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
|Choi, Jiho; Clement, Kendell; Huebner, Aaron J et al. (2017) DUSP9 Modulates DNA Hypomethylation in Female Mouse Pluripotent Stem Cells. Cell Stem Cell 20:706-719.e7|
|Merkle, Florian T; Ghosh, Sulagna; Kamitaki, Nolan et al. (2017) Human pluripotent stem cells recurrently acquire and expand dominant negative P53 mutations. Nature 545:229-233|
|Smith, Zachary D; Shi, Jiantao; Gu, Hongcang et al. (2017) Epigenetic restriction of extraembryonic lineages mirrors the somatic transition to cancer. Nature 549:543-547|
|Melé, Marta; Mattioli, Kaia; Mallard, William et al. (2017) Chromatin environment, transcriptional regulation, and splicing distinguish lincRNAs and mRNAs. Genome Res 27:27-37|
|Lin, Shuibin; Choe, Junho; Du, Peng et al. (2016) The m(6)A Methyltransferase METTL3 Promotes Translation in Human Cancer Cells. Mol Cell 62:335-345|
|Groff, Abigail F; Sanchez-Gomez, Diana B; Soruco, Marcela M L et al. (2016) In Vivo Characterization of Linc-p21 Reveals Functional cis-Regulatory DNA Elements. Cell Rep 16:2178-2186|
|Santos, David P; Kiskinis, Evangelos; Eggan, Kevin et al. (2016) Comprehensive Protocols for CRISPR/Cas9-based Gene Editing in Human Pluripotent Stem Cells. Curr Protoc Stem Cell Biol 38:5B.6.1-5B.6.60|
|Hacisuleyman, Ezgi; Shukla, Chinmay J; Weiner, Catherine L et al. (2016) Function and evolution of local repeats in the Firre locus. Nat Commun 7:11021|
|Liu, Lin L; Brumbaugh, Justin; Bar-Nur, Ori et al. (2016) Probabilistic Modeling of Reprogramming to Induced Pluripotent Stem Cells. Cell Rep 17:3395-3406|
|Tsankov, Alexander M; Akopian, Veronika; Pop, Ramona et al. (2015) A qPCR ScoreCard quantifies the differentiation potential of human pluripotent stem cells. Nat Biotechnol 33:1182-92|
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