Cell memory plays a key role during differentiation and disease. It relies on epigenetic inheritance that is essential to propagate gene expression program through cell generation, in large part through maintaining the structure of chromatin in daughter cell. DNA replication is the major obstacle in conservation of chromatin structure. During replication, most proteins are thought to dissociate from DNA. A few molecules may remain associated with DNA, thus marking DNA regulatory elements for future maturation of chromatin into an open or compact conformation. The identity of these epigenetic marks is unknown. The best candidates are thought to be modified histones because they are assumed to transfer from the parental to daughter nucleosomes on nascent DNA. However, until recently, there were no experimental approaches to directly examine neither the nature of epigenetic marks, nor the order and timing of recruitment of chromosomal proteins to DNA following replication. Similarly, we know very little about how and when transcription resumes after DNA replication. We developed several new experimental approaches that allow addressing these key epigenetic issues, and found that the structure of chromatin is not as severely disrupted as is currently suggested. RNA Polymerase II and related general transcription and elongation factors are found on nascent DNA just after replication. Moreover, even immature RNAs are found in the proximity to nascent DNA suggesting that the RNA Pol II ? RNA complex is able to survive DNA replication. We also found that transcription resumes relatively quickly after DNA replication. Based on our published and preliminary results, we propose to test a new epigenetic concept suggesting that once transcription is established, most of the transcriptional apparatus may be associated with DNA through replication, thus serving as an epigenetic mark for active genes. This possibility, however, conflicts with the conventional model suggesting that transcription and replication complexes travel along DNA, since this will lead to collisions of these protein complexes. To resolve this contradiction, we will test the hypothesis that the stability of the transcriptional machinery through replication can be resolved if transcription and replication occur in the stationary nuclear sub-domains, transcription and replication factories, and that DNA is reeled through these protein factories. The results of these experiments will greatly contribute to our understanding of the epigenetic processes, and may have a major impact on developing new approaches in many biological and drug discovery fields.

Public Health Relevance

Epigenetic inheritance lies in the heart of gene regulation during normal cell differentiation, and when changed, it contributes to development of cancer and other diseases. The mechanisms of the complicated processes involved in the conservation of chromatin structure through the cell cycle are poorly understood. By developing new experimental and conceptual approaches, we propose to address key epigenetic issues that will be beneficial for general biological and health related issues.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Project (R01)
Project #
Application #
Study Section
Development - 2 Study Section (DEV2)
Program Officer
Adkins, Ronald
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
Thomas Jefferson University
Schools of Medicine
United States
Zip Code
Petruk, Svetlana; Cai, Jingli; Sussman, Robyn et al. (2017) Delayed Accumulation of H3K27me3 on Nascent DNA Is Essential for Recruitment of Transcription Factors at Early Stages of Stem Cell Differentiation. Mol Cell 66:247-257.e5
Akishina, Angelina A; Vorontsova, Julia E; Cherezov, Roman O et al. (2017) Xenobiotic-induced activation of human aryl hydrocarbon receptor target genes in Drosophila is mediated by the epigenetic chromatin modifiers. Oncotarget 8:102934-102947
Petruk, Svetlana; Mariani, Samanta A; De Dominici, Marco et al. (2017) Structure of Nascent Chromatin Is Essential for Hematopoietic Lineage Specification. Cell Rep 19:295-306
Petruk, Svetlana; Fenstermaker, Tyler K; Black, Kathryn L et al. (2016) Detection of RNA-DNA association by a proximity ligation-based method. Sci Rep 6:27313
L Black, Kathryn; Petruk, Svetlana; Fenstermaker, Tyler K et al. (2016) Chromatin proteins and RNA are associated with DNA during all phases of mitosis. Cell Discov 2:16038
Petruk, Svetlana; Black, Kathryn L; Kovermann, Sina K et al. (2013) Stepwise histone modifications are mediated by multiple enzymes that rapidly associate with nascent DNA during replication. Nat Commun 4:2841
Petruk, Svetlana; Sedkov, Yurii; Johnston, Danika M et al. (2012) TrxG and PcG proteins but not methylated histones remain associated with DNA through replication. Cell 150:922-33
Orlovsky, Kira; Kalinkovich, Alexander; Rozovskaia, Tanya et al. (2011) Down-regulation of homeobox genes MEIS1 and HOXA in MLL-rearranged acute leukemia impairs engraftment and reduces proliferation. Proc Natl Acad Sci U S A 108:7956-61
Johnston, Danika M; Sedkov, Yurii; Petruk, Svetlana et al. (2011) Ecdysone- and NO-mediated gene regulation by competing EcR/Usp and E75A nuclear receptors during Drosophila development. Mol Cell 44:51-61
Petruk, Svetlana; Smith, Sheryl T; Sedkov, Yurii et al. (2008) Association of trxG and PcG proteins with the bxd maintenance element depends on transcriptional activity. Development 135:2383-90

Showing the most recent 10 out of 12 publications