Genomics Glossary

Fluorescent in situ hybridization (FISH)

A technique in which a fluorescent dye is attached to a nucleotide probe that then binds to a specific site on a chromosome and makes itself visible by its fluorescence.

Gene family

A group of genes that has arisen by duplication and divergence of an ancestral gene. Some genes in the family may not have diverged. The members of a gene family may include expressed genes as well as non-expressed sequences. Such non-expressed sequences include pseudogenes.

Bacterial artificial chromosomes (BACs)

Artificial chromosomes used for sequencing that are derived from bacterial fertility factors (F plasmids).

Centromere

Constrictions in eukaryotic chromosomes on which the kinetochore lies. Also,the DNA sequence within the constriction that is responsible for appropriate function.

Chromosome jumping

A technique for isolating clones from a genomic library that are not contiguous but skip a region between known points on the chromosome.This is usually done to bypass regions that are difficult or impossible to "walk" through or regions known not to be of interest.

Chromosome walking

A technique for studying segments of DNA,lar ger than can be individually cloned,b y using overlapping cloned DNA.

Classical linkage map

A chromosomal map,measured in centimorgans,based on genetic crosses to locate the relative

distances between genes and their relative locations on chromosomes.

Clone

A group of cells arising from a single ancestor.

Density-gradient centrifugation

A method of separating molecular entities by their differential sedimentation in a centrifugal gradient.

Dideoxy method

A method of DNA sequencing that uses chain-terminating (dideoxy) nucleotides.

DNA fingerprint

A pattern of bands created on an electrophoretic gel of a DNA digest probed for a variable locus.

DNA sequencing

A process by which the sequence of nucleotides along a strand of DNA is determined.

Double digest

The product formed when two different restriction endonucleases act on the same segment of DNA.

Downstream A convention on DNA related to the position and direction of transcription by RNA polymerase (5'→3'). Downstream (in the 3' direction) is in the direction of transcription, whereas upstream (in the 5' direction) is in the direction from which the polymerase has come.

Electrophoresis

The separation of molecular entities by electric current.

Electroporation

A technique for transfecting cells by applying a high-voltage electric pulse.

Endonucleases

Enzymes that make nicks internally in the backbone of a polynucleotide.They hydrolyze internal phosphodiester bonds.

Euchromatin

Regions of eukaryotic chromosomes that are diffuse during interphase. Presumably the actively transcribing DNA of the chromosomes.

Exon

In a gene that has intervening sequences (introns), a region that is actually exported from the nucleus to be expressed or become part of a transfer or ribosomal RNA.

Exonucleases

Enzymes that digest nucleotides from the ends of polynucleotide molecules. They hydrolyze phosphodiester bonds of terminal nucleotides.

Fluorescent in situ hybridization (FISH)

A technique in which a fluorescent dye is attached to a nucleotide probe that then binds to a specific site on a chromosome and makes itself visible by its fluorescence.

G-bands

Eukaryotic chromosomal bands produced by treatment with Giemsa stain.

Gene

Inherited determinant of the phenotype. See cistron; locus.

Gene cloning

Production of large numbers of a piece of DNA after that piece of DNA is inserted into a vector and taken up by a cell. Cloning occurs as the vector replicates.

Gene family

A group of genes that has arisen by duplication and divergence of an ancestral gene. Some genes in the family may not have diverged. The members of a gene family may include expressed genes as well as non-expressed sequences. Such non-expressed sequences include pseudogenes.

Genetic Marker

A gene or DNA sequence having a known location on a chromosome and associated with a particular gene or trait.

It can be described as some sort of variation present can arise due to mutation or alteration in the genomic loci that can be observed. A genetic marker may be a short DNA sequence, such as a sequence surrounding a single base-pair change (SNP), or a long one, like microsatellites. Some commonly used types of genetic markers are RFLP, VNTR, Microsatellite Polymorphism, SNP, STR.

Genetic polymorphism

The occurrence together in the same population of more than one allele at the same locus,with the least frequent allele occurring more frequently than can be accounted for by mutation.

Genome

The entire genetic complement of a prokaryote or virus or the haploid genetic complement of a eukaryote.

Genomic library

A set of cloned fragments making up the entire genome of an organism or species.

Genomics

The study of the mapping and sequencing of genomes. Bioinformatics is the science of mining the data from these DNA sequences obtained from sequencing.

Giemsa stain

A complex of stains specific for the phosphate groups of DNA.

Heterokaryon

A cell that contains two or more nuclei from different origins.

Highly repetitive DNA

Very short sequences (typically < 100 bp) that are present many thousands of times in the genome, often organized as long tandem repeats.

Histones

Arginine- and lysine-rich basic proteins making up a substantial portion of eukaryotic nucleoprotein.

in vitro

Biological or chemical work done in the test tube (literally,"in glass") rather than in living systems.

Introns (intervening sequences)

DNA sequences within a gene that are transcribed but removed prior to translation.

JunkDNA

DNA that is not useful to the organism, made up of untranscribed and parasitic sequences (selfish DNA).

Karyotype

The chromosome complement of a cell. See idiogram.

Leader

The length of messenger RNA from the 5' end to the initiation codon, AUG.

Locus

The position of a gene on a chromosome (plural: loci ).

Long interspersed elements (LINEs)

Sequences of DNA,up to seven thousand base pairs in length, interspersed in eukaryotic chromosomes in many copies.

Mapping

The process of locating the positions of genes on chromosomes.

Microsatellite DNA

Repeats of very short sequences of DNA, such as CACACACA, dispersed throughout the eukaryotic genome. The loci can be studied by polymerase chain reaction amplification.

