Region ◽

Cis Acting ◽

Rrna Transcription ◽

Stable Maintenance

We have analyzed the cis-acting sequences that regulate rRNA gene (rDNA) replication in Tetrahymena thermophila. The macronucleus of this ciliated protozoan contains 9,000 copies of a 21-kbp minichromosome in the form of a palindrome comprising two copies of the rDNA. These are derived from a single chromosomally integrated copy during conjugation through selective amplification and are maintained by replicating once per cell cycle during vegetative growth. We have developed a transformation vector and carried out a deletion analysis to determine the minimal sequences required for replication, amplification, and/or stable maintenance of the rDNA molecule. Using constructs containing progressively longer deletions, we show that only a small portion (approximately 900 bp) of the rDNA is needed for extrachromosomal replication and stable maintenance of this molecule. This core region is very near but does not include the rRNA transcription initiation site or its putative promoter, indicating that replication is not dependent on normal rRNA transcription. It includes two nearly identical nuclease-sensitive domains (D1 and D2), one of which (D1) corresponds to the physical origin of replication determined previously. Deletion of both domains abolishes replication, whereas deletion of either domain allows the molecules to replicate, indicating that only one domain is required. In addition to this core region, we have found several DNA segments, including a tandem array of a 21-nucleotide repeat (type II repeats) and sequences within the rRNA coding region, that play distinctive and important roles in maintaining the rDNA at a high copy number.

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Genomic footprinting of a yeast tRNA gene reveals stable complexes over the 5'-flanking region

Molecular and Cellular Biology ◽

10.1128/mcb.9.8.3244-3252.1989 ◽

1989 ◽

Vol 9 (8) ◽

pp. 3244-3252

Author(s):

J M Huibregtse ◽

D R Engelke

Keyword(s):

Stationary Phase ◽

Transcription Initiation ◽

Initiation Site ◽

Dnase I ◽

Transcription Initiation Site ◽

Upstream Region ◽

Stable Complex ◽

Coding Region ◽

Flanking Region ◽

Genomic Footprinting

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Expression of NF-L and NF-M in fibroblasts reveals coassembly of neurofilament and vimentin subunits.

The Journal of Cell Biology ◽

10.1083/jcb.108.2.579 ◽

1989 ◽

Vol 108 (2) ◽

pp. 579-593 ◽

Cited By ~ 81

Author(s):

M J Monteiro ◽

D W Cleveland

Keyword(s):

Transcription Initiation ◽

Initiation Site ◽

Cellular Protein ◽

Cell Protein ◽

Coding Region ◽

Animal Cells ◽

Murine Sarcoma Virus ◽

Sarcoma Virus ◽

Specific Factors

We have used transient and stable DNA transfection to force synthesis of the mouse NF-L and NF-M genes in nonneuronal cultured animal cells. When the authentic NF-L gene (containing 1.7 kb of sequences 5' to the transcription initiation site) was transfected into L cells, correctly initiated NF-L mRNA was produced from the transfected gene but not the endogenous NF-L genes. Therefore, the normal restriction of NF-L expression to neurons cannot derive exclusively from absence in nonneuronal cells of neuron-specific transcription factors. When the NF-L coding region was linked to the strong promoter from Moloney Murine Sarcoma virus, we obtained high levels of synthesis of NF-L subunits (accumulating to as much as 9% of cell protein in stable cell lines). Although NF-L and NF-M polypeptides are normally expressed exclusively in postmitotic neurons, NF-L or NF-M polypeptides expressed in fibroblasts were efficiently assembled into intermediate filament arrays, thus demonstrating the competence of both NF-L and NF-M to assemble in vivo in the absence of additional neuron-specific factors. As judged by immunofluorescence localization and by the alteration in the solubility of the endogenous vimentin filaments, filaments containing NF-L appeared to be copolymers with vimentin. Neither the alteration in the properties of the vimentin array nor the accumulation of NF-L to a level that made it the second most abundant cellular protein (after actin) had any observable effect on cell viability or growth rate.

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Co-inheritance of HBB:c.−106G > C, a rare single nucleotide variation at position −56 relative to transcription initiation site, with other known mutations in the globin clusters

Hematology ◽

10.1080/10245332.2017.1403737 ◽

2017 ◽

Vol 23 (6) ◽

pp. 368-372

Author(s):

Margherita Vinciguerra ◽

Cristina Passarello ◽

Filippo Cassarà ◽

Filippo Leto ◽

Monica Cannata ◽

...

Keyword(s):

Transcription Initiation ◽

Initiation Site ◽

Transcription Initiation Site ◽

Nucleotide Variation ◽

Single Nucleotide Variation ◽

Single Nucleotide

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Cloning of the gene encoding the human erythropoietin receptor

Blood ◽

10.1182/blood.v78.10.2557.bloodjournal78102557 ◽

1991 ◽

Vol 78 (10) ◽

pp. 2557-2563 ◽

Cited By ~ 1

Author(s):

L Maouche ◽

C Tournamille ◽

C Hattab ◽

G Boffa ◽

JP Cartron ◽

...

