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Subtelomeres are segments of DNA between telomeric caps and chromatin.
| | This article needs additional citations for verification .(April 2016) |
Subtelomeres are segments of DNA between telomeric caps and chromatin.
Telomeres are specialized protein–DNA constructs present at the ends of eukaryotic chromosomes, which prevent them from degradation and end-to-end chromosomal fusion. Most vertebrate telomeric DNA consists of long (T T A G G G)n repeats of variable length, often around 3-20kb. Subtelomeres are segments of DNA between telomeric caps and chromatin. In vertebrates, each chromosome has two subtelomeres immediately adjacent to the long (TTAGGG)n repeats. Subtelomeres are considered to be the most distal (farthest from the centromere) region of unique DNA on a chromosome, and they are unusually dynamic and variable mosaics of multichromosomal blocks of sequence. The subtelomeres of such diverse species as humans, Plasmodium falciparum , Drosophila melanogaster , and Saccharomyces cerevisiae are structurally similar in that they are composed of various repeated elements, but the extent of the subtelomeres and the sequence of the elements vary greatly among organisms. [1] In yeast (S. cerevisiae), subtelomeres are composed of two domains: the proximal and distal (telomeric) domains. The two domains differ in sequence content and extent of homology to other chromosome ends, and they are often separated by a stretch of degenerate telomere repeats (TTAGGG) and an element called 'core X', which is found at all chromosome ends and contains an autonomously replicating sequence (ARS) and an ABF1 binding site. [2] [3] The proximal domain is composed of variable interchromosomal duplications (<1-30 kb); this region can contain genes such Pho, Mel, and Mal. [4] The distal domain is composed of 0-4 tandem copies of the highly conserved Y' element; the number and chromosomal distribution of Y′ elements varies among yeast strains. [5] Between the core X and the Y' element or the core X and TTAGGG sequence there is often a set of 4 subtelomeric repeats elements (STR): STR-A, STR-B, STR-C and STR-D which consists of multiple copies of the vertebrate telomeric motif TTAGGG. [6] This two-domain structure is remarkably similar to the subtelomere structure in human chromosomes 20p, 4q and 18p in which proximal and distal subtelomeric domains are separated by a stretch of degenerate TTAGGG repeats, but the picture that emerges from studies of the subtelomeres of other human chromosomes indicates that the two-domain model does not apply universally. [1]
This structure with repeated sequences is responsible for frequent duplication events, which create new genes, and recombination events, at the origin of combination diversity. These properties generate diversity at an individual scale and therefore contribute to adaptation of organisms to their environments. For example, in Plasmodium falciparum during interphase of the erythrocytic stage, the chromosomic extremities are gathered at the cell nucleus periphery, where they undergo frequent deletion and telomere position effect (TPE). This event, in addition to expansion and deletion of subtelomeric repeats, gives rise to chromosome size polymorphisms and thus, subtelomeres undergo epigenetic and genetic controls. Because of the properties of subtelomeres, Plasmodium falciparum evades host immunity by varying the antigenic and adhesive character of infected erythrocytes (see Subtelomeric transcripts). [7] [8]
Variation of subtelomeric regions are mostly variation on STRs, due to recombination of large-scale stretches delimited by (TTAGGG)n-like repeated sequences, which play an important role in recombination and transcription. Haplotype (DNA sequence variants) and length differences are therefore observed between individuals.
