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What are memories made of? How Polycomb and Trithorax proteins mediate epigenetic memory

Subjects

Key Points

  • The conserved Polycomb group (PcG) and Trithorax group (TrxG) proteins are transcriptional regulators, with several hundred target genes. Disruption of PcG or TrxG protein function can cause developmental defects and cancer.

  • The PcG and TrxG proteins are recruited to cis-regulatory elements called Polycomb/Trithorax response elements (PREs). The PcG and TrxG proteins act antagonistically through PREs to maintain silent and active gene expression states, respectively. These states are initiated by transcription factors that act at enhancers and are maintained by PcG and TrxG proteins at the PRE.

  • Epigenetic memory is defined as the maintenance of gene expression states through cell generations in the absence of the initiating signals. PREs were first discovered in flies, in which they can mediate epigenetic memory of both silent and active states of their associated genes. Epigenetic memory has not yet been tested for mammalian PREs.

  • Silent and activated states are each ensured by several self-reinforcing molecular mechanisms that act on chromatin and are mediated by the PcG and TrxG proteins. These include covalent modifications of chromatin, structural changes and modulation of RNA polymerase II activity. Mechanisms of silencing and activation antagonize each other.

  • During the cell cycle, replication and mitosis are the stages at which epigenetic memory is most likely to be erased. Each stage presents a different molecular challenge to memory.

  • During replication, newly assembled chromatin is acetylated and may favour an active PRE but challenge a silent one. Several PcG and TrxG proteins remain bound to replicating chromatin and may transmit memory to daughter strands.

  • During mitosis, many proteins dissociate from chromatin and transcription shuts down. This may favour a silent PRE but challenge an active one. Several PcG and TrxG proteins remain bound to mitotic chromatin and may 'bookmark' silent and active states.

  • Many PcG and TrxG target genes are dynamically regulated during development and do not display long-term epigenetic memory. For these targets, the PcG and TrxG proteins may reinforce or amplify transcriptional levels over shorter timescales. This may add robustness to gene regulation.

Abstract

In any biological system with memory, the state of the system depends on its history. Epigenetic memory maintains gene expression states through cell generations without a change in DNA sequence and in the absence of initiating signals. It is immensely powerful in biological systems — it adds long-term stability to gene expression states and increases the robustness of gene regulatory networks. The Polycomb group (PcG) and Trithorax group (TrxG) proteins can confer long-term, mitotically heritable memory by sustaining silent and active gene expression states, respectively. Several recent studies have advanced our understanding of the molecular mechanisms of this epigenetic memory during DNA replication and mitosis.

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Figure 1: PREs mediate memory during embryogenesis.
Figure 2: PREs mediate memory from embryogenesis into larval stages.
Figure 3: Memory of active transcriptional states.
Figure 4: Mechanisms of silencing and activation.
Figure 5: Replication of silent and active states in chromatin.
Figure 6: Chromatin undergoes profound changes during mitosis.
Figure 7: PREs as thresholding elements.

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Acknowledgements

The authors apologize to colleagues whose publications were not cited owing to space limitations. They would like to thank M. Rehmsmeier and members of the Ringrose laboratory for discussions and feedback during the preparation of this manuscript. P.A.S. was funded by the EU FP6 Network of Excellence, 'The Epigenome'and the EU FP7 Network of Excellence 'Epigenesys'. The L.R. laboratory is supported by the Austrian Academy of Sciences. This article is dedicated to the memory of Audrey Ringrose (23.03.1931–01.02.2014).

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Molecular components of silent and active PREs and their potential for memory. (PDF 762 kb)

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Glossary

Epigenetic memory

The maintenance of active or silent gene expression states through cell generations, without a change in DNA sequence and in the absence of the initiating signals.

Genome-wide profiling

Mapping of binding sites for proteins or sites of histone or DNA modification on a genome-wide scale. It uses tiling microarrays or high-throughput sequencing and is usually based on chromatin immunoprecipitation.

Gal4–UAS system

(Gal4–upstream activating sequence system). A dual system for gene regulation, which is mostly used in flies. The UAS is placed upstream of the gene of interest and is only activated after expression of the yeast Gal4 protein, which is placed under the control of a promoter of choice.

Bistable

A system that exhibits bistable behaviour has two extreme states that are stable, whereas intermediate states are unstable. Thus, the system can switch between these two stable states.

Polycomb repressive complex 1

(PRC1). In flies, PRC1 contains Polycomb (Pc), Posterior Sex comb (Psc), Polyhomeotic (Ph), Sex combs extra (Sce) and accessory proteins. In vertebrates, PRC1 contains chromobox homologue (CBX) proteins, B lymphoma Mo-MLV insertion region 1 homologue (BMI1), PH, RING finger protein 1A (RING1A) or RING1B, and accessory proteins. Vertebrate PRC1 proteins are highly diverse.

