Shortening Of Chromosomes Research Articles

The regulation of the DNA damage response at telomeres: focus on kinases.

The natural ends of linear chromosomes resemble those of accidental double-strand breaks (DSBs). DSBs induce a multifaceted cellular response that promotes the repair of lesions and slows down cell cycle progression. This response is not elicited at chromosome ends, which are organized in nucleoprotein structures called telomeres. Besides counteracting DSB response through specialized telomere-binding proteins, telomeres also prevent chromosome shortening. Despite of the different fate of telomeres and DSBs, many proteins involved in the DSB response also localize at telomeres and participate in telomere homeostasis. In particular, the DSB master regulators Tel1/ATM and Mec1/ATR contribute to telomere length maintenance and arrest cell cycle progression when chromosome ends shorten, thus promoting a tumor-suppressive process known as replicative senescence. During senescence, the actions of both these apical kinases and telomere-binding proteins allow checkpoint activation while bulk DNA repair activities at telomeres are still inhibited. Checkpoint-mediated cell cycle arrest also prevents further telomere erosion and deprotection that would favor chromosome rearrangements, which are known to increase cancer-associated genome instability. This review summarizes recent insights into functions and regulation of Tel1/ATM and Mec1/ATR at telomeres both in the presence and in the absence of telomerase, focusing mainly on discoveries in budding yeast.

Distinct Roles for Condensin's Two ATPase Sites in Chromosome Condensation.

SummaryCondensin is a conserved SMC complex that uses its ATPase machinery to structure genomes, but how it does so is largely unknown. We show that condensin’s ATPase has a dual role in chromosome condensation. Mutation of one ATPase site impairs condensation, while mutating the second site results in hyperactive condensin that compacts DNA faster than wild-type, both in vivo and in vitro. Whereas one site drives loop formation, the second site is involved in the formation of more stable higher-order Z loop structures. Using hyperactive condensin I, we reveal that condensin II is not intrinsically needed for the shortening of mitotic chromosomes. Condensin II rather is required for a straight chromosomal axis and enables faithful chromosome segregation by counteracting the formation of ultrafine DNA bridges. SMC complexes with distinct roles for each ATPase site likely reflect a universal principle that enables these molecular machines to intricately control chromosome architecture.

Telomeres in Interstitial Lung Disease: The Short and the Long of It.

Telomeres are repetitive nucleotide sequences that cap linear chromosomes, thereby limiting progressive chromosomal shortening during cell replication. In conjunction with environmental factors, common single-nucleotide polymorphisms and rare and ultra-rare telomere-related mutations are associated with accelerated telomere shortening resulting in organ dysfunction, including interstitial lung disease (ILD). The most common telomere-related mutation-associated ILD is idiopathic pulmonary fibrosis (IPF). Up to one-third of individuals with familial IPF have shortened telomeres and/or carry a telomere-related mutation, and 1 in 10 individuals with sporadic IPF have telomere-related mutations. Regardless of ILD phenotype, individuals with short telomeres and/or known telomere-related mutations have more rapid disease progression and shorter lung transplant-free survival. Management should include initiation of antifibrotic agents for those with an IPF phenotype and early referral to a transplant center. Patients with ILD being considered for transplant should be screened for short telomeres if there is a significant family history of pulmonary fibrosis or evidence of extrapulmonary organ dysfunction associated with a short telomere syndrome. Post-transplant management of recipients with telomere-related mutations should include careful adjustment of immunosuppression regimens on the basis of bone marrow reserve. Data on the impact of shortened telomeres on post-transplant outcomes, however, remain mixed.

Reproductive history and blood cell telomere length.

Telomeres are repetitive nucleotide sequences that protect against chromosomal shortening. They are replenished by telomerase, an enzyme that may be activated by estrogen. Women have longer telomeres than men; this difference might be due to estrogen exposure. We hypothesized that reproductive histories reflecting greater estrogen exposure will be associated with longer blood cell telomeres. Among women in the Sister Study (n= 1,048), we examined telomere length in relation to self-reported data on reproductive history. The difference between age at menarche and last menstrual period was used to approximate the reproductive period. Relative telomere length (rTL) was measured using qPCR. After adjustment, rTL decreased with longer reproductive period (β= -0.019, 95% CI: -0.04, -0.00, p= 0.03). Premenopausal women had shorter rTL than postmenopausal women (β= -0.051, 95% CI: -0.12, 0.01, p= 0.13). Longer breastfeeding duration was associated with longer rTL (β= 0.027, 95% CI: 0.01, 0.05, p=0.01); increasing parity was associated with shorter rTL (β = -0.016, 95% CI: -0.03, 0.00, p=0.07). Duration of exogenous hormone use was not associated with rTL. Reproductive histories reflecting greater endogenous estrogen exposure were associated with shorter rTL. Our findings suggest that longer telomeres in women are unlikely to be explained by greater estrogen exposure.

