High fidelity epigenetic inheritance: Information theoretic model predicts threshold filling of histone modifications post replication

During cell devision, maintaining the epigenetic information encoded in histone modification patterns is crucial for survival and identity of cells. The faithful inheritance of the histone marks from the parental to the daughter strands is a puzzle, given that each strand gets only half of the paren...

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Bibliographic Details
Published in:PLoS computational biology 2022-02, Vol.18 (2), p.e1009861-e1009861
Main Authors: Ramakrishnan, Nithya, Pillai, Sibi Raj B, Padinhateeri, Ranjith
Format: Article
Language:English
Subjects:
Algorithms
Biology and Life Sciences
Cell survival
Chromatin
Communication theory
Deoxyribonucleic acid
DNA
DNA biosynthesis
DNA replication
DNA Replication - genetics
Earth Sciences
Enzymes
Epigenesis, Genetic - genetics
Epigenetic inheritance
Epigenetics
Gene expression
Genetic aspects
Genetic research
Heredity
Histone Code - genetics
Histones
Histones - genetics
Histones - metabolism
Information theory
Inheritance Patterns
Markov analysis
Noise
Nucleosomes
Nucleosomes - genetics
Parameter modification
Physical Sciences
Proteins
Replication
Research and Analysis Methods
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Summary:During cell devision, maintaining the epigenetic information encoded in histone modification patterns is crucial for survival and identity of cells. The faithful inheritance of the histone marks from the parental to the daughter strands is a puzzle, given that each strand gets only half of the parental nucleosomes. Mapping DNA replication and reconstruction of modifications to equivalent problems in communication of information, we ask how well enzymes can recover the parental modifications, if they were ideal computing machines. Studying a parameter regime where realistic enzymes can function, our analysis predicts that enzymes may implement a critical threshold filling algorithm which fills unmodified regions of length at most k. This algorithm, motivated from communication theory, is derived from the maximum à posteriori probability (MAP) decoding which identifies the most probable modification sequence based on available observations. Simulations using our method produce modification patterns similar to what has been observed in recent experiments. We also show that our results can be naturally extended to explain inheritance of spatially distinct antagonistic modifications.
ISSN:1553-7358
1553-734X
1553-7358
DOI:10.1371/journal.pcbi.1009861