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RAPID SIGNED

Chromatin dynamics resolved by rapid protein labeling and bioorthogonal capture

Total Cost €

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EC-Contrib. €

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Partnership

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 RAPID project word cloud

Explore the words cloud of the RAPID project. It provides you a very rough idea of what is the project "RAPID" about.

epigenetic    polycomb    descriptions    sequencing    division    rules    heterochromatin    cycle    readouts    linked    time    labeling    model    cells    eukaryotic    propensity    chase    landscape    interstitial    multitude    experiments    seq    epigenomic    suited    functionally    protein    lineage    proteins    maintained    genome    packaging    mesc    genetics    domains    occupancy    chromatin    combination    minutes    uniquely    histone    days    dimensional    signals    spectrometry    gene    relative    termed    evolution    regulated    dimension    microscopy    cellular    expression    selective    stability    pioneers    mass    integrates    epigenomics    pluripotency    mouse    propagation    memory    little    embryonic    stable    modulated    inheritance    fast    chip    pluripotent    sensitive    cell    population    developmentally    dynamic    ranging    rapid    heritable    stem    specification    capturing    marks    fundamental    replication    pulse    gen    snapshots    employ    flexible    form    collect    dynamics    resolved    period    introduces    coupled    modification   

Project "RAPID" data sheet

The following table provides information about the project.

Coordinator
KAROLINSKA INSTITUTET 

Organization address
address: Nobels Vag 5
city: STOCKHOLM
postcode: 17177
website: www.ki.se

contact info
title: n.a.
name: n.a.
surname: n.a.
function: n.a.
email: n.a.
telephone: n.a.
fax: n.a.

 Coordinator Country Sweden [SE]
 Total cost 1˙846˙360 €
 EC max contribution 1˙846˙360 € (100%)
 Programme 1. H2020-EU.1.1. (EXCELLENT SCIENCE - European Research Council (ERC))
 Code Call ERC-2016-STG
 Funding Scheme ERC-STG
 Starting year 2017
 Duration (year-month-day) from 2017-01-01   to  2021-12-31

 Partnership

Take a look of project's partnership.

# participants  country  role  EC contrib. [€] 
1    KAROLINSKA INSTITUTET SE (STOCKHOLM) coordinator 1˙846˙360.00

Map

 Project objective

Histone proteins provide a dynamic packaging system for the eukaryotic genome. Chromatin integrates a multitude of signals to control gene expression, only some of which have the propensity to be maintained through replication and cell division. For our understanding of cellular memory and epigenetic inheritance we need to know what features characterize a stable, heritable chromatin state throughout the cell cycle. State-of-the-art methods such as ChIP-Seq provide population-based snapshots of the epigenomic landscape but little information on the stability and relative importance of each studied feature or modification. This project pioneers a rapid, sensitive and selective protein labeling method (termed RAPID) for capturing genome-wide chromatin dynamics resolved over a period of time ranging from minutes to days. RAPID introduces a flexible time dimension in the form of pulse or pulse-chase experiments for studying genome-wide occupancy of a protein of interest by next-gen sequencing. It can also be coupled to other readouts such as mass spectrometry or microscopy. RAPID is uniquely suited for studying cell cycle-linked processes, by defining when and where stable ‘marks’ are set in chromatin. I will employ mouse embryonic stem cell (mESC) as a model system for pluripotency and lineage specification. RAPID will define fundamental rules for inheritance of histone and other chromatin-associated proteins and how they are modulated by the fast cell cycle of pluripotent cells. Using RAPID in combination with other state-of-the art genetics and epigenomics, I will collect multi-dimensional descriptions of the dynamic evolution and propagation of functionally relevant chromatin states, such as interstitial heterochromatin and developmentally regulated Polycomb domains.

 Publications

year authors and title journal last update
List of publications.
2018 Birthe Meineke, Johannes Heimgärtner, Lorenzo Lafranchi, Simon J Elsässer
Methanomethylophilus alvus Mx1201 provides basis for mutual orthogonal pyrrolysyl tRNA/aminoacyl-tRNA synthetase pairs in mammalian cells
published pages: , ISSN: , DOI: 10.1101/371757
BioRxiv Preprint 2019-06-13
2019 Banushree Kumar, Simon J Elsässer
Quantitative multiplexed ChIP reveals global alterations that shape promoter bivalency in ground state embryonic stem cells
published pages: , ISSN: , DOI: 10.1101/557082
BioRxiv Preprint 2019-08-29
2018 Birthe Meineke, Johannes Heimgärtner, Lorenzo Lafranchi, Simon J. Elsässer
Methanomethylophilus alvus Mx1201 Provides Basis for Mutual Orthogonal Pyrrolysyl tRNA/Aminoacyl-tRNA Synthetase Pairs in Mammalian Cells
published pages: 3087-3096, ISSN: 1554-8929, DOI: 10.1021/acschembio.8b00571
ACS Chemical Biology 13/11 2019-08-29

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