I11 Personalised nutrition, nutraceuticals and multi-omic diagnostics to precisely prevent ageing at the fundamental genome level and optimise tissue regeneration

Damage to the genome at the chromosomal, telomere, and mitochondrial DNA level is the most fundamental pathology that accelerates ageing and the onset of degenerative diseases such as cancer, cardiovascular disease and dementia. Cells that have higher levels of chromosomal DNA damage, telomere shortening and mitochondrial DNA deletions have reduced capacity for DNA replication and are more likely to undergo senescence. As a consequence regenerative capacity of tissues is diminished. The processes of high fidelity DNA replication, DNA repair and chromosome segregation during mitosis require several vitamins (e.g. folate, vitamin B12, vitamin B6, niacin) and minerals (e.g. Mg, Zn). Furthermore, antioxidant vitamins (e.g. vitamins A,C,E) and phytonutrients (e.g. catechin, caffeic acid) as well as minerals required as cofactors of antioxidant enzymes (Zn, Mn, Cu, Se), are essential to mitigate against the accumulation of base damage and DNA strand breaks that cause DNA replication stress and chromosome abnormalities. Several common polymorphisms in genes that code for proteins required for the absorption and metabolism of these essential nutrients influence individual dietary requirements and their biological effects are measurable using multi-omics technologies. The presentation will provide an overview of the field of personalised nutrition for DNA damage prevention using supplements, nutraceuticals and dietary patterns and the use of multi-omics to determine efficacy and safety at the individual level.

DNA Replication Origins and Fork Progression at Mammalian Telomeres.

Telomeres are essential chromosomal regions that prevent critical shortening of linear chromosomes and genomic instability in eukaryotic cells. The bulk of telomeric DNA is replicated by semi-conservative DNA replication in the same way as the rest of the genome. However, recent findings revealed that replication of telomeric repeats is a potential cause of chromosomal instability, because DNA replication through telomeres is challenged by the repetitive telomeric sequences and specific structures that hamper the replication fork. In this review, we summarize current understanding of the mechanisms by which telomeres are faithfully and safely replicated in mammalian cells. Various telomere-associated proteins ensure efficient telomere replication at different steps, such as licensing of replication origins, passage of replication forks, proper fork restart after replication stress, and dissolution of post-replicative structures. In particular, shelterin proteins have central roles in the control of telomere replication. Through physical interactions, accessory proteins are recruited to maintain telomere integrity during DNA replication. Dormant replication origins and/or homology-directed repair may rescue inappropriate fork stalling or collapse that can cause defects in telomere structure and functions.

Ctf4 Is a Hub in the Eukaryotic Replisome that Links Multiple CIP-Box Proteins to the CMG Helicase

SummaryReplisome assembly at eukaryotic replication forks connects the DNA helicase to DNA polymerases and many other factors. The helicase binds the leading-strand polymerase directly, but is connected to the Pol α lagging-strand polymerase by the trimeric adaptor Ctf4. Here, we identify new Ctf4 partners in addition to Pol α and helicase, all of which contain a “Ctf4-interacting-peptide” or CIP-box. Crystallographic analysis classifies CIP-boxes into two related groups that target different sites on Ctf4. Mutations in the CIP-box motifs of the Dna2 nuclease or the rDNA-associated protein Tof2 do not perturb DNA synthesis genome-wide, but instead lead to a dramatic shortening of chromosome 12 that contains the large array of rDNA repeats. Our data reveal unexpected complexity of Ctf4 function, as a hub that connects multiple accessory factors to the replisome. Most strikingly, Ctf4-dependent recruitment of CIP-box proteins couples other processes to DNA synthesis, including rDNA copy-number regulation.

Insertion of Retrotransposons at Chromosome Ends: Adaptive Response to Chromosome Maintenance.

The telomerase complex is a specialized reverse transcriptase (RT) that inserts tandem DNA arrays at the linear chromosome ends and contributes to the protection of the genetic information in eukaryotic genomes. Telomerases are phylogenetically related to retrotransposons, encoding also the RT activity required for the amplification of their sequences throughout the genome. Intriguingly the telomerase gene is lost from the Drosophila genome and tandem retrotransposons replace telomeric sequences at the chromosome extremities. This observation suggests the versatility of RT activity in counteracting the chromosome shortening associated with genome replication and that retrotransposons can provide this activity in case of a dysfunctional telomerase. In this review paper, we describe the major classes of retroelements present in eukaryotic genomes in order to point out the differences and similarities with the telomerase complex. In a second part, we discuss the insertion of retroelements at the ends of chromosomes as an adaptive response for dysfunctional telomeres.

