DOCSLIB.ORG

FANCD2 Binding Identifies Conserved Fragile Sites at Large Transcribed

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
FANCD2 Binding Identifies Conserved Fragile Sites at Large Transcribed 1280–1294 Nucleic Acids Research, 2018, Vol. 46, No. 3 Published online 14 December 2017 doi: 10.1093/nar/gkx1260 FANCD2 binding identifies conserved fragile sites at large transcribed genes in avian cells Constanze Pentzold1, Shiraz Ali Shah1, Niels Richard Hansen2, Benoˆıt Le Tallec3, Andaine Seguin-Orlando4,5, Michelle Debatisse6, Michael Lisby1,7 and Vibe H. Oestergaard1,* 1Department of Biology; University of Copenhagen; Copenhagen N 2200, Denmark, 2Department of Mathematical Sciences, University of Copenhagen, Copenhagen 2100, Denmark, 3Institut de Biologie de l’Ecole Normale Superieure´ (IBENS), CNRS-UMR8197 – Inserm U1024, Paris F-75005, France, 4Center for GeoGenetics, Natural Downloaded from https://academic.oup.com/nar/article/46/3/1280/4739372 by guest on 01 October 2021 History Museum of Denmark; University of Copenhagen; Copenhagen 1350, Denmark, 5Danish National High-throughput DNA Sequencing Centre, University of Copenhagen, Øster Farimagsgade 2D, Copenhagen K 1353, Denmark, 6Institut Gustave Roussy, UMR 8200, 94800 Villejuif, France and 7Center for Chromosome Stability, Department of Cellular and Molecular Medicine, University of Copenhagen, Blegdamsvej 3b, DK-2200 Copenhagen N, Denmark Received September 27, 2017; Revised December 01, 2017; Editorial Decision December 05, 2017; Accepted December 05, 2017 ABSTRACT INTRODUCTION Common Chromosomal Fragile Sites (CFSs) are spe- During mitosis, a copy of the genome is passed on to each cific genomic regions prone to form breaks on of the two daughter cells. Mitosis constitutes a short win- metaphase chromosomes in response to replication dow of the entire cell cycle, but is of immense importance for genome integrity. In response to severe replication stress, stress. Moreover, CFSs are mutational hotspots in / cancer genomes, showing that the mutational mech- the G2 M checkpoint will normally arrest cells in G2 phase but under conditions of mild replication stress, certain re- anisms that operate at CFSs are highly active in gions in the genome escape checkpoint detection and en- cancer cells. Orthologs of human CFSs are found ter mitosis in an underreplicated state (1–5). This leads to in a number of other mammals, but the extent of the formation of microscopically visible breaks and gaps CFS conservation beyond the mammalian lineage is on metaphase chromosomes (6). Genomic regions prone to unclear. Characterization of CFSs from distantly re- form gaps and breaks in response to replication stress are lated organisms can provide new insight into the bi- named chromosomal fragile sites (6). Interestingly, chro- ology underlying CFSs. Here, we have mapped CFSs mosomal fragile sites are hotspots for large deletions and in an avian cell line. We find that, overall the most rearrangements in cancer genomes (7–10). The genome of significant CFSs coincide with extremely large con- healthy individuals contains two classes of chromosomal served genes, from which very long transcripts are fragile sites; (i) common fragile sites (CFSs) and (ii) early produced. However, no significant correlation be- replicating fragile sites (ERFSs) (8,11). Underreplicated re- gions that persist in mitosis pose a problem to disjunction tween any sequence characteristics and CFSs is of sister chromatids and accordingly CFSs can remain in- found. Moreover, we identified putative early repli- terlinked by ultrafine DNA bridges (UFBs) or chromatin cating fragile sites (ERFSs), which is a distinct class bridges during anaphase (3,12,13). of fragile sites and we developed a fluctuation anal- Since CFSs were first discovered, a variety of features ysis revealing high mutation rates at the CFS gene have been suggested to be involved in their breakage and PARK2, with deletions as the most prevalent muta- mutagenesis. Firstly, it has