Endogenous Chromosomes Research Articles

Metabolism of halauxifen acid is regulated by genes located on wheat chromosome 5A

Abstract Allohexaploid wheat (Triticum aestivum L.) is tolerant to halauxifen-methyl (HM) via rapid detoxification of the phytotoxic form of HM, halauxifen acid (HA), to non-phytotoxic metabolites. Previous research utilizing ‘Chinese Spring’ (CS) wheat, alien substitution (i.e., endogenous chromosome pair substituted with a homoeologous pair from diploid Sears’ goatgrass (Aegilops searsii M. Feldman & M. Kislev) (AS), or nullisomic-tetrasomic (NT) lines indicated plants lacking chromosome 5A are more sensitive than CS to HM. We hypothesized the increased HM sensitivity of these plants results from losing gene(s) on chromosome 5A associated with HA metabolism, which leads to a reduced HA detoxification rate relative to CS. To compare HA abundance among AS, CS, alien substitution, and NT lines during a time course, two excised-leaf studies using unlabeled HM and liquid chromatography–mass spectrometry analyses were performed. Aegilops searsii accumulated more HA than CS did, and each substitution line at 8, 12, and 24 h after treatment (HAT). Furthermore, only the wheat substitution line lacking chromosome 5A displayed greater abundance of HA relative to CS (2.4- to 3.8-fold, depending on the time point). In contrast, HA abundances in lines possessing chromosome 5A were not different than HA abundances in CS at all time points. When NT lines were compared with CS, the nullisomic 5D-tetrasomic 5A (N5D-T5A) line displayed similar HA abundance, whereas the nullisomic 5A-tetrasomic 5D (N5A-T5D) accumulated approximately 3-fold more HA at 12 and 24 HAT. These results biochemically support the hypothesis that genes encoding HA-detoxifying enzyme(s) are located on wheat chromosome 5A and corroborate findings from previous greenhouse phenotypic experiments. Future experimentation is needed to identify and characterize genes and enzymes on wheat chromosome 5A involved with HA detoxification, which may include cytochrome P450 monooxygenases, unknown oxidases, UDP-dependent glucosyltransferases, or, potentially, transcription factors that regulate expression of these genes associated with HA detoxification.

Chromosome Transplantation: Opportunities and Limitations.

There are thousands of rare genetic diseases that could be treated with classical gene therapy strategies such as the addition of the defective gene via viral or non-viral delivery or by direct gene editing. However, several genetic defects are too complex for these approaches. These "genomic mutations" include aneuploidies, intra and inter chromosomal rearrangements, large deletions, or inversion and copy number variations. Chromosome transplantation (CT) refers to the precise substitution of an endogenous chromosome with an exogenous one. By the addition of an exogenous chromosome and the concomitant elimination of the endogenous one, every genetic defect, irrespective of its nature, could be resolved. In the current review, we analyze the state of the art of this technique and discuss its possible application to human pathology. CT might not be limited to the treatment of human diseases. By working on sex chromosomes, we showed that female cells can be obtained from male cells, since chromosome-transplanted cells can lose either sex chromosome, giving rise to 46,XY or 46,XX diploid cells, a modification that could be exploited to obtain female gametes from male cells. Moreover, CT could be used in veterinary biology, since entire chromosomes containing an advantageous locus could be transferred to animals of zootechnical interest without altering their specific genetic background and the need for long and complex interbreeding. CT could also be useful to rescue extinct species if only male cells were available. Finally, the generation of "synthetic" cells could be achieved by repeated CT into a recipient cell. CT is an additional tool for genetic modification of mammalian cells.

Plasmid parB contributes to uropathogenic Escherichia coli colonization in vivo by acting on biofilm formation and global gene regulation.

