genetics Genetics is the study of genes, genetic variation, and heredity in organisms.Hartl D, Jones E (2005) It is an important branch in biology because heredity is vital to organisms' evolution. Gregor Mendel, a Moravian Augustinians, Augustinian ...

, eukaryotic chromosome fine structure refers to the

structure A structure is an arrangement and organization of interrelated elements in a material object or system, or the object or system so organized. Material structures include man-made objects such as buildings and machines and natural objects such as ...

sequences In mathematics, a sequence is an enumerated collection of objects in which repetitions are allowed and order matters. Like a set, it contains members (also called ''elements'', or ''terms''). The number of elements (possibly infinite) is call ...

for the

chromosomes A chromosome is a package of DNA containing part or all of the genetic material of an organism. In most chromosomes, the very long thin DNA fibers are coated with nucleosome-forming packaging proteins; in eukaryotic cells, the most importa ...

eukaryotic The eukaryotes ( ) constitute the Domain (biology), domain of Eukaryota or Eukarya, organisms whose Cell (biology), cells have a membrane-bound cell nucleus, nucleus. All animals, plants, Fungus, fungi, seaweeds, and many unicellular organisms ...

organisms. Some fine sequences are included in more than one class, so the classification listed is not intended to be completely separate.

Chromosomal characteristics

Some sequences are required for a properly functioning chromosome: *

Centromere The centromere links a pair of sister chromatids together during cell division. This constricted region of chromosome connects the sister chromatids, creating a short arm (p) and a long arm (q) on the chromatids. During mitosis, spindle fiber ...

: Used during cell division as the attachment point for the spindle fibers. *

Telomere A telomere (; ) is a region of repetitive nucleotide sequences associated with specialized proteins at the ends of linear chromosomes (see #Sequences, Sequences). Telomeres are a widespread genetic feature most commonly found in eukaryotes. In ...

: Used to maintain chromosomal integrity by capping off the ends of the linear chromosomes. This region is a

microsatellite A microsatellite is a tract of repetitive DNA in which certain Sequence motif, DNA motifs (ranging in length from one to six or more base pairs) are repeated, typically 5–50 times. Microsatellites occur at thousands of locations within an organ ...

, 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).Pryde FE, Gorham HC, Louis EJ (1997) Chromosome ends: all the same under their caps. Curr Opin Genet Dev 7(6):822-828 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 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: * Enhancer 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 TATA and CAAT boxes, GC elements, and an initiator. *

Exon An exon is any part of a gene that will form a part of the final mature RNA produced by that gene after introns have been removed by RNA splicing. The term ''exon'' refers to both the DNA sequence within a gene and to the corresponding sequence ...

s are the part of the transcript that will eventually be transported to the cytoplasm for translation. When discussing gene with

alternate splicing Alternative splicing, alternative RNA splicing, or differential splicing, is an alternative splicing process during gene expression that allows a single gene to produce different splice variants. For example, some exons of a gene may be included ...

, 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' UTR The 5′ untranslated region (also known as 5′ UTR, leader sequence, transcript leader, or leader RNA) is the region of a messenger RNA (mRNA) that is directly Upstream and downstream (DNA), upstream from the initiation codon. This region is im ...

) can serve several functions, including mRNA transport, and initiation of translation (including, portions of the

Kozak sequence The Kozak consensus sequence (Kozak consensus or Kozak sequence) is a Nucleic acid sequence, nucleic acid motif that functions as the protein Translation (biology), translation initiation site in most eukaryotic Messenger RNA, mRNA transcripts. Reg ...

). They are never translated into the protein (excepting various mutations). **The 3' region downstream from the stop codon is separated into two parts: ***

3' UTR In molecular genetics, the three prime untranslated region (3′-UTR) is the section of messenger RNA (mRNA) that immediately follows the translation (biology), translation termination codon. The 3′-UTR often contains regulatory regions that P ...

is never translated, but serves to add mRNA stability. It is also the attachment site for the

poly-A tail Polyadenylation is the addition of a poly(A) tail to an RNA transcript, typically a messenger RNA (mRNA). The poly(A) tail consists of multiple adenosine monophosphates; in other words, it is a stretch of RNA that has only adenine bases. In euka ...

. 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

, 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. *

Intron An intron is any nucleotide sequence within a gene that is not expressed or operative in the final RNA product. The word ''intron'' is derived from the term ''intragenic region'', i.e., a region inside a gene."The notion of the cistron .e., gen ...

s are intervening sequences between the exons that are never translated. Some sequences inside introns function as

miRNA Micro ribonucleic acid (microRNA, miRNA, μRNA) are small, single-stranded, non-coding RNA molecules containing 21–23 nucleotides. Found in plants, animals, and even some viruses, miRNAs are involved in RNA silencing and post-transcri ...

, and there are even some cases of small genes residing completely within the intron of a large gene. For some genes (such as the

antibody An antibody (Ab) or immunoglobulin (Ig) is a large, Y-shaped protein belonging to the immunoglobulin superfamily which is used by the immune system to identify and neutralize antigens such as pathogenic bacteria, bacteria and viruses, includin ...

