Papers by Mehmet U bikkul
SpringerLink, 2016
The genome has a special relationship with the nuclear envelope in cells. Much of the genome is a... more The genome has a special relationship with the nuclear envelope in cells. Much of the genome is anchored at the nuclear periphery, tethered by chromatin binding proteins such nuclear lamins and other integral membrane proteins. Even though there are global assays such as DAM-ID or ChIP to assess what parts of the genome are associated with the nuclear envelope, it is also essential to be able to visualize regions of the genome in order to reveal their individual relationships with nuclear structures in single cells. This is executed by fluorescence in situ hybridization (FISH) in 2-dimensional flattened nuclei (2D-FISH) or 3-dimensionally preserved cells (3D-FISH) in combination with indirect immunofluorescence to reveal structural proteins. This chapter explains the protocols for 2D-and 3D-FISH in combination with indirect immunofluorescence and discusses options for image capture and analysis. Due to the nuclear envelope proteins being part of the non-extractable nucleoskeleton, we also describe how to prepare DNA halos through salt extraction and how they can be used to study genome behavior and association when combined with 2D-FISH.
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Biogerontology, 2018
Hutchinson–Gilford progeria syndrome (HGPS) is a rare and fatal premature ageing disease in child... more Hutchinson–Gilford progeria syndrome (HGPS) is a rare and fatal premature ageing disease in children. HGPS is one of several progeroid syndromes caused by mutations in the LMNA gene encoding the nuclear structural proteins lamins A and C. In classic HGPS the mutation G608G leads to the formation of a toxic lamin A protein called progerin. During post-translational processing progerin remains farnesylated owing to the mutation interfering with a step whereby the farnesyl moiety is removed by the enzyme ZMPSTE24. Permanent farnesylation of progerin is thought to be responsible for the proteins toxicity. Farnesyl is generated through the mevalonate pathway and three drugs that interfere with this pathway and hence the farnesylation of proteins have been administered to HGPS children in clinical trials. These are a farnesyltransferase inhibitor (FTI), statin and a bisphosphonate. Further experimental studies have revealed that other drugs such as N-acetyl cysteine, rapamycin and IGF-1 may be of use in treating HGPS through other pathways. We have shown previously that FTIs restore chromosome positioning in interphase HGPS nuclei. Mis-localisa-tion of chromosomes could affect the cells ability to regulate proper genome function. Using nine different drug treatments representing drug regimes in the clinic we have shown that combinatorial treatments containing FTIs are most effective in restoring specific chromosome positioning towards the nuclear periphery and in tethering telomeres to the nucleoskeleton. On the other hand, rapamycin was found to be detrimental to telomere tethering, it was, nonetheless, the most effective at inducing DNA damage repair, as revealed by COMET analyses. Keywords Hutchinson–Gilford progeria syndrome Á Genome organisation Á COMET assay Á DNA damage Á Farnesyltransferase inhibitors Á Rapamycin
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Books by Mehmet U bikkul
SpringerLink, 2013
Interphase chromosomes are nonrandomly positioned in the nuclei of
normal cells. They occupy spec... more Interphase chromosomes are nonrandomly positioned in the nuclei of
normal cells. They occupy specifi c locations with respect to a radial distribution
from the nuclear edge to the nuclear interior. Furthermore, there is some evidence
that interphase chromosomes reproducibly have the same neighbors that can be
involved in creating translocations which lead to cancer. Not only are chromosomes
nonrandomly positioned but they are anchored to certain regions of the cell nucleus
by cellular structures such as the nuclear lamina and the nucleolus. Global screening
of the genome has identifi ed both lamina-associated domains and nucleolarassociated
domains. Increasingly, researchers are fi nding that interphase chromosomes
are mislocalized in disease situations. The consequences of chromosome
mislocalization are not yet that clear, but gene expression can be affected with interphase
chromosomes being located in another compartment of the nucleus, changing
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Thesis Chapters by Mehmet U bikkul
Brunel University, 2016
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Papers by Mehmet U bikkul
Books by Mehmet U bikkul
normal cells. They occupy specifi c locations with respect to a radial distribution
from the nuclear edge to the nuclear interior. Furthermore, there is some evidence
that interphase chromosomes reproducibly have the same neighbors that can be
involved in creating translocations which lead to cancer. Not only are chromosomes
nonrandomly positioned but they are anchored to certain regions of the cell nucleus
by cellular structures such as the nuclear lamina and the nucleolus. Global screening
of the genome has identifi ed both lamina-associated domains and nucleolarassociated
domains. Increasingly, researchers are fi nding that interphase chromosomes
are mislocalized in disease situations. The consequences of chromosome
mislocalization are not yet that clear, but gene expression can be affected with interphase
chromosomes being located in another compartment of the nucleus, changing
Thesis Chapters by Mehmet U bikkul
normal cells. They occupy specifi c locations with respect to a radial distribution
from the nuclear edge to the nuclear interior. Furthermore, there is some evidence
that interphase chromosomes reproducibly have the same neighbors that can be
involved in creating translocations which lead to cancer. Not only are chromosomes
nonrandomly positioned but they are anchored to certain regions of the cell nucleus
by cellular structures such as the nuclear lamina and the nucleolus. Global screening
of the genome has identifi ed both lamina-associated domains and nucleolarassociated
domains. Increasingly, researchers are fi nding that interphase chromosomes
are mislocalized in disease situations. The consequences of chromosome
mislocalization are not yet that clear, but gene expression can be affected with interphase
chromosomes being located in another compartment of the nucleus, changing