The endogenous plasmid pUTI89 harbored by the uropathogenic Escherichia coli (UPEC) strain UTI89 plays an important role in the acute stage of infection. The partitioning gene parB is important for stable inheritance of pUTI89. However, the function of partitioning genes located on the plasmid in pathogenesis of UPEC still needs to be further investigated. In the present study, we observed that disruption of the parB gene leads to a deficiency in biofilm formation in vitro. Moreover, in a mixed infection with the wild type strain and the parB mutant, in an ascending UTI mouse model, the mutant displayed a lower bacterial burden in the bladder and kidneys, not only at the acute infection stage but also extending to 72 hours post infection. However, in the single infection test, the reduced colonization ability of the parB mutant was only observed at six hpi in the bladder, but not in the kidneys. The colonization capacity in vivo of the parB-complemented strain was recovered. qRT-PCR assay suggested that ParB could be a global regulator, influencing the expression of genes located on both the endogenous plasmid and chromosome, while the gene parA or the operon parAB could not. Our study demonstrates that parB contributes to the virulence of UPEC by influencing biofilm formation and proposes that the parB gene of the endogenous plasmid could regulate gene expression globally.

Asymmetric chromatin retention and nuclear envelopes separate chromosomes in fused cells in vivo

Hybrid cells derived through fertilization or somatic cell fusion recognize and separate chromosomes of different origins. The underlying mechanisms are unknown but could prevent aneuploidy and tumor formation. Here, we acutely induce fusion between Drosophila neural stem cells (neuroblasts; NBs) and differentiating ganglion mother cells (GMCs) in vivo to define how epigenetically distinct chromatin is recognized and segregated. We find that NB-GMC hybrid cells align both endogenous (neuroblast-origin) and ectopic (GMC-origin) chromosomes at the metaphase plate through centrosome derived dual-spindles. Physical separation of endogenous and ectopic chromatin is achieved through asymmetric, microtubule-dependent chromatin retention in interphase and physical boundaries imposed by nuclear envelopes. The chromatin separation mechanisms described here could apply to the first zygotic division in insects, arthropods, and vertebrates or potentially inform biased chromatid segregation in stem cells.

Aurora B/C-dependent phosphorylation promotes Rec8 cleavage in mammalian oocytes

To generate haploid gametes, cohesin is removed in a stepwise manner from chromosome arms in meiosis I and the centromere region in meiosis II to segregate chromosomes and sister chromatids, respectively. Meiotic cohesin removal requires cleavage of the meiosis-specific kleisin subunit Rec8 by the protease separase.1,2 In yeast and C.elegans, Rec8 on chromosome arms has to be phosphorylated to be cleaved in meiosis I,3-7 whereas Rec8 at the centromere is protected from cleavage by the action of PP2A-B56.8-10 However, in mammalian meiosis, it is unknown whether Rec8 has to be equally phosphorylated for cleavage, and if so, the identity of the relevant kinase(s). This is due to technical challenges, as Rec8 is poorly conserved, preventing a direct translation of the knowledge gained from model systems such as yeast and C.elegans to mammals. Additionally, there is no turnover of Rec8 after cohesion establishment, preventing phosphomutant analysis of functional Rec8. To address the very basic question of whether Rec8 cleavage requires its phosphorylation in mammals, we adapted a biosensor that detects separase activity to study Rec8 cleavage in single mouse oocytes by live imaging. Crucially, through phosphomutant analysis, we identified phosphorylation sites in Rec8 promoting cleavage. We found that Rec8 cleavage depends on Aurora B/C kinase activities and identified an aminoacid residue that is phosphorylated invivo. Accordingly, inhibition of AuroraB/C kinases during meiotic maturation impairs endogenous Rec8 phosphorylation and chromosome segregation.

Formation of artificial chromosomes in Caenorhabditis elegans and analyses of their segregation in mitosis, DNA sequence composition and holocentromere organization.

