Heterochromatin comprises tightly compacted repetitive regions of eukaryotic chromosomes. It is inherited through mitosis and has roles in transcriptional silencing, centromere specification and genome integrity, which profoundly impact epigenetic mechanisms in human health and disease. We have found that the epigenetic inheritance of heterochromatin in fission yeast requires RNA interference (RNAi) to guide histone modification, which occurs during the DNA replication phase of the cell cycle. In the fission yeast S.pombe centromeric repeats have an alternating arrangement of small RNA clusters and origins of replication that makes collision of the transcription and replication machineries all but inevitable. We propose that RNA interference promotes release of RNA polymerase (PolII) during S phase, allowing completion of centromeric DNA replication by the leading strand DNA polymerase. DNA Polymerase epsilon directly recruits the histone-modifying Rik1 complex and so can spread heterochromatin along with DNA replication. In the absence of RNAi, stalled forks are repaired by homologous recombination (HR) without histone modification, so that HR is essential in the absence of RNAi. This model may explain the participation of non-coding RNA and DNA replication in many examples of epigenetic silencing, including paramutation in plants, and imprinting and X-inactivation in mammals. S.pombe is an outstanding model system for cell cycle research, heterochromatic silencing, and RNAi. We will examine the roles of DNA replication, RNA Polymerase release, DNA recombination and repair in heterochromatic histone modification mediated by RNAi. We will utilize models of heterochromatic nucleation and RNAi, as well as chromosome profiling and genetic analysis, to test our hypothesis. We will build on our recent results concerning the roles of the Rik1 complex and Centromere-binding protein B in DNA replication and repair, as well as RNA interference.

Public Health Relevance

Epigenetic mechanisms alter gene function independent of DNA sequence, and have profound effects on health and disease. RNA interference impacts these mechanisms by guiding the modification of histones associated with the DNA, ensuring specificity and avoiding inappropriate gene silencing. We have found that replication of the chromosome during cell division occurs at the same time as RNA interference, and that these mechanisms interact to cause silencing. The key molecules involved are conserved from yeast to humans, and are implicated in childhood disease, mental retardation, aging and cancer. Our findings suggest that therapies that target these molecules may also impact gene expression and chromosome organization. We will investigate the underlying mechanism to determine the causes and consequences of RNAi- mediated modification of chromatin during the DNA replication phase of the cell cycle.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM076396-07
Application #
8582065
Study Section
Molecular Genetics B Study Section (MGB)
Program Officer
Carter, Anthony D
Project Start
2007-08-01
Project End
2015-11-30
Budget Start
2013-12-01
Budget End
2014-11-30
Support Year
7
Fiscal Year
2014
Total Cost
$362,003
Indirect Cost
$170,467
Name
Cold Spring Harbor Laboratory
Department
Type
DUNS #
065968786
City
Cold Spring Harbor
State
NY
Country
United States
Zip Code
11724
Pichugina, T; Sugawara, T; Kaykov, A et al. (2016) A diffusion model for the coordination of DNA replication in Schizosaccharomyces pombe. Sci Rep 6:18757
Heard, Edith; Martienssen, Robert A (2014) Transgenerational epigenetic inheritance: myths and mechanisms. Cell 157:95-109
Grand, R S; Martienssen, R; O'Sullivan, J M (2014) Potential roles for interactions between the mitochondrial and nuclear DNA throughout the cell cycle of Schizosaccharomyces pombe. Mitochondrion 17:141-9
Grand, Ralph S; Pichugina, Tatyana; Gehlen, Lutz R et al. (2014) Chromosome conformation maps in fission yeast reveal cell cycle dependent sub nuclear structure. Nucleic Acids Res 42:12585-99
Castel, Stephane E; Ren, Jie; Bhattacharjee, Sonali et al. (2014) Dicer promotes transcription termination at sites of replication stress to maintain genome stability. Cell 159:572-83
Kuscu, Canan; Zaratiegui, Mikel; Kim, Hyun Soo et al. (2014) CRL4-like Clr4 complex in Schizosaccharomyces pombe depends on an exposed surface of Dos1 for heterochromatin silencing. Proc Natl Acad Sci U S A 111:1795-800
Castel, Stephane E; Martienssen, Robert A (2013) RNA interference in the nucleus: roles for small RNAs in transcription, epigenetics and beyond. Nat Rev Genet 14:100-12
Ren, Jie; Martienssen, Robert A (2012) Silent decision: HP1 protein escorts heterochromatic RNAs to their destiny. EMBO J 31:3237-8
Zaratiegui, Mikel; Martienssen, Robert A (2012) SnapShot: small RNA-mediated epigenetic modifications. Cell 151:456-456.e1
Holmes, Allyson; Roseaulin, Laura; Schurra, Catherine et al. (2012) Lsd1 and lsd2 control programmed replication fork pauses and imprinting in fission yeast. Cell Rep 2:1513-20

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