been proposed that specific DNA tion. Finally, we show that avian homologs of the hu- features, such as AT-richness or increased flexibility of the man CFS genes despite their fragility have resisted double helix could cause difficult-to-replicate secondary the general intron size reduction observed in birds structures (14–17). Secondly, CFSs are generally late repli- suggesting that CFSs have a conserved biological cating and this was suggested to make them specifically vul- function. nerable to replication stress (18). In line with this idea, it was also shown that some CFSs have a scarcity of replica- *To whom correspondence should be addressed. Tel: +45 3533 0444; Fax: +45 3532 2128; Email: [email protected] Present address: Constanze Pentzold, Institute of Human Genetics, Jena University Hospital, DE-07747 Jena, Germany. C The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact [email protected] Nucleic Acids Research, 2018, Vol. 46, No. 3 1281 tion origins (19,20) and consequently they cannot respond Generation of targeting constructs for FANCD2, PARK2 and to replication stress by firing backup origins, which would OVAL make these genomic regions more prone to enter mitosis The construct for GS-tagging (protein G-streptavidin bind- in an underreplicated state (11). Consistently, CFS fragility ing peptide/tandem affinity purification tag) of endogenous varies from one cell type to another, implying that epige- chicken FANCD2 (FANCD2, Gene ID: 415935) was gener- netic features rather than the DNA sequence per se is caus- ated by first, amplifying the 3 homology arm using primers ing fragility (9). Finally, many CFSs coincide with large VO300 and VO301; and the 5 homology arm using the transcribed genes, where potential collisions between repli- primers VO302 and VO303. Next, the 3’ homology arm cation and transcription machineries can delay replication was cloned into pBluescript SK+ (Agilent Technologies) as (21–23). ERFSs, on the other hand, are early replicating, a SpeI/NotI fragment. Then, a sequence encoding an N- gene dense regions, where high transcription activity of sev- terminal GS-tag (31) was inserted as a BamHI/XbaI frag- eral genes may sensitize the region to replication stress (8). ment. Thereafter, the 5 arm was inserted as a SalI/BamHI FANCD2 has an important role in CFS maintenance fragment and finally, the resistance cassette was inserted as Downloaded from https://academic.oup.com/nar/article/46/3/1280/4739372 by guest on 01 October 2021 (24,25) and localizes to CFSs during mitosis in human a BamHI fragment. The GS targeting construct was lin- cells even in the absence of breakage (12,13). FANCD2 earized with NotI before transfection. prevents replication fork stalling at the AT-rich cores of The BSR, PURO,andNEO resistance genes were excised FRA16D (housing the WWOX gene) and FRA6E (hous- from pLOX-BSR, pLOX-PURO and pLOX-NEO, respec- ing the PARK2 gene), and specific examination of FRA16D tively (32) using BamHI. also shows that FANCD2 deficiency leads to accumula- For assembly of the PARK2 (PARK2, Gene ID: 421577) tion of RNA-DNA hybrids at this CFS (25). Moreover, knock-in construct (pCP2), the 5 and 3 homology arms FANCD2 is a key component of the Fanconi Anemia path- were PCR amplified using primer pairs CP43-CP44 and way that protects cells against genotoxic agents such as CP45-CP46, respectively. Then they were individually sub- DNA interstrand cross-linkers and aldehydes (26). cloned into pCR® 2.1-TOPO® TA vector (Invitrogen) in Traditionally, CFSs have been defined and mapped cy- the listed order using restriction sites KpnI–NotI or NotI– togenetically (11,27) and are mainly characterized in hu- XhoI, respectively. The HyTK cassette was excised by NotI mans, other primates and mice (9,22,28–30). Here, we per- from the original vector (kindly provided by Christine Farr) formed ChIP-seq of FANCD2 from cells subjected to repli- (33). The PARK2 targeting construct was linearized with cation stress to map fragile sites genome-wide in