To investigate how exogenous DNA concatemerizes to form episomal artificial chromosomes (ACs), acquire equal segregation ability and maintain stable holocentromeres, we injected DNA sequences with different features, including sequences that are repetitive or complex, and sequences with different AT-contents, into the gonad of Caenorhabditis elegans to form ACs in embryos, and monitored AC mitotic segregation. We demonstrated that AT-poor sequences (26% AT-content) delayed the acquisition of segregation competency of newly formed ACs. We also co-injected fragmented Saccharomyces cerevisiae genomic DNA, differentially expressed fluorescent markers and ubiquitously expressed selectable marker to construct a less repetitive, more complex AC. We sequenced the whole genome of a strain which propagates this AC through multiple generations, and de novo assembled the AC sequences. We discovered CENP-AHCP-3 domains/peaks are distributed along the AC, as in endogenous chromosomes, suggesting a holocentric architecture. We found that CENP-AHCP-3 binds to the unexpressed marker genes and many fragmented yeast sequences, but is excluded in the yeast extremely high-AT-content centromeric and mitochondrial DNA (> 83% AT-content) on the AC. We identified A-rich motifs in CENP-AHCP-3 domains/peaks on the AC and on endogenous chromosomes, which have some similarity with each other and similarity to some non-germline transcription factor binding sites.

RbAp46/48LIN-53 and HAT-1 are required for initial CENP-AHCP-3 deposition and de novo holocentromere formation on artificial chromosomes in Caenorhabditis elegans embryos.

Foreign DNA microinjected into the Caenorhabditis elegans syncytial gonad forms episomal extra-chromosomal arrays, or artificial chromosomes (ACs), in embryos. Short, linear DNA fragments injected concatemerize into high molecular weight (HMW) DNA arrays that are visible as punctate DAPI-stained foci in oocytes, and they undergo chromatinization and centromerization in embryos. The inner centromere, inner kinetochore and spindle checkpoint components, including AIR-2, CENP-AHCP-3, Mis18BP1KNL-2 and BUB-1, respectively, assemble onto the nascent ACs during the first mitosis. The DNA replication efficiency of ACs improves over several cell cycles, which correlates with the improvement of kinetochore bi-orientation and proper segregation of ACs. Depletion of condensin II subunits, like CAPG-2 and SMC-4, but not the replicative helicase component, MCM-2, reduces de novo CENP-AHCP-3 level on nascent ACs. Furthermore, H3K9ac, H4K5ac and H4K12ac are highly enriched on newly chromatinized ACs. RbAp46/48LIN-53 and HAT-1, which affect the acetylation of histone H3 and H4, are essential for chromatinization, de novo centromere formation and segregation competency of nascent ACs. RbAp46/48LIN-53 or HAT-1 depletion causes the loss of both CENP-AHCP-3 and Mis18BP1KNL-2 initial deposition at de novo centromeres on ACs. This phenomenon is different from centromere maintenance on endogenous chromosomes, where Mis18BP1KNL-2 functions upstream of RbAp46/48LIN-53.

MYC Promotes Bone Marrow Stem Cell Dysfunction in Fanconi Anemia.

Bone marrow failure (BMF) in Fanconi anemia (FA) patients results from dysfunctional hematopoietic stem and progenitor cells (HSPCs). To identify determinants of BMF, we performed single-cell transcriptome profiling of primary HSPCs from FA patients. In addition to overexpression of p53 and TGF-β pathway genes, we identified high levels of MYC expression. We correspondingly observed coexistence of distinct HSPC subpopulations expressing high levels of TP53 or MYC in FA bone marrow (BM). Inhibiting MYC expression with the BET bromodomain inhibitor (+)-JQ1 reduced the clonogenic potential of FA patient HSPCs but rescued physiological and genotoxic stress in HSPCs from FA mice, showing that MYC promotes proliferation while increasing DNA damage. MYC-high HSPCs showed significant downregulation of cell adhesion genes, consistent with enhanced egress of FA HSPCs from bone marrow to peripheral blood. We speculate that MYC overexpression impairs HSPC function in FA patients and contributes to exhaustion in FA bone marrow.

