The mouse inner cell mass (ICM) and the embryonic stem (ES) cells derived from it contain two active X chromosomes. Similarly, nuclear reprogramming resets the state of X chromosome inactivation (XCI) in mouse induced pluripotent stem (IPS) cells, which also transcribe both of their X chromosomes. However, the proper status of dosage compensation in human pluripotent stem cells remains to be clarified. As the transcriptional networks that propagates the pluripotent state in mouse ES cells has been tightly linked to the regulation of X chromosome inactivation, it will be of substantial interest to determine whether these gene regulatory processes are also tightly coupled within human pluripotent stem cells. In addition, many diseases result from mutations in X-linked genes. As there is substantial interest in using reprogrammed cells for modeling these conditions in vitro, it will be critically important to understand the state of dosage compensation in both human IPS cells and their differentiated derivatives. Here we propose to combine reprogramming, stem cell and genomic approaches to understand the behavior of the inactive X chromosome during the generation, maintenance and differentiation of human IPS cells.
Our specific aims are to:
Aim 1) To determine whether female IPS cells inherit the inactive X chromosome of the somatic cells from which they are derived and to determine how stably they maintain this inactive X in the course of long-term culture.
Aim 2) To determine whether the loss of cytological hallmarks of X chromosome inactivation is accompanied by X-chromosome-wide relaxation of DNA methylation, chromatin structure and transcriptional silencing.
Aim 3) We will determine the specific culture conditions that contribute to instability of X chromosome inactivation that we have observed and identify culture conditions that allow proper maintenance of X chromosome-wide heterochromatin.
Human pluripotent stem cells represent a significant opportuninty to better understand and treatmost any degenertive disease. However, if we are to use these stem cells for medical applications, we must understand the fundemental properties. He we propose to look at the process of X chromosome inactivation in human iPS cells. Understanding X chromosome biology will be essential for the use IPS cells in modeling dlsaasRS nau.sfifl mv X chrnmnsnmfi miitatinn.g
|Hacisuleyman, Ezgi; Goff, Loyal A; Trapnell, Cole et al. (2014) Topological organization of multichromosomal regions by the long intergenic noncoding RNA Firre. Nat Struct Mol Biol 21:198-206|
|Rinn, John; Guttman, Mitchell (2014) RNA Function. RNA and dynamic nuclear organization. Science 345:1240-1|
|Smith, Zachary D; Chan, Michelle M; Humm, Kathryn C et al. (2014) DNA methylation dynamics of the human preimplantation embryo. Nature 511:611-5|
|Lu, Yu; Loh, Yuin-Han; Li, Hu et al. (2014) Alternative splicing of MBD2 supports self-renewal in human pluripotent stem cells. Cell Stem Cell 15:92-101|
|Trapnell, Cole; Cacchiarelli, Davide; Grimsby, Jonna et al. (2014) The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells. Nat Biotechnol 32:381-6|
|Ichida, Justin K; TCW, Julia; T C W, Julia et al. (2014) Notch inhibition allows oncogene-independent generation of iPS cells. Nat Chem Biol 10:632-9|
|Federation, Alexander J; Bradner, James E; Meissner, Alexander (2014) The use of small molecules in somatic-cell reprogramming. Trends Cell Biol 24:179-87|
|Karnik, Rahul; Meissner, Alexander (2013) Browsing (Epi)genomes: a guide to data resources and epigenome browsers for stem cell researchers. Cell Stem Cell 13:14-21|
|Sun, Lei; Goff, Loyal A; Trapnell, Cole et al. (2013) Long noncoding RNAs regulate adipogenesis. Proc Natl Acad Sci U S A 110:3387-92|
|Smith, Zachary D; Meissner, Alexander (2013) DNA methylation: roles in mammalian development. Nat Rev Genet 14:204-20|
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