Subtelomeric transcripts largely consist of either pseudogenes (transcribed genes producing RNA sequences not translated into protein) or gene families. In humans, they code for olfactory receptors, immunoglobulin heavy chains, and zinc-finger proteins. In other species, several parasites such as Plasmodium and Trypanosoma brucei have developed sophisticated evasion mechanisms to adapt to the hostile environment posed by the host, such as exposing variable surface antigens to escape the immune system. Genes coding for surface antigens in these organisms are located at subtelomeric regions, and it has been speculated that this preferred location facilitates gene switching and expression, and the generation of new variants. [9] [10] For example, the genes belonging to the var family in Plasmodium falciparum (agent of malaria) are mostly localized in subtelomeric regions. Antigenic variation is orchestrated by epigenetic factors, including monoallelic var transcription at separate spatial domains at the nuclear periphery (nuclear pore), differential histone marks on otherwise identical var genes, and var silencing mediated by telomeric heterochromatin. Other factors such as non-coding RNA produced in subtelomeric regions adjacent or within var genes may contribute as well to antigenic variation. [11] [12] In Trypanosoma brucei (agent of sleeping sickness), variable surface glycoprotein (VSG) antigenic variation is a relevant mechanism used by the parasite to evade the host immune system. VSG expression is exclusively subtelomeric and occurs either by in situ activation of a silent VSG gene or by DNA rearrangement that inserts an internal silent copy of a VSG gene into an active telomeric expression site. To contrast with Plasmodium falciparum, in Trypanosoma brucei, antigenic variation is orchestrated by epigenetic and genetic factors. [13] [14]
In Pneumocystis jirovecii major surface glycoprotein (MSG) gene family cause antigenic variation. MSG genes are like boxes at chromosome ends, and only the MSG gene at the unique locus UCS (upstream conserved sequence) is transcribed. Different MSG genes can occupy the expression site (UCS), suggesting that recombination can take a gene from a pool of silent donors and install it at the expression site, possibly via crossovers, activating transcription of a new MSG gene, and changing the surface antigen of Pneumocystis jirovecii. Switching at the expression site is probably facilitated by the subtelomeric locations of expressed and silent MSG genes. A second subtelomeric gene family, MSR, is not strictly regulated at the transcriptional level, but may contribute to phenotypic diversity. Antigenic variation in P. jirovecii is dominated by genetic regulation. [15] [16]
Loss of telomeric DNA through repeated cycles of cell division is associated with senescence or somatic cell aging. In contrast, germ line and cancer cells possess an enzyme, telomerase, which prevents telomere degradation and maintains telomere integrity, causing these types of cells to be very long-lived.
In humans, the role of subtelomere disorders is demonstrated in facioscapulohumeral muscular dystrophy (FSHD), Alzheimer's disease, epilepsy [17] and peculiar syndromic diseases (malformation and mental retardation). For example, FSHD is associated with a deletion in the subtelomeric region of chromosome 4q. A series of 10 to >100 kb repeats is located in the normal 4q subtelomere, but FSHD patients have only 1–10 repeat units. This deletion is thought to cause disease owing to a position effect that influences the transcription of nearby genes, rather than through the loss of the repeat array itself. [1]
Subtelomeres are homologous to other subtelomeres that are located at different chromosomes and are a type of transposable element, DNA segments that can move around the genome. Although subtelomeres are pseudogenes and do not code for protein, they provide an evolutionary advantage by diversifying genes. The duplication, recombination, and deletion of subtelomeres allow for the creation of new genes and new chromosomal properties. [1] The advantages of subtelomeres have been studied in different species such as Plasmodium falciparum , [1] Drosophila melanogaster , [1] and Saccharomyces cerevisiae , [1] since they have similar genetic elements to humans, not accounting for length and sequence. [1] Subtelomeres might have the same role in plants since the same advantage have been found in a common bean plant known as Phaseolus vulgaris . [18]
