We now have the capability to reprogram a somatic cell to a pluripotent state, a so-called """"""""induced pluripotent stem cells"""""""" (iPSCs), which have many of the attributes of embryonic stem cells (ESCs). These include self- renewal and the ability to be directed to the three germ layers. Importantly, iPSCs retain the genetic composition of parental cells, and as a consequence their potential utility as autologous donors for cell therapy and in vitro disease modeling has been recognized. The epigenetic states in iPSCs are similar to ESCs but they differ, especially with respect to methylation. These include differentially methylated regions and incomplete erasure of parental DNA methylation (epigenetic memory), these in turn have repercussions in differentiation potential resulting in unpredictable behavior o iPSC-derivatives. To safeguard against these undesirable side-effects it is crucial to investigate the reprogramming process at the epigenetic level, with the ultimate goal of generating desirable iPSCs. Among the proteins involved in DNA methylation and demethylation, is the hemi-methylated DNA binding protein NP95, which increases reprogramming efficiency and can substitute for c-Myc. Accompanied with these observations, NP95 increases H3K4me3 as well as hydroxymethylcytosine (hmC). These implicate a novel function for NP95 in transcriptional activation during reprogramming, contrary to reported involvement in maintenance of methylated DNA and heterochromatic regions. This proposal will address a number of gaps in our knowledge of reprogramming, by providing crucial insight into the function of NP95. This will be achieved by implementing these specific aims: (1) Determine whether NP95 increases SET1 activity. We will establish whether NP95 stabilizes the SET1 complex or directly activates the catalytic activity of Set1/COMPASS complex and identify the domains critical for SET1 activity. (2) Determine whether NP95 recruits Set1a for H3K4me3 marks. We will assess the ability of NP95 to recruit Set1 complex to targets and mediates euchromatin gene activation. This will be achieved with ChIP-seq against NP95, Set1 and H3K4me3. The TTD domain of NP95 is known to interact with modified histone H3. It will be interrogated to assess its role in H3K4me3 formation during reprogramming. (3) Determine whether NP95 reads hmC for H3K4me3 formation. In ESCs, hmC marks the loci of active genes. The hmC marks are produced by TET proteins induced during the reprogramming process. Recent studies have shown that NP95 binds to hmC as well as mC. We will confirm these observations and further develop this by examining the formation of mC and hmC by NP95 during reprogramming. This proposal will significantly impact on the reprogramming field by providing for the first time a detailed study of molecular events during reprogramming. Additionally we will dissect the novel function of NP95 in transcriptional activation during reprogramming and pluripotent stem cells. Ultimately our data will be critical in generating clinically safe, appropriately reprogrammed iPSCs for cell therapy and disease modeling.

Public Health Relevance

Induced pluripotent stem cells (iPSCs) generated by reprogramming hold great promise for regenerative medicine and disease modeling. Genetic and epigenetic aberrations accompany reprogramming, raising concerns of clinical utilities of iPSCs. We propose to investigate the function of an epigenetic regulator NP95 in reprogramming, aiming to generate clinically safe iPSCs.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Project (R01)
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Development - 2 Study Section (DEV2)
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Carter, Anthony D
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Yale University
Schools of Medicine
New Haven
United States
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Kim, Kun-Yong; Tanaka, Yoshiaki; Su, Juan et al. (2018) Uhrf1 regulates active transcriptional marks at bivalent domains in pluripotent stem cells through Setd1a. Nat Commun 9:2583
Patterson, Benjamin; Tanaka, Yoshiaki; Park, In-Hyun (2017) New Advances in Human X chromosome status from a Developmental and Stem Cell Biology. Tissue Eng Regen Med 14:643-652
Xiang, Yangfei; Tanaka, Yoshiaki; Patterson, Benjamin et al. (2017) Fusion of Regionally Specified hPSC-Derived Organoids Models Human Brain Development and Interneuron Migration. Cell Stem Cell 21:383-398.e7
Hysolli, Eriona; Tanaka, Yoshiaki; Su, Juan et al. (2016) Regulation of the DNA Methylation Landscape in Human Somatic Cell Reprogramming by the miR-29 Family. Stem Cell Reports 7:43-54
Liu, Renjing; Kim, Kun-Yong; Jung, Yong-Wook et al. (2016) Dnmt1 regulates the myogenic lineage specification of muscle stem cells. Sci Rep 6:35355
Xiang, Yangfei; Kim, Kun-Yong; Gelernter, Joel et al. (2015) Ethanol upregulates NMDA receptor subunit gene expression in human embryonic stem cell-derived cortical neurons. PLoS One 10:e0134907
Greer, Celeste B; Tanaka, Yoshiaki; Kim, Yoon Jung et al. (2015) Histone Deacetylases Positively Regulate Transcription through the Elongation Machinery. Cell Rep 13:1444-1455
Tanaka, Yoshiaki; Hysolli, Eriona; Su, Juan et al. (2015) Transcriptome Signature and Regulation in Human Somatic Cell Reprogramming. Stem Cell Reports 4:1125-39