Translocation: What is it? History, Generation of New Chromosomes, Karyotypes and Classification

It refers to the displacement of a segment of a chromosome to a new place in the genome.

Translocations generate new chromosomes. In a translocation, a segment of a chromosome is transferred to a non-homologous chromosome or to a new site on the same chromosome.

Translocations place genes in new linkage relationships and generate chromosomes without normal mating partners.

When scientists compare the genomes of closely related species, they can see that translocations have occurred many times during the course of evolution.

However, translocations that give the organism an adaptive advantage are very rare. Translocations are more often associated with negative consequences, such as aneuploidy, infertility, or cancer.

Scientists can now use molecular probes to analyze translocations, and the results provide new insights into the molecular origins of various diseases, including cancer.

History

In 1973, Janet Rowley identified an aberrant chromosome as the cause of chronic myelogenous leukemia (CML). This momentous discovery forever changed the field of cancer biology by showing that a chromosomal defect could cause cancer.

The now famous Philadelphia chromosome consists of a reciprocal fusion of parts of chromosome 9 and chromosome 22 and is a prototypical example of a cancer-causing chromosomal translocation.

Juxtaposition of the ABL gene, which encodes a tyrosine kinase, on chromosome 9 and the BCR gene on chromosome 22, leads to the generation of a chimeric fusion protein with constitutive oncogenic kinase activity.

Since the discovery of the Philadelphia chromosome, thousands of chromosomal translocations have been characterized.

In addition to the generation of fusion proteins as in the case of BCR-ABL, translocations can lead to the alteration or poor regulation of genes as seen in Burkitt’s lymphoma.

Where the enhancer elements of one of the three immunoglobulin loci (IGH, IGK or IGL) are juxtaposed to the MYC gene leading to its constitutive activation.

While chromosomal translocations have been particularly well characterized in blood cancers such as CML, they are equally relevant and frequent in solid tumors and in non-cancerous diseases, including infertility and schizophrenia.

Forming a translocation requires three basic steps:

  1. The appearance of multiple DNA double-stranded breaks on different chromosomes.
  2. The physical association of the broken ends.
  3. The union of the broken chromosomes of the pair.

Despite the indisputable pathological relevance of translocations, how these steps occur in vivo and in the context of the intact cell has remained largely unknown.

Recent work is beginning to shed light on two key questions: what determines which chromosomes undergo translocation with each other, and what determines where the chromosomes break in the first place?

Translocations generate new chromosomes

Translocations were first detected cytologically in the late 19th and early 20th centuries as novel chromosomes that appeared prominently in tumor cells.

Some of the oldest and most complete descriptions of tumor cell chromosomes were provided by the great German cytologist Theodor Boveri, considered by many to be the premier cancer geneticist.

Based on his observations of tumors, Boveri postulated that tumor cells possess “growth-promoting chromosomes” that play a role in malignancy.

At that time, cytological markers were not available for human chromosomes, so Boveri was not able to identify specific chromosomal changes in tumors. Today, we know that Boveri’s ideas were correct.

Translocations are indeed common in cancer cells, and some translocations produce oncogenes that are responsible for malignant transformation.

With the development of genetic and cytological models in the early 20th century, the existence of translocations became firmly established.

Geneticists discovered that genes were physically linked on chromosomes, and that the strength of the genetic link could be used to provide a rough map of each chromosome.

Occasionally, however, geneticists discovered mutations in which genes on two different chromosomes behaved as if they were physically linked.

Furthermore, the number of these mutations could increase by orders of magnitude when the organisms were treated with X-rays.

Examination of the chromosomes of these organisms provided an explanation for the appearance of new groups of bonds; specifically, new chromosomes appeared, and existing chromosomes had been altered.

Furthermore, in organisms such as Drosophila and corn, for which cytological markers were available, the scientists observed that the new chromosomes contained parts of normal chromosomes.

Thus, they were able to infer that disruptions had occurred in the normal chromosomes and that the broken ends of the non-homologous chromosomes had fused, producing translocations.

These early observations provided the basis for our modern understanding of translocations. We now appreciate that translocations require double strand breaks (DSBs) in DNA at two locations.