Different varieties of subtelomeres are frequently rearranging during meiotic and mitotic recombination, indicating that subtelomeres are frequently shuffling, which causes new and rapid genetic changes in chromosomes. [1] In Saccharomyces cerevisiae, 15kb region of chromosome 7L in subtelomeres maintained cell viability in the removal of telomerase, while the removal of the last 15kb increased chromosome senescence. [19] The knockout of subtelomeres in fission yeast, Schizosaccharomyces pombe , cells does not impede mitosis and meiosis from occurring, indicating that subtelomeres are not necessary for cell division. [20] They are not needed for the procession of mitosis and meiosis yet, subtelomeres take advantage of cellular DNA recombination. The knockout of subtelomeres in Schizosaccharomyces pombe cells does not affect the regulation of multiple stress responses, when treated with high doses of hydroxyurea, camptothecin, ultraviolet radiation, and thiabendazole. [20] Knockout of Subtelomeres in Schizosaccharomyces pombe cells did not affect the length of telomeres, indicating that they play no role it the regulation of length. [20] However, subtelomeres strongly influences the replication timing of telomeres. [21] Knockout of subtelomeres in Schizosaccharomyces pombe cells after the loss of telomerase does not affect cell survival, indicating that subtelomeres are not necessary for cell survival. [20] An explanation as to why subtelomeres are not necessary after the loss of telomerase is because the chromosomes can use intra or inter-chromosomal circularization [22] or HAATI [23] to maintain chromosomal stabilization. However, the use of inter-chromosomal circularization engenders chromosome instability by creating two centromeres in a single chromosome, causing chromosomal breakage during mitosis. In response to this, the chromosome could induce centromere inactivation to impede the formation of two centromeres, but this would induce heterochromatin formation in centromeres. Heterochromatin can be deleterious if it gets into a location that it is not supposed to be in. Subtelomeres are responsible to block heterochromatin from getting into the euchromatin region. Subtelomeres can mitigate the effects of heterochromatin invasion, by distributing heterochromatin around the ends of the subtelomeres. Without subtelomeres, heterochromatin would spread around the region of subtelomeres, getting too close to important genes. At this distance, heterochromatin can silence genes that are nearby, resulting in a higher sensitivity to osmotic stress. [20]
Subtelomeres carry out essential functions with Shugoshin protein. Shugoshin is a centromere protein for chromosome segregation during meiosis and mitosis. There are two types of Shugoshin protein: SGOL1 and SGOL2. Sgo1 is only expressed in meiosis 1 for centromeric cohesion of the sister chromosomes, [24] while Sgo2, expressed in meiosis and mitosis, is responsible for the segregation of chromosomes at centromeres in the M phase. In fission yeast, Sgo2 is localized not only in centromeres, but also in subtelomeres. Sgo2 interacts with subtelomeres during interphase; middle of the G2 phase and plays a major role in forming "knob", which is a highly condensed chromatin body. Sgo2 remains in subtelomeres, whose cells lack telomere DNA. Sgo2 represses the expression of subtelomeric genes that is in a different pass-way from the H3K9me3- Swi6-mediated heterochromatin. Sgo2 has also repressive effects for timing of subtelomeres replication by suppressing Sld3, [25] a replication factor, at the start of the replication. [26] Thus, Sgo2 regulate gene expressions and replication to ensure proper subtelomeric gene expression and replication timing.
Subtelomere analysis, especially sequencing and profiling of patient subtelomeres, is difficult because of the repeated sequences, length of stretches, and lack of databases on the topic.
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 attach to the centromere via the kinetochore.
Heterochromatin is a tightly packed form of DNA or condensed DNA, which comes in multiple varieties. These varieties lie on a continuum between the two extremes of constitutive heterochromatin and facultative heterochromatin. Both play a role in the expression of genes. Because it is tightly packed, it was thought to be inaccessible to polymerases and therefore not transcribed; however, according to Volpe et al. (2002), and many other papers since, much of this DNA is in fact transcribed, but it is continuously turned over via RNA-induced transcriptional silencing (RITS). Recent studies with electron microscopy and OsO4 staining reveal that the dense packing is not due to the chromatin.
Saccharomyces cerevisiae is a species of yeast. The species has been instrumental in winemaking, baking, and brewing since ancient times. It is believed to have been originally isolated from the skin of grapes. It is one of the most intensively studied eukaryotic model organisms in molecular and cell biology, much like Escherichia coli as the model bacterium. It is the microorganism behind the most common type of fermentation. S. cerevisiae cells are round to ovoid, 5–10 μm in diameter. It reproduces by budding.
