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Chromatin3D SIGNED

Chromatin Dynamics in Development and Disease

Total Cost €

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EC-Contrib. €

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Partnership

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Project "Chromatin3D" data sheet

The following table provides information about the project.

Coordinator
IDRYMA TECHNOLOGIAS KAI EREVNAS 

Organization address
address: N PLASTIRA STR 100
city: IRAKLEIO
postcode: 70013
website: www.forth.gr

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 Greece [EL]
 Project website http://www.chromatin3d.eu/
 Total cost 3˙782˙583 €
 EC max contribution 3˙782˙583 € (100%)
 Programme 1. H2020-EU.1.3.1. (Fostering new skills by means of excellent initial training of researchers)
 Code Call H2020-MSCA-ITN-2014
 Funding Scheme MSCA-ITN-ETN
 Starting year 2015
 Duration (year-month-day) from 2015-01-01   to  2018-12-31

 Partnership

Take a look of project's partnership.

# participants  country  role  EC contrib. [€] 
1    IDRYMA TECHNOLOGIAS KAI EREVNAS EL (IRAKLEIO) coordinator 969˙547.00
2    KAROLINSKA INSTITUTET SE (STOCKHOLM) participant 527˙318.00
3    AvantiCell Science Ltd UK (AYR) participant 273˙287.00
4    THE UNIVERSITY OF EDINBURGH UK (EDINBURGH) participant 273˙287.00
5    WEIZMANN INSTITUTE OF SCIENCE IL (REHOVOT) participant 260˙300.00
6    DIAGENODE BE (SERAING) participant 250˙560.00
7    LUDWIG-MAXIMILIANS-UNIVERSITAET MUENCHEN DE (MUENCHEN) participant 249˙216.00
8    MOSAIQUES DIAGNOSTICS GMBH DE (HANNOVER) participant 249˙216.00
9    FUNDACIO INSTITUT D'INVESTIGACIO BIOMEDICA DE BELLVITGE ES (L'HOSPITALET DE LLOBREGAT) participant 247˙872.00
10    UD-GENOMED MEDICAL GENOMIC TECHNOLOGIES KUTATAS-FEJLESZTESI ES SZOLGALTATO KFT HU (DEBRECEN) participant 223˙913.00
11    FONDAZIONE ISTITUTO ITALIANO DI TECNOLOGIA IT (GENOVA) participant 164˙872.00
12    ISTITUTO EUROPEO DI ONCOLOGIA SRL IT (MILANO) participant 93˙188.00
13    BIOMEDICAL SCIENCES RESEARCH CENTER ALEXANDER FLEMING EL (VARI-ATHENS) participant 0.00
14    EXIQON AS DK (VEDBAEK) partner 0.00
15    LIFEGLIMMER GMBH DE (BERLIN) partner 0.00
16    SB Science Management UG DE (BERLIN) partner 0.00
17    YELLOW RESEARCH NL (AMSTERDAM) partner 0.00

Map

 Project objective

The cell nucleus is organized and compartmentalized into a highly ordered structure that contains DNA, RNA, chromosomal and histone proteins which make up a structure called chromatin. The dynamics associated with these various components are responsible for regulating physiological processes and the overall stability of the genome. The destabilization of such regulatory mechanisms that act on the chromatin structure are implicated in pathologies such as cancer. Higher order organization of chromatin results in chromosomes which occupy discrete territories within the cell nucleus. Most nuclear processes occur or at least being initiated onto the chromosomes which makes them the main organizing factors in the nucleus. Several proteins that are involved in the replication of DNA, gene transcription and the processing of RNA are found enriched in discrete focal structures. An emerging question is how these structures assemble and are maintained in the absence of membranes and moreover what are the kinetics of stable binding and/or rapid exchange of their components. The dynamic assembly and modification of chromatin during developmental processes as well as the deregulation of such chromatin dynamics during the onset of disease lacks mechanistic insights at present. To address these questions we have put forward a multidisciplinary approach which involves molecular, cellular and systems level approaches by assembling a group of scientists from academia and industry with cross disciplinary expertise and capabilities.