The frequency of these double-stranded breaks is greatly increased by ionizing radiation, which is still used experimentally to generate translocations.

Cells do not tolerate double chain breaks; These ruptures cause cells to stop in mitosis or to undergo apoptosis.

Therefore, the appearance of double strand breaks activates the cellular DNA repair machinery that catalyzes the joining of the ends of the broken chromosome. A variety of rearrangements can result from this union.

For example, the precise joining of the broken ends can regenerate a normal chromosome. Deletions, duplications, and inversions can occur when joining involves two broken ends on the same chromosome.

Also, translocations can occur when the broken ends of two non-homologous chromosomes come together. The final non-homologous binding is often imprecise, so some nucleotides can be completely lost during the binding process.

Karyotypes are used to classify translocations

Translocations involving human chromosomes are of great clinical interest because they have been linked to a number of disorders, including mental retardation, infertility, and cancer.

Translocations are usually detected when a cytogeneticist examines a karyotype, which is an ordered arrangement of an individual’s metaphase chromosomes.

In standard karyotypes, chromosomes that have been stained with Giemsa stain after special treatment reveal a characteristic set of bands along their length.

Translocations manifest as a change in the length or banding pattern of a chromosomal arm. Over time, cytogenetists have discovered hundreds, if not thousands, of different human translocations.

To describe these rearrangements, cytogenetists have developed a standardized nomenclature that allows researchers to focus on the chromosomal regions that are affected by translocations.

Non-reciprocal translocations are one-way translocations in which a chromosomal segment is transferred to a non-homologous chromosome.

Reciprocal translocations, on the other hand, involve the exchange of segments of two non-homologous chromosomes.

If no genetic material is lost during the exchange, the translocation is considered a balanced translocation. A reciprocal translocation that has occurred between chromosome 12 and chromosome 17.

The first set of parentheses identifies the two chromosomes involved in the translocation, and the second set of parentheses indicates the breakpoints in the arms of the chromosome.

Therefore, this particular translocation involved the p13.1 region of chromosome 12 and the p13 region of chromosome 17. The rearranged chromosomes that result from a translocation are called derived (der) chromosomes.

In this particular translocation, the rearranged chromosome is called der (12) t (12; 17), because the centromere of the derived chromosome is derived from chromosome 12.

Yet another category of translocations are Robertsonian translocations, in which the long q arms of two acrocentric chromosomes are joined at a single centromere.

Chromosomal p arms are lost during Robertsonian translocations, but because acrocentric chromosomes have very short p arms that are repetitive, there are no phenotypic consequences.

A Robertsonian translocation between chromosomes 14 and 21 that has generated the derived chromosome (14; 21). This particular translocation is interesting because it is commonly seen in patients with the familial form of Down syndrome.

Familial Down syndrome is much less common than the form in which patients have 47 chromosomes due to the presence of an extra copy of chromosome 21.

Patients with familial Down syndrome have 46 chromosomes, including two normal copies of chromosome 21 and a Robertsonian translocation with material from chromosome 21

Familial Down patients usually inherit the translocation chromosome from an unaffected parent, which has only 45 chromosomes, including the Robertsonian chromosome and a normal copy of chromosome 21.

What determines the choice of transfer partners?

The genesis of a chromosomal translocation requires that two double-stranded breaks come into physical contact to allow the illegitimate joining of the ends of the chromosome.

Since the physical interaction of the chromosomal loci involved is a fundamental step in the formation of translocations, it is likely that their spatial arrangement contributes directly to the frequency of translocation. Cytogenetic and biochemical evidence supports this notion.

Cytogenetic studies

Numerous cytogenetic studies have indicated a strong correlation between the spatial proximity of chromosomes or genes and their translocation frequencies by showing that proximal genome sites are more likely to form translocations than distal ones.

As an example, in mouse lymphoma, translocations often involve chromosomes 12, 14, and 15, and these chromosomes are found with high frequency in a space cluster in normal mouse splenocytes when mapped by fluorescent in situ hybridization (FISH). .