Schizosaccharomyces pombe, also called "fission yeast", is a species of yeast used in traditional brewing and as a model organism in molecular and cell biology. It is a unicellular eukaryote, whose cells are rod-shaped. Cells typically measure 3 to 4 micrometres in diameter and 7 to 14 micrometres in length. Its genome, which is approximately 14.1 million base pairs, is estimated to contain 4,970 protein-coding genes and at least 450 non-coding RNAs.
Yeast artificial chromosomes (YACs) are genetically engineered chromosomes derived from the DNA of the yeast, Saccharomyces cerevisiae, which is then ligated into a bacterial plasmid. By inserting large fragments of DNA, from 100–1000 kb, the inserted sequences can be cloned and physically mapped using a process called chromosome walking. This is the process that was initially used for the Human Genome Project, however due to stability issues, YACs were abandoned for the use of Bacterial artificial chromosomes (BAC). Beginning with the initial research of the Rankin et al., Strul et al., and Hsaio et al., the inherently fragile chromosome was stabilized by discovering the necessary autonomously replicating sequence (ARS); a refined YAC utilizing this data was described in 1983 by Murray et al.
A minisatellite is a tract of repetitive DNA in which certain DNA motifs are typically repeated 5-50 times. Minisatellites occur at more than 1,000 locations in the human genome and they are notable for their high mutation rate and high diversity in the population. Minisatellites are prominent in the centromeres and telomeres of chromosomes, the latter protecting the chromosomes from damage. The name "satellite" refers to the early observation that centrifugation of genomic DNA in a test tube separates a prominent layer of bulk DNA from accompanying "satellite" layers of repetitive DNA. Minisatellites are small sequences of DNA that do not encode proteins but appear throughout the genome hundreds of times, with many repeated copies lying next to each other.
Constitutive heterochromatin domains are regions of DNA found throughout the chromosomes of eukaryotes. The majority of constitutive heterochromatin is found at the pericentromeric regions of chromosomes, but is also found at the telomeres and throughout the chromosomes. In humans there is significantly more constitutive heterochromatin found on chromosomes 1, 9, 16, 19 and Y. Constitutive heterochromatin is composed mainly of high copy number tandem repeats known as satellite repeats, minisatellite and microsatellite repeats, and transposon repeats. In humans these regions account for about 200Mb or 6.5% of the total human genome, but their repeat composition makes them difficult to sequence, so only small regions have been sequenced.
Non-homologous end joining (NHEJ) is a pathway that repairs double-strand breaks in DNA. NHEJ is referred to as "non-homologous" because the break ends are directly ligated without the need for a homologous template, in contrast to homology directed repair(HDR), which requires a homologous sequence to guide repair. NHEJ is active in both non-dividing and proliferating cells, while HDR is not readily accessible in non-dividing cells. The term "non-homologous end joining" was coined in 1996 by Moore and Haber.
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.
A dicentric chromosome is an abnormal chromosome with two centromeres. It is formed through the fusion of two chromosome segments, each with a centromere, resulting in the loss of acentric fragments and the formation of dicentric fragments. The formation of dicentric chromosomes has been attributed to genetic processes, such as Robertsonian translocation and paracentric inversion. Dicentric chromosomes have important roles in the mitotic stability of chromosomes and the formation of pseudodicentric chromosomes. Their existence has been linked to certain natural phenomena such as irradiation and have been documented to underlie certain clinical syndromes, notably Kabuki syndrome. The formation of dicentric chromosomes and their implications on centromere function are studied in certain clinical cytogenetics laboratories.
Antigenic variation or antigenic alteration refers to the mechanism by which an infectious agent such as a protozoan, bacterium or virus alters the proteins or carbohydrates on its surface and thus avoids a host immune response, making it one of the mechanisms of antigenic escape. It is related to phase variation. Antigenic variation not only enables the pathogen to avoid the immune response in its current host, but also allows re-infection of previously infected hosts. Immunity to re-infection is based on recognition of the antigens carried by the pathogen, which are "remembered" by the acquired immune response. If the pathogen's dominant antigen can be altered, the pathogen can then evade the host's acquired immune system. Antigenic variation can occur by altering a variety of surface molecules including proteins and carbohydrates. Antigenic variation can result from gene conversion, site-specific DNA inversions, hypermutation, or recombination of sequence cassettes. The result is that even a clonal population of pathogens expresses a heterogeneous phenotype. Many of the proteins known to show antigenic or phase variation are related to virulence.
