Eukaryotic chromosome fine structure
Encyclopedia
Eukaryotic chromosome fine structure refers to the structure of sequences for eukaryotic chromosomes. Some fine sequences are included in more than one class, so the classification listed is not intended to be completely separate.
Throughout the eukaryotic kingdom, the overall structure of chromosome ends is conserved and is characterized by the telomeric tract - a series of short G-rich repeats. This is succeeded by an extensive subtelomeric region consisting of various types and lengths of repeats - the telomere associated sequences (TAS). These regions are generally low in gene density, low in transcription, low in recombination, late replicating, are involved in protecting the end from degradation and end-to-end fusions and in completing replication. The subtelomeric repeats can rescue chromosome ends when telomerase fails, buffer subtelomerically located genes against transcriptional silencing and protect the genome from deleterious rearrangements due to ectopic recombination. They may also be involved in fillers for increasing chromosome size to some minimum threshold level necessary for chromosome stability; act as barriers against transcriptional silencing; provide a location for the adaptive amplification of genes; and be involved in secondary mechanism of telomere maintenance via recombination when telomerase activity is absent.
Other RNAs are transcribed and not translated, but have undiscovered functions.
are tandem repeats, with sequences that are found interspersed across the genome. They can be classified based on the length of the repeat as:
Both of these types are classified as retrotransposons.
s are sequences in the DNA that are the result of retrotransposition of RNA. LINEs and SINEs are examples where the sequences are repeats, but there are non-repeated sequences that can also be retrotransposons.
Chromosomal characteristics
Some sequences are required for a properly functioning chromosome:- CentromereCentromereA centromere is a region of DNA typically found near the middle of a chromosome where two identical sister chromatids come closest in contact. It is involved in cell division as the point of mitotic spindle attachment...
: Used during cell division as the attachment point for the spindle fibers. - TelomereTelomereA telomere is a region of repetitive DNA sequences at the end of a chromosome, which protects the end of the chromosome from deterioration or from fusion with neighboring chromosomes. Its name is derived from the Greek nouns telos "end" and merοs "part"...
: Used to maintain chromosomal integrity by capping off the ends of the linear chromosomes. This region is a microsatellite, but its function is more specific than a simple tandem repeat.
Throughout the eukaryotic kingdom, the overall structure of chromosome ends is conserved and is characterized by the telomeric tract - a series of short G-rich repeats. This is succeeded by an extensive subtelomeric region consisting of various types and lengths of repeats - the telomere associated sequences (TAS). These regions are generally low in gene density, low in transcription, low in recombination, late replicating, are involved in protecting the end from degradation and end-to-end fusions and in completing replication. The subtelomeric repeats can rescue chromosome ends when telomerase fails, buffer subtelomerically located genes against transcriptional silencing and protect the genome from deleterious rearrangements due to ectopic recombination. They may also be involved in fillers for increasing chromosome size to some minimum threshold level necessary for chromosome stability; act as barriers against transcriptional silencing; provide a location for the adaptive amplification of genes; and be involved in secondary mechanism of telomere maintenance via recombination when telomerase activity is absent.
Structural sequences
Other sequences are used in replication or during interphase with the physical structure of the chromosome.- Ori, or OriginOri (genetics)Ori is the DNA sequence that signals for the origin of replication, sometimes referred to simply as origin. In E. coli, ori is some 250 nucleotides in length for the chromosomal origin...
: Origins of replication. - MAR: Matrix attachment regions, where the DNA attaches to the nuclear matrix.
Protein-coding genes
Regions of the genome with protein-coding genes include several elements:- EnhancerEnhancer (genetics)In genetics, an enhancer is a short region of DNA that can be bound with proteins to enhance transcription levels of genes in a gene cluster...
regions (normally up to a few thousand basepairs upstream of transcription). - Promoter regions (normally less than a couple of hundred basepairs upstream of transcription) include elements such as the TATATATA boxThe TATA box is a DNA sequence found in the promoter region of genes in archaea and eukaryotes; approximately 24% of human genes contain a TATA box within the core promoter....
and CAATCAAT boxIn molecular biology, a CCAAT box is a distinct pattern of nucleotides with GGCCAATCT consensus sequence that occur upstream by 75-80 bases to the initial transcription site. The CAAT box signals the binding site for the RNA transcription factor, and is typically accompanied by a conserved...
boxes, GC elements, an initiator, etc. - ExonExonAn exon is a nucleic acid sequence that is represented in the mature form of an RNA molecule either after portions of a precursor RNA have been removed by cis-splicing or when two or more precursor RNA molecules have been ligated by trans-splicing. The mature RNA molecule can be a messenger RNA...
s are the part of the transcript that will eventually be transported to the cytoplasm for translation. When discussing gene with alternate splicing, an exon is a portion of the transcript that could be translated, given the correct splicing conditions. The exons can be divided into three parts- The coding region is the portion of the mRNA that will eventually be translated.
- Upstream untranslated region (5' UTRFive prime untranslated regionA messenger ribonucleic acid molecule codes for a protein through translation. The mRNA also contains regions that are not translated: in eukaryotes these include the 5' untranslated region, 3' untranslated region, 5' cap and poly-A tail....