Chromosome Transplantation: A Possible Approach to Treat Human X-linked Disorders

Many human genetic diseases are associated with gross mutations such as aneuploidies, deletions, duplications, or inversions. For these “structural” disorders, conventional gene therapy, based on viral vectors and/or on programmable nuclease-mediated homologous recombination, is still unsatisfactory. To correct such disorders, chromosome transplantation (CT), defined as the perfect substitution of an endogenous defective chromosome with an exogenous normal one, could be applied. CT re-establishes a normal diploid cell, leaving no marker of the procedure, as we have recently shown in mouse pluripotent stem cells. To prove the feasibility of the CT approach in human cells, we used human induced pluripotent stem cells (hiPSCs) reprogrammed from Lesch-Nyhan (LN) disease patients, taking advantage of their mutation in the X-linked HPRT gene, making the LN cells selectable and distinguishable from the resistant corrected normal cells. In this study, we demonstrate, for the first time, that CT is feasible in hiPSCs: the normal exogenous X chromosome was first transferred using an improved chromosome transfer system, and the extra sex chromosome was spontaneously lost. These CT cells were functionally corrected and maintained their pluripotency and differentiation capability. By inactivation of the autologous HPRT gene, CT paves the way to the correction of hiPSCs from several X-linked disorders.

Genetic and epigenetic effects on centromere establishment.

Endogenous chromosomes contain centromeres to direct equal chromosomal segregation in mitosis and meiosis. The location and function of existing centromeres is usually maintained through cell cycles and generations. Recent studies have investigated how the centromere-specific histone H3 variant CENP-A is assembled and replenished after DNA replication to epigenetically propagate the centromere identity. However, existing centromeres occasionally become inactivated, with or without change in underlying DNA sequences, or lost after chromosomal rearrangements, resulting in acentric chromosomes. New centromeres, known as neocentromeres, may form on ectopic, non-centromeric chromosomal regions to rescue acentric chromosomes from being lost, or form dicentric chromosomes if the original centromere is still active. In addition, de novo centromeres can form after chromatinization of purified DNA that is exogenously introduced into cells. Here, we review the phenomena of naturally occurring and experimentally induced new centromeres and summarize the genetic (DNA sequence) and epigenetic features of these new centromeres. We compare the characteristics of new and native centromeres to understand whether there are different requirements for centromere establishment and propagation. Based on our understanding of the mechanisms of new centromere formation, we discuss the perspectives of developing more stably segregating human artificial chromosomes to facilitate gene delivery in therapeutics and research.

Engineering synthetic mini-chromosomes to study chromosome segregation in budding yeast

Chromosomes need to be replicated and partitioned into daughter cells during cellular division. Failure to do so leads to aneuploidy, which has been linked to medical conditions such as cancer. Cohesin, a ring-shaped protein complex, holds the replicated sister chromatids together to ensure their accurate segregation. In Saccharomyces cerevisiae a large pool of cohesin is loaded at centromeres. Introducing the centromeric sequence to circular and linear DNA has been exploited to allow propagation of extra-chromosomal DNA. However, these extra-chromosomal DNA do not segregate as well as endogenous chromosomes and the reasons for this are unknown. Interestingly, small circular chromosomes are more stable than their linear counterparts. Furthermore, the stability of linear chromosomes increases with chromosome length. The DNA sequence itself appears to be important as linear chromosomes containing endogenous DNA are more stable than chromosomes derived from artificial DNA of similar lengths. During our project, we sought to identify cis-acting DNA elements, other than the centromere, that are important for chromosome segregation. We have developed a synthetic biology approach to engineer a library of synthetic circular and linear chromosomes of various lengths containing unnatural DNA (designed to lack features of known elements such as transcription units). These chromosomes act as a “blank canvas” where candidate DNA elements are introduced to test their functionality. Our design, build and test cycle has allowed us to determine how chromosome length, circularization and DNA sequence influence chromosome segregation and the minimal requirements for building the optimal synthetic chromosome. Our latest findings will be presented.

