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

2016 ◽  
Vol 26 (18) ◽  
pp. 2527-2534 ◽  
Author(s):  
Xiang Deng ◽  
Oxana A. Zhironkina ◽  
Varvara D. Cherepanynets ◽  
Olga S. Strelkova ◽  
Igor I. Kireev ◽  
...  
Keyword(s):  
Dna Replication ◽  
Large Scale ◽  
Chromatin Fibers ◽  
Dynamic Plasticity

scholarly journals Large-scale chromatin structure of inducible genes: transcription on a condensed, linear template

2009 ◽  
Vol 185 (1) ◽  
pp. 87-100 ◽  
Author(s):  
Yan Hu ◽  
Igor Kireev ◽  
Matt Plutz ◽  
Nazanin Ashourian ◽  
Andrew S. Belmont
Keyword(s):  
Chromatin Structure ◽  
Transcriptional Activation ◽  
Large Scale ◽  
Nuclear Speckles ◽  
Interphase Chromosome ◽  
Chromosome Conformation ◽  
Dynamic Events ◽  
Classical Models ◽  
Chromatin Fibers

The structure of interphase chromosomes, and in particular the changes in large-scale chromatin structure accompanying transcriptional activation, remain poorly characterized. Here we use light microscopy and in vivo immunogold labeling to directly visualize the interphase chromosome conformation of 1–2 Mbp chromatin domains formed by multi-copy BAC transgenes containing 130–220 kb of genomic DNA surrounding the DHFR, Hsp70, or MT gene loci. We demonstrate near-endogenous transcription levels in the context of large-scale chromatin fibers compacted nonuniformly well above the 30-nm chromatin fiber. An approximately 1.5–3-fold extension of these large-scale chromatin fibers accompanies transcriptional induction and active genes remain mobile. Heat shock–induced Hsp70 transgenes associate with the exterior of nuclear speckles, with Hsp70 transcripts accumulating within the speckle. Live-cell imaging reveals distinct dynamic events, with Hsp70 transgenes associating with adjacent speckles, nucleating new speckles, or moving to preexisting speckles. Our results call for reexamination of classical models of interphase chromosome organization.

scholarly journals Interphase Cell Cycle Dynamics of a Late-Replicating, Heterochromatic Homogeneously Staining Region: Precise Choreography of Condensation/Decondensation and Nuclear Positioning

1998 ◽  
Vol 140 (5) ◽  
pp. 975-989 ◽  
Author(s):  
Gang Li ◽  
Gail Sudlow ◽  
Andrew S. Belmont
Keyword(s):  
Cell Cycle ◽  
Dna Replication ◽  
Dna Sequences ◽  
Large Scale ◽  
S Phase ◽  
Interphase Cell ◽  
Compact Mass ◽  
Lac Operator ◽  
Cell Cycle Dynamics

Recently we described a new method for in situ localization of specific DNA sequences, based on lac operator/repressor recognition (Robinett, C.C., A. Straight, G. Li, C. Willhelm, G. Sudlow, A. Murray, and A.S. Belmont. 1996. J. Cell Biol. 135:1685–1700). We have applied this methodology to visualize the cell cycle dynamics of an ∼90 Mbp, late-replicating, heterochromatic homogeneously staining region (HSR) in CHO cells, combining immunostaining with direct in vivo observations. Between anaphase and early G1, the HSR extends approximately twofold to a linear, ∼0.3-μm-diam chromatid, and then recondenses to a compact mass adjacent to the nuclear envelope. No further changes in HSR conformation or position are seen through mid-S phase. However, HSR DNA replication is preceded by a decondensation and movement of the HSR into the nuclear interior 4–6 h into S phase. During DNA replication the HSR resolves into linear chromatids and then recondenses into a compact mass; this is followed by a third extension of the HSR during G2/ prophase. Surprisingly, compaction of the HSR is extremely high at all stages of interphase. Preliminary ultrastructural analysis of the HSR suggests at least three levels of large-scale chromatin organization above the 30-nm fiber.

scholarly journals A tel2 Mutation That Destabilizes the Tel2-Tti1-Tti2 Complex Eliminates Rad3ATR Kinase Signaling in the DNA Replication Checkpoint and Leads to Telomere Shortening in Fission Yeast

