GLOSSARY

ARS: Autonomously replicating sequence; the origin of replication in yeast. Autoradiography: The detection of radioactive molecules (eg, DNA, RNA, protein) by visualization of their effects on photographic or x-ray film. Bacteriophage: A virus that infects a bacterium. Blunt-ended DNA: Two strands of a DNA duplex having ends that are flush with each other. cDNA: A single-stranded DNA molecule that is complementary to an mRNA molecule and is synthesized from it by the action of reverse transcriptase. Chimeric molecule: A molecule (eg, DNA, RNA, protein) containing sequences derived from two different species. Clone: A large number of organisms, cells or molecules that are identical with a single parental organism cell or molecule. Copy number variation (CNV): Change in the copy number of specific genomic regions of DNA between two or more individuals. CNVs can be as large as 106 bp of DNA and include deletions or insertions. Cosmid: A plasmid into which the DNA sequences from bacteriophage lambda that are necessary for the packaging of DNA (cos sites) have been inserted; this permits the plasmid DNA to be packaged in vitro. ENCODE Project: Encyclopedia of DNA Elements Project; an effort of multiple laboratories throughout the world to provide a detailed, biochemically informative representation of the human genome using high throughput sequencing methods to identify and catalog the functional elements within a single restricted portion (~1%; 30,000,000 bp) of one human chromosome. Endonuclease: An enzyme that cleaves internal bonds in DNA or RNA. Epigenetic code: The patterns of modification of chromosomal DNA (ie, cytosine methylation) and nucleosomal histone post-translational modifications. These changes in modification status can lead to dramatic alterations in gene expression. Notably though, the actual underlying DNA sequence involved does not change. Excinuclease: The excision nuclease involved in nucleotide exchange repair of DNA. Exon: The sequence of a gene that is represented (expressed) as mRNA. Exonuclease: An enzyme that cleaves nucleotides from either the 3' or 5' ends of DNA or RNA. Fingerprinting: The use of RFLPs or repeat sequence DNA to establish a unique pattern of DNA fragments for an individual. FISH: Fluorescence in situ hybidization, a method used to map the location of specific DNA sequences within fixed nuclei. Footprinting: DNA with protein bound is resistant to digestion by DNase enzymes. When a sequencing reaction is performed using such DNA, a protected area, representing the "footprint" of the bound protein, will be detected because nucleases are unable to cleave the DNA directly bound by the protein. Hairpin: A double-helical stretch formed by base pairing between neighboring complementary

if a radioactive nucleoside triphosphate is employed. DNA with RNA. Oligonucleotide: A short. Probe: A molecule used to detect the presence of a specific fragment of DNA or RNA in. 21–22 nucleotide long RNA species derived from RNA polymerase II transcription units. are thought to play crucial roles in gene regulation. Nick translation: A technique for labeling DNA based on the ability of the DNA polymerase from E coli to degrade a strand of DNA that has been nicked and then to resynthesize the strand. Hybridization: The specific reassociation of complementary strands of nucleic acids (DNA with DNA. 500–1500 bp in length via RNA processing. Ligation: The enzyme-catalyzed joining in phosphodiester linkage of two stretches of DNA or RNA into one. generally introduced by the techniques of recombinant DNA technology. Lines: Long interspersed repeat sequences. tRNA genes can also contain introns. Microsatellite repeat sequences: Dispersed or group repeat sequences of 2–5 bp repeated up to 50 times. in aggregate. Northern blot: A method for transferring RNA from an agarose or polyacrylamide gel to a nitrocellulose filter. These RNAs. Libraries may be either genomic DNA (in which both introns and exons are represented) or cDNA (in which only exons are represented). Plasmid: A small. Palindrome: A sequence of duplex DNA that is the same when the two strands are read in opposite directions. May occur at 50–100 thousand locations in the genome. Polymerase chain reaction (PCR): An enzymatic method for the repeated copying (and thus amplification) of the two strands of DNA that make up a particular gene sequence. PAC: A high-capacity (70–95 kb) cloning vector based upon the lytic E coli bacteriophage P1 that replicates in bacteria as an extrachromosomal element. the entire genome. Insert: An additional length of base pairs in DNA. Primosome: The mobile complex of helicase and primase that is involved in DNA replication. Ori: The origin of DNA replication. Intron: The sequence of an mRNA-encoding gene that is transcribed but excised before translation. Microsatellite polymorphism: Heterozygosity of a certain microsatellite repeat in an individual. the respective enzymes are DNA and RNA ligases. Library: A collection of cloned fragments that represents. the rebuilt strand becomes labeled and can be used as a radioactive probe.sequences of a single strand of DNA or RNA. or RNA with RNA). on which the RNA can be detected by a suitable probe. miRNAs: MicroRNAs. circular molecule of DNA that replicates independently of the host DNA. recently discovered. extrachromosomal. a bacterial colony that is formed from a genetic library or during analysis by blot transfer . for instance. defined sequence of nucleotides joined together in the typical phosphodiester linkage.

