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Our genetic analyses of these phenomena lead us to propose that DDM1-dependent maintenance of silent chromatin, and Pol IV-dependent RNA silencing are overlapping processes that repress aberrant 5S rDNA transcription and contribute to 5S rDNA heterochromatic organization.
Analysis of 5S aberrant transcripts revealed that 5S LT1 accumulates to higher levels in nrpd1 ddm1 and rdr2 doubleouble mutants than in ddm1 alone; this indicates that both DDM1 maintenance of silent chromatin and siRNA-dependent silencing contribute to suppression of aberrant transcripts (Figure 3B).
Another HDAC candidate of interest is Sir2, an HDAC critical for establishment and maintenance of silent chromatin [reviewed in Rusche et al. (2003)].
Histone methylations such as H3 K9, H3 K27, and H4 K20 are mainly involved in the formation and maintenance of silent heterochromatin state, whereas methylations at H3 K4, H3 K36, and H3 K79 are associated with actively transcribing euchromatic regions.
Esc2, a member of a conserved family of proteins that contain SUMO-like domains, interacts with Sir2 through a SUMO-binding motif and is required for the maintenance of silent chromatin structure at rDNA [ 82].
In C. albicans, deletion of one copy of SIR2 affects the rDNA silencing (Fig. 4C), indicating that like S. cerevisiae, Candida SIR2 is involved in the maintenance of silent chromatin.
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In the case of the Igf2r gene, this DNA methylation mark is not necessary for initiation or maintenance of the silent state but seems to play a role in re-enforcing the silent state [ 35, 74].
DNA methylation is important for the maintenance of the silent state of genes on the inactive X chromosome (Xi).
To begin exploring the role of ATF7IP in XCI, we first investigated the consequences of Atf7ip depletion on the maintenance of the silent state of the Xi in somatic cells.
To monitor the functional effect of Atf7ip knockdown on the maintenance of the silent state of the Xi, we developed a new Xi-linked reporter that is highly sensitive for Xi-reactivation.
In contrast, however, the genomic nucleating sequences that direct inactivation of the X chromosome in female mammals are dispensable for continued maintenance of the silent chromatin state throughout development (Brown and Willard 1994).
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