the avian Eam1105I (AhdI) before transfection. cell line DT40. By cytogenetic analyses using fluorescence in The vector for targeting the chicken ovalbumin gene lo- situ hybridization (FISH) we confirm that the most signif- cus 2 (OVAL, Gene ID: 396058) was assembled by first icant peaks from our ChIP-seq are bona fide CFSs. More- subcloning the 3 homology arm in the XhoI/KpnI site over, we identify a number of gene-dense highly expressed of pBlueScript SK+ (Fermentas GmbH). The 5 homology regions likely corresponding to DT40 ERFSs. Additionally, arm was subcloned in the NotI/SpeI site of pLOX-PURO we have developed a fluctuation assay to estimate the site- (32). Thereafter, the 3 and 5 homology arms were assem- specific mutation rate at a CFS. bled into one vector by subcloning a KpnI/ClaI fragment This study provides a genome-wide map of CFSs and pu- to generate pML27. The HyTK counterselection gene was tative ERFSs, plotted together with replication timing and XhoI-adapted by PCR, using the original vector (33)as transcription level as well as other features suggested to con- template. To finally insert the HyTK counterselection gene tribute to CFS fragility. We do not find significant correla- between the OVAL homology arms, the adapted HyTK gene tion with any of the tested sequence features formerly sug- was cloned into the XhoI site of pML27, resulting in the fi- gested to induce fragility, but our results support that tran- nal targeting vector pCP9. The OVAL targeting construct scription is involved in fragility at both CFSs and ERFSs. was linearized with Eam1105I (AhdI) before transfection. Specifically, transcribed genes over 500 kb always coincide Plasmids and primers used in this study are listed in sup- with CFSs. Moreover, we report the conservation of long in- plemental methods, respectively. tron sizes in CFSs within the two major branches of the am- niotes – the synapsids to become mammals and the saurop- Chromatin immunoprecipitation followed by massively paral- sids to become birds and reptiles.
Load more

Recommended publications
  • Cisplatin and Phenanthriplatin Modulate Long-Noncoding
    www.nature.com/scientificreports OPEN Cisplatin and phenanthriplatin modulate long‑noncoding RNA expression in A549 and IMR90 cells revealing regulation of microRNAs, Wnt/β‑catenin and TGF‑β signaling Jerry D. Monroe1,2, Satya A. Moolani2,3, Elvin N. Irihamye2,4, Katheryn E. Lett1, Michael D. Hebert1, Yann Gibert1* & Michael E. Smith2* The monofunctional platinum(II) complex, phenanthriplatin, acts by blocking transcription, but its regulatory efects on long‑noncoding RNAs (lncRNAs) have not been elucidated relative to traditional platinum‑based chemotherapeutics, e.g., cisplatin. Here, we treated A549 non‑small cell lung cancer and IMR90 lung fbroblast cells for 24 h with either cisplatin, phenanthriplatin or a solvent control, and then performed microarray analysis to identify regulated lncRNAs. RNA22 v2 microRNA software was subsequently used to identify microRNAs (miRNAs) that might be suppressed by the most regulated lncRNAs. We found that miR‑25‑5p, ‑30a‑3p, ‑138‑5p, ‑149‑3p, ‑185‑5p, ‑378j, ‑608, ‑650, ‑708‑5p, ‑1253, ‑1254, ‑4458, and ‑4516, were predicted to target the cisplatin upregulated lncRNAs, IMMP2L‑1, CBR3‑1 and ATAD2B‑5, and the phenanthriplatin downregulated lncRNAs, AGO2‑1, COX7A1‑2 and SLC26A3‑1. Then, we used qRT‑PCR to measure the expression of miR‑25‑5p, ‑378j, ‑4516 (A549) and miR‑149‑3p, ‑608, and ‑4458 (IMR90) to identify distinct signaling efects associated with cisplatin and phenanthriplatin. The signaling pathways associated with these miRNAs suggests that phenanthriplatin may modulate Wnt/β‑catenin and TGF‑β signaling through the MAPK/ ERK and PTEN/AKT pathways diferently than cisplatin. Further, as some of these miRNAs may be subject to dissimilar lncRNA targeting in A549 and IMR90 cells, the monofunctional complex may not cause toxicity in normal lung compared to cancer cells by acting through distinct lncRNA and miRNA networks.
