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  • 1
    Electronic Resource
    Electronic Resource
    Dense Alu clustering and a potential new member of the NFκB family within a 90 kilobase HLA Class III segment (1993)
    [s.l.] : Nature Publishing Group
    Nature genetics 3 (1993), S. 137-145 
    Details
    ISSN: 1546-1718
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Medicine
    Notes: [Auszug] We have conducted a detailed structural analysis of 90 kilobases (kb) of the HLA Class III region from the Bat2 gene at the centromeric end to 23 kb beyond TNF. A single contig of 80 kb was sequenced entirely with a group of four smaller contigs covering 10 kb being only partly sequenced. This ...
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1038/ng0293-137
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  • 2
    Electronic Resource
    Electronic Resource
    Distinct catalytic and non-catalytic roles of ARGONAUTE4 in RNA-directed DNA methylation (2006)
    [s.l.] : Nature Publishing Group
    Nature 443 (2006), S. 1008-1012 
    Details
    ISSN: 1476-4687
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Notes: [Auszug] DNA methylation has important functions in stable, transcriptional gene silencing, immobilization of transposable elements and genome organization. In Arabidopsis, DNA methylation can be induced by double-stranded RNA through the RNA interference (RNAi) pathway, a response known as ...
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1038/nature05198
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  • 3
    Electronic Resource
    Electronic Resource
    Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences (2007)
    [s.l.] : Nature Publishing Group
    Nature 447 (2007), S. 167-177 
    Details
    ISSN: 1476-4687
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Notes: [Auszug] We report a high-quality draft of the genome sequence of the grey, short-tailed opossum (Monodelphis domestica). As the first metatherian (‘marsupial’) species to be sequenced, the opossum provides a unique perspective on the organization and evolution of mammalian genomes. Distinctive ...
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1038/nature05805
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  • 4
    Electronic Resource
    Electronic Resource
    Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzae (2005)
    [s.l.] : Nature Publishing Group
    Nature 438 (2005), S. 1105-1115 
    Details
    ISSN: 1476-4687
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Notes: [Auszug] The aspergilli comprise a diverse group of filamentous fungi spanning over 200 million years of evolution. Here we report the genome sequence of the model organism Aspergillus nidulans, and a comparative study with Aspergillus fumigatus, a serious human pathogen, and Aspergillus oryzae, used in the ...
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1038/nature04341
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  • 5
    Electronic Resource
    Electronic Resource
    Integration of Retroposable Elements in Mammals: Selection of Target Sites (1996)
    Springer
    Journal of molecular evolution 43 (1996), S. 685-689 
    Details
    ISSN: 1432-1432
    Keywords: Key words: Retroposons — Integration targets — Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract. Genomic DNA fragments generated by the reverse transcription of cellular RNA are called retroposons. Because they are flanked by short repeats, mammalian retroposons are believed to integrate at staggered chromosomal breaks. Recently, a significant sequence pattern associated with the integration of Alu and ID repeats was identified (Jurka 1996). It is represented by the 5′ TTAAAA consensus sequence around the 5′ ends of flanking repeats of Alu, ID, as well as, of B1 and B2 retroposed elements as shown in this paper. This consensus is a potential target for enzymatic nicking which probably occurs in the complementary strand between 3′ AA and the following 3′ TTTT bases. The first four bases of the flanking repeats corresponding to the 3′ TTTT consensus sequence show some sequence variations that may be affected by complementary base pairing between the A-rich RNA tails and the DNA target sequences prior to nicking and reverse transcription. We discuss potential evidence for such base pairing based on correlated variations in nucleotide composition of different tail and target regions.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02202117
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  • 6
    Electronic Resource
    Electronic Resource
    Integration of retroposable elements in mammals: Selection of target sites (1996)
    Springer
    Journal of molecular evolution 43 (1996), S. 685-689 
    Details
    ISSN: 1432-1432
    Keywords: Retroposons ; Integration targets ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Genomic DNA fragments generated by the reverse transcription of cellular RNA are called retroposons. Because they are flanked by short repeats, mammalian retroposons are believed to integrate at staggered chromosomal breaks. Recently, a significant sequence pattern associated with the integration of Alu and ID repeats was identified (Jurka 1996). It is represented by the 5′ TTAAAA consensus sequence around the 5′ ends of flanking repeats of Alu, ID, as well as, of B1 and B2 retroposed elements as shown in this paper. This consensus is a potential target for enzymatic nicking which probably occurs in the complementary strand between 3′ AA and the following 3′ TTTT bases. The first four bases of the flanking repeats corresponding to the 3′ TTTT consensus sequence show some sequence variations that may be affected by complementary base pairing between the A-rich RNA tails and the DNA target sequences prior to nicking and reverse transcription. We discuss potential evidence for such base pairing based on correlated variations in nucleotide composition of different tail and target regions.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02202117
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  • 7
    Electronic Resource
    Electronic Resource
    The Length Distribution of Perfect Dimer Repetitive DNA Is Consistent with Its Evolution by an Unbiased Single-Step Mutation Process (1997)
    Springer
    Journal of molecular evolution 44 (1997), S. 414 -421 
    Details
    ISSN: 1432-1432
    Keywords: Key words: Repeats — Repetitive DNA — Microsatellites — Evolution — Dimers