 Deliverables

List of deliverables.
I. Scientific writing and presentation course Other 2020-03-17 11:29:12
Podcasts & Videocasts Websites, patent fillings, videos etc. 2020-03-17 11:29:11
Visits and secondments of ESRs Other 2020-03-17 11:29:11
Workshop 4: “Epigenetic modifiers and genome integrity” Other 2020-03-17 11:29:12
Bioethics Course Other 2020-03-17 11:29:11
Final Network Conference Other 2020-03-17 11:29:12
Attendance of ESRs in international conferences & symposia Other 2020-03-17 11:29:11
Workshop 2: “Cancer Epigenomics” Other 2020-03-17 11:29:11
Business and entrepreneurship course Other 2020-03-17 11:29:11
Workshop 3: “Developmental Programming and Reprogramming” Other 2020-03-17 11:29:11
Project Management course Other 2020-03-17 11:29:09
1st Chromatin3D Summer School Other 2020-03-17 11:29:09
Open Lab Day Other 2020-03-17 11:29:09
Workshop 1: “Folding chromatin in Three Dimensions” Other 2020-03-17 11:29:09
Facebook Chromatin3D page Websites, patent fillings, videos etc. 2020-03-17 11:29:09
Chromatin3D Newsletter Websites, patent fillings, videos etc. 2020-03-17 11:29:10
Communication course Other 2020-03-17 11:29:09
Recruitment of ESRs Other 2020-03-17 11:29:09
Chromatin3D website Websites, patent fillings, videos etc. 2020-03-17 11:29:09
International Course on Laboratory Animal Science Other 2020-03-17 11:29:09

Take a look to the deliverables list in detail:  detailed list of Chromatin3D deliverables.