2019 ◽  
Vol 39 (20) ◽  
Author(s):  
Yong-jie Xu ◽  
Saman Khan ◽  
Adam C. Didier ◽  
Michal Wozniak ◽  
Yufeng Liu ◽  
...  
Keyword(s):  
Dna Replication ◽  
Fission Yeast ◽  
Large Scale ◽  
Gene Encoding ◽  
Telomere Shortening ◽  
Signaling Mechanism ◽  
Replication Checkpoint ◽  
Checkpoint Signaling ◽  
Enhanced Sensitivity ◽  
Dna Replication Checkpoint

ABSTRACT In response to perturbed DNA replication, ATR (ataxia telangiectasia and Rad3-related) kinase is activated to initiate the checkpoint signaling necessary for maintaining genome integrity and cell survival. To better understand the signaling mechanism, we carried out a large-scale genetic screen in fission yeast looking for mutants with enhanced sensitivity to hydroxyurea. From a collection of ∼370 primary mutants, we found a few mutants in which Rad3 (ATR ortholog)-mediated phospho-signaling was significantly compromised. One such mutant carried an uncharacterized mutation in tel2, a gene encoding an essential and highly conserved eukaryotic protein. Previous studies in various biological models have shown that Tel2 mainly functions in Tel2-Tti1-Tti2 (TTT) complex that regulates the steady-state levels of all phosphatidylinositol 3-kinase-like protein kinases, including ATR. We show here that although the levels of Rad3 and Rad3-mediated phospho-signaling in DNA damage checkpoint were moderately reduced in the tel2 mutant, the phospho-signaling in the DNA replication checkpoint was almost completely eliminated. In addition, the tel2 mutation caused telomere shortening. Since the interactions of Tel2 with Tti1 and Tti2 were significantly weakened by the mutation, destabilization of the TTT complex likely contributes to the observed checkpoint and telomere defects.

scholarly journals DNA replication and the GINS complex: localization on extended chromatin fibers

2009 ◽  
Vol 2 (1) ◽  
Author(s):  
Stephanie M Cohen ◽  
Paul D Chastain ◽  
Marila Cordeiro-Stone ◽  
David G Kaufman
Keyword(s):  
Dna Replication ◽  
Chromatin Fibers

scholarly journals Comparative Analysis of DNA Replication Timing Reveals Conserved Large-Scale Chromosomal Architecture

PLoS Genetics ◽  
2010 ◽  
Vol 6 (7) ◽  
pp. e1001011 ◽  
Author(s):  
Eitan Yaffe ◽  
Shlomit Farkash-Amar ◽  
Andreas Polten ◽  
Zohar Yakhini ◽  
Amos Tanay ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Dna Replication ◽  
Large Scale ◽  
Replication Timing ◽  
Chromosomal Architecture ◽  
Dna Replication Timing

scholarly journals Large-scale contractions of Friedreich’s ataxia GAA repeats in yeast occur during DNA replication due to their triplex-forming ability

2020 ◽  
Vol 117 (3) ◽  
pp. 1628-1637 ◽  
Author(s):  
Alexandra N. Khristich ◽  
Jillian F. Armenia ◽  
Robert M. Matera ◽  
Anna A. Kolchinski ◽  
Sergei M. Mirkin
Keyword(s):  
Dna Replication ◽  
Genetic Analysis ◽  
Dna Polymerase ◽  
Mirror Symmetry ◽  
Large Scale ◽  
Catalytic Domain ◽  
Friedreich’S Ataxia ◽  
Hereditary Disease ◽  
Friedreich's Ataxia ◽  
Lagging Strand

