Trinucleotide repeats are prevalent among cancer-related genes

Regulatory role of Non-canonical DNA Polymorphisms in human genome and their relevance in Cancer

DNA has the ability to form polymorphic structures like canonical duplex DNA and non-canonical triplex DNA, Cruciform, Z-DNA, G-quadruplex (G4), i-motifs, and hairpin structures. The alteration in the form of DNA polymorphism in the response to environmental changes influences the gene expression. Non-canonical structures are engaged in various biological functions, including chromatin epigenetic and gene expression regulation via transcription and translation, as well as DNA repair and recombination. The presence of non-canonical structures in the regulatory region of the gene alters the gene expression and affects the cellular machinery. Formation of non-canonical structure in the regulatory site of cancer-related genes either inhibits or dysregulate the gene function and promote tumour formation. In the current article, we review the influence of non-canonical structure on the regulatory mechanisms in human genome. Moreover, we have also discussed the relevance of non-canonical structures in cancer and provided information on the drugs used for their treatment by targeting these structures.

Long-read sequencing technology indicates genome-wide effects of non-B DNA on polymerization speed and error rate

DNA conformation may deviate from the classical B-form in ∼13% of the human genome. Non-B DNA regulates many cellular processes; however, its effects on DNA polymerization speed and accuracy have not been investigated genome-wide. Such an inquiry is critical for understanding neurological diseases and cancer genome instability. Here, we present the first simultaneous examination of DNA polymerization kinetics and errors in the human genome sequenced with Single-Molecule Real-Time (SMRT) technology. We show that polymerization speed differs between non-B and B-DNA: It decelerates at G-quadruplexes and fluctuates periodically at disease-causing tandem repeats. Analyzing polymerization kinetics profiles, we predict and validate experimentally non-B DNA formation for a novel motif. We demonstrate that several non-B motifs affect sequencing errors (e.g., G-quadruplexes increase error rates), and that sequencing errors are positively associated with polymerase slowdown. Finally, we show that highly divergent G4 motifs have pronounced polymerization slowdown and high sequencing error rates, suggesting similar mechanisms for sequencing errors and germline mutations.

Trinucleotide Repeat Expansion Diseases, RNAi, and Cancer

Many neurodegenerative diseases are caused by unstable trinucleotide repeat (TNR) expansions located in disease-associated genes. siRNAs based on CAG repeat expansions effectively kill cancer cell lines in vitro through RNAi. They also cause significant reduction in tumor growth in a human ovarian cancer mouse model with no toxicity to the treated mice. This suggests that cancer cells are particularly sensitive to CAG TNR-derived siRNAs, and explains a reported inverse correlation between the length of CAG TNRs and reduced global cancer incidences in some CAG TNR diseases. This review discusses both mutant proteins and mutant RNAs as a cause of TNR diseases, with a focus on RNAi and its role in contributing to disease pathology and in suppressing cancer.

Drugging Undruggable Molecular Cancer Targets

Cancer, more than any other human disease, now has a surfeit of potential molecular targets poised for therapeutic exploitation. Currently, a number of attractive and validated cancer targets remain outside of the reach of pharmacological regulation. Some have been described as undruggable, at least by traditional strategies. In this article, we outline the basis for the undruggable moniker, propose a reclassification of these targets as undrugged, and highlight three general classes of this imposing group as exemplars with some attendant strategies currently being explored to reclassify them. Expanding the spectrum of disease-relevant targets to pharmacological manipulation is central to reducing cancer morbidity and mortality.

Environmental stress induces trinucleotide repeat mutagenesis in human cells

The dynamic mutability of microsatellite repeats is implicated in the modification of gene function and disease phenotype. Studies of the enhanced instability of long trinucleotide repeats (TNRs)-the cause of multiple human diseases-have revealed a remarkable complexity of mutagenic mechanisms. Here, we show that cold, heat, hypoxic, and oxidative stresses induce mutagenesis of a long CAG repeat tract in human cells. We show that stress-response factors mediate the stress-induced mutagenesis (SIM) of CAG repeats. We show further that SIM of CAG repeats does not involve mismatch repair, nucleotide excision repair, or transcription, processes that are known to promote TNR mutagenesis in other pathways of instability. Instead, we find that these stresses stimulate DNA rereplication, increasing the proportion of cells with >4 C-value (C) DNA content. Knockdown of the replication origin-licensing factor CDT1 eliminates both stress-induced rereplication and CAG repeat mutagenesis. In addition, direct induction of rereplication in the absence of stress also increases the proportion of cells with >4C DNA content and promotes repeat mutagenesis. Thus, environmental stress triggers a unique pathway for TNR mutagenesis that likely is mediated by DNA rereplication. This pathway may impact normal cells as they encounter stresses in their environment or during development or abnormal cells as they evolve metastatic potential.