Aging and Immortality

AGING AND IMMORTALITY BY DANIEL JIAO T he oldest verified person lived to 122 years old and died in 1997 but even today we have people claiming to be even older such as Mbah Gotho who states he is 145 years old. The current worldwide average expectancy is 71 years old but the variety of ages we live to is enormous. We still have much to learn about what leads to these differences in life spans leading us to question what aging is. Numerous studies have been done inves- tigating the various causes of aging such as telomerase, mitochondrial signaling, sensory signaling, diet, and microRNAs. Telomerase is an RNA dependent DNA polymerase which is used to lengthen the ends of chromosomes by adding base pairs. The ends of each of the arms of the chromosome are called telomeres and they protect the cell from losing important coding regions on chromosomes. Base pairs are lost from the chromosome ends upon each division which slowly shorten the telomere. This continues until a point at which the cell can no longer divide which is called cellular senescence. The cell is then able to kill itself by the apoptotic pathway when the critical length is met during cellular senescence. In the end all telomeres are controlled by the telomerase activity and erosion during cell division and it is one of the reason why organisms such as humans cannot live forever currently. The idea that the shortening of telomeres and apoptosis is important in regulation of tumor suppression is strongly supported Investigations into the telomeres of different organisms such as lobsters can provide greater insight into their role and functions in aging. Lobster are known to have indeterminate growth meaning that they continue to grow until they die. This is un- like humans which have determinate growth and stop growing mostly after puberty. We can then think about chromosomal shortening and why lobsters are able to replicate their cells continuously but humans are not. The answer is the lobster’s telomerase which is con- tinuously produced even after maturation of the tissues which is unlike human cells which mostly exhibit no telomerase activity after differentiation. Telomerase is only one of the many factors that plays a role in aging however so even though lobsters theoretically can keep dividing their cells continuously they usually live 30-50 years depending on gender. The fact that lobsters do not live forever or for unreasonable years shows that other factors play huge roles in determining life span such as mutations, diseases, and diet. Berkeley Scientific Journal | FALL 2016

The influence of oxidative stress induced by iron on telomere length.

Oxidative stress can be induced by increased concentrations of iron in the body and consequently can cause shortening of telomeres. Telomeres, called mitotic clocks, are non-coding fragments at the end of chromosomes. During the replication of genetic material they are shortened, playing the role of ageing biomarkers in eukaryotes. In human endothelial cells, oxidative stress causes a decrease in telomerase activity. Shortening of chromosomes in telomeric parts was found in patients with primary hemochromatosis and in patients taking supplements containing iron. Increased level of transferrin saturation is associated with the presence of shorter telomeres in the chromosomes of leukocytes. The relationship between iron status and telomere length is still not fully understood.

Association between telomere length and chromosome 21 nondisjunction in the oocyte.

Chromosome 21 nondisjunction in oocytes is the most common cause of trisomy 21, the primary chromosomal abnormality responsible for Down syndrome (DS). This specific type of error is estimated to account for over 90 % of live births with DS, with maternal age being the best known risk factor for chromosome 21 nondisjunction. The loss of telomere length and the concomitant shortening of chromosomes are considered a biological marker for aging. Thus, we tested the hypothesis that mothers who had a maternal nondisjunction error leading to a live birth with DS (n = 404) have shorter telomeres than mothers with live births without DS (n = 42). In effect, our hypothesis suggests that mothers of children with DS will appear "biologically older" as compared to the mothers of euploid children. We applied a quantitative PCR assay to measure the genome-wide relative telomere length to test this hypothesis. The results of our study support the hypothesis that young mothers of DS babies are "biologically older" than mothers of euploid babies in the same age group and supports telomere length as a biomarker of age and hence risk for chromosome nondisjunction.

Human telomerase specialization for repeat synthesis by unique handling of primer-template duplex

With eukaryotic genome replication, incomplete telomere synthesis results in chromosome shortening and eventual compromise of genome stability. Telomerase counteracts this terminal sequence loss by synthesizing telomeric repeats through repeated cycles of reverse transcription of its internal RNA template. Using human telomerase domain-complementation assays for telomerase reverse transcriptase protein (TERT) and RNA in combination with the first direct footprinting assay for telomerase association with bound DNA, we resolve mechanisms by which TERT domains and RNA motifs direct repeat synthesis. Surprisingly, we find that product-template hybrid is sensed in a length- and sequence-dependent manner to set the template 5' boundary. We demonstrate that the TERT N-terminal (TEN) domain determines active-site use of the atypically short primer-template hybrid necessary for telomeric-repeat synthesis. Also against expectation, we show that the remainder of TERT (the TERT ring) supports functional recognition and physical protection of single-stranded DNA adjacent to the template hybrid. These findings establish unprecedented polymerase recognition specificities for DNA-RNA hybrid and single-stranded DNA and suggest a new perspective on the mechanisms of telomerase specialization for telomeric-repeat synthesis.