Similarly, human chromosomes 4, 13, and 18, which are all preferentially located on the nuclear periphery, frequently translocate with each other, but do not translocate with locally located chromosomes, with which they are not in physical proximity.

Interestingly, the frequency of translocation also correlates with the degree of crossover between chromosomes, strongly suggesting that the local arrangement of double strands breaks translocations.

The same type of correlation applies to individual genes. For example, the spatial proximity of the MYC gene, relative to its possible translocation partners IGH, IGK, and IGL in Burkitts lymphoma, is directly correlated with the observed frequency of these translocations in patients.

There are many other similar examples.

Both the spatial arrangement of genomes and the occurrence of translocations are specific to the type of tissue and cell.

Comparison of translocation patterns and spatial genome organization between tissues further supports a role for genome organization in translocations.

In particular, tissue-specific translocation frequencies correlate with tissue-specific organization patterns.

In mice, for example, chromosomes 12 and 15 that are frequently translocated in lymphomas are proximal in lymphocytes but not in hepatocytes, whereas chromosomes 5 and 6, which are frequently translocated in hepatomas, are proximal in hepatocytes, but not lymphocytes.

These correlations led to the proposal that tissue-specific genome organization is a major driver of chromosomal translocations.

Genomic studies

While these studies provide evidence of the contribution of spatial genome organization as a determining factor in the outcome of translocations, their correlative and retrospective analysis assumes that these regions form translocations, however, without directly demonstrating it.

Furthermore, tumorigenic translocations are often clonal and highly selected, so correlations may not accurately reflect the contribution of spatial organization to translocation frequency.

Several recent studies overcame this limitation by capturing the genetic landscape of translocations in the absence of selection.

Sequencing of translocation junctions, formed by experimentally induced single double strand breaks at the c-myc or Igh locus in primary B lymphocytes.

It indicates that translocations occur more frequently on the same chromosome, while translocations with other chromosomes are much rarer.

Considering that regions of the genome on the same chromosome are more proximal than loci on other chromosomes, these results highlight the notion that the relative distance of translocation partners determines the formation of translocations.

This interpretation is supported by studies that used chromosome conformation capture techniques to map genome-wide physical interactions.

Spatial proximity and translocations

Two models have been presented on how translocations are formed within the 3D nuclear space.

The “break first” model envisions that double-stranded breaks from distant locations can move toward each other over long distances and then join together to form a permanent translocation.

In an alternative “contact first” model, the junction of the broken ends occurs preferentially between chromosomal loci that are in close proximity before the breaks are formed.

Morphological and biochemical observations strongly support the contact-first model. Additional evidence comes from studies showing that double chain breaks have limited mobility within the nucleus of mammals.

Typically, in mammalian cells, a double strand break undergoes limited local movement with a mean squared shift of ~ 1 µm2 / hr, comparable to that of a locus in an intact chromatin fiber.

In contrast, similar experiments in yeast S. cerevisiae indicated higher chromosomal mobility from persistent double strand breaks compared to intact chromosomal loci.

The observed increase depended on factors involved in the stages of the homologous recombination (HR) repair pathway, presumably to facilitate homologous pairing during recombination.

Along with the finding that the 53BP1 double-stranded mammalian breakdown protein promotes the final binding of dysfunctional telomeres by increasing the mobility of local chromatin.

However, even in the much smaller yeast nucleus, spatial proximity appears to play a role in determining recombination results.

By the fact that the MAT mating locus preferentially recombines with its most proximal potential partner rather than a distant potential partner.

Although cytogenetic observations, whole genome mapping and movement studies suggest that most translocations can be explained by the contact model in the first place.

Distal cuts may also form translocations, but probably at a reduced frequency.

An argument in favor of translocation formation from distal breaks is the observation of long-range, apparently directed movement of gene loci.

In living cells and the observed ability of chromosomal domains containing double-stranded breaks to move several microns and clump together within the mammalian nucleus.

In addition, in S. cerevisiae multiple double-stranded breaks are joined at common repair centers.

Although this focal set of repair proteins can increase their local concentration and affect repair efficiency, the spatial proximity of the involved breaks can also facilitate illegitimate misbinding.