    [Show full text]
  • ARTICLE Doi:10.1038/Nature10523
    ARTICLE doi:10.1038/nature10523 Spatio-temporal transcriptome of the human brain Hyo Jung Kang1*, Yuka Imamura Kawasawa1*, Feng Cheng1*, Ying Zhu1*, Xuming Xu1*, Mingfeng Li1*, Andre´ M. M. Sousa1,2, Mihovil Pletikos1,3, Kyle A. Meyer1, Goran Sedmak1,3, Tobias Guennel4, Yurae Shin1, Matthew B. Johnson1,Zˇeljka Krsnik1, Simone Mayer1,5, Sofia Fertuzinhos1, Sheila Umlauf6, Steven N. Lisgo7, Alexander Vortmeyer8, Daniel R. Weinberger9, Shrikant Mane6, Thomas M. Hyde9,10, Anita Huttner8, Mark Reimers4, Joel E. Kleinman9 & Nenad Sˇestan1 Brain development and function depend on the precise regulation of gene expression. However, our understanding of the complexity and dynamics of the transcriptome of the human brain is incomplete. Here we report the generation and analysis of exon-level transcriptome and associated genotyping data, representing males and females of different ethnicities, from multiple brain regions and neocortical areas of developing and adult post-mortem human brains. We found that 86 per cent of the genes analysed were expressed, and that 90 per cent of these were differentially regulated at the whole-transcript or exon level across brain regions and/or time. The majority of these spatio-temporal differences were detected before birth, with subsequent increases in the similarity among regional transcriptomes. The transcriptome is organized into distinct co-expression networks, and shows sex-biased gene expression and exon usage. We also profiled trajectories of genes associated with neurobiological categories and diseases, and identified associations between single nucleotide polymorphisms and gene expression. This study provides a comprehensive data set on the human brain transcriptome and insights into the transcriptional foundations of human neurodevelopment.
    [Show full text]
  • How to Rule the Nucleus: Divide Et Impera
    Available online at www.sciencedirect.com ScienceDirect How to rule the nucleus: divide et impera 1 1 1,2 Irina Solovei , Katharina Thanisch and Yana Feodorova Genome-wide molecular studies have provided new insights conserved and serve as functional platforms for into the organization of nuclear chromatin by revealing the physical interactions between regulatory elements [6– presence of chromatin domains of differing transcriptional 8]. Various other domains, such as lamina-associated activity, frequency of cis-interactions, proximity to scaffolding domains (LADs) [9,10 ,11], nucleolus-associated structures and replication timing. These studies have not only domains (NADs) [12] or pericentromere-associated brought our understanding of genome function to a new level, domains (PADs) [13 ], have been implicated in organiz- but also offered functional insight for many phenomena ing and anchoring the genome within the nucleus. In observed in microscopic studies. In this review, we discuss the cycling cells, genomic regions with time-coordinated major principles of nuclear organization based on the spatial replication form replication domains [14–17]. segregation of euchromatin and heterochromatin, as well as the dynamic genome rearrangements occurring during cell Although the fine details of genome organization and its differentiation and development. We hope to unite the existing functional connections to transcription regulation have molecular and microscopic data on genome organization to get been thoroughly discussed in a plethora of recent reviews a holistic view of the nucleus, and propose a model, in which (e.g., this COCB issue, see also [17–24], it remains a repeat repertoire together with scaffolding structures blueprint challenge to integrate the genomics-based and microsco- the functional nuclear architecture.