Replication stress limits developmental potential of human preimplantation embryos

Human preimplantation embryos show abnormal nucleation and DNA damage, compromising cell cycle progression and developmental potential. The molecular mechanisms and timing of these abnormalities are unknown. We identified endogenous DNA damage and repair mechanisms in human embryos and developed a murine model to study developmental consequences of replication stress in preimplantation embryos. Prospective laboratory study of human and mouse embryos Endogenous DNA damage and repair pathways were evaluated in humans using donated oocytes (n=25) and embryos (n=20). Immunofluorescent staining detected DNA damage (γH2AX, RPA), repair (RPAS33, RPA S4/S8, Rad51, 53BP1), and micronucleation. Consequences of genomic instability were studied in a murine model using aphidicolin, a DNA polymerase inhibitor that increases endogenous chromosome fragility1. Mouse zygotes (n=500) were briefly exposed to aphidicolin in the first cell cycle, then evaluated at 1-cell, 2-cell, 4-8-cell and blastocyst stage. Immunofluorescent staining detected DNA damage and repair. Cleavage progression, blastulation and embryo quality were assessed versus controls. Human and mouse karyotypes were determined with NGS. Human preimplantation embryos show endogenous DNA damage, demonstrated by γH2AX, RPA and abnormal nucleation. Cleavage embryos had significantly greater foci and micronucleation vs blastocysts (γH2AX cleavage mean 2.3 vs blastocyst 1.0, p <0.0001; RPA cleavage mean 1.7 vs 0.3, p<0.0001; abnormal nucleation cleavage mean 15.9% vs blastocyst 4.2%, p<0.0001). DNA damage foci coincided with RPAS33, indicating RPA phosphorylation by G2 checkpoint kinase ATR, Rad51, indicating repair by homologous recombination, and 53BP1, indicating unrepaired DNA is passed to daughter cells. Aphidicolin-induced replication delay resulted in DNA damage (γH2AX and RPA), and RPAS33, indicating an ATR-dependent G2 checkpoint. Additional DNA repair mechanisms included Rad51 and 53BP1, similar to human embryos. Though some unreplicated DNA is tolerated in mitosis and compatible with euploidy, aphidicolin-induced under replication in the first cell cycle precipitated instability in later cell cycles, leading to decreased blastulation (45% after 8h aphidicolin vs 91.8% control, p<0.0001), and poor quality embryos as evidenced by significantly fewer total cells and inner cell mass with significantly greater DNA damage and micronucleation with increasing duration of aphidicolin exposure compared to controls. DNA damage responses to incomplete replication in G2 (ATR and Rad51), and the G1 response to unreplicated DNA (53BP1) mirror endogenous repair activity in human preimplantation embryos. Developmental consequences of replication stress likely persist beyond the preimplantation stage and may contribute to failed implantation or miscarriage. The murine model of genomic instability enables further study of these processes and the development of targeted therapeutics.

Point centromere activity requires an optimal level of centromeric noncoding RNA

In budding yeast, which possesses simple point centromeres, we discovered that all of its centromeres express long noncoding RNAs (cenRNAs), especially in S phase. Induction of cenRNAs coincides with CENP-ACse4 loading time and is dependent on DNA replication. Centromeric transcription is repressed by centromere-binding factor Cbf1 and histone H2A variant H2A.ZHtz1 Deletion of CBF1 and H2A.ZHTZ1 results in an up-regulation of cenRNAs; an increased loss of a minichromosome; elevated aneuploidy; a down-regulation of the protein levels of centromeric proteins CENP-ACse4, CENP-A chaperone HJURPScm3, CENP-CMif2, SurvivinBir1, and INCENPSli15; and a reduced chromatin localization of CENP-ACse4, CENP-CMif2, and Aurora BIpl1 When the RNA interference system was introduced to knock down all cenRNAs from the endogenous chromosomes, but not the cenRNA from the circular minichromosome, an increase in minichromosome loss was still observed, suggesting that cenRNA functions in trans to regulate centromere activity. CenRNA knockdown partially alleviates minichromosome loss in cbf1Δ, htz1Δ, and cbf1Δ htz1Δ in a dose-dependent manner, demonstrating that cenRNA level is tightly regulated to epigenetically control point centromere function.

