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In ES cells, many known PRC targets are differentiation genes and PRC target specificity is conferred by cell-type-specific transcription factors such as JARID2.
Still, in most of the PRC target loci in ES cells, the activating H3K4me3 mark is also present.
The polycomb (PRC) complex is responsible for deposition of H3K27me3, and, in HSCs, PRC target genes often succumb to age-related DNA methylation (Sun et al., 2014a).
EZH2 also interacts with Dnmts, and another PRC2 protein, EED, interacts with HDAC1 and HDAC2 (3); both are necessary for a stable repressive state for PRC target gene promoters (6, 7).
Weinberg and associates [ 23] observed that the target genes of PRC are also repressed in various human cancers, and that the repression of PRC target genes also predicts poorly differentiated human tumors.
When these data sets were tested using expression profiling data sets from human cancer patients, the activation of ES-cell-specific gene sets (such as ES-expressed) and the repression of PRC target genes were significantly enriched in poorly differentiated human tumors.
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At active PRC targets, PRCs are also tightly interlinked with unproductive RNAPII-S5p complexes.
At silent developmental PRC targets, PRCs are tightly interlinked with RNAPII-S5p complexes at promoters and throughout coding regions, which produce transcripts that do not mature into mRNA, and from which protein is not produced.
The range of expression levels at PRC targets suggests that PRCs do not act as absolute silencers, but may regulate the extent of RNAPII transcriptional activity, as described in Drosophila (Enderle et al., 2011; Schwartz and Pirrotta, 2008).
Functional PRC-mediated repression of active PRC targets was confirmed, as the same proportion (∼30%) of PRCa and PRCr genes show substantial derepression after Ring1B knockout (p < 10−54, one-tailed Fisher's exact test; Figure 6A).
We show that this group of PRC targets switches between active and PRC-repressed states within the ESC population, and that many have roles in metabolism.
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