    [Show full text]
  • Supplementary Table S4. FGA Co-Expressed Gene List in LUAD
    Supplementary Table S4. FGA co-expressed gene list in LUAD tumors Symbol R Locus Description FGG 0.919 4q28 fibrinogen gamma chain FGL1 0.635 8p22 fibrinogen-like 1 SLC7A2 0.536 8p22 solute carrier family 7 (cationic amino acid transporter, y+ system), member 2 DUSP4 0.521 8p12-p11 dual specificity phosphatase 4 HAL 0.51 12q22-q24.1histidine ammonia-lyase PDE4D 0.499 5q12 phosphodiesterase 4D, cAMP-specific FURIN 0.497 15q26.1 furin (paired basic amino acid cleaving enzyme) CPS1 0.49 2q35 carbamoyl-phosphate synthase 1, mitochondrial TESC 0.478 12q24.22 tescalcin INHA 0.465 2q35 inhibin, alpha S100P 0.461 4p16 S100 calcium binding protein P VPS37A 0.447 8p22 vacuolar protein sorting 37 homolog A (S. cerevisiae) SLC16A14 0.447 2q36.3 solute carrier family 16, member 14 PPARGC1A 0.443 4p15.1 peroxisome proliferator-activated receptor gamma, coactivator 1 alpha SIK1 0.435 21q22.3 salt-inducible kinase 1 IRS2 0.434 13q34 insulin receptor substrate 2 RND1 0.433 12q12 Rho family GTPase 1 HGD 0.433 3q13.33 homogentisate 1,2-dioxygenase PTP4A1 0.432 6q12 protein tyrosine phosphatase type IVA, member 1 C8orf4 0.428 8p11.2 chromosome 8 open reading frame 4 DDC 0.427 7p12.2 dopa decarboxylase (aromatic L-amino acid decarboxylase) TACC2 0.427 10q26 transforming, acidic coiled-coil containing protein 2 MUC13 0.422 3q21.2 mucin 13, cell surface associated C5 0.412 9q33-q34 complement component 5 NR4A2 0.412 2q22-q23 nuclear receptor subfamily 4, group A, member 2 EYS 0.411 6q12 eyes shut homolog (Drosophila) GPX2 0.406 14q24.1 glutathione peroxidase
    [Show full text]
  • Dynamics of DNA Replication in a Eukaryotic Cell
    Dynamics of DNA replication in a eukaryotic cell Thomas Kellya,1 and A. John Callegaria,2 aProgram in Molecular Biology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065 Contributed by Thomas Kelly, December 26, 2018 (sent for review October 30, 2018; reviewed by Paul Nurse and Nicholas Rhind) Each genomic locus in a eukaryotic cell has a distinct average time A deeper understanding of the dynamics of eukaryotic DNA of replication during S phase that depends on the spatial and replication will require a quantitative model describing the spatial temporal pattern of replication initiation events. Replication distribution of potential initiation sites and the time course of their timing can affect genomic integrity because late replication is activation during S phase. The fission yeast Schizosaccharomyces associated with an increased mutation rate. For most eukaryotes, pombe represents a useful system for developing such a model the features of the genome that specify the location and timing of because its genome has many characteristics in common with initiation events are unknown. To investigate these features for that of other eukaryotes. Early genetic studies identified seg- Schizosaccharomyces pombe the fission yeast, , we developed an ments of the S. pombe genome, called autonomously replicating integrative model to analyze large single-molecule and global ge- sequence (ars) elements, that function as origins of DNA repli- nomic datasets. The model provides an accurate description of the > S. pombe cation (14). These elements are large ( 1 kb) and rich in A and complex dynamics of DNA replication at high resolution. T residues but do not contain a common sequence motif (15, 16).