Keyword(s):

Sequence Homology ◽

Transcription Initiation ◽

Stop Codon ◽

Fetal Liver ◽

Splice Junction ◽

Initiation Site ◽

Erythropoietin Receptor ◽

Cdna Libraries ◽

Coding Region ◽

Human Erythropoietin

The genomic and complementary DNAs of the human erythropoietin receptor (hEpo-R) have been isolated and characterized from a genomic placental library and from two cDNA libraries prepared from bone marrow and fetal liver. The five different partial cDNAs isolated were aberrant in the predicted reading frames as compared with the Epo-R protein sequence, because all retained insert sequences that may represent splicing intermediates (three clones), cloning artifact (one clone), or a new sequence at a splice junction (one clone) of the gene. The cDNAs were used to isolate several genomic clones encompassing the complete hEpo-R gene. This gene, which encodes a 508-amino acid polypeptide chain of predicted M(r) 55,000, is organized into eight exons spread over 6 kb of DNA and exhibited a high degree of sequence homology (81.6% in the coding region) and structural organization with its murine counterpart. Primer extension analysis indicated that the transcription initiation site is located 141 bp upstream of the initiation codon. Sequence homology 320 bp upstream of the cap site was significantly lower (60%) and diverged completely further upstream as compared with the murine gene. Similarly, the human and murine sequences were largely divergent downstream of the stop codon, indicating that a strong conservation during evolution was restricted to the coding sequence of the Epo-R protein. The 320-bp region upstream of the cap site does not contain the typical TATA or CAAT boxes present in many tissue-specific genes, but does include potential binding sites for the ubiquitous Sp1 and the erythroid-specific GATA-1 trans-activating factors. These boxes are well conserved in sequence and position relative to the cap site within the promoter region of the human and murine genes, but the CACCC boxes present in the murine gene are absent in the human gene.

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L1 Antisense Promoter Drives Tissue-Specific Transcription of Human Genes

Journal of Biomedicine and Biotechnology ◽

10.1155/jbb/2006/71753 ◽

2006 ◽

Vol 2006 ◽

pp. 1-16 ◽

Cited By ~ 69

Author(s):

Kert Mätlik ◽

Kaja Redik ◽

Mart Speek

Keyword(s):

Transcription Initiation ◽

Regulatory Elements ◽

Initiation Site ◽

Coding Region ◽

Tissue Specific ◽

Multiple Loci ◽

Complex Interactions ◽

Chimeric Transcripts ◽

Human Genes

Transcription of transposable elements interspersed in the genome is controlled by complex interactions between their regulatory elements and host factors. However, the same regulatory elements may be occasionally used for the transcription of host genes. One such example is the human L1 retrotransposon, which contains an antisense promoter (ASP) driving transcription into adjacent genes yielding chimeric transcripts. We have characterized 49 chimeric mRNAs corresponding to sense and antisense strands of human genes. Here we show that L1 ASP is capable of functioning as an alternative promoter, giving rise to a chimeric transcript whose coding region is identical to the ORF of mRNA of the following genes:KIAA1797,CLCN5, andSLCO1A2. Furthermore, in these cases the activity of L1 ASP is tissue-specific and may expand the expression pattern of the respective gene. The activity of L1 ASP is tissue-specific also in cases where L1 ASP produces antisense RNAs complementary toCOL11A1andBOLLmRNAs. Simultaneous assessment of the activity of L1 ASPs in multiple loci revealed the presence of L1 ASP-derived transcripts in all human tissues examined. We also demonstrate that L1 ASP can act as a promoter in vivo and predict that it has a heterogeneous transcription initiation site. Our data suggest that L1 ASP-driven transcription may increase the transcriptional flexibility of several human genes.

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Complementary Roles of Yeast Rad4p and Rad34p in Nucleotide Excision Repair of Active and Inactive rRNA Gene Chromatin

Molecular and Cellular Biology ◽

10.1128/mcb.00137-08 ◽

2008 ◽

Vol 28 (24) ◽

pp. 7504-7513 ◽

Cited By ~ 17

Author(s):

Maxime Tremblay ◽

Yumin Teng ◽

Michel Paquette ◽

Raymond Waters ◽

Antonio Conconi

Keyword(s):

Nucleotide Excision Repair ◽

Transcription Initiation ◽

Excision Repair ◽

Initiation Site ◽

Dna Lesions ◽

Transcription Initiation Site ◽

Rrna Gene ◽

Open Chromatin ◽

Coding Region ◽

Nucleotide Excision

ABSTRACT Nucleotide excision repair (NER) removes a plethora of DNA lesions. It is performed by a large multisubunit protein complex that finds and repairs damaged DNA in different chromatin contexts and nuclear domains. The nucleolus is the most transcriptionally active domain, and in yeast, transcription-coupled NER occurs in RNA polymerase I-transcribed genes (rDNA). Here we have analyzed the roles of two members of the xeroderma pigmentosum group C family of proteins, Rad4p and Rad34p, during NER in the active and inactive rDNA. We report that Rad4p is essential for repair in the intergenic spacer, the inactive rDNA coding region, and for strand-specific repair at the transcription initiation site, whereas Rad34p is not. Rad34p is necessary for transcription-coupled NER that starts about 40 nucleotides downstream of the transcription initiation site of the active rDNA, whereas Rad4p is not. Thus, although Rad4p and Rad34p share sequence homology, their roles in NER in the rDNA locus are almost entirely distinct and complementary. These results provide evidences that transcription-coupled NER and global genome NER participate in the removal of UV-induced DNA lesions from the transcribed strand of active rDNA. Furthermore, nonnucleosome rDNA is repaired faster than nucleosome rDNA, indicating that an open chromatin structure facilitates NER in vivo.

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