@article {38325, title = {A guild of 45 CRISPR-associated (Cas) protein families and multiple CRISPR/Cas subtypes exist in prokaryotic genomes}, journal = {PLoS computational biologyPLOS Computational Biology}, volume = {1}, year = {2005}, note = {http://www.ncbi.nlm.nih.gov/pubmed/16292354?dopt=Abstract}, type = {10.1371/journal.pcbi.0010060}, abstract = {Clustered regularly interspaced short palindromic repeats (CRISPRs) are a family of DNA direct repeats found in many prokaryotic genomes. Repeats of 21-37 bp typically show weak dyad symmetry and are separated by regularly sized, nonrepetitive spacer sequences. Four CRISPR-associated (Cas) protein families, designated Cas1 to Cas4, are strictly associated with CRISPR elements and always occur near a repeat cluster. Some spacers originate from mobile genetic elements and are thought to confer "immunity" against the elements that harbor these sequences. In the present study, we have systematically investigated uncharacterized proteins encoded in the vicinity of these CRISPRs and found many additional protein families that are strictly associated with CRISPR loci across multiple prokaryotic species. Multiple sequence alignments and hidden Markov models have been built for 45 Cas protein families. These models identify family members with high sensitivity and selectivity and classify key regulators of development, DevR and DevS, in Myxococcus xanthus as Cas proteins. These identifications show that CRISPR/cas gene regions can be quite large, with up to 20 different, tandem-arranged cas genes next to a repeat cluster or filling the region between two repeat clusters. Distinctive subsets of the collection of Cas proteins recur in phylogenetically distant species and correlate with characteristic repeat periodicity. The analyses presented here support initial proposals of mobility of these units, along with the likelihood that loci of different subtypes interact with one another as well as with host cell defensive, replicative, and regulatory systems. It is evident from this analysis that CRISPR/cas loci are larger, more complex, and more heterogeneous than previously appreciated.}, keywords = {Genes, Archaeal, Genes, Bacterial, Genes, Fungal, Genome, Genome, Bacterial, Haloarcula marismortui, Markov chains, Multigene Family, Oligonucleotide Array Sequence Analysis, Phylogeny, Prokaryotic Cells, Proteins, Repetitive Sequences, Nucleic Acid, Yersinia pestis}, author = {Haft, Daniel H. and J. Selengut and Mongodin, Emmanuel F. and Nelson, Karen E.} } @article {49699, title = {P element-mediated in vivo deletion analysis of white-apricot: deletions between direct repeats are strongly favored.}, journal = {Genetics}, volume = {136}, year = {1994}, month = {1994 Mar}, pages = {1001-11}, abstract = {

We have isolated and characterized deletions arising within a P transposon, P[hswa], in the presence of P transposase. P[hswa] carries white-apricot (wa) sequences, including a complete copia element, under the control of an hsp70 promoter, and resembles the original wa allele in eye color phenotype. In the presence of P transposase, P[hswa] shows a high overall rate (approximately 3\%) of germline mutations that result in increased eye pigmentation. Of 234 derivatives of P[hswa] with greatly increased eye pigmentation, at least 205 carried deletions within copia. Of these, 201 were precise deletions between the directly repeated 276-nucleotide copia long terminal repeats (LTRs), and four were unique deletions. High rates of transposase-induced precise deletion were observed within another P transposon carrying unrelated 599 nucleotide repeats (yeast 2 mu FLP; recombinase target sites) separated by 5.7 kb. Our observation that P element-mediated deletion formation occurs preferentially between direct repeats suggests general methods for controlling deletion formation.

}, keywords = {Alleles, Animals, Animals, Genetically Modified, Base Sequence, Crosses, Genetic, DNA, DNA Transposable Elements, Drosophila, Eye Color, Female, Genes, Insect, Male, Molecular Sequence Data, Nucleotidyltransferases, PHENOTYPE, Recombination, Genetic, Repetitive Sequences, Nucleic Acid, Sequence Deletion, Transformation, Genetic, Transposases}, issn = {0016-6731}, author = {Kurkulos, M and Weinberg, J M and Roy, D and Mount, S M} } @article {49703, title = {Polyadenylylation in copia requires unusually distant upstream sequences.}, journal = {Proc Natl Acad Sci U S A}, volume = {88}, year = {1991}, month = {1991 Apr 15}, pages = {3038-42}, abstract = {

Retroviruses and related genetic elements generate terminally redundant RNA products by differential polyadenylylation within a long terminal repeat. Expression of the white-apricot (wa) allele of Drosophila melanogaster, which carries an insertion of the 5.1-kilobase retrovirus-like transposable element copia in a small intron, is influenced by signals within copia. By using this indicator, we have isolated a 518-base-pair deletion, 312 base pairs upstream of the copia polyadenylylation site, that is phenotypically like much larger deletions and eliminates RNA species polyadenylylated in copia. This requirement of distant upstream sequences for copia polyadenylylation has implications for the expression of many genetic elements bearing long terminal repeats.