    [Show full text]
  • Abstracts from the 50Th European Society of Human Genetics Conference: Electronic Posters
    European Journal of Human Genetics (2019) 26:820–1023 https://doi.org/10.1038/s41431-018-0248-6 ABSTRACT Abstracts from the 50th European Society of Human Genetics Conference: Electronic Posters Copenhagen, Denmark, May 27–30, 2017 Published online: 1 October 2018 © European Society of Human Genetics 2018 The ESHG 2017 marks the 50th Anniversary of the first ESHG Conference which took place in Copenhagen in 1967. Additional information about the event may be found on the conference website: https://2017.eshg.org/ Sponsorship: Publication of this supplement is sponsored by the European Society of Human Genetics. All authors were asked to address any potential bias in their abstract and to declare any competing financial interests. These disclosures are listed at the end of each abstract. Contributions of up to EUR 10 000 (ten thousand euros, or equivalent value in kind) per year per company are considered "modest". Contributions above EUR 10 000 per year are considered "significant". 1234567890();,: 1234567890();,: E-P01 Reproductive Genetics/Prenatal and fetal echocardiography. The molecular karyotyping Genetics revealed a gain in 8p11.22-p23.1 region with a size of 27.2 Mb containing 122 OMIM gene and a loss in 8p23.1- E-P01.02 p23.3 region with a size of 6.8 Mb containing 15 OMIM Prenatal diagnosis in a case of 8p inverted gene. The findings were correlated with 8p inverted dupli- duplication deletion syndrome cation deletion syndrome. Conclusion: Our study empha- sizes the importance of using additional molecular O¨. Kırbıyık, K. M. Erdog˘an, O¨.O¨zer Kaya, B. O¨zyılmaz, cytogenetic methods in clinical follow-up of complex Y.
    [Show full text]
  • REVIEW ARTICLE the Genetics of Autism
    REVIEW ARTICLE The Genetics of Autism Rebecca Muhle, BA*; Stephanie V. Trentacoste, BA*; and Isabelle Rapin, MD‡ ABSTRACT. Autism is a complex, behaviorally de- tribution of a few well characterized X-linked disorders, fined, static disorder of the immature brain that is of male-to-male transmission in a number of families rules great concern to the practicing pediatrician because of an out X-linkage as the prevailing mode of inheritance. The astonishing 556% reported increase in pediatric preva- recurrence rate in siblings of affected children is ϳ2% to lence between 1991 and 1997, to a prevalence higher than 8%, much higher than the prevalence rate in the general that of spina bifida, cancer, or Down syndrome. This population but much lower than in single-gene diseases. jump is probably attributable to heightened awareness Twin studies reported 60% concordance for classic au- and changing diagnostic criteria rather than to new en- tism in monozygotic (MZ) twins versus 0 in dizygotic vironmental influences. Autism is not a disease but a (DZ) twins, the higher MZ concordance attesting to ge- syndrome with multiple nongenetic and genetic causes. netic inheritance as the predominant causative agent. By autism (the autistic spectrum disorders [ASDs]), we Reevaluation for a broader autistic phenotype that in- mean the wide spectrum of developmental disorders cluded communication and social disorders increased characterized by impairments in 3 behavioral domains: 1) concordance remarkably from 60% to 92% in MZ twins social interaction; 2) language, communication, and and from 0% to 10% in DZ pairs. This suggests that imaginative play; and 3) range of interests and activities.
    [Show full text]
  • Experimental Eye Research 129 (2014) 93E106
    Experimental Eye Research 129 (2014) 93e106 Contents lists available at ScienceDirect Experimental Eye Research journal homepage: www.elsevier.com/locate/yexer Transcriptomic analysis across nasal, temporal, and macular regions of human neural retina and RPE/choroid by RNA-Seq S. Scott Whitmore a, b, Alex H. Wagner a, c, Adam P. DeLuca a, b, Arlene V. Drack a, b, Edwin M. Stone a, b, Budd A. Tucker a, b, Shemin Zeng a, b, Terry A. Braun a, b, c, * Robert F. Mullins a, b, Todd E. Scheetz a, b, c, a Stephen A. Wynn Institute for Vision Research, The University of Iowa, Iowa City, IA, USA b Department of Ophthalmology and Visual Sciences, Carver College of Medicine, The University of Iowa, Iowa City, IA, USA c Department of Biomedical Engineering, College of Engineering, The University of Iowa, Iowa City, IA, USA article info abstract Article history: Proper spatial differentiation of retinal cell types is necessary for normal human vision. Many retinal Received 14 September 2014 diseases, such as Best disease and male germ cell associated kinase (MAK)-associated retinitis pigmen- Received in revised form tosa, preferentially affect distinct topographic regions of the retina. While much is known about the 31 October 2014 distribution of cell types in the retina, the distribution of molecular components across the posterior pole Accepted in revised form 4 November 2014 of the eye has not been well-studied. To investigate regional difference in molecular composition of Available online 5 November 2014 ocular tissues, we assessed differential gene expression across the temporal, macular, and nasal retina and retinal pigment epithelium (RPE)/choroid of human eyes using RNA-Seq.