Regions of homozygosity and their impact on complex diseases and traits

Regions of homozygosity (ROHs) are more abundant in the human genome than previously thought. These regions are without heterozygosity, i.e. all the genetic variations within the regions have two identical alleles. At present there are no standardized criteria for defining the ROHs resulting in the different studies using their own criteria in the analysis of homozygosity. Compared to the era of genotyping microsatellite markers, the advent of high-density single nucleotide polymorphism genotyping arrays has provided an unparalleled opportunity to comprehensively detect these regions in the whole genome in different populations. Several studies have identified ROHs which were associated with complex phenotypes such as schizophrenia, late-onset of Alzheimer's disease and height. Collectively, these studies have conclusively shown the abundance of ROHs larger than 1 Mb in outbred populations. The homozygosity association approach holds great promise in identifying genetic susceptibility loci harboring recessive variants for complex diseases and traits.

Triplet repeat length bias and variation in the human transcriptome

Length variation in short tandem repeats (STRs) is an important family of DNA polymorphisms with numerous applications in genetics, medicine, forensics, and evolutionary analysis. Several major diseases have been associated with length variation of trinucleotide (triplet) repeats including Huntington's disease, hereditary ataxias and spinobulbar muscular atrophy. Using the reference human genome, we have catalogued all triplet repeats in genic regions. This data revealed a bias in noncoding DNA repeat lengths. It also enabled a survey of repeat-length polymorphisms (RLPs) in human genomes and a comparison of the rate of polymorphism in humans versus divergence from chimpanzee. For short repeats, this analysis of three human genomes reveals a relatively low RLP rate in exons and, somewhat surprisingly, in introns. All short RLPs observed in multiple genomes are biallelic (at least in this small sample). In contrast, long repeats are highly polymorphic and some long RLPs are multiallelic. For long repeats, the chimpanzee sequence frequently differs from all observed human alleles. This suggests a high expansion/contraction rate in all long repeats. Expansions and contractions are not, however, affected by natural selection discernable from our comparison of human-chimpanzee divergence with human RLPs. Our catalog of human triplet repeats and their surrounding flanking regions can be used to produce a cost-effective whole-genome assay to test individuals. This repeat assay could someday complement SNP arrays for producing tests that assess the risk of an individual to develop a disease, or become part of personalized genomic strategy that provides therapeutic guidance with respect to drug response.

Non-B DNA conformations as determinants of mutagenesis and human disease

Repetitive DNA motifs may fold into non-B DNA structures, including cruciforms/hairpins, triplexes, slipped conformations, quadruplexes, and left-handed Z-DNA, thereby representing chromosomal targets for DNA repair, recombination, and aberrant DNA synthesis leading to repeat expansion or genomic rearrangements associated with neurodegenerative and genomic disorders. Hairpins and quadruplexes also determined the relative abundances of simple sequence repeats (SSR) in vertebrate genomes, whereas strong base stacking has permitted the expansion of purine.pyrimidine-rich SSR during evolutionary time. SSR are enriched in regulatory and cancer-related gene classes, where they have been actively recruited to participate in both gene and protein functions. SSR polymorphic alleles in the population are associated with cancer susceptibility, including within genes that appear to share regulatory circuits involving reactive oxygen species.

Genome-wide analysis of histidine repeats reveals their role in the localization of human proteins to the nuclear speckles compartment

Single amino acid repeats are prevalent in eukaryote organisms, although the role of many such sequences is still poorly understood. We have performed a comprehensive analysis of the proteins containing homopolymeric histidine tracts in the human genome and identified 86 human proteins that contain stretches of five or more histidines. Most of them are endowed with DNA- and RNA-related functions, and, in addition, there is an overrepresentation of proteins expressed in the brain and/or nervous system development. An analysis of their subcellular localization shows that 15 of the 22 nuclear proteins identified accumulate in the nuclear subcompartment known as nuclear speckles. This localization is lost when the histidine repeat is deleted, and significantly, closely related paralogous proteins without histidine repeats also fail to localize to nuclear speckles. Hence, the histidine tract appears to be directly involved in targeting proteins to this compartment. The removal of DNA-binding domains or treatment with RNA polymerase II inhibitors induces the re-localization of several polyhistidine-containing proteins from the nucleoplasm to nuclear speckles. These findings highlight the dynamic relationship between sites of transcription and nuclear speckles. Therefore, we define the histidine repeats as a novel targeting signal for nuclear speckles, and we suggest that these repeats are a way of generating evolutionary diversification in gene duplicates. These data contribute to our better understanding of the physiological role of single amino acid repeats in proteins.

Single amino acid repeats are common in eukaryotic proteins. Some of them are associated with developmental and neurodegenerative disorders in humans, suggesting that they play important functions. However, the role of many of these repeats is unknown. Here, we have studied histidine repeats from a bioinformatics as well as a functional point of view. We found that only 86 proteins in the human genome contain stretches of five or more histidines, and that most of these proteins have functions related with RNA synthesis. When studying where these proteins localize in the cell, we found that a significant proportion accumulate in a subnuclear organelle known as nuclear speckles, via the histidine repeat. This is a structure where proteins related to the synthesis and processing of RNA accumulate. In some cases, the localization is transient and depends on the transcriptional requirements of the cell. Our findings are important because they identify a common cellular function for stretches of histidine residues, and they support the notion that histidine repeats contribute to generate evolutionary diversification. Finally, and considering that some of the proteins with histidine stretches are key elements in essential developmental processes, variation in these repeats would be expected to contribute to human disease.