) can serve several functions, including mRNA transport, and initiation of translation (including, portions of the Kozak sequence). They are never translated into the protein (excepting various mutations). - The 3' region downstream from the stop codon is separated into two parts:
- 3' UTRThree prime untranslated regionIn molecular genetics, the three prime untranslated region is a particular section of messenger RNA . It is preceeded by the coding region....
is never translated, but serves to add mRNA stability. It is also the attachment site for the poly-A tail. The poly-A tail is used in the initiation of translation and also seems to have an effect on the long-term stability (aging) of the mRNA. - An unnamed region after the poly-A tail, but before the actual site for transcription termination, is spliced off during transcription, and so does not become part of the 3' UTR. Its function, if any, is unknown.
- 3' UTR
- IntronIntronAn 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 are intervening sequences between the exons that are never translated. Some sequences inside introns function as miRNAMirnaMirna may refer to:geographical entities* Mirna , a river in Istria, Croatia* Mirna , a river in Slovenia, tributary of the river Sava* Mirna , a settlement in the municipality of Mirna in Southeastern Sloveniapeople...
, and there are even some cases of small genes residing completely within the intron of a large gene. For some genes (such as the antibodyAntibodyAn antibody, also known as an immunoglobulin, is a large Y-shaped protein used by the immune system to identify and neutralize foreign objects such as bacteria and viruses. The antibody recognizes a unique part of the foreign target, termed an antigen...
genes), internal control regions are found inside introns. These situations, however, are treated as exceptions.
Genes that are used as RNA
Many regions of the DNA are transcribed with RNA as the functional form:- rRNA: Ribosomal RNA are used in the ribosomeRibosomeA ribosome is a component of cells that assembles the twenty specific amino acid molecules to form the particular protein molecule determined by the nucleotide sequence of an RNA molecule....
. - tRNA: Transfer RNA are used in the translationTranslationTranslation is the communication of the meaning of a source-language text by means of an equivalent target-language text. Whereas interpreting undoubtedly antedates writing, translation began only after the appearance of written literature; there exist partial translations of the Sumerian Epic of...
process by bringing amino acidAmino acidAmino acids are molecules containing an amine group, a carboxylic acid group and a side-chain that varies between different amino acids. The key elements of an amino acid are carbon, hydrogen, oxygen, and nitrogen...
s to the ribosome. - snRNA: Small nuclear RNA are used in spliceosomeSpliceosomeA spliceosome is a complex of snRNA and protein subunits that removes introns from a transcribed pre-mRNA segment. This process is generally referred to as splicing.-Composition:...
s to help the processing of pre-mRNA. - gRNAGuide RNAGuide RNAs are the RNAs that guide the insertion or deletion of uridine residues into mitochondrial mRNAs in kinetoplastid protists in a process known as RNA editing.-Overview of gRNA-directed editing:...
: Guide RNA are used in RNA editingRNA editingThe term RNA editing describes those molecular processes in which the information content in an RNA molecule is altered through a chemical change in the base makeup. To date, such changes have been observed in tRNA, rRNA, mRNA and microRNA molecules of eukaryotes but not prokaryotes...
. - miRNAMirnaMirna may refer to:geographical entities* Mirna , a river in Istria, Croatia* Mirna , a river in Slovenia, tributary of the river Sava* Mirna , a settlement in the municipality of Mirna in Southeastern Sloveniapeople...
: Micro RNA are small (approximately 24 nucleotides) that are used in gene silencingGene silencingGene silencing is a general term describing epigenetic processes of gene regulation. The term gene silencing is generally used to describe the "switching off" of a gene by a mechanism other than genetic modification...
. - snoRNA: Small nucleolar RNA are used to help process and construct the ribosome.
Other RNAs are transcribed and not translated, but have undiscovered functions.
Repeated sequences
Repeated sequences are of two basic types: unique sequences that are repeated in one area; and repeated sequences that are interspersed throughout the genome.Satellites
Satellites are unique sequences that are repeated in tandem in one area. Depending on the length of the repeat, they are classified as either:- MinisatelliteMinisatelliteA minisatellite is a section of DNA that consists of a short series of bases 10-60 bp. These occur at more than 1,000 locations in the human genome...
: Short repeats of nucleotides. - Microsatellite: Very short repeats of nucleotides. Some trinucleotide repeats are found in coding regions (see, Trinucleotide repeat disorder). Most are found in noncoding regions. Their function is unknown, if they have any specific function. They are used as molecular markers and in DNA fingerprinting.
Interspersed sequences
Interspersed sequencesInterspersed repeat
Interspersed repetitive DNA is found in all eukaryotic genomes. Certain classes of these sequences propagate themselves by RNA mediated transposition, and they have been called retrotransposons. Interspersed repetitive DNA elements allow new genes to evolve. They do this by uncoupling similar DNA...
are tandem repeats, with sequences that are found interspersed across the genome. They can be classified based on the length of the repeat as:
- SINESinéMaurice Sinet , known as Siné, is a French cartoonist.As a young man he studied drawing and graphic arts, while earning a living as a cabaret singer. After his military service he started publishing his drawings and also worked as a photo-retoucher for porn magazines. His first published drawing...
: Short interspersed sequences. The repeats are normally a few hundred base pairs in length. These sequences constitute about 13% of the human genome with the specific AluAlu sequenceAn 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...
sequence accounting for about 10%. - LINE: Long interspersed sequences. The repeats are normally several thousand base pairs in length. These sequences constitute about 21% of the human genome.
Both of these types are classified as retrotransposons.
Retrotransposons
RetrotransposonRetrotransposon
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 are sequences in the DNA that are the result of retrotransposition of RNA. LINEs and SINEs are examples where the sequences are repeats, but there are non-repeated sequences that can also be retrotransposons.