To examine whether the hsi2-4-dependent changes in histone methylation marks are associated with both the Kan R and Kan S transgene loci, ChIP-qPCR analyses were performed on various regions of the endogenous GSTF8 gene and the GSTF8 LUC transgene in Kan R, Kan S, hsi2-4-Kan R and hsi2-4-Kan seedlingsgseedlings
Furthermore, fundamental differences exist between single-locus ChIP approaches and ChIP-chip experiments, and these differences require new methods of analysis.
When we compared our findings to other reports of genome-wide location analysis for ERα in MCF7 cells, we similarly found no evidence for recruitment of ERα to the PCNA gene locus using ChIP-on-chip or alternative genomic approaches such as ChIP-DSL and ChIP-PET [44], [70], [71].
We were, however, not able to map Piwi specifically to target loci using ChIP experiments.
DOI: http://dx.doi.org/10.7554/eLife.06671.013 10.7554/eLiFigure71.014 Figure 6 figure supplement 2. ChIP-PCR assays for selected flowering genes and heterochromatic loci confirm ChIP-qPCR.
3. Further investigations, such as protein interaction assessment with ATR and mapping FMRP chromatin loci with ChIP-seq, will provide deeper insight of FMRP nuclear function.
There is an overemphasis on locus-specific ChIP studies that lacked measures of statistical significance.
The 'chip_loci' table stores identified YY1-binding loci from ChIP-based experiments and related annotations such as the number of predicted motifs within each locus, the nearest genes and so forth.
In order to study the kinetics of Stat6 binding to lysosomal loci, Stat6 ChIP-seq peaks from different time points after IL-4 addition were aligned to genomic maps of the genes whose mRNA levels were analyzed in Figure 6.
A ChIPseq analysis performed by Farnham and co-workers [19] and a locus-specific ChIP performed in this study show the binding of KAP1 to the TNDM1 ICR and in vitro binding assays demonstrate that this sequence is indeed able to bind hZFP57 if methylated.
Next, we investigated the allele specificity of the conserved histone variant H2A.Z at the DLGAP4 locus using ChIP, followed by bisulfite allelic sequencing in two carriers and found unexpectedly that the H2A.Z antibody enriched specifically for the undisrupted and hypo/unmethylated DLGAP4 allele (chr20) in translocation carriers (Fig. 3B and C).