    [Show full text]
  • Genome-Wide Dynamics of Replication Timing Revealed by in Vitro Models of Mouse Embryogenesis
    Downloaded from genome.cshlp.org on September 26, 2021 - Published by Cold Spring Harbor Laboratory Press Article Genome-wide dynamics of replication timing revealed by in vitro models of mouse embryogenesis Ichiro Hiratani,1 Tyrone Ryba,1 Mari Itoh,1 Joy Rathjen,2 Michael Kulik,3 Bernadett Papp,4 Eden Fussner,5 David P. Bazett-Jones,5 Kathrin Plath,4 Stephen Dalton,3 Peter D. Rathjen,2 and David M. Gilbert1,6 1Department of Biological Science, Florida State University, Tallahassee, Florida 32306, USA; 2Department of Zoology, University of Melbourne, Parkville, Victoria 3010, Australia; 3Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602, USA; 4University of California Los Angeles, David Geffen School of Medicine, Department of Biological Chemistry, Jonsson Comprehensive Cancer Center, Molecular Biology Institute, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, Los Angeles, California 90024, USA; 5Program in Genetics and Genome Biology, The Hospital for Sick Children, Research Institute, Toronto, Ontario M5G 1L7, Canada Differentiation of mouse embryonic stem cells (mESCs) is accompanied by changes in replication timing. To explore the relationship between replication timing and cell fate transitions, we constructed genome-wide replication-timing profiles of 22 independent mouse cell lines representing 10 stages of early mouse development, and transcription profiles for seven of these stages. Replication profiles were cell-type specific, with 45% of the genome exhibiting significant changes at some point during development that were generally coordinated with changes in transcription. Comparison of early and late epiblast cell culture models revealed a set of early-to-late replication switches completed at a stage equivalent to the post- implantation epiblast, prior to germ layer specification and down-regulation of key pluripotency transcription factors [POU5F1 (also known as OCT4)/NANOG/SOX2] and coinciding with the emergence of compact chromatin near the nuclear periphery.
    [Show full text]
  • Working on Genomic Stability: from the S-Phase to Mitosis
    G C A T T A C G G C A T genes Review Working on Genomic Stability: From the S-Phase to Mitosis Sara Ovejero 1,2,3,* , Avelino Bueno 1,4 and María P. Sacristán 1,4,* 1 Instituto de Biología Molecular y Celular del Cáncer (IBMCC), Universidad de Salamanca-CSIC, Campus Miguel de Unamuno, 37007 Salamanca, Spain; [email protected] 2 Institute of Human Genetics, CNRS, University of Montpellier, 34000 Montpellier, France 3 Department of Biological Hematology, CHU Montpellier, 34295 Montpellier, France 4 Departamento de Microbiología y Genética, Universidad de Salamanca, Campus Miguel de Unamuno, 37007 Salamanca, Spain * Correspondence: [email protected] (S.O.); [email protected] (M.P.S.); Tel.: +34-923-294808 (M.P.S.) Received: 31 January 2020; Accepted: 18 February 2020; Published: 20 February 2020 Abstract: Fidelity in chromosome duplication and segregation is indispensable for maintaining genomic stability and the perpetuation of life. Challenges to genome integrity jeopardize cell survival and are at the root of different types of pathologies, such as cancer. The following three main sources of genomic instability exist: DNA damage, replicative stress, and chromosome segregation defects. In response to these challenges, eukaryotic cells have evolved control mechanisms, also known as checkpoint systems, which sense under-replicated or damaged DNA and activate specialized DNA repair machineries. Cells make use of these checkpoints throughout interphase to shield genome integrity before mitosis. Later on, when the cells enter into mitosis, the spindle assembly checkpoint (SAC) is activated and remains active until the chromosomes are properly attached to the spindle apparatus to ensure an equal segregation among daughter cells.
