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The association of NFI with boundaries suggested that it may indeed contribute to the formation of chromatin barriers, but that its binding may not be sufficient to promote boundaries at all genomic loci, as occupied binding sites also occur within chromatin domains.
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Nonetheless, these observations strongly suggest that the IR-L element can promote boundary activity.
Our analysis using our synthetic reporter tool suggested that two parallel pathways to promote boundary function of the IR element.
We conclude that Epe1 and TFIIIC to work in two parallel pathways to promote boundary function of the IR elements.
Although validating that the endogenous IR element requires the two redundant pathways to promote boundary activity, we discovered that the function of a single boundary is essential for normal cell growth.
These observations indicate that redundant pathways promote boundary functions to ensure proper cell growth by suppressing the intrinsic toxicity of heterochromatin spread that can be produced from the inactivation of a single boundary.
These faint phenotypes could be due to the fact that heterochromatin induced in our system is intrinsically too weak to spread over the IR-L element or that Epe1 and TFIIIC work in two redundant pathways to promote boundary function.
TFIIIC-binding sites have been reported to promote boundary activity of both the tRNA gene cluster of the inner centromere and of the IR element (Noma et al. 2006).
When a 1.1-kb DNA fragment containing the IRC sequence element from the left boundary of cen1+ was placed into the reporter construct, there was no change in the amount of growth on YS+5-FOA compared with the reporter without an insert, indicating that IRC element does not promote boundary function in this system.
Experimental response: ChIP-seq for CP190 in mixed cells and parasegment 7. Location in revised manuscript: Figure 2 Since CP190 is in a protein complex with CTCF and can alter local chromatin structure in a way that may promote boundary function, we thought it would be a worthwhile target of investigation.
We also use the system to demonstrate that HP1/Swi6 promotes boundary activity in addition to promoting silencing and acts in the same pathway as Epe1.
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