Polycomb repressive complex 2

(PRC2). In flies, PRC2 contains enhancer of zeste (E(z)), Suppressor of zeste 12 (SU(z)12), Extra sex combs (Esc) and Nucleosome-remodelling factor 55 kDa subunit (Nurf55; also known as Caf1). In vertebrates, PRC2 contains enhancer of zeste homologue 2 (EZH2), suppressor of zeste homologue 12 (SUZ12), embryonic ectoderm development (EED), Rb-associated protein 46 (RbAp46; also known as RBBP7), RbAp48 (also known as RBBP4) and Jumonji/ARID domain-containing protein 2 (JARID2).

Histone Lys methylation

Covalent modification of specific Lys residues of histone proteins by addition of up to three methyl groups.

Histone Lys acetylation

Covalent addition of an acetyl group to Lys residues of histones. Many Lys residues can be acetylated and, unlike methylation, acetylation changes the charge of the Lys. By masking the positive charge of Lys, acetylation reduces electrostatic interactions between DNA and histone tails, thus increasing accessibility.

Histone Lys ubiquitylation

Covalent addition of an ubiquitin molecule to Lys residues of histones. The Polycomb repressive complex 1(PRC1) monoubiquitylates histone H2A at Lys118 (Lys119 in vertebrates). This adds a large (76 amino acid) molecule to the DNA–histone interface.

FLP recombinase

A site-specific recombinase that is used to engineer specific DNA rearrangements in living organisms.

Chromatin immunoprecipitation

(ChIP). Method for detecting sites of chromatin binding. Cells or tissues are crosslinked to preserve chromatin–protein interactions, and the protein of interest is immunoprecipitated with an antibody. Quantification of the precipitated DNA by PCR or profiling methods indicates enrichments of the protein of interest.

Chromatin remodelers

Enzymes or complexes that alter nucleosomal positions, composition, conformation or presence using ATP hydrolysis, which enables changes in the accessibility of DNA to other molecules.

CREB-binding protein

(CBP). Transcriptional activator that couples chromatin remodelling to transcription factor recognition. CBP and its close relative p300 have histone acetyltransferase activity.

SET domain

(Su(var)3–9, E(z), Trx domain). A conserved 130–140 amino acid domain, which was initially characterized in the Drosophila melanogaster proteins Suppressor of variegation 3–9 (Su(var)3–9), Enhancer of zeste (E(z)) and Trithorax (Trx). These and other SET domains have histone methyltransferase activity with different specificities and may also methylate non-histone proteins.

Nucleosomes

The basic packaging units of DNA. These consist of two copies each of histones H2A, H2B, H3 and H4 that are wrapped by 147 bp of DNA, which passes 1.67 times around the histone octamer.

Bivalent chromatin

Bivalent chromatin contains histone modifications that are catalysed by both activators (trimethylated Lys4 of histone 3 (H3K4)) and repressors (trimethylated H3K27). It is thought to be 'poised' to become stably activated or repressed after differentiation when one of the marks is removed.

Elutriation

A process for separating particles on the basis of their size, shape and density. Cell cultures can be fractionated into cells that are in G1, S phase, and G2 or M phase, which have increasingly large size. Elutriation bypasses the drug treatments that are required for cell synchronization.

Chromodomain

(Chromatin organization modifier domain). A conserved domain of 60 amino acids, which was originally identified in Drosophila melanogaster proteins that modify variegation. Different chromodomains bind to specifically modified histone tails and/or RNA.

H3–H4 tetramers

H3 and H4 histones are assembled into new chromatin as an H3–H4 tetramer.

H2A–H2B dimers

H2A and H2B histones are assembled into new chromatin as two H2A–H2B dimers per nucleosome.

Cdc2–cyclin B kinase

Cdc2 is a cyclin-dependent kinase which, as a heterodimer with cyclin B, is responsible for the execution of the M phase of the cell cycle.

FRAP

(Fluorescene recovery after photobleaching). A method for determining kinetic parameters of fluorescently tagged proteins in living cells. The speed with which fluorescent proteins move into a region in which fluorescence has been bleached provides information on binding and diffusion behaviour.

Residence time

Average time that a given molecule spends in an interaction. For proteins, residence time can be extracted from fluorescence recovery after photobleaching (FRAP) experiments and is inversely proportional to the dissociation rate.

Heterochromatin protein 1

(HP1). An essential component of heterochromatin in fission yeast (Swi6), mammals (HP1) and Drosophila melanogaster (HP1). It contains a chromodomain (chromatin organization modifier domain) that specifically binds to methylated Lys9 of histone H3.

Reprogramming by nuclear transfer

Somatic cell nuclei are introduced into enucleated cells of a different identity. This can erase epigenetic memory and alter the identity of the donor nucleus.

H3.3

A variant of histone H3, which is expressed throughout the cell cycle and is incorporated into chromatin independently of replication, for example at sites of active transcription. H3.3 and H3 differ by only four amino acids.

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Steffen, P., Ringrose, L. What are memories made of? How Polycomb and Trithorax proteins mediate epigenetic memory. Nat Rev Mol Cell Biol 15, 340–356 (2014). https://doi.org/10.1038/nrm3789

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