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Publications

Fresh off the press:

Collart, C., Christov, C.P., Smith, J.C., and Krude, T. (2011).
The mid-blastula transition defines the onset of Y RNA-dependent DNA replication in Xenopus laevis. Mol Cell Biol 31, 3857-3870.

Abstract
Non-coding Y RNAs are essential for the initiation of chromosomal DNA replication in mammalian cell extracts, but their role in this process during early vertebrate development is unknown. Here, we use antisense morpholino nucleotides (MOs) to investigate Y RNA function in Xenopus laevis and zebrafish embryos. We show that embryos in which Y RNA function is inhibited by MOs develop normally until the mid-blastula transition (MBT) but then fail to replicate their DNA and die before gastrulation. Consistent with this observation, Y RNA function is not required for DNA replication in Xenopus egg extracts, but is required for replication in a post-MBT cell line. Y RNAs do not bind chromatin in karyomeres before MBT, but associate with interphase nuclei after MBT in an origin recognition complex (ORC)-dependent manner. Y RNA-specific MOs inhibit the association of Y RNAs with ORC, Cdt1 and HMGA1a proteins, suggesting that these molecular associations are essential for Y RNA function in DNA replication. The MBT is thus a transition point between Y RNA-independent and Y RNA-dependent control of vertebrate DNA replication. Our data suggest that in vertebrates Y RNAs function as a developmentally regulated layer of control over the evolutionarily conserved eukaryotic DNA replication machinery.

This paper has been highlighted in a news article on the MRC-NIMR website:
"The onset of Y RNA-dependent DNA replication in Xenopus laevis"

 

Zhang, A.T., Langley, A.R., Christov, C.P., Kheir, E., Shafee, T., Gardiner, T.J., and Krude, T. (2011).
Dynamic interaction of Y RNAs with chromatin and initiation proteins during human DNA replication. J Cell Sci 124, 2058-2069.

Abstract
Non-coding Y RNAs are required for the initiation of chromosomal DNA replication in mammalian cells. It is unknown how they perform this function or if they associate with a nuclear structure during DNA replication. Here, we investigate the association of Y RNAs with chromatin and their interaction with replication proteins during DNA replication in a human cell-free system. Our results show that fluorescently labelled Y RNAs associate with unreplicated euchromatin in late G1 phase cell nuclei before the initiation of DNA replication. Following initiation, Y RNAs are displaced locally from nascent and replicated DNA present in replication foci. In intact human cells, a substantial fraction of endogenous Y RNAs are associated with G1 phase nuclei, but not with G2 phase nuclei. Y RNAs interact and colocalise with the origin recognition complex (ORC), the pre-replication complex (pre-RC) protein Cdt1, and other proteins implicated in the initiation of DNA replication. These data support a molecular 'catch and release' mechanism for Y RNA function during the initiation of chromosomal DNA replication, which is consistent with Y RNAs acting as replication licensing factors.

This paper has been highlighted in the Journal of Cell Science section 'In this Issue':
"Y RNAs give license to copy"

 


Full publication list:

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Selected recent journal articles:

Krude, T. (2010).
Non-coding RNAs: New players in the field of eukaryotic DNA replication. Subcell Biochem 50, 105-118.

Langley, A.R., Chambers, H., Christov, C.P., and Krude, T. (2010).
Ribonucleoprotein Particles Containing Non-Coding Y RNAs, Ro60, La and Nucleolin Are Not Required for Y RNA Function in DNA Replication. PLoS ONE 5, e13673.

Gardiner, T.J., Christov, C.P., Langley, A.R., and Krude, T. (2009).
A conserved motif of vertebrate Y RNAs essential for chromosomal DNA replication. RNA 15, 1375-1385.

Krude, T., Christov, C.P., Hyrien, O., and Marheineke, K. (2009).
Y RNA functions at the initiation step of mammalian chromosomal DNA replication. J Cell Sci 122, 2836-2845.

Marheineke, K., Goldar, A., Krude, T., and Hyrien, O. (2009).
Use of DNA combing to study DNA replication in xenopus and human cell-free systems. Methods Mol Biol 521, 575-603.

Christov, C.P., Trivier, E., and Krude, T. (2008).
Noncoding human Y RNAs are overexpressed in tumours and required for cell proliferation. Br J Cancer 98, 981-988.

Klinge, S., Hirst, J., Maman, J. D., Krude, T., and Pellegrini, L. (2007).
An iron-sulfur domain of the eukaryotic primase is essential for RNA primer synthesis. Nat Struct Mol Biol 14, 875-877.

Christov, C. P., Gardiner, T. J., Szüts, D., and Krude, T. (2006).
Functional requirement of non-coding Y RNAs for human chromosomal DNA replication. Mol Cell Biol 26, 6993-7004.

Krude, T. (2006).
Initiation of chromosomal DNA replication in mammalian cell-free systems. Cell Cycle 5, 2115-2122.
Click here for an open access to the pdf of this review

Nabatiyan, A., Szüts, D., and Krude, T. (2006).
Induction of CAF-1 expression in response to DNA strand breaks in quiescent human cells.
Mol Cell Biol 26, 1839-1849.

Marheineke, K., Hyrien, O., and Krude, T. (2005).
Visualization of bidirectional initiation of chromosomal DNA replication in a human cell free system. Nucleic Acids Res 33, 6931-6941.

Szüts, D., Christov, C., Kitching, L., and Krude, T. (2005).
Distinct populations of human PCNA are required for initiation of chromosomal DNA replication and concurrent DNA repair. Exp Cell Res 311, 240-250.

Szüts, D., and Krude, T. (2004).
Cell cycle arrest at the initiation step of human chromosomal DNA replication causes DNA damage. J Cell Sci 117, 4897-4908.

Nabatiyan, A., and Krude, T. (2004).
Silencing of Chromatin Assembly Factor 1 in human cells leads to cell death and loss of chromatin assembly during DNA synthesis. Mol Cell Biol 24, 2853-2862.

Szüts, D., Kitching, L., Christov, C., Budd, A., Peak-Chew, S., and Krude, T. (2003).
RPA is an initiation factor for human chromosomal DNA replication. Nucleic Acids Res 31, 1725-1734.

Keller, C., Hyrien, O., Knippers, R., and Krude, T. (2002).
Site-specific and temporally controlled initiation of DNA replication in a human cell-free system. Nucleic Acids Res 30, 2114-2123.

Laman, H., Coverley, D., Krude, T., Laskey, R., and Jones, N. (2001).
Viral cyclin-cyclin-dependent kinase 6 complexes initiate nuclear DNA replication. Mol Cell Biol 21, 624-635.

Krude, T. (2000).
Initiation of human DNA replication in vitro using nuclei from cells arrested at an initiation-competent state. J Biol Chem 275, 13699-13707.

Krude, T. (1999).
Mimosine arrests proliferating human cells before onset of DNA replication in a dose-dependent manner. Exp Cell Res 247, 148-159.

Krude, T., Jackman, M., Pines, J., and Laskey, R.A. (1997).
Cyclin/Cdk-dependent initiation of DNA replication in a human cell-free system.
Cell 88, 109-119.



 


Books:

Krude, T., Editor (2003).
DNA: Changing Science and Society
Cambridge University Press,
200 pages,
ISBN 0521823781

 

 

 


Book reviews:

Krude, T. (2007).
Controlling the cycle. BioEssays 29, 605-606.

Review of:
Primers in Biology: The cell cycle. Principles of control. (2007)
By David O Morgan
New Science Press Ltd., in association with Oxford University Press and Sinauer Associates, Inc., 297 pages, ISBN 978-0-19-920610-0.