On the origin of the Alu family of repeated sequences

Organization of the gene encoding cellular nucleic acid-binding protein

The human cellular CNBP gene locus has been sequenced and is comprised of 6453 bp from the transcription start point (tsp) to the polyadenylation signal, and an additional 201 bp of 5' and 259 bp of 3' flanking sequences. The gene consists of five exons, four of which contain coding information for two alternatively spliced products, CNPB alpha and beta. The open reading frame (ORF) of 177 amino acids (aa) is encoded by exons 2 through 4 (CNBP alpha, M(r) 19463). The protein contains seven zinc-finger (Zf) domains. CNBP beta lacks seven aa in the linker region between the first two Zf, because of the use of an alternative 5' donor site within exon 2. The sixth Zf is the only Zf domain that is not completely encoded within a single exon and is interrupted by an intron (intron 4). The 5' untranslated region (UTR) contains 849 bp and is interrupted by intron 1. The 3' UTR, ending at the polyadenylation signal, is 857 bp long and is contained within exon 5. One Alu repeat was identified within intron 1, the largest intron of CNBP.

Porcine TNF: a review

One of the classical animal model systems in the study of important cardiovascular diseases, such as septic shock is that of swine. Important mediators of such disease states are different cytokines, among them tumor necrosis factor alpha (TNF-alpha) and beta (TNF-beta). This review aims to summarize the current knowledge about the primary structure and the regulation of the porcine TNF genes, as well as methods used to measure their respective proteins.

The complete sequence of the human beta-myosin heavy chain gene and a comparative analysis of its product

We have isolated and sequenced the gene and the cDNA coding for the human cardiac beta-myosin heavy chain (designated MYH7). The gene is 22,883 bp long. The 1935 amino acids of this protein (Mr223,111) are encoded by 38 exons. The 5' untranslated region (86 bp) is split by two introns. The 3' untranslated region is 114 bp long. Three Alu repeats were identified within the gene and a fourth one in the 3' flanking intergenic region. The molecular organization of this gene reflects the conservative pattern with respect to size, coding ratio, and number or position of introns characteristic of vertebrate sarcomeric myosin heavy chain genes. The protein sequence of the human beta-heavy chain was compared with corresponding (homologous) sequences of rabbit, rat, and hamster as well as with the (heterologous) embryonic heavy chain sequences of rat, chicken, and man. The results show that protein subregions responsible for basic functions of myosin heavy chains (nucleotide binding and actin binding) are very similar in homologous and heterologous heavy chains. Regions that differ in their primary sequences in heterologous heavy chains appear to be highly conserved within mammalian beta-myosin heavy chains. Constant and variable subregions of heavy chains are discussed in terms of functional significance and evolutionary relatedness.

RNA-mediated gene duplication: the rat preproinsulin I gene is a functional retroposon

Rats and mice have two, equally expressed, nonallelic genes encoding preproinsulin (genes I and II). Cytological hybridization with metaphase chromosomes indicated that both genes reside on rat chromosome I but are approximately 100,000 kilobases apart. In mice the two genes reside on two different chromosomes. DNA sequence comparisons of the gene-flanking regions in rats and mice indicated that the preproinsulin gene I has lost one of the two introns present in gene II, is flanked by a long (41-base) direct repeat, and has a remnant of a polydeoxyadenylate acid tract preceding the downstream direct repeat. These structural features indicated that gene I was generated by an RNA-mediated duplication-transposition event involving a transcript of gene II which was initiated upstream from the normal capping site. Sequence divergence analysis indicated that the pair of the original gene and its retroposed, but functional, counterpart (which appeared about 35 million years ago) is maintained by strong negative selection operating primarily on the segments encoding the chains of the mature hormone, whereas the segments encoding the parts of the polypeptide that are eliminated during processing and also the introns and the flanking regions are evolving neutrally.

The multiple origins of human Alu sequences

I have analyzed a collection of published human Alu sequences. The compiled sequences show several unexpected features, including a uniform pattern of divergence from their consensus sequence, a mutual divergence that is not correlated with their age, and common features in the genomic DNA flanking the 5' ends of the elements. I suggest that the Alu family of sequences derives from a large pool of precursors and not from a single precursor similar to the family consensus sequence, and that new elements integrate into the genome selectively at oligo-A-rich sites.

The population biology of transposable elements

A transposable element can be defined as a DNA sequence capable of moving to new sites in the genome. Such DNA sequences have been described in a wide range of organisms. The evolutionary processes affecting transposable elements can thus be divided into two categories: changes in sequence and changes in genomic location. As with other types of evolutionary change, the nature of the evolutionary process will be reflected in the extent and type of genetic variation existing in wild populations. Quantitative models of the evolution of transposable element sequences and positions will be outlined, and related to relevant data. The extent to which models designed to describe obvious transposable elements such as the mobile sequences of Drosophila are also applicable to interspersed repetitive DNAs from other species will be discussed.

RNA-mediated gene duplication: the rat preproinsulin I gene is a functional retroposon

Rats and mice have two, equally expressed, nonallelic genes encoding preproinsulin (genes I and II). Cytological hybridization with metaphase chromosomes indicated that both genes reside on rat chromosome I but are approximately 100,000 kilobases apart. In mice the two genes reside on two different chromosomes. DNA sequence comparisons of the gene-flanking regions in rats and mice indicated that the preproinsulin gene I has lost one of the two introns present in gene II, is flanked by a long (41-base) direct repeat, and has a remnant of a polydeoxyadenylate acid tract preceding the downstream direct repeat. These structural features indicated that gene I was generated by an RNA-mediated duplication-transposition event involving a transcript of gene II which was initiated upstream from the normal capping site. Sequence divergence analysis indicated that the pair of the original gene and its retroposed, but functional, counterpart (which appeared about 35 million years ago) is maintained by strong negative selection operating primarily on the segments encoding the chains of the mature hormone, whereas the segments encoding the parts of the polypeptide that are eliminated during processing and also the introns and the flanking regions are evolving neutrally.