and were primarily unmethylated in D3 cells (approximately 5% of CpG methylated)

and were primarily unmethylated in D3 cells (approximately 5% of CpG methylated). analysis is usually provided in the Materials and Methods S1 file.(DOCX) pone.0097820.s001.docx (99K) GUID:?482190EA-6050-40F0-AAEE-ED41CAEAFE88 Figure S2: ChIP analysis across three antibody concentrations for JMJD3. ChIP assays using a range of JMJD3 antibody concentrations were carried out on chromatin extracts from A) D3 mouse ES cells (was then quantified by qPCR. Binding values of non-immune IgG were subtracted from the binding values of JMJD3 antibody. The data is usually presented as the amount of DNA specifically bound relative to the total amount of DNA, expressed as a percentage. The results of an analysis of variance are stated in the text. The results are the mean and standard deviation of three impartial experiments. The results of an analysis of variance are stated in the text. Information around the materials and methods used for this analysis is usually provided in the Materials and Methods S1 file.(DOCX) pone.0097820.s002.docx (94K) GUID:?53FF838C-F331-4F6E-84F0-CAD13FBE240B Table S1: Validation of the microarry data by qRT-PCR. (PDF) pone.0097820.s003.pdf (12K) GUID:?E2EA1EC3-ED7D-424F-8DD9-A90AA0BBC2C9 Table S2: Quantitative RT-PCR primer sequences. (PDF) pone.0097820.s004.pdf (13K) GUID:?20F69090-8AFF-42B6-A068-C846312C8093 Table S3: Bisulfite PCR primer sequences. (PDF) pone.0097820.s005.pdf (8.8K) Nedocromil sodium GUID:?A46DCD9E-C0A5-46C7-BD39-EEF3E820694E Table S4: Primary antibodies and immunoglobulins used in ChIP. (PDF) pone.0097820.s006.pdf (26K) GUID:?98BE95ED-6AF8-4343-908F-3F382ED29B6E Table S5: Quantitative PCR primer sequences of gene promoters. (PDF) pone.0097820.s007.pdf (12K) GUID:?344A2BB5-C21E-409E-89CB-E69FD8E0F0B7 Table S6: Gene Ontology enrichment analysis of genes upregulated in one cell line relative to the other. (PDF) pone.0097820.s008.pdf (13K) GUID:?521C51CF-02B6-4F10-8A3F-C2F3FAAB650F Materials and Methods S1: (DOCX) pone.0097820.s009.docx (16K) GUID:?792D6B06-4420-4005-B0AE-5CF03698B367 Abstract This study assesses changes in activator and repressor modifications to histones associated with the core transcription factor genes most highly upregulated or downregulated in pancreatic -cells relative to expression in an embryonic stem cell line. Epigenetic analysis of the and (pluripotency) and and (pancreatic -cells) transcription factor genes in embryonic stem cells and a -cell line (MIN6) showed the pluripotency genes were enriched for active (histone 3 trimethylated at lysine 4 and histone 3 acetylated at lysine 9) and depleted of repressor modifications (histone 3 trimethylated at lysine 27 Rabbit polyclonal to ZBTB49 and histone 3 trimethylated at lysine 9) around the transcription start site in mouse embryonic stem cells (D3), and this was reversed in MIN6 cells. The -cell transcription factors were bivalently enriched for activating (histone 3 trimethylated at lysine 4) and repressor (histone 3 trimethylated at lysine 27) modifications in embryonic stem cells but were monovalent for the activator modification (histone 3 trimethylated at lysine 4) in the -cells. The polycomb repressor Nedocromil sodium complex 2 acts as a histone 3 lysine 27 methylase and an essential component of this complex, SUZ12, was enriched at the -cell transcription factors Nedocromil sodium in embryonic stem cells and was reduced MIN6. Knock-down of SUZ12 in embryonic stem cells, however, did not reduce the level of histone 3 trimethylated at lysine 27 at -cell transcription factor loci or break the transcriptional repression of these genes in embryonic stem cells. This study shows the reduction in the total SUZ12 level was not a sufficient cause of the resolution of the epigenetic bivalency of -cell transcription factors in embryonic stem cells. Introduction There is a marked difference in the pattern of transcription from the genome between pluripotent cells (as exemplified by embryonic stem cells (ES cells) and each of the range of differentiated cell types that make up the body [1]C[3]. The pluripotent state requires the expression of a core set of transcription factors that include NANOG, POU5F1 (hereafter known as OCT4), UTF1 and SOX2 [4], [5]. Differentiation from the pluripotent state is usually accompanied by the repression of these core transcription factors and the active expression of different sets of transcription factors. The identity and timing of expression of new transcription factors defines the lineage formed during differentiation. A range of covalent histone modifications within regulatory regions of genes are major determinants of gene expressivity [6], [7] and acetylation and methylation of specific lysine (K) residues on histone H3 have been the most extensively studied. Acetylation of H3K9 (H3K9ac) and tri-methylation of H3K4 (H3K4me3) are associated with an open, euchromatin structure that permits easier access of transcription factors and the activation of gene transcription [8]C[10]. Conversely, H3K27 and H3K9 tri-methylation (H3K27me3 and H3K9me3) generally serve as repressive chromatin modifications by the creation of a more closed conformation and these modifications are commonly associated with the formation of repressive heterochromatin [11], [12]. Genome-wide mapping.