Histone H3K9 and H4 Acetylations and Transcription Facilitate the Initial CENP-AHCP\u22123 Deposition and De Novo Centromere Establishment in Caenorhabditis elegans Artificial Chromosomes

BackgroundThe centromere is the specialized chromatin region that directs chromosome segregation. The kinetochore assembles on the centromere, attaching chromosomes to microtubules in mitosis. The centromere position is usually maintained through cell cycles and generations. However, new centromeres, known as neocentromeres, can occasionally form on ectopic regions when the original centromere is inactivated or lost due to chromosomal rearrangements. Centromere repositioning can occur during evolution. Moreover, de novo centromeres can form on exogenously transformed DNA in human cells at a low frequency, which then segregates faithfully as human artificial chromosomes (HACs). How centromeres are maintained, inactivated and activated is unclear. A conserved histone H3 variant, CENP-A, epigenetically marks functional centromeres, interspersing with H3. Several histone modifications enriched at centromeres are required for centromere function, but their role in new centromere formation is less clear. Studying the mechanism of new centromere formation has been challenging because these events are difficult to detect immediately, requiring weeks for HAC selection.ResultsDNA injected into the Caenorhabditis elegans gonad can concatemerize to form artificial chromosomes (ACs) in embryos, which first undergo passive inheritance, but soon autonomously segregate within a few cell cycles, more rapidly and frequently than HACs. Using this in vivo model, we injected LacO repeats DNA, visualized ACs by expressing GFP::LacI, and monitored equal AC segregation in real time, which represents functional centromere formation. Histone H3K9 and H4 acetylations are enriched on new ACs when compared to endogenous chromosomes. By fusing histone deacetylase HDA-1 to GFP::LacI, we tethered HDA-1 to ACs specifically, reducing AC histone acetylations, reducing AC equal segregation frequency, and reducing initial kinetochroe protein CENP-AHCP−3 and NDC-80 deposition, indicating that histone acetylations facilitate efficient centromere establishment. Similarly, inhibition of RNA polymerase II-mediated transcription also delays initial CENP-AHCP-3 loading.ConclusionsAcetylated histones on chromatin and transcription can create an open chromatin environment, enhancing nucleosome disassembly and assembly, and potentially contribute to centromere establishment. Alternatively, acetylation of soluble H4 may stimulate the initial deposition of CENP-AHCP−3-H4 nucleosomes. Our findings shed light on the mechanism of de novo centromere activation.