    [Show full text]
  • Dimensional Space of Plant Nuclei Němečková Al
    bioRxiv preprint doi: https://doi.org/10.1101/2020.04.02.021857; this version posted April 2, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-ND 4.0 International license. 1 DNA replication and chromosome positioning throughout the interphase in three- 2 dimensional space of plant nuclei 3 4 5 Němečková Alžběta, Veronika Koláčková, Vrána Jan, Doležel Jaroslav, Hřibová Eva* 6 7 8 Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region 9 Hana for Biotechnological and Agricultural Research, Olomouc, Czech Republic 10 11 Short Title: DNA replication and interphase chromosome positioning 12 13 *Corresponding Author: 14 Eva Hřibová 15 Institute of Experimental Botany 16 Šlechtitelů 31 17 779 00 Olomouc 18 Czech Republic 19 Tel: +420 585 238 713 20 E-mail:[email protected] 21 22 E-mail addresses: 23 Němečková A. - [email protected] 24 Koláčková V. - [email protected] 25 Vrána J. - [email protected] 26 Doležel J. - [email protected] 27 28 29 Highlight 30 Telomere and centromere replication timing and interphase chromosome positioning in seven 31 grass species differing in genome size indicates a more complex relation between genome size 32 and the chromosome positioning. 33 34 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.04.02.021857; this version posted April 2, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.
    [Show full text]
  • Impact of Disseminated Neuroblastoma Cells on the Identification of the Relapse-Seeding Clone
    Author Manuscript Published OnlineFirst on February 22, 2017; DOI: 10.1158/1078-0432.CCR-16-2082 Author manuscripts have been peer reviewed and accepted for publication but have not yet been edited. Impact of disseminated neuroblastoma cells on the identification of the relapse-seeding clone M. Reza Abbasi1, Fikret Rifatbegovic1, Clemens Brunner1, Georg Mann2, Andrea Ziegler1, Ulrike Pötschger1, Roman Crazzolara3, Marek Ussowicz4, Martin Benesch5, Georg Ebetsberger-Dachs6, Godfrey C.F. Chan7, Neil Jones8, Ruth Ladenstein1,9, Inge M. Ambros1, Peter F. Ambros1,9 1CCRI, Children’s Cancer Research Institute, Vienna, Austria; 2St. Anna Children’s Hospital, Vienna, Austria; 3Department of Pediatrics, Medical University of Innsbruck, Innsbruck, Austria; 4Department of Pediatric Hematology and Oncology, Wroclaw Medical University, Wroclaw, Poland; 5Department of Pediatrics and Adolescent Medicine, Medical University of Graz, Graz, Austria; 6Department of Pediatrics, Kepler University Clinic Linz, Linz, Austria; 7Department of Pediatrics and Adolescent Medicine, University of Hong Kong, Hong Kong; 8Department of Pediatrics and Adolescent Medicine, Paracelsus Medical University, Salzburg, Austria; 9Department of Pediatrics, Medical University of Vienna, Vienna, Austria. Running title: Genomics of disseminated neuroblastoma cells Keywords: Neuroblastoma, disseminated tumor cells, bone marrow, tumor evolution, tumor heterogeneity Financial Support: St. Anna Kinderkrebsforschung; Austrian National Bank (ÖNB), Grant Nos. 15114, 16611; Austrian Science
    [Show full text]