Eukaryotic chromosome fine structure refers to the structure of sequences for

eukaryotic Eukaryotes () are organisms whose Cell (biology), cells have a cell nucleus, nucleus. All animals, plants, fungi, and many unicellular organisms, are Eukaryotes. They belong to the group of organisms Eukaryota or Eukarya, which is one of the ...

chromosomes A chromosome is a long DNA molecule with part or all of the genetic material of an organism. In most chromosomes the very long thin DNA fibers are coated with packaging proteins; in eukaryotic cells the most important of these proteins are ...

. 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 fibers ...

: 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. Although there are different architectures, telomeres, in a broad sense, are a widespread genetic feature mos ...

: 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).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. * Exons 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' 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 from the initiation codon. This region is important for the regulation of t ...

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

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

miRNA MicroRNA (miRNA) are small, single-stranded, non-coding RNA molecules containing 21 to 23 nucleotides. Found in plants, animals and some viruses, miRNAs are involved in RNA silencing and post-transcriptional regulation of gene expression. miR ...

, 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), also known as an immunoglobulin (Ig), is a large, Y-shaped protein used by the immune system to identify and neutralize foreign objects such as pathogenic bacteria and viruses. The antibody recognizes a unique molecule of the ...

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 ribosoma ...

: Ribosomal RNA are used in the ribosome. *

tRNA Transfer RNA (abbreviated tRNA and formerly referred to as sRNA, for soluble RNA) is an adaptor molecule composed of RNA, typically 76 to 90 nucleotides in length (in eukaryotes), that serves as the physical link between the mRNA and the amino ...

: Transfer RNA are used in the

translation Translation is the communication of the meaning of a source-language text by means of an equivalent target-language text. The English language draws a terminological distinction (which does not exist in every language) between ''transla ...

process by bringing

amino acid Amino acids are organic compounds that contain both amino and carboxylic acid functional groups. Although hundreds of amino acids exist in nature, by far the most important are the alpha-amino acids, which comprise proteins. Only 22 alpha 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 transcri ...

: 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 specif ...

s to help the processing of pre-mRNA. *

gRNA A guide RNA (gRNA) is a piece of RNA that functions as a guide for RNA- or DNA-targeting enzymes, with which it forms complexes. Very often these enzymes will delete, insert or otherwise alter the targeted RNA or DNA. They occur naturally, se ...

: 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 organism ...

. *

: 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 or translation and is often used in research. In particular, methods used to silence ge ...

. *

snoRNA In molecular biology, Small nucleolar RNAs (snoRNAs) are a class of small RNA molecules that primarily guide chemical modifications of other RNAs, mainly ribosomal RNAs, transfer RNAs and small nuclear RNAs. There are two main classes of 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: *

Minisatellite A minisatellite is a tract of repetitive DNA in which certain DNA motifs (ranging in length from 10–60 base pairs) are typically repeated 5-50 times. Minisatellites occur at more than 1,000 locations in the human genome and they are notable for ...

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

Trinucleotide repeat disorder Trinucleotide repeat disorders, also known as microsatellite expansion diseases, are a set of over 50 genetic disorders caused by trinucleotide repeat expansion, a kind of mutation in which repeats of three nucleotides ( trinucleotide repeats) in ...

). 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 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: 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 or transposons via RNA intermediates) are a type of genetic component that copy and paste themselves into different genomic locations ( transposon) by converting RNA back into DNA throug ...

Retrotransposons

Retrotransposon Retrotransposons (also called Class I transposable elements or transposons via RNA intermediates) are a type of genetic component that copy and paste themselves into different genomic locations (transposon) by converting RNA back into DNA through ...

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 Genetics