Biomaterial Database

Developmentally programmed DNA rearrangement in Tetrahymena thermophila: isolation and sequence characterization of three new alternative deletion systems. 1996

M F Chau, and E Orias

Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara 93106, USA.

Extensive developmentally programmed DNA rearrangements, including thousands of internal deletions, occur in the differentiating somatic macronucleus in Tetrahymena thermophila. Some deletion systems involve the use of multiple alternative deletion sites. We report here the cloning and the sequences of three new alternative deletion systems (RR, RP and B) obtained using genomic subtraction. The RP and RR deletion systems are 2 kb apart on chromosome 1R, and both involve the removal of < 2 kb of micronuclear sequences. The B deletion system is on chromosome 5 and involves a deletion of > 5 kb. All three deleted regions are very AT rich (approximately 80%) and do not appear to encode any protein. Sequences of the regions flanking the deletion junctions of all three systems revealed no sequence similarity among them nor with any previously reported deletion systems, suggesting that different cis-acting elements are involved for rearrangement. Unlike other deletion systems in ciliates, the B deletion system lacks short terminal direct repeats. Our results suggest an average of at least one alternative deletion system per 134 kb of micronuclear DNA and lead to an estimate that at least 25% of all deletion systems in Tetrahymena utilize alternative ends. The genomic subtraction method employed in this study could prove useful for the isolation of alternatively deleted DNA in special-purpose cases in Tetrahymena and other ciliates. The hybridization parameters for genomic subtraction worked out here for highly AT-rich DNA may have wider usefulness.

UI	MeSH Term	Description	Entries
D008969	Molecular Sequence Data	Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.	Sequence Data, Molecular,Molecular Sequencing Data,Data, Molecular Sequence,Data, Molecular Sequencing,Sequencing Data, Molecular
D003001	Cloning, Molecular	The insertion of recombinant DNA molecules from prokaryotic and/or eukaryotic sources into a replicating vehicle, such as a plasmid or virus vector, and the introduction of the resultant hybrid molecules into recipient cells without altering the viability of those cells.	Molecular Cloning
D005820	Genetic Testing	Detection of a MUTATION; GENOTYPE; KARYOTYPE; or specific ALLELES associated with genetic traits, heritable diseases, or predisposition to a disease, or that may lead to the disease in descendants. It includes prenatal genetic testing.	Genetic Predisposition Testing,Genetic Screening,Predictive Genetic Testing,Predictive Testing, Genetic,Testing, Genetic Predisposition,Genetic Predictive Testing,Genetic Screenings,Genetic Testing, Predictive,Predisposition Testing, Genetic,Screening, Genetic,Screenings, Genetic,Testing, Genetic,Testing, Genetic Predictive,Testing, Predictive Genetic
D000818	Animals	Unicellular or multicellular, heterotrophic organisms, that have sensation and the power of voluntary movement. Under the older five kingdom paradigm, Animalia was one of the kingdoms. Under the modern three domain model, Animalia represents one of the many groups in the domain EUKARYOTA.	Animal,Metazoa,Animalia
D001483	Base Sequence	The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.	DNA Sequence,Nucleotide Sequence,RNA Sequence,DNA Sequences,Base Sequences,Nucleotide Sequences,RNA Sequences,Sequence, Base,Sequence, DNA,Sequence, Nucleotide,Sequence, RNA,Sequences, Base,Sequences, DNA,Sequences, Nucleotide,Sequences, RNA
D015139	Blotting, Southern	A method (first developed by E.M. Southern) for detection of DNA that has been electrophoretically separated and immobilized by blotting on nitrocellulose or other type of paper or nylon membrane followed by hybridization with labeled NUCLEIC ACID PROBES.	Southern Blotting,Blot, Southern,Southern Blot
D015183	Restriction Mapping	Use of restriction endonucleases to analyze and generate a physical map of genomes, genes, or other segments of DNA.	Endonuclease Mapping, Restriction,Enzyme Mapping, Restriction,Site Mapping, Restriction,Analysis, Restriction Enzyme,Enzyme Analysis, Restriction,Restriction Enzyme Analysis,Analyses, Restriction Enzyme,Endonuclease Mappings, Restriction,Enzyme Analyses, Restriction,Enzyme Mappings, Restriction,Mapping, Restriction,Mapping, Restriction Endonuclease,Mapping, Restriction Enzyme,Mapping, Restriction Site,Mappings, Restriction,Mappings, Restriction Endonuclease,Mappings, Restriction Enzyme,Mappings, Restriction Site,Restriction Endonuclease Mapping,Restriction Endonuclease Mappings,Restriction Enzyme Analyses,Restriction Enzyme Mapping,Restriction Enzyme Mappings,Restriction Mappings,Restriction Site Mapping,Restriction Site Mappings,Site Mappings, Restriction
D015321	Gene Rearrangement	The ordered rearrangement of gene regions by DNA recombination such as that which occurs normally during development.	DNA Rearrangement,DNA Rearrangements,Gene Rearrangements,Rearrangement, DNA,Rearrangement, Gene,Rearrangements, DNA,Rearrangements, Gene
D016054	DNA, Protozoan	Deoxyribonucleic acid that makes up the genetic material of protozoa.	Protozoan DNA
D016808	Tetrahymena thermophila	A species of ciliate protozoa used in genetic and cytological research.	Tetrahymena thermophilas,thermophilas, Tetrahymena