HEROIC (High-throughput Epigenetic Regulatory Organisation In Chromatin) 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|
|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
|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)|
The HEROIC project is funded by a European Commission FP6 grant. More details, including a participants list, can be found on the HEROIC website.