Friedreich’s ataxia (FRDA) is a human hereditary disease caused by the presence of expanded (GAA)n repeats in the first intron of the FXN gene [V. Campuzano et al., Science 271, 1423–1427 (1996)]. In somatic tissues of FRDA patients, (GAA)n repeat tracts are highly unstable, with contractions more common than expansions [R. Sharma et al., Hum. Mol. Genet. 11, 2175–2187 (2002)]. Here we describe an experimental system to characterize GAA repeat contractions in yeast and to conduct a genetic analysis of this process. We found that large-scale contraction is a one-step process, resulting in a median loss of ∼60 triplet repeats. Our genetic analysis revealed that contractions occur during DNA replication, rather than by various DNA repair pathways. Repeats contract in the course of lagging-strand synthesis: The processivity subunit of DNA polymerase δ, Pol32, and the catalytic domain of Rev1, a translesion polymerase, act together in the same pathway to counteract contractions. Accumulation of single-stranded DNA (ssDNA) in the lagging-strand template greatly increases the probability that (GAA)n repeats contract, which in turn promotes repeat instability in rfa1, rad27, and dna2 mutants. Finally, by comparing contraction rates for homopurine-homopyrimidine repeats differing in their mirror symmetry, we found that contractions depend on a repeat’s triplex-forming ability. We propose that accumulation of ssDNA in the lagging-strand template fosters the formation of a triplex between the nascent and fold-back template strands of the repeat. Occasional jumps of DNA polymerase through this triplex hurdle, result in repeat contractions in the nascent lagging strand.

scholarly journals Nuclear Reorganization of Mammalian DNA Synthesis Prior to Cell Cycle Exit

2004 ◽  
Vol 24 (2) ◽  
pp. 595-607 ◽  
Author(s):  
David A. Barbie ◽  
Brian A. Kudlow ◽  
Richard Frock ◽  
Jiyong Zhao ◽  
Brett R. Johnson ◽  
...  
Keyword(s):  
Cell Cycle ◽  
Dna Replication ◽  
Dna Synthesis ◽  
Mammalian Cells ◽  
Large Scale ◽  
Replicative Senescence ◽  
S Phase ◽  
Serum Starvation ◽  
Cell Cycle Exit ◽  
Replication Foci

ABSTRACT In primary mammalian cells, DNA replication initiates in a small number of perinucleolar, lamin A/C-associated foci. During S-phase progression in proliferating cells, replication foci distribute to hundreds of sites throughout the nucleus. In contrast, we find that the limited perinucleolar replication sites persist throughout S phase as cells prepare to exit the cell cycle in response to contact inhibition, serum starvation, or replicative senescence. Proteins known to be involved in DNA synthesis, such as PCNA and DNA polymerase δ, are concentrated in perinucleolar foci throughout S phase under these conditions. Moreover, chromosomal loci are redirected toward the nucleolus and overlap with the perinucleolar replication foci in cells poised to undergo cell cycle exit. These same loci remain in the periphery of the nucleus during replication under highly proliferative conditions. These results suggest that mammalian cells undergo a large-scale reorganization of chromatin during the rounds of DNA replication that precede cell cycle exit.

Recent development of Ori-Finder system and DoriC database for microbial replication origins

2018 ◽  
Vol 20 (4) ◽  
pp. 1114-1124 ◽  
Author(s):  
Hao Luo ◽  
Chun-Lan Quan ◽  
Chong Peng ◽  
Feng Gao
Keyword(s):  
Dna Replication ◽  
Large Scale ◽  
Research Field ◽  
Replication Origins ◽  
Manual Curation ◽  
Domains Of Life ◽  
Curve Method ◽  
Dna Replication Origins ◽  
And Function ◽  
Z Curve

Abstract DNA replication begins at replication origins in all three domains of life. Identification and characterization of replication origins are important not only in providing insights into the structure and function of the replication origins but also in understanding the regulatory mechanisms of the initiation step in DNA replication. The Z-curve method has been used in the identification of replication origins in archaeal genomes successfully since 2002. Furthermore, the Web servers of Ori-Finder and Ori-Finder 2 have been developed to predict replication origins in both bacterial and archaeal genomes based on the Z-curve method, and the replication origins with manual curation have been collected into an online database, DoriC. Ori-Finder system and DoriC database are currently used in the research field of DNA replication origins in prokaryotes, including: (i) identification of oriC regions in bacterial and archaeal genomes; (ii) discovery and analysis of the conserved sequences within oriC regions; and (iii) strand-biased analysis of bacterial genomes. Up to now, more and more predicted results by Ori-Finder system were supported by subsequent experiments, and Ori-Finder system has been used to identify the replication origins in > 100 newly sequenced prokaryotes in their genome reports. In addition, the data in DoriC database have been widely used in the large-scale analyses of replication origins and strand bias in prokaryotic genomes. Here, we review the development of Ori-Finder system and DoriC database as well as their applications. Some future directions and aspects for extending the application of Ori-Finder and DoriC are also presented.

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