Mechanisms of Trf1/Trf2 Binding Properties and DNA Sequence Recognition as Studied by Molecular Dynamics

Telomeres are complex nucleoprotein structures, formed at the ends of linear chromosomes as means of termini protection and stabilization. They were developped in response to the so-called termini replication problem, which caused steady shortening of Eukaryota chromosomes over the course of cell divisions. In numerous species, including humans, telomeric DNA consists of tandem 5'-TTAGGG-3' repeats of various length (ca. 10 kbp in case of human chromosomes); this portion of non-coding DNA can be lost during proliferation with no loss in genetic information. Constitutively proliferating cells, however, need to produce telomerase -- a ribonucleoprotein which is able to elongate the termini by use of its own RNA template. Telomere-deficient chromosomes might undergo ligation by cellular mechanisms of DNA repair and, further, trigger apoptosis; at the same time, telomere shortening is considered to be a cellular marker of aging. These two reasons make telomeres subject to particular attention in fields of drug design and senescence research.The telomere structure is stabilized by a number of distinct proteins, building up the shelterin complex. Two of these are responsible for specifically recruiting the complex to the telomeric sequence: Telomere repeat-binding factors 1 and 2 (TRF1 and TRF2). Here we present a detailed comparative Molecular Dynamics study of their mechanism of binding and sequence recognition. A decomposed free energy profile is used to quantify the key determinants of binding. We reproduce the experimental affinity data on the fully atomic scale, and propose a novel mechanism of sequence specificity. Moreover, we have computed a 2D PMF profile that enables us to draw conclusions about the association-dissociaton dynamics.

Chromosome Territories Meet a Condensin

Chromosome Territories Meet a Condensin

The relative ratio of condensin I to II determines chromosome shapes

To understand how chromosome shapes are determined by actions of condensins and cohesin, we devised a series of protocols in which their levels are precisely changed in Xenopus egg extracts. When the relative ratio of condensin I to II is forced to be smaller, embryonic chromosomes become shorter and thicker, being reminiscent of somatic chromosomes. Further depletion of condensin II unveils its contribution to axial shortening of chromosomes. Cohesin helps juxtapose sister chromatid arms by collaborating with condensin I and counteracting condensin II. Thus, chromosome shaping is achieved by an exquisite balance among condensin I and II and cohesin.

Telomeraz Enziminin Tanı ve Tedavide Kullanım Alanı

There are structures on the tip of eukaryotic chromosomes known as telomer. These non-translated repeat sequences participate in the stabilization of chromosomes. These structures shorten 10-12 bp in each replication. However, there is an enzyme which takes effect to prevent the shortening of chromosomes. This enzyme is found in germ cells, embriyonic stem cells, single celled eukaryotes and cancerous cells. Telomer has important roles on aging and cancer. In the last decade, medical sciences focus on the probability of use of telomerase enzyme retarding the aging course and inerease life expectancy. In addition, the presence of the enzyme in cancerous cells suggests the use of this enzyme for cancer diagnosis as a biomarker. The telomerase enzymes may also be used in cancer treatment. Studies on the prevention of ability of finite division of the cancer cells by the inactivation of the telomerase enzyme are promising.

Length Does Not Matter

The role of telomeres in maintaining genetic stability was first described by Blackburn1 in 1991. Telomeres and their associated proteins provide protection against DNA degradation because 40 to 200 bp of the telomere's tandem repeats are lost on each successive cell division, resulting in the progressive shortening of chromosomes. Telomeres also help to regulate the “cellular clock” because critically short telomeres trigger a cell cycle checkpoint, resulting in replicative senescence (ie, a natural process for terminally differentiated somatic cells, yet undesirable for hematopoietic cells, which require the potential for regulated proliferation throughout life).2 Thus, exquisite regulation of telomerase is required for extension of telomeres under appropriate conditions in immune cells. Indeed, overexpression or underexpression of telomerase or its reverse transcriptase catalytic domain, human telomerase reverse transcriptase (hTERT), is associated with numerous chronic inflammatory and autoimmune disorders,3 underscoring the importance of telomerase activity in immune cell function. See accompanying article on page 245 Nearly 10 years ago, Stewart et al4 demonstrated a novel role for telomerase in the promotion of tumorigenesis. By using an hTERT-mutant protein unable to extend telomere length, the researchers showed that TERT, together with transforming protein p21 (H-RAS), induced tumorigenesis independently of effects on telomeres. Adding further complexity to telomerase activity, recent work from Park et al5 showed that TERT associates with Brahma-related gene …

Telomerase activity-independent function of TERT allows glioma cells to attain cancer stem cell characteristics by inducing EGFR expression.