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 ribonucleic acid (rRNA) is a type of non-coding RNA which is the primary component of ribosomes, essential to all cells. rRNA is a ribozyme which carries out protein synthesis in ribosomes. Ribosomal RNA is transcribed from ribosomal ...

: Ribosomal RNA are used in the

ribosome Ribosomes () are molecular machine, macromolecular machines, found within all cell (biology), cells, that perform Translation (biology), biological protein synthesis (messenger RNA translation). Ribosomes link amino acids together in the order s ...

. *

tRNA Transfer ribonucleic acid (tRNA), formerly referred to as soluble ribonucleic acid (sRNA), is an adaptor molecule composed of RNA, typically 76 to 90 nucleotides in length (in eukaryotes). In a cell, it provides the physical link between the gene ...

: Transfer RNA are used in the

translation Translation is the communication of the semantics, meaning of a #Source and target languages, source-language text by means of an Dynamic and formal equivalence, equivalent #Source and target languages, target-language text. The English la ...

process by bringing

amino acid Amino acids are organic compounds that contain both amino and carboxylic acid functional groups. Although over 500 amino acids exist in nature, by far the most important are the 22 α-amino acids incorporated into proteins. Only these 22 a ...

s to the ribosome. *

snRNA Small nuclear RNA (snRNA) is a class of small RNA molecules that are found within the splicing speckles and Cajal bodies of the cell nucleus in eukaryotic cells. The length of an average snRNA is approximately 150 nucleotides. They are transcrib ...

: Small nuclear RNA are used in

spliceosome A spliceosome is a large ribonucleoprotein (RNP) complex found primarily within the nucleus of eukaryotic cells. The spliceosome is assembled from small nuclear RNAs ( snRNA) and numerous proteins. Small nuclear RNA (snRNA) molecules bind to sp ...

s to help the processing of pre-mRNA. * gRNA: Guide RNA are used in

RNA editing RNA editing (also RNA modification) is a molecular process through which some cells can make discrete changes to specific nucleotide sequences within an RNA molecule after it has been generated by RNA polymerase. It occurs in all living organisms ...

. *

: Micro RNA are small (approximately 24 nucleotides) that are used in

gene silencing Gene silencing is the regulation of gene expression in a cell to prevent the expression of a certain gene. Gene silencing can occur during either Transcription (genetics), transcription or Translation (biology), translation and is often used in res ...

. * 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 A satellite or an artificial satellite is an object, typically a spacecraft, placed into orbit around a celestial body. They have a variety of uses, including communication relay, weather forecasting, navigation ( GPS), broadcasting, scientif ...

are unique sequences that are repeated in tandem in one area. Depending on the length of the repeat, they are classified as either: *

Minisatellite In genetics, a minisatellite is a tract of repetitive DNA in which certain DNA motifs (ranging in length from 10–60 base pairs) are typically repeated two to several hundred times. Minisatellites occur at more than 1,000 locations in the huma ...

: Short repeats of nucleotides. *

Microsatellite A microsatellite is a tract of repetitive DNA in which certain Sequence motif, DNA motifs (ranging in length from one to six or more base pairs) are repeated, typically 5–50 times. Microsatellites occur at thousands of locations within an organ ...

: Very short repeats of nucleotides. Some trinucleotide repeats are found in coding regions (see,

Trinucleotide repeat disorder In genetics, trinucleotide repeat disorders, a subset of microsatellite expansion diseases (also known as repeat expansion disorders), are a set of over 30 genetic disorders caused by trinucleotide repeat expansion, a kind of mutation in which ...

). Most are found in noncoding regions. Their function is unknown, if they have any specific function. They are used as

molecular marker In molecular biology and other fields, a molecular marker is a molecule, sampled from some source, that gives information about its source. For example, DNA is a molecular marker that gives information about the organism from which it was taken. ...

s and in

DNA fingerprinting DNA profiling (also called DNA fingerprinting and genetic fingerprinting) is the process of determining an individual's deoxyribonucleic acid (DNA) characteristics. DNA analysis intended to identify a species, rather than an individual, is cal ...

Interspersed sequences

Interspersed sequences are nonadjacent repeats, with sequences that are found dispersed across the genome. They can be classified based on the length of the repeat as: *

SINE In mathematics, sine and cosine are trigonometric functions of an angle. The sine and cosine of an acute angle are defined in the context of a right triangle: for the specified angle, its sine is the ratio of the length of the side opposite th ...

: Short interspersed sequences. The repeats are normally a few hundred base pairs in length. These sequences constitute about 13% of the human genomePierce, B. A. (2005). Genetics: A conceptual approach. Freeman. Page 311 with the specific '' Alu'' 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 (also called Class I transposable elements) are transposable element, mobile elements which move in the host genome by converting their transcribed RNA into DNA through reverse transcription. Thus, they differ from Class II trans ...

Retrotransposons

Retrotransposon Retrotransposons (also called Class I transposable elements) are mobile elements which move in the host genome by converting their transcribed RNA into DNA through reverse transcription. Thus, they differ from Class II transposable elements, or ...

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.

Other sequences

Typical eukaryotic chromosomes contain much more DNA than is classified in the categories above. The DNA may be used as spacing, or have other as-yet-unknown function. Or, they may simply be random sequences of no consequence.

References

Notes

{{Reflist Chromosomes