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Gastrointestinal NursingVol. 16, No. 1 NewsNewsSue LearnerSue LearnerSearch for more papers by this authorSue LearnerPublished Online:9 Feb 2018https://doi.org/10.12968/gasn.2018.16.1.8AboutSectionsView articleView Full TextPDF/EPUB ToolsAdd to favoritesDownload CitationsTrack CitationsPermissions ShareShare onFacebookTwitterLinked InEmail View article References Health Matters. NHS bowel scope uptake boosted by a fifth when patients sent reassuring reminders. 2018. https://tinyurl.com/y96usr8b (accessed 31 January 2018) Google ScholarKerrison RS, McGregor LM, Counsell N et al.. Use of two self-referral reminders and a theory-based leaflet to increase the uptake of flexible sigmoidoscopy in the English bowel scope screening program: results from a randomized controlled trial in London. Ann Behav Med. 2018; 52. https://doi.org/https://doi.org/10.1093/abm/kax068 Google ScholarPastel E, Price E, Sjöholm K et al.. Lysyl oxidase and adipose tissue dysfunction. Metabolism. 2018; 78:118–27. https://doi.org/https://doi.org/10.1016/j.metabol.2017.10.002 Crossref, Google ScholarUniversity of Exeter. Obese fat becomes ‘inflamed’ and scarred, which may make weight loss harder. 2018. https://tinyurl.com/y98ksbsv (accessed 22 Jan 2018) Google ScholarReges O, Greenland P, Dicker D et al.. Association of bariatric surgery using laparoscopic banding, roux-en-Y gastric bypass, or laparoscopic sleeve gastrectomy vs usual care obesity management with all-cause mortality. JAMA. 2018; 319(3):279. https://doi.org/https://doi.org/10.1001/jama.2017.20513 Crossref, Google ScholarThomas C, Hooper L, Petty R et al.. 10 years on: new evidence on TV marketing and junk food consumption amongst 11-19 year olds 10 years after broadcast regulations. 2018. https://tinyurl.com/y7d3oknt (accessed 31 January 2018) Google ScholarGaraycoechea JI, Crossan GP, Langevin F et al.. Alcohol and endogenous aldehydes damage chromosomes and mutate stem cells. Nature. 2018; 553(7687):171–7. https://doi.org/https://doi.org/10.1038/nature25154 Crossref, Google ScholarMacmillan Cancer Support. Willful ignorance: Macmillan reveals the shocking state of UK wills. 2018. https://tinyurl.com/yd59gx57 (accessed 31 January 2018) Google ScholarWhale K, Cramer H, Joinson C. Left behind and left out: the impact of the school environment on young people with continence problems. Br J Health Psychol. 2017. https://doi.org/https://doi.org/10.1111/bjhp.12284 Google Scholar FiguresReferencesRelatedDetails 2 February 2018Volume 16Issue 1ISSN (print): 1479-5248ISSN (online): 2052-2835 Metrics History Published online 9 February 2018 Published in print 2 February 2018 Information© MA Healthcare LimitedPDF download

Alcohol and endogenous aldehydes damage chromosomes and mutate stem cells.

Haematopoietic stem cells renew blood. Accumulation of DNA damage in these cells promotes their decline, while misrepair of this damage initiates malignancies. Here we describe the features and mutational landscape of DNA damage caused by acetaldehyde, an endogenous and alcohol-derived metabolite. This damage results in DNA double-stranded breaks that, despite stimulating recombination repair, also cause chromosome rearrangements. We combined transplantation of single haematopoietic stem cells with whole-genome sequencing to show that this damage occurs in stem cells, leading to deletions and rearrangements that are indicative of microhomology-mediated end-joining repair. Moreover, deletion of p53 completely rescues the survival of aldehyde-stressed and mutated haematopoietic stem cells, but does not change the pattern or the intensity of genome instability within individual stem cells. These findings characterize the mutation of the stem-cell genome by an alcohol-derived and endogenous source of DNA damage. Furthermore, we identify how the choice of DNA-repair pathway and a stringent p53 response limit the transmission of aldehyde-induced mutations in stem cells.

Using Pulsed-Field Gel Electrophoresis to Analyze Schizosaccharomyces pombe Chromosomes and Chromosomal Elements.

Pulsed field gel electrophoresis (PFGE) uses alternatively oriented pulsed electrical fields to separate large DNA molecules. Here, we describe PFGE protocols and conditions for separating and visualizing chromosomes between 0.5 and 6 Mb (optimal for analyzing the endogenous fission yeast chromosomes of 5.7, 4.6, and 3.5 Mb), and for shorter chromosomal elements of between 50 and 600 kb, such as the 530 kb Ch16 minichromosome. In addition to determining chromosome size, this technique has a wide range of applications, including determining whether DNA replication or repair is complete, defining the molecular karyotype of cells, analyzing chromosomal rearrangements, assigning genes or constructs to particular chromosomes, and isolating DNA from specific chromosomes.