Telomerase reverse transcriptase (TERT), the catalytic subunit of the enzyme telomerase, is robustly expressed in cancer cells. TERT enables cells to avoid chromosome shortening during repeated replication by maintaining telomere length. However, several lines of evidence indicate that many cancer cells exhibit shorter telomere length than normal tissues, implying an additional function of TERT in tumor formation and progression. Here, we report a telomerase activity-independent function of TERT that induces cancer stemness in glioma cells. Overexpression of TERT712, a telomerase activity-deficient form of TERT, in U87MG cells promoted cell self-renewal in vitro, and induced EGFR expression and formation of gliomas exhibiting cellular heterogeneity in vivo. In patients with glioblastoma multiforme, TERT expression showed a high correlation with EGFR expression, which is closely linked to the stemness gene signature. Induction of differentiation and TERT-knockdown in glioma stem cells led to a marked reduction in EGFR expression, cancer stemness, and anticancer drug resistance. Together, our findings indicate that TERT plays a crucial role in tumor progression by promoting cancer stemness through expression of EGFR.

Telomere Shortening and Regenerative Capacity after Acute Kidney Injury

With advances in modern medicine leading to improved health, the percentage of the population who are elderly is increasing. Associated with increasing age is a decline in renal function and loss of renal mass.1 These alterations in renal function predict increasing risk for mortality.2 The aging kidney also associates with multiple disease states, such as cardiovascular disease,3 cancer,4 and cognitive dysfunction,5 which increase susceptibility to ischemic acute kidney injury (AKI), from which the elderly are less likely to recover.6 Telomere attrition is implicated in many diseases associated with aging, including cardiovascular disease; however, an association between telomere shortening and decreased renal repair and regeneration after injury is largely unknown.7 The role of telomeres, repetitive DNA elements located at the end of chromosomes, is to prevent unwanted chromosome shortening and recombination. The length of telomeres is regulated by telomerase, which adds tandem TTAGGG repeats to the end of chromosomes to minimize shortening.8 Unfortunately, the majority of human cell types have limited telomerase activity, and, as we age, our telomeres shorten progressively with every cell division, eventually becoming critically short and resulting in senescence and apoptosis. This has serious implications for organ repair, regeneration, and recovery from injury. In this issue of JASN , Westhoff et al. …

Conformation of Telomerase RNP Established through Footprinting and Single-Molecule FRET

Telomerase, a ribonucleoprotein (RNP) expressed in all highly proliferating cells, is comprised of telomerase RNA, telomerase reverse transcriptase (TERT) and other protein cofactors. The complex compensates for the chromosomal shortening that arises with each round of DNA replication. Since mutations altering telomerase expression, assembly and regulation cause multiple human diseases, it is of utmost importance to understand telomerase at the structural level. However, while the structure of TERT in the absence of RNA has been recently published, the full RNP structure remains unknown.Using a combination of single-molecule FRET and ensemble footprinting, we are probing the functional structure of telomerase RNP. In particular, we have determined the active conformation adopted by two conserved regions of telomerase RNA - the stemloop IV and the pseudoknot - upon assembly with TERT and other protein cofactors.The pseudoknot, unformed in naked telomerase RNA, was folded in active RNPs. Proper pseudoknot folding was required for catalysis, as demonstrated by mutations that abolished telomerase activity when formation of either pseudoknot stem was disallowed. Conversely, compensatory mutations that reinstated basepairing in the pseudoknot region also restored telomerase activity.Binding of TERT, in addition to allowing pseudoknot formation, brought loop IV into the proximity of the pseudoknot without affecting its conformation. Mutations in the loop IV region that abolished TERT binding and telomerase activity resulted in an extended RNA conformation with a substantially larger loop IV-pseudoknot distance, as well as protection of the pseudoknot by RNP proteins. Interestingly, the telomerase holoenzyme protein p65 could compensate for these effects of loop IV mutations, restoring the loop IV-TERT interaction, the folded conformation of stemloop IV and telomerase activity.These results suggest that proper conformations of the pseudoknot and stemloop IV of telomerase RNA are critical for enzyme activity.