Genomic organization
Encyclopedia
Organism
s have a vast array of ways in which their respective genome
s are organized. A comparison of the genomic organization of six major model organisms shows size expansion with the increase of complexity
of the organism. There is a more than 300-fold difference between the genome sizes of yeast
and mammal
s, but only a modest 4- to 5-fold increase in overall gene
number (see the figure on the right). However, the ratio of coding to noncoding and repetitive sequences is indicative of the complexity of the genome: The largely "open" genomes of unicellular fungi have relatively little noncoding DNA
compared with the highly heterochromatic
genomes of multicellular organisms.
In particular, mammals have accumulated considerable repetitive elements and noncoding regions, which account for the majority of their DNA sequences (52% non-coding and 44% repetitive DNA). Only 1.2% of the mammalian genome thus encodes for protein
function. This massive expansion of repetitive and noncoding sequences in multicellular organisms is most likely due to the incorporation of invasive elements, such as DNA transposon
s, retrotransposon
s, and other repetitive elements. The expansion of repetitive elements (such as Alu sequence
s) has even infiltrated the transcriptional
units of the mammalian genome. This results in transcription units that are frequently much larger (30-200 kb), commonly containing multiple promoters and DNA repeats within untranslated intron
s.
The vast expansion of the genome with noncoding and repetitive DNA in higher eukaryote
s implies more extensive epigenetic
silencing mechanisms. Studies of the genomic organization is thought to be the future of genomic medicine
, which will provide the opportunity for personalized prognoses
in clinics.
Organism
In biology, an organism is any contiguous living system . In at least some form, all organisms are capable of response to stimuli, reproduction, growth and development, and maintenance of homoeostasis as a stable whole.An organism may either be unicellular or, as in the case of humans, comprise...
s have a vast array of ways in which their respective genome
Genome
In modern molecular biology and genetics, the genome is the entirety of an organism's hereditary information. It is encoded either in DNA or, for many types of virus, in RNA. The genome includes both the genes and the non-coding sequences of the DNA/RNA....
s are organized. A comparison of the genomic organization of six major model organisms shows size expansion with the increase of complexity
Complexity
In general usage, complexity tends to be used to characterize something with many parts in intricate arrangement. The study of these complex linkages is the main goal of complex systems theory. In science there are at this time a number of approaches to characterizing complexity, many of which are...
of the organism. There is a more than 300-fold difference between the genome sizes of yeast
Yeast
Yeasts are eukaryotic micro-organisms classified in the kingdom Fungi, with 1,500 species currently described estimated to be only 1% of all fungal species. Most reproduce asexually by mitosis, and many do so by an asymmetric division process called budding...
and mammal
Mammal
Mammals are members of a class of air-breathing vertebrate animals characterised by the possession of endothermy, hair, three middle ear bones, and mammary glands functional in mothers with young...
s, but only a modest 4- to 5-fold increase in overall gene
Gene
A gene is a molecular unit of heredity of a living organism. It is a name given to some stretches of DNA and RNA that code for a type of protein or for an RNA chain that has a function in the organism. Living beings depend on genes, as they specify all proteins and functional RNA chains...
number (see the figure on the right). However, the ratio of coding to noncoding and repetitive sequences is indicative of the complexity of the genome: The largely "open" genomes of unicellular fungi have relatively little noncoding DNA
DNA
Deoxyribonucleic acid is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms . The DNA segments that carry this genetic information are called genes, but other DNA sequences have structural purposes, or are involved in...
compared with the highly heterochromatic
Heterochromatin
Heterochromatin is a tightly packed form of DNA, which comes in different varieties. These varieties lie on a continuum between the two extremes of constitutive and facultative heterochromatin...
genomes of multicellular organisms.
In particular, mammals have accumulated considerable repetitive elements and noncoding regions, which account for the majority of their DNA sequences (52% non-coding and 44% repetitive DNA). Only 1.2% of the mammalian genome thus encodes for protein
Protein
Proteins are biochemical compounds consisting of one or more polypeptides typically folded into a globular or fibrous form, facilitating a biological function. A polypeptide is a single linear polymer chain of amino acids bonded together by peptide bonds between the carboxyl and amino groups of...
function. This massive expansion of repetitive and noncoding sequences in multicellular organisms is most likely due to the incorporation of invasive elements, such as DNA transposon
Transposon
Transposable elements are sequences of DNA that can move or transpose themselves to new positions within the genome of a single cell. The mechanism of transposition can be either "copy and paste" or "cut and paste". Transposition can create phenotypically significant mutations and alter the cell's...
s, retrotransposon
Retrotransposon
Retrotransposons are genetic elements that can amplify themselves in a genome and are ubiquitous components of the DNA of many eukaryotic organisms. They are a subclass of transposon. They are particularly abundant in plants, where they are often a principal component of nuclear DNA...
s, and other repetitive elements. The expansion of repetitive elements (such as Alu sequence
Alu sequence
An Alu element is a short stretch of DNA originally characterized by the action of the Alu restriction endonuclease. Alu elements of different kinds occur in large numbers in primate genomes. In fact, Alu elements are the most abundant mobile elements in the human genome. They are derived from the...
s) has even infiltrated the transcriptional
Transcription (genetics)
Transcription is the process of creating a complementary RNA copy of a sequence of DNA. Both RNA and DNA are nucleic acids, which use base pairs of nucleotides as a complementary language that can be converted back and forth from DNA to RNA by the action of the correct enzymes...
units of the mammalian genome. This results in transcription units that are frequently much larger (30-200 kb), commonly containing multiple promoters and DNA repeats within untranslated intron
Intron
An intron is any nucleotide sequence within a gene that is removed by RNA splicing to generate the final mature RNA product of a gene. The term intron refers to both the DNA sequence within a gene, and the corresponding sequence in RNA transcripts. Sequences that are joined together in the final...
s.
The vast expansion of the genome with noncoding and repetitive DNA in higher eukaryote
Eukaryote
A eukaryote is an organism whose cells contain complex structures enclosed within membranes. Eukaryotes may more formally be referred to as the taxon Eukarya or Eukaryota. The defining membrane-bound structure that sets eukaryotic cells apart from prokaryotic cells is the nucleus, or nuclear...
s implies more extensive epigenetic
Epigenetics
In biology, and specifically genetics, epigenetics is the study of heritable changes in gene expression or cellular phenotype caused by mechanisms other than changes in the underlying DNA sequence – hence the name epi- -genetics...
silencing mechanisms. Studies of the genomic organization is thought to be the future of genomic medicine
Medicine
Medicine is the science and art of healing. It encompasses a variety of health care practices evolved to maintain and restore health by the prevention and treatment of illness....
, which will provide the opportunity for personalized prognoses
Prognosis
Prognosis is a medical term to describe the likely outcome of an illness.When applied to large statistical populations, prognostic estimates can be very accurate: for example the statement "45% of patients with severe septic shock will die within 28 days" can be made with some confidence, because...
in clinics.
See also
- Genome Comparison
- Genome projectGenome projectGenome projects are scientific endeavours that ultimately aim to determine the complete genome sequence of an organism and to annotate protein-coding genes and other important genome-encoded features...
- List of sequenced eukaryotic genomes
- Molecular evolutionMolecular evolutionMolecular evolution is in part a process of evolution at the scale of DNA, RNA, and proteins. Molecular evolution emerged as a scientific field in the 1960s as researchers from molecular biology, evolutionary biology and population genetics sought to understand recent discoveries on the structure...