Why do chromosomes break where they break?

While the spatial and temporal proximity of chromosomes is an essential determinant in the formation of translocations, it remains largely unclear which upstream factors predispose genomic regions to breakage and translocations in the first place.

Circumstantial evidence suggests that DNA sequence characteristics as well as chromatin properties may facilitate susceptibility to breakdown of genome regions.

DNA sequence

The characteristics of DNA that influence breakage may be related to sequence and / or structure.

In support of this idea, certain DNA sequences are recognized by endogenous nucleases that lead to the formation of double-stranded breaks and translocations.

RAG1 / 2 are endonucleases that create double strand breaks during V (D) J recombination in B and T cells.

Translocations can form when RAG enzymes misrecognize sequences that resemble recombination signal sequences (RSS) normally found in the V (D) J regions.

In germinal center B cells, deaminase recognizes a single chain sequence motif during transcription of regions involved in somatic hypermutation and class switch recombination and promotes double strand breaks to generate antibody diversity.

However, misrecognition of non-Ig targets can lead to translocations.

Deaminase-induced translocations were first seen in germinal center-derived B-cell lymphomas, but have recently been discovered in other B-cell lymphomas, as well as some solid tumors.

It has also been suggested that deaminase contributes to translocations in ways other than misrecognition of recombination signal sequences.

In prostate cancer, deaminase co-recruits with androgen receptor (AR) linked to androgen receptor-binding DNA sequences, sensitizing them to double-strand breaks and leading to the formation of translocations in the presence of genotoxic stress.

Furthermore, several genomic studies have implicated off-target deaminase binding sites that may play a role in the formation of translocations.

These observations suggest that sequence misrecognition by cellular endonucleases promotes genome breakage.

What are the sequences most prone to breakage?

The CpG islands are a candidate.

Although they represent only 1% of the human genome, CpG dinucleotides are present in 40-70% of the bcl-2 and bcl-1 breakpoints in pro-B and pre-B lymphocytes, suggesting that CpGs are the target of deaminase and RAG endonucleases.

However, CpGs are not associated with translocations in other cell types, including lymphoid myeloid progenitors, mature B cells, and T cells.

This suggests that if the CpG islands facilitate breakage, their presence is not enough to promote them and it does not do so in all tissues.

Alu repeats constituting an estimated 11% of the human genome have been proposed to serve as recombination sites for translocations by virtue of non-allelic homologous recombination.

However, in a system designed to quantify translocations, the introduction of identical or divergent Alu repeats adjacent to induced double strand break sites did not alter the frequency of translocations.

Suggesting that the presence of homology per se is not a driver of the translocation frequency.

In support, the presence of Alu elements at sequenced translocation junctions in patient cases has been rare and anecdotal, further suggesting that Alu elements are not universal markers of breakpoints.

Common brittle sites (CFS) have also been linked to translocations.

Common brittle sites are cytologically defined regions of chromosomes that contain gaps and metaphase constrictions under partial replication stress, and these regions have been shown to be prone to breakage.

A recent large-scale analysis of 746 cancer cell lines revealed a strong match of fragile sites with regions of homozygous cancer-causing deletions that strongly support their role in tumorigenesis.

A possible link between brittle sites and translocation formation comes from the observation that exposure of thyroid cells to chemicals that induce brittle sites promotes RET / PTC translocations.

Although no single mechanism appears to explain the appearance of common brittle sites, some common sequence features have been identified.

Common brittle sites are enriched in AT-dinucleotide repeat chains that give these regions high DNA helix flexibility and the ability to form stable non-B DNA secondary structures, which can inhibit DNA replication.

In fact, it has been postulated that translocations form in AT palindromic sequences through a mechanism involving cruciform DNA structures that can be disrupted.

And computational analysis of five translocation genes (CBFB, HMGA1, LAMA4, MLL, and AFF4) revealed significantly higher AT content than the control regions.

More direct evidence for DNA secondary structures in breaks and translocations was the discovery that the major breakpoint region of bcl-2 adopts a stable non-B DNA structure that is driven by recombinantly activated genes in an independent manner. of the sequence.