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract. We have examined the length distribution of perfect dimer repeats, where perfect means uninterrupted by any other base, using data from GenBank on primates and rodents. Virtually no lengths greater than 30 repeats are found, except for rodent AG repeats, which extend to 35. Comparable numbers of long AC and AG repeats suggest that they have not been selected for special functions or DNA structures. We have compared the data with predictions of two models: (1) a Bernoulli Model in which bases are assumed equally likely and distributed at random and (2) an Unbiased Random Walk Model (URWM) in which repeats are permitted to change length by plus or minus one unit, with equal probabilities, and in which base substitutions are allowed to destroy long perfect repeats, producing two shorter perfect repeats. The source of repeats is assumed to be from single base substutions from neighboring sequences, i.e., those differing from the perfect repeat by a single base. Mutation rates either independent of repeat length or proportional to length were considered. An upper limit to the lengths L≈ 30 is assumed and isolated dimers are assumed unable to expand, so that there are absorbing barriers to the random walk at lengths 1 and L+ 1, and a steady state of lengths is reached. With these assumptions and estimated values for the rates of length mutation and base substitution, reasonable agreement is found with the data for lengths 〉 5 repeats. Shorter repeats, of lengths ≤ 3 are in general agreement with the Bernoulli Model. By reducing the rate of length mutations for n≤ 5, it is possible to obtain reasonable agreement with the full range of data. For these reduced rates, the times between length mutations become comparable to those suggested for a bottleneck in the evolution of Homo sapiens, which may be the reason for low heterozygosity of short repeats.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/PL00006161
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  • 8
    Electronic Resource
    Electronic Resource
    The Long Terminal Repeat of an Endogenous Retrovirus Induces Alternative Splicing and Encodes an Additional Carboxy-Terminal Sequence in the Human Leptin Receptor (1999)
    Springer
    Journal of molecular evolution 48 (1999), S. 248-251 
    Details
    ISSN: 1432-1432
    Keywords: Key words: Leptin receptor — Retrovirus — Long terminal repeats — Alternative splicing
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract. The evolution of mammalian protein structure and regulation, specifically transcriptional and posttranscriptional regulation, may include among its tools the use of abundant retroviral long terminal repeats (LTRs). In particular, LTRs may be turned into switches for alternative splicing. This type of regulatory pathway is illustrated by the alternative splicing in the human leptin receptor (OBR). The human leptin receptor is involved in the control of important biological processes including energy expenditure, production of sex hormones, and activation of hemopoietic cells. OBRa and OBRb are the two major, alternatively spliced forms of the leptin receptor, called the ``short form'' and the ``long form,'' respectively. We report that the OBRa short form is the result of a double splicing event which occurs within the LTR of the endogenous retrovirus HERV-K. Working as a switch of alternative splicing, this LTR also encodes the terminal 67 amino acid residues in OBRa. We suggest the possibility of transcriptional and posttranscriptional regulation of OBR expression by steroids that bind the LTR.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/PL00013153
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  • 9
    Electronic Resource
    Electronic Resource
    The BC200 RNA Gene and Its Neural Expression Are Conserved in Anthropoidea (Primates) (1998)
    Springer
    Journal of molecular evolution 47 (1998), S. 677-685 
    Details
    ISSN: 1432-1432
    Keywords: Key words: Primates — Anthropoidea — Monomeric Alu repetitive element — Exaptation — BC200 small cytoplasmic RNA — Neural expression — Ribonucleoprotein complex (RNP)
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract. The gene encoding BC200 RNA arose from a monomeric Alu element. Subsequently, the RNA had been recruited or exapted into a function of the nervous system. Here we confirm the presence of the BC200 gene in several primate species among the Anthropoidea. The period following the divergence of New World monkeys and Old World monkeys from their common ancestor is characterized by a significantly higher substitution rate in the examined 5′ flanking region than in the BC200 RNA coding region itself. Furthermore, the conservation of CpG dimers in the RNA coding region (200 bp) is drastically increased compared to the 5′ flanking region (∼400 bp) over all 12 species examined. Finally, the brain-specific expression pattern of BC200 RNA and its presence as a ribonucleoprotein particle (RNP) are conserved in Old World and New World monkeys. Our studies indicate that the gene encoding BC200 RNA was created at least 35–55 million years ago and its presence, mode of expression, and association with protein(s) as an RNP are under selective pressure.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/PL00006426
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  • 10
    Electronic Resource
    Electronic Resource
    Globular proteins, GU wobbling, and the evolution of the genetic code (1982)
    Springer
    Journal of molecular evolution 19 (1982), S. 20-27 
    Details
    ISSN: 1432-1432
    Keywords: GU base pairing ; RNA replication ; Globular proteins ; Genetic code ; Evolution
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary It has previously been shown that the formation of GU base pairs in RNA copying processes leads to an accumulation of G and U in both strands of the replicating RNA, which results in a non-random distribution of base triplets. In the present paper, this distribution is calculated, and, using the χ2-test, a correlation between the distribution of triplets and the amino acid composition of the evolutionarily conservative interior regions of selected globular proteins is established. It is suggested that GU wobbling in early replication of RNA could have led to the observed amino acid composition of present-day protein interiors. If this hypothesis is correct, the GU wobbling must have been very extensive in the imprecisely replicating RNA, even reaching values close to the critical for stability of its double-helical structure. Implications of the hypothesis both for the evolution of the genetic code and of proteins are discussed.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02100220
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