Project acronym ROADTOIPS
Project Dissection of molecular signature transformation during the process of pluripotency induction
Researcher (PI) Keisuke Kaji
Host Institution (HI) THE UNIVERSITY OF EDINBURGH
Call Details Starting Grant (StG), LS3, ERC-2010-StG_20091118
Summary Induced pluripotent stem cells (iPSCs) are expected to have an enormous impact on medical research. However, the efficiency of reprogramming is still low and far from routine. Nevertheless, reprogramming with defined factors, Oct4, Sox2, Klf4 and c-Myc, is not a random event. Cells positive for SSEA-1, a marker of undifferentiated mouse ES cells (ESC), appear from cells which have lost the fibroblast marker Thy-1, prior to acquiring other pluripotent markers, e.g. Oct4, Nanog. Similarly, TRA-1-60 positive fully reprogrammed human iPSCs appear from SSEA-4 positive populations. Based on these observations, I hypothesize that there are essential ordered stages that the cells must undergo as they are directed toward pluripotency.
To explore this hypothesis, I plan to perform three projects:
1. Identifying gene expression signatures during the successful reprogramming process.
2. Investigating serial changes of reprogramming factor binding, chromatin modifications and chromatin structure on the route to a pluripotent state.
3. Functional analysis of the candidate gene(s) identified for successful reprogramming.
Based on my latest publication in Nature, I have developed an original highly efficient reprogramming system, in which almost all cells differentiated by retinoic acid treatment generate iPSCs by day 12 post reprogramming factor induction. The homogenous culture allowed by this system enables the unique execution of the objectives above, and for the first time will shed light on the molecular mechanisms of the reprogramming process. Accurate and more informed understanding of these ordered processes will allow derivation of strategies to improve the reprogramming technology.
Summary
Induced pluripotent stem cells (iPSCs) are expected to have an enormous impact on medical research. However, the efficiency of reprogramming is still low and far from routine. Nevertheless, reprogramming with defined factors, Oct4, Sox2, Klf4 and c-Myc, is not a random event. Cells positive for SSEA-1, a marker of undifferentiated mouse ES cells (ESC), appear from cells which have lost the fibroblast marker Thy-1, prior to acquiring other pluripotent markers, e.g. Oct4, Nanog. Similarly, TRA-1-60 positive fully reprogrammed human iPSCs appear from SSEA-4 positive populations. Based on these observations, I hypothesize that there are essential ordered stages that the cells must undergo as they are directed toward pluripotency.
To explore this hypothesis, I plan to perform three projects:
1. Identifying gene expression signatures during the successful reprogramming process.
2. Investigating serial changes of reprogramming factor binding, chromatin modifications and chromatin structure on the route to a pluripotent state.
3. Functional analysis of the candidate gene(s) identified for successful reprogramming.
Based on my latest publication in Nature, I have developed an original highly efficient reprogramming system, in which almost all cells differentiated by retinoic acid treatment generate iPSCs by day 12 post reprogramming factor induction. The homogenous culture allowed by this system enables the unique execution of the objectives above, and for the first time will shed light on the molecular mechanisms of the reprogramming process. Accurate and more informed understanding of these ordered processes will allow derivation of strategies to improve the reprogramming technology.
Max ERC Funding
1 359 000 €
Duration
Start date: 2010-12-01, End date: 2015-11-30
Project acronym SMI-DDR
Project Single Molecule Imaging of the DNA Damage Response in Live Cells
Researcher (PI) Antony Carr
Host Institution (HI) THE UNIVERSITY OF SUSSEX
Call Details Advanced Grant (AdG), LS3, ERC-2010-AdG_20100317
Summary "Accurate DNA replication is key to maintaining genomic stability. Replication is immensely complex requiring error-free duplication of several billion bases each time a human cell divides. The DNA replication machinery must deal with a wide range of DNA damage, aberrant secondary structures and DNA:protein complexes; obstacles that cause replication forks to arrest. Arrested replication complexes are actively stabilised by checkpoint pathways, but in some cases component proteins still dissociate from the site of DNA incorporation, resulting in fork ¿collapse¿. Collapsed forks can be restarted by homologous recombination (HR)-based processes, but are strongly associated with gross chromosomal rearrangements. Thus, the advantage gained by restarting a collapsed fork comes at the expense of an increased potential for genome instability.
Structural, biochemical, and molecular techniques identified the main components and regulators of these processes, but are inherently limited to studying the system in bulk, thereby averaging events and limiting our understanding of the dynamics and behaviour of molecular participants. To overcome these limitations and to study single molecules at a single arrested or collapsed fork I propose to develop an nTIRF-PALM ¿super-resolution¿ microscopy platform that will allow the identification of individual protein molecule as well as very small numbers of molecules at <50 nanometer resolution inside the nucleus of a living eukaryotic cell. I propose to apply this methodology to the model organism fission yeast (S. pombe) to study the organization and structure of normal and restarted replication forks. To achieve this I propose to extend the development of site-specific and temporally controlled replication fork arrest systems to manipulate a single replication fork at a defined DNA locus. By creating a variety of fluorescent protein tags we will record ""molecular movies"" to provide insight into the dynamics and reaction mechanisms."
Summary
"Accurate DNA replication is key to maintaining genomic stability. Replication is immensely complex requiring error-free duplication of several billion bases each time a human cell divides. The DNA replication machinery must deal with a wide range of DNA damage, aberrant secondary structures and DNA:protein complexes; obstacles that cause replication forks to arrest. Arrested replication complexes are actively stabilised by checkpoint pathways, but in some cases component proteins still dissociate from the site of DNA incorporation, resulting in fork ¿collapse¿. Collapsed forks can be restarted by homologous recombination (HR)-based processes, but are strongly associated with gross chromosomal rearrangements. Thus, the advantage gained by restarting a collapsed fork comes at the expense of an increased potential for genome instability.
Structural, biochemical, and molecular techniques identified the main components and regulators of these processes, but are inherently limited to studying the system in bulk, thereby averaging events and limiting our understanding of the dynamics and behaviour of molecular participants. To overcome these limitations and to study single molecules at a single arrested or collapsed fork I propose to develop an nTIRF-PALM ¿super-resolution¿ microscopy platform that will allow the identification of individual protein molecule as well as very small numbers of molecules at <50 nanometer resolution inside the nucleus of a living eukaryotic cell. I propose to apply this methodology to the model organism fission yeast (S. pombe) to study the organization and structure of normal and restarted replication forks. To achieve this I propose to extend the development of site-specific and temporally controlled replication fork arrest systems to manipulate a single replication fork at a defined DNA locus. By creating a variety of fluorescent protein tags we will record ""molecular movies"" to provide insight into the dynamics and reaction mechanisms."
Max ERC Funding
2 366 576 €
Duration
Start date: 2011-05-01, End date: 2016-04-30