The Ty5 is a type of retrotransposon native to the Saccharomyces cerevisiae organism.
Telomeric repeat-binding factor 1 is a protein that in humans is encoded by the TERF1 gene.
Telomere-binding proteins function to bind telomeric DNA in various species. In particular, telomere-binding protein refers to TTAGGG repeat binding factor-1 (TERF1) and TTAGGG repeat binding factor-2 (TERF2). Telomere sequences in humans are composed of TTAGGG sequences which provide protection and replication of chromosome ends to prevent degradation. Telomere-binding proteins can generate a T-loop to protect chromosome ends. TRFs are double-stranded proteins which are known to induce bending, looping, and pairing of DNA which aids in the formation of T-loops. They directly bind to TTAGGG repeat sequence in the DNA. There are also subtelomeric regions present for regulation. However, in humans, there are six subunits forming a complex known as shelterin.
A mega-telomere, is an extremely long telomere sequence that sits on the end of chromosomes and prevents the loss of genetic information during cell replication. Like regular telomeres, mega-telomeres are made of a repetitive sequence of DNA and associated proteins, and are located on the ends of chromosomes. However, mega-telomeres are substantially longer than regular telomeres, ranging in size from 50 kilobases to several megabases.
Shelterin is a protein complex known to protect telomeres in many eukaryotes from DNA repair mechanisms, as well as to regulate telomerase activity. In mammals and other vertebrates, telomeric DNA consists of repeating double-stranded 5'-TTAGGG-3' (G-strand) sequences along with the 3'-AATCCC-5' (C-strand) complement, ending with a 50-400 nucleotide 3' (G-strand) overhang. Much of the final double-stranded portion of the telomere forms a T-loop (Telomere-loop) that is invaded by the 3' (G-strand) overhang to form a small D-loop (Displacement-loop).
Telomeric repeat–containing RNA (TERRA) is a long non-coding RNA transcribed from telomeres - repetitive nucleotide regions found on the ends of chromosomes that function to protect DNA from deterioration or fusion with neighboring chromosomes. TERRA has been shown to be ubiquitously expressed in almost all cell types containing linear chromosomes - including humans, mice, and yeasts. While the exact function of TERRA is still an active area of research, it is generally believed to play a role in regulating telomerase activity as well as maintaining the heterochromatic state at the ends of chromosomes. TERRA interaction with other associated telomeric proteins has also been shown to help regulate telomere integrity in a length-dependent manner.
SilentInformationRegulator (SIR) proteins are involved in regulating gene expression. SIR proteins organize heterochromatin near telomeres, rDNA, and at silent loci including hidden mating type loci in yeast. The SIR family of genes encodes catalytic and non-catalytic proteins that are involved in de-acetylation of histone tails and the subsequent condensation of chromatin around a SIR protein scaffold. Some SIR family members are conserved from yeast to humans.
Robin Campbell Allshire is Professor of Chromosome Biology at University of Edinburgh and a Wellcome Trust Principal Research Fellow. His research group at the Wellcome Trust Centre for Cell Biology focuses on the epigenetic mechanisms governing the assembly of specialised domains of chromatin and their transmission through cell division.
RRM3 is a gene that encodes a 5′-to-3′ DNA helicase known affect multiple cellular replication and repair processes and is most commonly studied in Saccharomyces cerevisiae. RRM3 formally stands for Ribosomal DNArecombination mutation 3. The gene codes for nuclear protein Rrm3p, which is 723 amino acids in length, and is part of a Pif1p DNA helicase sub-family that is conserved from yeasts to humans. RRM3 and its encoded protein have been shown to be vital for cellular replication, specifically associating with replication forks genome-wide. RRM3 is located on chromosome 8 in yeast cells and codes for 723 amino acids producing a protein that weighs 81,581 Da.