}, keywords = {Animals, Base Sequence, Blotting, Northern, DNA Transposable Elements, Drosophila melanogaster, Eye Color, Molecular Sequence Data, Oligonucleotides, Polymerase Chain Reaction, Regulatory Sequences, Nucleic Acid, Repetitive Sequences, Nucleic Acid, RNA Processing, Post-Transcriptional, RNA, Messenger}, issn = {0027-8424}, author = {Kurkulos, M and Weinberg, J M and Pepling, M E and Mount, S M} } @article {49710, title = {Complete nucleotide sequence of the Drosophila transposable element copia: homology between copia and retroviral proteins.}, journal = {Mol Cell Biol}, volume = {5}, year = {1985}, month = {1985 Jul}, pages = {1630-8}, abstract = {

We have determined the complete nucleotide sequence of the copia element present at the white-apricot allele of the white locus in Drosophila melanogaster. This transposable element is 5,146 nucleotides long and contains a single long open reading frame of 4,227 nucleotides. Analysis of the coding potential of the large open reading frame, which appears to encode a polyprotein, revealed weak homology to a number of retroviral proteins, including a protease, nucleic acid-binding protein, and reverse transcriptase. Better homology existed between another part of the copia open reading frame and a region of the retroviral pol gene recently shown to be distinct from reverse transcriptase and required for the integration of circular DNA forms of the retroviral genome to form proviruses. Comparison of the copia sequence with those of the Saccharomyces cerevisiae transposable element Ty, several vertebrate retroviruses, and the D. melanogaster copia-like element 17.6 showed that Ty was most similar to copia, sharing amino acid sequence homology and organizational features not found in the other genetic elements.

}, keywords = {Amino Acid Sequence, Animals, Base Sequence, Codon, DNA Helicases, DNA Transposable Elements, Drosophila melanogaster, Gene Expression Regulation, Gene Products, gag, Integrases, Repetitive Sequences, Nucleic Acid, Retroviridae, RNA-Directed DNA Polymerase, Viral Envelope Proteins, Viral Proteins}, issn = {0270-7306}, author = {Mount, S M and Rubin, G M} } @article {49715, title = {Pseudogenes for human small nuclear RNA U3 appear to arise by integration of self-primed reverse transcripts of the RNA into new chromosomal sites.}, journal = {Cell}, volume = {32}, year = {1983}, month = {1983 Feb}, pages = {461-72}, abstract = {

We find that both human and rat U3 snRNA can function as self-priming templates for AMV reverse transcriptase in vitro. The 74 base cDNA is primed by the 3{\textquoteright} end of intact U3 snRNA, and spans the characteristically truncated 69 or 70 base U3 sequence found in four different human U3 pseudogenes. The ability of human and rat U3 snRNA to self-prime is consistent with a U3 secondary structure model derived by a comparison between rat U3 snRNA and the homologous D2 snRNA from Dictyostelium discoideum. We propose that U3 pseudogenes are generated in vivo by integration of a self-primed cDNA copy of U3 snRNA at new chromosomal sites. We also consider the possibility that the same cDNA mediates gene conversion at the 5{\textquoteright} end of bona fide U3 genes where, over the entire region spanned by the U3 cDNA, the two rat U3 sequence variants U3A and U3B are identical.

}, keywords = {Animals, Base Sequence, DNA, genes, HUMANS, Nucleic Acid Conformation, Rats, Recombination, Genetic, Repetitive Sequences, Nucleic Acid, RNA, RNA, Small Nuclear, RNA-Directed DNA Polymerase, Templates, Genetic, Transcription, Genetic}, issn = {0092-8674}, author = {Bernstein, L B and Mount, S M and Weiner, A M} } @article {49717, title = {A catalogue of splice junction sequences.}, journal = {Nucleic Acids Res}, volume = {10}, year = {1982}, month = {1982 Jan 22}, pages = {459-72}, abstract = {

Splice junction sequences from a large number of nuclear and viral genes encoding protein have been collected. The sequence CAAG/GTAGAGT was found to be a consensus of 139 exon-intron boundaries (or donor sequences) and (TC)nNCTAG/G was found to be a consensus of 130 intron-exon boundaries (or acceptor sequences). The possible role of splice junction sequences as signals for processing is discussed.

}, keywords = {Animals, Base Sequence, genes, Genes, Viral, HUMANS, Repetitive Sequences, Nucleic Acid, RNA Splicing, Species Specificity}, issn = {0305-1048}, author = {Mount, S M} }