R-Spondin chromosome rearrangements drive Wnt-dependent tumour initiation and maintenance in the intestine

Defining the genetic drivers of cancer progression is a key in understanding disease biology and developing effective targeted therapies. Chromosome rearrangements are a common feature of human malignancies, but whether they represent bona fide cancer drivers and therapeutically actionable targets, requires functional testing. Here, we describe the generation of transgenic, inducible CRISPR-based mouse systems to engineer and study recurrent colon cancer-associated EIF3E–RSPO2 and PTPRK–RSPO3 chromosome rearrangements in vivo. We show that both Rspo2 and Rspo3 fusion events are sufficient to initiate hyperplasia and tumour development in vivo, without additional cooperating genetic events. Rspo-fusion tumours are entirely Wnt-dependent, as treatment with an inhibitor of Wnt secretion, LGK974, drives rapid tumour clearance from the intestinal mucosa without effects on normal intestinal crypts. Altogether, our study provides direct evidence that endogenous Rspo2 and Rspo3 chromosome rearrangements can initiate and maintain tumour development, and indicate a viable therapeutic window for LGK974 treatment of RSPO-fusion cancers.

Centromere Silencing Mechanisms.

Centromere function is essential for genome stability and chromosome inheritance. Typically, each chromosome has a single locus that consistently serves as the site of centromere formation and kinetochore assembly. Decades of research have defined the DNA sequence and protein components of functional centromeres, and the interdependencies of specific protein complexes for proper centromere assembly. Less is known about how centromeres are disassembled or functionally silenced. Centromere silencing, or inactivation, is particularly relevant in the cases of dicentric chromosomes that occur via genome rearrangements that place two centromeres on the same chromosome. Dicentrics are usually unstable unless one centromere is inactivated, thereby allowing the structurally dicentric chromosome to behave like one of the monocentric, endogenous chromosomes. The molecular basis for centromere inactivation is not well understood, although studies in model organisms and in humans suggest that both genomic and epigenetic mechanisms are involved. In this chapter, we review recent studies using synthetic chromosomes and engineered or induced dicentrics from various organisms to define the molecular processes that are involved in the complex process of centromere inactivation.

Cytology of DNA Replication Reveals Dynamic Plasticity of Large-Scale Chromatin Fibers

In higher eukaryotic interphase nuclei, the 100- to>1,000-fold linear compaction of chromatin is difficult to reconcile with its function as a template for transcription, replication, and repair. It is challenging to imagine how DNA and RNA polymerases with their associated molecular machinery would move along the DNA template without transient decondensation of observed large-scale chromatin "chromonema" fibers [1]. Transcription or "replication factory" models [2], in which polymerases remain fixed while DNA is reeled through, are similarly difficult to conceptualize without transient decondensation of these chromonema fibers. Here, we show how a dynamic plasticity of chromatin folding within large-scale chromatin fibers allows DNA replication to take place without significantchanges in the global large-scale chromatin compaction or shape of these large-scale chromatin fibers. Time-lapse imaging of lac-operator-tagged chromosome regions shows no major change inthe overall compaction of these chromosome regions during their DNA replication. Improved pulse-chase labeling of endogenous interphase chromosomes yields a model in which the global compaction and shape of large-Mbp chromatin domains remains largely invariant during DNA replication, with DNA within these domains undergoing significant movements and redistribution as they move into and then out of adjacent replication foci. In contrast to hierarchical folding models, this dynamic plasticity of large-scale chromatin organization explains how localized changes in DNA topology allow DNA replication to take place without an accompanying global unfolding of large-scale chromatin fibers while suggesting a possible mechanism for maintaining epigenetic programming of large-scale chromatin domains throughout DNA replication.