The HEROIC Project

High-throughput Epigenetic Regulatory Organisation In Chromatin

HEROIC Logo HEROIC is an Integrated Project supported by a grant from the European Commission as part of the sixth Framework programme (FP6). HEROIC encompasses 13 established research groups, from 8 European countries (The Netherlands, Austria, Sweden, Germany, United Kingdom, Belgium, Spain and France) all striving to further strengthen epigenetic research.

Epigenetics is the study of reversible heritable changes in gene function that occur without a change in the sequence of DNA. The basic unit of the chromatin is the nucleosome, a nucleoprotein complex containing approximately 147 base pairs of DNA wrapped around an octamer of histones. This octamer comprises a central core of Histone H3 and Histone H4 heterodimers and an outer core of Histone H2A and Histone H2B heterodimers. Each nucleosome is linked to the next by small strands of linker DNA.

The 3D structure of chromatin modulates the accessibility and recruitment of regulatory factors to the underlying DNA and is therefore critical to gene expression regulation. The 3D structure of the chromatin may be altered in its components by, for example, the presence of repressors, activators, chromatin remodeling complexes, and/or incorporation of histone variants. Moreover, the DNA itself can be covalently modified by methylation at cytosine residues and histone tails can be post-translationally modified, e.g. acetylation, methylation, ubiquitylation etc. Understanding epigenetics will have an impact on our understanding of human disease, cancer, ageing and stem cells.

The main body of the HEROIC consortium investigation was performed in Mouse. The resultant data sets are catalogued in the following table:

Data Set Details
Lab Data Set Type PubMed Status Archive/Browser
Barlow MEF H3ac, H4ac, H4K20me1, H3K27me3, H3K9me3, H4K20me3, H3K4me2, H3K4me3 and H3K9ac ChIP-Chip 19047520 Complete GSE11335
Stunnenburg ES cells Histone modifications (X chromosome inactivation) ChIP-Chip 19581487 Complete GSE15814
Stunnenburg HeLa cells GFP fusion proteins ChIP-Seq Manuscript under revision GSE20303
Stunnenburg HeLa cells GFP fusion proteins ChIP-Seq Under analysis
Stunnenburg ES cells Transcription Factors (Suz12, Ezh2 and Ring1b) X chromosome inactivation ChIP-Seq Under analysis
Stunnenburg ES cells H3K9me3, SetDB1 KO ChIP-Seq Under analysis
Stunnenburg ES cells RNA profiling during X-inactivation RNA-Seq Under analysis
Stunnenburg ES cells MLL KO; H3K4me3 and H3K27me3 ChIP-Seq Manuscript in preparation
Stunnenburg ES cells MLL KO; expression profiling RNA-Seq Manuscript in preparation
Stunnenburg ES cells Arid1a KO; H3K9/14Ac profiling ChIP-Seq Under analysis
Stunnenburg ES cells RNA-Seq Imprinted genes RNA-Seq Under analysis
Graf A robust and highly efficient immune cell reprogramming system. Expression 19896445 Complete GSE17316
Beck Mouse tissue methylation (Batman) profiles for DRG, E14, HB_SC, Heart, Kidney, Limbs, Liver, NSC, SC, Skeletal muscle, Spleen. Medip-ChIP Complete Ensembl
Beck Mouse age methylation (Batman) profiles taken at age 80 and 450, 3 replicates. Medip-ChIP Complete Ensembl
Beck 18 methylomes of Mouse ES & NP TDG heterozygotes and knockouts Medip-Seq Manuscription in preparation GSE27468
Ensembl/UCSC
Beck Methylation profiling of human spermatozoa Medip-Seq 18612301 Complete E-TABM-482
Beck DNA methylation reference profiles of 13 normal somatic tissues, placenta, sperm, and an immortalized cell line Medip-ChIP 18577705 Complete E-TABM-445
Beck MeDIP-seq methylomes of malignant peripheral nerve sheath tumours (MPNST), benign Neurofibromas and normal Schwann cells Medip-Seq 21324880 Complete GSE21714
Epigenomics AG DNA Differential Methylation Hybridisation, adult mouse tissue, fetal mouse tissue, stem cells DMH Manuscript in preparation TSV files (FTP)

Acknowledgements

EU LogoThe HEROIC project is funded by a European Commission FP6 grant. More details, including a participants list, can be found on the HEROIC website.

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