Separation of replication and transcription domains in nucleoli

Smirnov, Evgeny; Borkovec, Josef; Kováčik, Ľubomír; Svidenská, Silvie; Schröfel, Adam; Skalnı́ková, Magdalena; Švindrych, Zdeněk; Křížek, Pavel; Ovesný, Martin; Hagen, Guy M.; Jůda, Pavel; Michalova, Kyra; Cardoso, M. C.; Cmarko, Dušan; Raška, Ivan

doi:10.1016/j.jsb.2014.10.001

Cited by 38 publications

(47 citation statements)

References 36 publications

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“…Although the majority of transcriptional activity in eukaryotes occurs during G1 phase, there are transcriptionally active loci in S phase, and these loci seem to be spatially separated from replicating regions [202]. Transcription and replication of rRNA genes (rDNA) in mammalian cells are an excellent example of such coordination [203,204]. Each rDNA locus undergoes a temporal sequence of reprogramming from active transcription to active replication.…”

Section: Coordination Between Transcription and Replication Machinmentioning

confidence: 99%

“…Following replication, the rDNA loci are reprogrammed for transcription [205]. In terms of spatial separation, actively transcribed rRNA genes are exclusively localized in the interior of the nucleolus [206,207], and replicating loci seem to be physically separated from their transcription by fibrillar centers that provide a structural barrier between domains [203]. In S. cerevisiae , actively transcribed genes localize near nuclear pores [208,209].…”

Section: Coordination Between Transcription and Replication Machinmentioning

confidence: 99%

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Regulation of DNA Replication through Natural Impediments in the Eukaryotic Genome

Gadaleta

Noguchi

2017

Genes

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All living organisms need to duplicate their genetic information while protecting it from unwanted mutations, which can lead to genetic disorders and cancer development. Inaccuracies during DNA replication are the major cause of genomic instability, as replication forks are prone to stalling and collapse, resulting in DNA damage. The presence of exogenous DNA damaging agents as well as endogenous difficult-to-replicate DNA regions containing DNA–protein complexes, repetitive DNA, secondary DNA structures, or transcribing RNA polymerases, increases the risk of genomic instability and thus threatens cell survival. Therefore, understanding the cellular mechanisms required to preserve the genetic information during S phase is of paramount importance. In this review, we will discuss our current understanding of how cells cope with these natural impediments in order to prevent DNA damage and genomic instability during DNA replication.

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Section: Coordination Between Transcription and Replication Machinmentioning

confidence: 99%

Section: Coordination Between Transcription and Replication Machinmentioning

confidence: 99%

Regulation of DNA Replication through Natural Impediments in the Eukaryotic Genome

Gadaleta

Noguchi

2017

Genes

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“…This dye is more commonly used in (d)STORM studies [32] and is provided for purposes of comparison of the single molecule parameters. For this experiment we used an Alexa 532labeled antibody to detect RNA molecules in the nucleus of a HeLa cell as previously described [33]. The raw data is useful in this context because it was acquired with the same microscope setup and detector.…”

Section: Contextmentioning

confidence: 99%

“…In each experiment, a sequence of 1,419-10,000 images was acquired with an exposure time of 40 -100 ms and an EM gain of 50-300. For imaging Alexa 532, we used a 1 W, 532 nm laser (Dragon laser) and an appropriate fluorescence emission filter (569-610 nm, Chroma) as previously described [33].…”

Section: Single Molecule Microscopymentioning

confidence: 99%

Quantitative super-resolution single molecule microscopy dataset of YFP-tagged growth factor receptors

Lozano-Pérez

Pospíšil

Fliegel

et al. 2018

Preprint

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BackgroundSuper-resolution single molecule localization microscopy (SMLM) is a method for achieving resolution beyond the classical limit in optical microscopes (approx. 200 nm laterally). Yellow fluorescent protein (YFP) has been used for super-resolution single molecule localization microscopy, but less frequently than other fluorescent probes. Working with YFP in SMLM is a challenge because a lower number of photons are emitted per molecule compared to organic dyes which are more commonly used. Publically available experimental data can facilitate development of new data analysis algorithms.FindingsFour complete, freely available single molecule super-resolution microscopy datasets on YFP-tagged growth factor receptors expressed in a human cell line are presented including both raw and analyzed data. We report methods for sample preparation, for data acquisition, and for data analysis, as well as examples of the acquired images. We also analyzed the SMLM data sets using a different method: super-resolution optical fluctuation imaging (SOFI). The two modes of analysis offer complementary information about the sample. A fifth single molecule super-resolution microscopy dataset acquired with the dye Alexa 532 is included for comparison purposes.ConclusionThis dataset has potential for extensive reuse. Complete raw data from SMLM experiments has typically not been published. The YFP data exhibits low signal to noise ratios, making data analysis a challenge. These data sets will be useful to investigators developing their own algorithms for SMLM, SOFI, and related methods. The data will also be useful for researchers investigating growth factor receptors such as ErbB3.

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“…Traditional colocalization analysis of laser scanning confocal microscopy images has several limitations (Ronneberger et al 2008), however, SMLM methods offer a new paradigm for colocalization studies due to the coordinate-based nature of the data (Gunkel et al 2009;Malkusch et al 2012;Smirnov et al 2014). Colocalization analysis is a commonly used approach to measure spatial overlap between two (or more) different fluorescent labels, each having a different emission wavelength.…”

Section: Further Analysismentioning

confidence: 99%

Image Analysis for Single-Molecule Localization Microscopy

2016

Super-Resolution Imaging in Biomedicine

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Separation of replication and transcription domains in nucleoli

Cited by 38 publications

References 36 publications

Regulation of DNA Replication through Natural Impediments in the Eukaryotic Genome

Regulation of DNA Replication through Natural Impediments in the Eukaryotic Genome

Quantitative super-resolution single molecule microscopy dataset of YFP-tagged growth factor receptors

Image Analysis for Single-Molecule Localization Microscopy

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