By containing stable single-stranded regions, this DNA structure promotes recombination-activated gene-mediated cleavage of the bcl-2 locus and the formation of the t (14; 18) translocation in follicular lymphoma.

This secondary structure can be a “G-quadruplex”, a four-stranded DNA structure that can spontaneously form in G-rich sequences.

Additional support that non-B DNA structures contribute to genomic instability and translocations comes from studies in mice in which integration of sequences that form triplex H-DNA or left-handed Z-DNA increased break, deletion, and translocation events. chromosomal.

The topological characteristics of DNA can also contribute to susceptibility to breakage. Topoisomerase II (TOP2) generates a transient double-stranded break to regulate DNA underlinking and overcoiling, for example in mitotic chromosomes and in replication, but also during transcription.

The normally beneficial function of topoisomerase II can, however, sometimes have detrimental effects.

The beta isoform of topoisomerase II has been shown to associate with the androgen receptor upon transcriptional activation and trigger double-stranded disruptions at the TMPRSS2 and ERG breakpoints in prostate cancer.

Chromatin structure and histone modifications

Circumstantial evidence suggests that various aspects of chromatin may play a role in susceptibility and chromosome break translocations.

Genome mapping of the translocation regions after a double-stranded break is introduced at the c-myc or Igh locus in primary B lymphocytes found that double-stranded breaks occur mainly in the transcriptionally active regions.

Along the same lines, two studies have documented breakpoints at or near transcriptionally active regions of the genome.

In anaplastic large cell lymphoma, several genes near the translocation breakpoints are highly expressed before translocations occur.

Similarly, the androgen receptor ligand, a potent transcriptional activator, binds to the TMPRSS2, ERG, and ETV breakpoints, which are involved in translocations in prostate cancer and, under genotoxic stress, induce translocations.

One interpretation of these observations is that chromatin remodeling and transcription factor binding may predispose genomic regions to breakage and translocations.

Histone modifications modulate transcription, replication, double strand break repair, and recombination, making them potential candidates for double strand break susceptibility and translocation mechanisms.

H3K4me3 has been implicated in both the recombinantly activated gene and deaminase-mediated double-chain breaking mechanisms.

The recombinantly activated gene 2 plant homeodomain finger 2 binds to H3K4me3 at the Ig locus in V (D) J recombination, and mutation of this domain greatly decreases the efficiency of recombination.

Furthermore, H3K4me3 stimulates the activity of the recombinantly activated gene at sites other than its natural recognition site, especially at cryptic sites.

In T cells, H3K4me3 peaks at cryptic recombination-activated gene binding sites at certain translocation breakpoints and this binding has been proposed to promote translocations in T cell leukemias.

Similarly, genomic analysis of deaminase-induced cleavage sites identifies four non-immunoglobulin genes that accumulate high rates of mutations and participate in translocations.

Like the deaminase-cleaved natural immunoglobulin target genes, three of these four non-immunoglobulin genes exhibited H3K4me3 enrichment at their cleavage sites, as well as clusters of repeated DNA sequences.

Genome-wide changes of H4K20 monomethylation in mice led to defective double strand break repair, Ig class switch recombination, and translocations involving the IgH locus.

H3K79 methylation has also been implicated in DNA recombination and possibly translocation formation.

In prostate cancer cells, the androgen receptor ligand induces the enrichment of H3K79me2 in the cutoff regions and the overexpression of the H3K79 DOT1L methyltranferase increases the frequency of translocations in the presence of androgen and genotoxic stress.

Genomic mapping of a set of histone modifications in a prostate cancer cell line has indicated a possible enrichment of the active chromatin labels, H3K4me3, H3K36me3 and acetylated H3, on the TMPRSS2-ERG translocation region.

Furthermore, regions corresponding to prostate breakpoints other than TMPRSS2-ERG showed a completely different pattern in that these active labels were depleted and instead enriched for the repressive H3K27me3 label.

This indicates that the relationship between histone marks and breakage susceptibility is complex.

However, the sum of these observations points to the possibility of a combined effect of DNA sequence characteristics, chromatin structure, and histone modifications on susceptibility to chromosome breakage.