New and Old Histones in Epigenetic Cell Memory

Project Information

HISTONEMEMORY

Grant agreement ID: 724436

DOI

10.3030/724436

Project closed

EC signature date 13 March 2017

Start date 1 May 2017

End date 30 April 2022

Funded under

• EXCELLENT SCIENCE - European Research Council (ERC)

Total cost

€ 1 999 750,00

EU contribution

€ 1 999 750,00

Coordinated by

KOBENHAVNS UNIVERSITET
Denmark

Periodic Reporting for period 4 - HISTONEMEMORY (New and Old Histones in Epigenetic Cell Memory)

Reporting period: 2021-11-01 to 2022-04-30

Summary of the context and overall objectives of the project

Cell type specific organization of DNA into chromatin is an important determinant of gene expression and cell identity. During cell division, epigenetic information in chromatin must be transmitted to daughter cells in order to maintain cell identity or commit to a developmental program. However, it remains unknown how epigenetic states are inherited during cell division. Elucidating molecular mechanisms underlying epigenetic cell memory thus represents a major challenge in biology critical to understand development and disease.
Chromatin undergoes genome-wide disruption during DNA replication and histone marks are diluted 2-fold due to new histone deposition. Yet, how this impacts on establishment and maintenance of gene expression programs is not known. We hypothesize that chromatin replication represents a critical window for epigenetic cell memory and cell fate decisions, and predict that three histone-based processes play critical roles in guarding cell identity: 1) new histone deposition to regulate nucleosome occupancy and transcription factor (TF) binding, 2) accurate transmission of old modified histones by dedicated recycling machinery, and 3) recruitment of regulatory proteins to new and old histones to direct epigenome maintenance. To dissect these events mechanistically and test causal roles in cell fate decisions, we have set up a research program integrating explorative proteomics and histone chaperone structure-function analysis with stem cell biology and new cutting-edge genomic tools developed by my research group. We have identified novel mechanisms in chromatin assembly and histone inheritance, and revealed that inheritance of histone modifications plays a critical role maintaining normal genome regulation and supporting embryonic differentiation.

Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far

We have discovered that MCM2, part of the replicative helicase, is responsible for segregation of parental histones to lagging strand and ensuring balanced transmission of histone post-translational modifications (PTMs) to both DNA strands (Petryk et al., 2018, Science). Using mouse ES cells expressing MCM2 histone binding mutants as a powerful and unique tool, we have revealed a critical role of histone-based inheritance in genome regulation and cell fate decisions.
We have uncovered a new histone chaperone DNAJC9 and identified its dual functionality as a molecular chaperone and histone chaperone that facilitates histone transactions in different cellular environments (Hammond et al., 2021, Mol Cell). This work demonstrates that heat shock molecular chaperones support histone supply chains from synthesis to deposition.
In a structure-function study of the NASP histone chaperone, we characterize two distinct histone binding modes and reveal the molecular basis for how NASP protects soluble histones from degradation (Bao, Carraro et al., Nucleic Acis Res 2022).

Progress beyond the state of the art and expected potential impact (including the socio-economic impact and the wider societal implications of the project so far)

Our research has provided a major advance in understanding epigenetic cell memory by 1) identifying novel mechanisms of histone chaperoning and deposition, and 2) addressing how the inheritance of histone modifications during DNA replication impacts gene regulation and cell fate decisions.

Figure for publishable summary