21–25 nt in length generated by selective nucleolytic degradation of double-stranded RNAs of cellular or viral origin. Reverse transcription: RNA-directed synthesis of DNA. This family of RNAs is best known for its role in mRNA processing. and U6) and many proteins. common probes are cDNA molecules. Sines: Short interspersed repeat sequences. synthetic oligodeoxynucleotides of defined sequence. above). The spliceosome consists of at least five small nuclear RNAs (snRNA. Proteome: The entire collection of expressed proteins in an organism. snRNA: Small nuclear RNA. Tandem: Used to describe multiple copies of the same sequence (eg. Restriction enzyme: An endodeoxynuclease that causes cleavage of both strands of DNA at highly specific sites dictated by the base sequence. on which the DNA can be detected by a suitable probe (eg. catalyzed by reverse transcriptase. U4. RT-PCR: A method used to quantitate mRNA levels that relies upon a first step of cDNA copying of mRNAs catalyzed by reverse transcriptase prior to PCR amplification and quantitation. Splicing: The removal of introns from RNA accompanied by the joining of its exons. Refers to the fact that single nucleotide genetic variation in genome sequence exists at discrete loci throughout the chromosomes. Transcription: Template DNA-directed synthesis of nucleic acids. DNA) that lie adjacent to one another. Hybridization with a complementary radioactive polynucleotide (eg. U1. or antibodies to specific proteins. Southern blot: A method for transferring DNA from an agarose gel to nitrocellulose filter.techniques. Terminal transferase: An enzyme that adds nucleotides of one type (eg. typically generated by transposition of a cDNA copy of an mRNA. deoxyadenonucleotidyl residues) to the 3' end of DNA strands. Sticky-ended DNA: Complementary single strands of DNA that protrude from opposite ends of a DNA duplex or from the ends of different duplex molecules (see also Blunt-ended DNA. complementary DNA or RNA). U2. U5." SNP: Single nucleotide polymorphism. Measurement of allelic SNP differences is useful for gene mapping studies. Signal: The end product observed when a specific sequence of DNA or RNA is detected by autoradiography or some other method. hence gene "knockdown. Pseudogene: An inactive segment of DNA arising by mutation of a parental active gene. Spliceosome: The macromolecular complex responsible for precursor mRNA splicing. typically DNA-directed synthesis . by Southern or Northern blotting) is commonly used to generate the signal. SiRNAs anneal to various specific sites within target in RNAs leading to mRNA degradation. Recombinant DNA: The altered DNA that results from the insertion of a sequence of deoxynucleotides not previously present into an existing molecule of DNA by enzymatic or chemical means. SiRNAs: Silencing RNAs. Southwestern blot: A method for detecting protein-DNA interactions by applying a labeled DNA probe to a transfer membrane that contains a renatured protein.

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