 Publications

year authors and title journal last update
List of publications.
2019 Pierbruno Ricci, Pedro Magalhães, Magdalena Krochmal, Martin Pejchinovski, Erica Daina, Maria Rosa Caruso, Laura Goea, Iwona Belczacka, Giuseppe Remuzzi, Muriel Umbhauer, Jens Drube, Lars Pape, Harald Mischak, Stéphane Decramer, Franz Schaefer, Joost P. Schanstra, Silvia Cereghini, Petra Zürbig
Urinary proteome signature of Renal Cysts and Diabetes syndrome in children
published pages: 9:2225, ISSN: 2045-2322, DOI: 10.1038/s41598-019-38713-5
Scientific Reports 9/1 2020-03-17
2018 Zelenka T.
Prostorová organizace chromatinu (3D chromatin organization)
published pages: Vesmír 97, 34, , ISSN: , DOI:
VESMIR Vesmír 97, 34, 2018/1 2020-03-17
2019 David Marx, Jochen Metzger, Jérôme Olagne, Iwona Belczacka, Stanislas Faguer, Magali Colombat, Holger Husi, William Mullen, Wilfried Gwinner, Sophie Caillard
Proteomics in Kidney Allograft Transplantation-Application of Molecular Pathway Analysis for Kidney Allograft Disease Phenotypic Biomarker Selection
published pages: 1800091, ISSN: 1862-8346, DOI: 10.1002/prca.201800091
PROTEOMICS - Clinical Applications 1800091C 2020-03-17
2018 Iwona Belczacka, Martin Pejchinovski, Magdalena Krochmal, Pedro Magalhães, Maria Frantzi, William Mullen, Antonia Vlahou, Harald Mischak, Vera Jankowski
Urinary Glycopeptide Analysis for the Investigation of Novel Biomarkers
published pages: 1800111, ISSN: 1862-8346, DOI: 10.1002/prca.201800111
PROTEOMICS - Clinical Applications 18 October 2018 2020-03-17
2018 Daphna Rothschild, Omer Weissbrod, Elad Barkan, Alexander Kurilshikov, Tal Korem, David Zeevi, Paul I. Costea, Anastasia Godneva, Iris N. Kalka, Noam Bar, Smadar Shilo, Dar Lador, Arnau Vich Vila, Niv Zmora, Meirav Pevsner-Fischer, David Israeli, Noa Kosower, Gal Malka, Bat Chen Wolf, Tali Avnit-Sagi, Maya Lotan-Pompan, Adina Weinberger, Zamir Halpern, Shai Carmi, Jingyuan Fu, Cisca Wijmenga, Alexandra Zhernakova, Eran Elinav, Eran Segal
Environment dominates over host genetics in shaping human gut microbiota
published pages: 210-215, ISSN: 0028-0836, DOI: 10.1038/nature25973
Nature 555/7695 2020-03-17
2018 Stavros Bashiardes, Anastasia Godneva, Eran Elinav, Eran Segal
Towards utilization of the human genome and microbiome for personalized nutrition
published pages: 57-63, ISSN: 0958-1669, DOI: 10.1016/j.copbio.2017.11.013
Current Opinion in Biotechnology 51 2020-03-17
2018 David Marx, Jochen Metzger, Martin Pejchinovski, Ryan Bruce Gil, Maria Frantzi, Agnieszka Latosinska, Iwona Belczacka, Silke Sophie Heinzmann, Holger Husi, Jerome Zoidakis, Matthias Klingele, Stefan Herget-Rosenthal
Proteomics and Metabolomics for AKI Diagnosis
published pages: 63-87, ISSN: 0270-9295, DOI: 10.1016/j.semnephrol.2017.09.007
Seminars in Nephrology 38/1 2020-03-17
2018 David J. Hanly, Manel Esteller, María Berdasco
Interplay between long non-coding RNAs and epigenetic machinery: emerging targets in cancer?
published pages: 20170074, ISSN: 0962-8436, DOI: 10.1098/rstb.2017.0074
Philosophical Transactions of the Royal Society B: Biological Sciences 373/1748 2020-03-17
2017 Iwona Belczacka, Agnieszka Latosinska, Jochen Metzger, David Marx, Antonia Vlahou, Harald Mischak, Maria Frantzi
Proteomics biomarkers for solid tumors: Current status and future prospects
published pages: 49-78, ISSN: 0277-7037, DOI: 10.1002/mas.21572
Mass Spectrometry Reviews 38/1 2020-03-17
2019 Zeevi, D., Korem T., Godneva, A., Bar, N. ,Segal, E
Structural variation in the gut microbiome associates with host health
published pages: , ISSN: 1476-4687, DOI: 10.1038/s41586-019-1065-y
Nature 27 March 2019 2020-03-17
2018 1) Belczacka I, Latosinska A, Frantzi M, and Harald Mischak H.
“Urinary CE-MS Peptide Marker Pattern for Detection of Solid Tumors – Beyond the Abstract”
published pages: May 10 2018, ISSN: , DOI:
UROTODAY May 10 2018 2020-03-17
2018 Maria Frantzi, Agnieszka Latosinska, Iwona Belczacka, Harald Mischak
Urinary proteomic biomarkers in oncology: ready for implementation?
published pages: 49-63, ISSN: 1478-9450, DOI: 10.1080/14789450.2018.1547193
Expert Review of Proteomics 16/1 2020-03-17
2018 Zsolt Czimmerer, Attila Horvath, Bence Daniel, Gergely Nagy, Ixchelt Cuaranta-Monroy, Mate Kiss, Zsuzsanna Kolostyak, Szilard Poliska, Laszlo Steiner, Nikolas Giannakis, Tamas Varga, Laszlo Nagy
Dynamic transcriptional control of macrophage miRNA signature via inflammation responsive enhancers revealed using a combination of next generation sequencing-based approaches
published pages: 14-28, ISSN: 1874-9399, DOI: 10.1016/j.bbagrm.2017.11.003
Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms 1861/1 2020-03-17
2018 Iwona Belczacka, Agnieszka Latosinska, Justyna Siwy, Jochen Metzger, Axel S. Merseburger, Harald Mischak, Antonia Vlahou, Maria Frantzi, Vera Jankowski
Urinary CE-MS peptide marker pattern for detection of solid tumors
published pages: 8:5227, ISSN: 2045-2322, DOI: 10.1038/s41598-018-23585-y
Scientific Reports 8/1 2020-03-17
2019 Attila Horvath, Bence Daniel, Lajos Szeles, Ixchelt Cuaranta-Monroy, Zsolt Czimmerer, Lilla Ozgyin, Laszlo Steiner, Mate Kiss, Zoltan Simandi, Szilard Poliska, Nikolas Giannakis, Emanuele Raineri, Ivo G Gut, Benedek Nagy, Laszlo Nagy
Labelled regulatory elements are pervasive features of the macrophage genome and are dynamically utilized by classical and alternative polarization signals
published pages: 2019 1, ISSN: 0305-1048, DOI: 10.1093/nar/gkz118
Nucleic Acids Research 2019 1 2020-03-17
2017 Alessandro Scacchetti, Laura Brueckner, Dhawal Jain, Tamas Schauer, Xu Zhang, Frank Schnorrer, Bas van Steensel, Tobias Straub, Peter B Becker
CHRAC/ACF contribute to the repressive ground state of chromatin
published pages: e201800024, ISSN: 2575-1077, DOI: 10.26508/lsa.201800024
Life Science Alliance 1/1 2020-03-17
2016 Stratigi K, Chatzidoukaki O, Garinis GA.
DNA damage-induced inflammation and nuclear architecture
published pages: , ISSN: 0047-6374, DOI: 10.1016/j.mad.2016.09.008
Mechanisms of Ageing and Development 2020-03-17

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