Moderately repetitive DNA

Relatively short sequences that are repeated typically 10-1000X in the genome. The sequences are dispersed throughout the genome.

Modern linkage map

A chromosomal map based on the positions of RFLP markers along its length.

Nucleosomes

Arrangements of DNA and histones forming regular spherical structures in eukaryotic chromatin.

Open reading frames (ORFs)

Sequence of codons between the initiation and termination codons in a gene.

Partial digest

A restriction digest that has not been allowed to go to completion, and thus contains pieces of DNA that have restriction endonuclease sites that have not been cleaved.

Physical map

A map in which distances are in physical units of base pairs.

Plasmid

An autonomous,self-replicating genetic particle,usuall y of double-stranded DNA.

Polymerase chain reaction (PCR)

A method to amplify DNA segments rapidly in temperature-controlled cycles of denaturation, primer binding, and replication.

Probe

In recombinant DNA work, a radioactive nucleic acid complementary to a region being searched for in a restriction digest or genomic library.

Pseudogenes

Defective copies of functional genes. These may be partial or complete duplicates derived from polypeptide-encoding genes or RNA genes.

The α-globin gene cluster consists of three functional genes and three pseudogenes. There is also an additional gene that is expressed but not incorporated into a hemoglobin molecule. In other words, this would be an example of an expressed pseudogene. The β-globin gene complex consists of five functional genes and one pseudogene.

Restriction endonucleases

Endonucleases that recognize certain DNA sequences, then cleave them. They protect cells from viral infection; they are useful in recombinant DNA work.

Restriction fragment length polymorphism (RFLP)

Variations (among individuals) in banding patterns of electrophoresed restriction digests.

Restriction map

A physical map of a piece of DNA showing recognition sites of specific restriction endonucleases separated by lengths marked in numbers of bases.

Restriction site

The sequence of DNA recognized by a restriction endonuclease.

Retrotransposons

Transposable genetic elements found in eukaryotic DNA that move through the reverse transcription of an RNA intermediate.

Retrotransposons

Transposable genetic elements found in eukaryotic DNA that move through the reverse transcription of an RNA intermediate.

RNA polymerase

The enzyme that polymerizes RNA by using DNA as a template. (Also known as transcriptase or RNA transcriptase.)

Satellite DNA

Highly repetitive eukaryotic DNA primarily located around centromeres. Satellite DNA usually has a different buoyant density than the rest of the cell's DNA.

Sequence-tagged sites (STSs)

DNA lengths of 100–500 base pairs that are unique in the genome. They are created by polymerase chain reaction amplification of primers that are then tested to be sure the sequence is unique.

Short interspersed elements (SINEs)

Sequences of DNA interspersed in eukaryotic chromosomes in many copies. Alu,a three hundred base-pair sequence, is found about half a million times in human DNA.

Shotgun cloning

The random cloning of pieces of the DNA of an organism without regard to the genes or sequences present in the cloned DNA.

single-nucleotide polymorphisms (SNPs)

Differences between individuals involving single base pairs that are located about every 1,000 bases along the human genome. SNPs are useful for mapping disease genes.

Small nuclear ribonucleoproteins (snRNPs)

Components of the spliceosome,the intron-removing apparatus in eukaryotic nuclei.

Small nucleolar ribonucleoprotein particles (snoRNPs)

Particles composed of RNA and protein found in the nucleolus that modify ribosomal RNAs, par ticularly by converting some uridines to pseudouridines and methylating some ribose sugars.

snRNPs

See small nuclear ribonucleoprotiens.

Southern blotting

A method,first devised by E.M. Southern, used to transfer DNA fragments from an agarose gel to a nitrocellulose gel for the purpose of DNA-DNA or DNA-RNA hybridization during recombinant DNA work.

Tandem

Having identical components arranged one behind the other.

Telomeres

The ends of linear chromosomes.

Terminator sequence

A sequence in DNA that signals the termination of transcription to RNA polymerase.

Trailer

The length of messenger RNA from the nonsense codon to the 3' end or, in polycistronic messenger RNAs, from a nonsense codon to the next gene's leader.

Transduction

A process whereby a cell can gain access to and incorporate foreign DNA brought in by a viral particle.

Transfection

The introduction of foreign DNA into eukaryotic cells.

Transformation

A process whereby prokaryotes take up DNA from the environment and incorporate it into their

genomes, or the conversion of a eukaryotic cell into a cancerous one.

transposable genetic element

A region of the genome, flanked by inverted repeats, a copy of which can be inserted at another place; also called a transposon or a jumping gene.

Transposon

See transposable genetic element.

Unequal crossing over

Nonreciprocal crossing over caused by the mismatching of homologous chromosomes. Usually occurs in regions of tandem repeats.

Unique DNA

A length of DNA with no repetitive nucleotide sequences.

Upstream

A convention on DNA related to the position and direction of transcription by RNA polymerase (5'→3'). Downstream (or 3' to) is in the direction of transcription whereas upstream (5' to) is in the direction from which the polymerase has come.

Variable-number-of-tandem-repeats (VNTR) loci

Loci that are hypervariable because of tandem repeats. Presumably, variability is generated by unequal crossing over.

Western blotting

A technique for probing for a particular protein using antibodies. See Southern blotting.

Whole-genome shotgun method

A method of sequencing entire genomes by breaking up the genomes into small pieces, sequencing the pieces, and then using computers to establish order by overlapping the sequences.

Yeast artificial chromosome (YAC)

Originating from a bacterial plasmid,a YAC contains additionally a yeast centromeric region (CEN) and a yeast origin of DNA replication (ARS).YACs are capable of including large pieces of foreign DNA during cloning.