TI - Relationships between Hnf1alpha-Dependent Locus Specific Chromatin Changes and Subnuclear Positioning . AB - Together with previous findings , our data shows that binding of Hnf1alpha to target loci promotes local histone tail hyperacetylation , methylation of H3-Lys4 and chromatin decondensation , while preventing methylation at H3-Lys27 [38] , [40] , [41] . H3-Lys27 methylation thus appears to represent a default state , consistent with genetic studies showing that the H3-Lys4-specific methyltransferase Trithorax suppresses default gene silencing mediated by methylated H3-Lys27 [55] . Concomitant with local chromatin changes , Hnf1alpha binding also causes the recruitment of targets to predominantly central subdomains that are enriched in PHOSphoserine-5 RNA polymerase II and concordant histone modifications ( see model in Figure 6 ) . How Hnf1alpha controls subnuclear positioning of its targets remains to be clarified . Treatment with the RNA polymerase II inhibitors alpha-amanitin and 5 , 6-dichlorobenzimidazole riboside ( DRB ) does not alter the preferential positioning of Kif12 in H3-Lys4me-rich/H3-Lys27me-poor domains in a beta cell line with normal Hnf1alpha expression (Figure S9) . This suggests that Kif12 compartmentalization is not solely dependent on ongoing transcriptional activity per se , and points to the involvement of other activator -dependent functions . Changes in local chromatin structure represent another potential mechanism . Our results showed that Hnf1alpha regulates not only local chromatin decompaction , but also the decondensation of the Cyp2j5 locus that is reflected by changes in distances between adjacent loci and relative to chromosomal territories . Our findings also show that the histone modification enrichment pattern of Hnf1alpha -dependent genes in nuclear domains with which they associate coincides with the local post-translational histone modification profile . This raises the possibility that histone modifications may be partly instrumental in gene positioning . Although similar measurements of locus positioning relative to histone modification domains have not been carried out before , two studies previously showed that treatment with histone deacetylase inhibitors causes repositioning of inactive genes away from the nuclear periphery [20] , [56] . Local histone modifications could affect compartmentalization of gene loci by regulating interactions with the nuclear lamina [56] and could also affect mobility , since acetylated histones have been previously shown to increase chromatin fiber flexibility [57] . Taken together , these findings support the proposal that local Hnf1alpha -dependent chromatin decompaction and histone modifications might result in augmented mobility and loop formation , thus increasing the likelihood of accessing and establishing dynamic interactions with components of transcriptionally active nuclear regions ( Figure 6 ) . Local activator -dependent changes in chromatin structure may thus play a role in regulating the spatial organization of the genome . Emerging evidence indicates that gene transcription is an integrated process involving multiple levels of regulation [2] , [3] . The data presented here link the in vivo function of an activator to different levels of regulation , namely the binding to specific target sequences , the local modification of target chromatin , and the positioning of targets in distinct subnuclear domains . This demonstration is provided in a genetic model of human diabetes , indicating cellular defects at multiple regulatory levels in a human transcriptional disease . Thus , our findings provide not only new insights into the complexity of trans-activator functions and transcriptional regulation , but are also important for understanding mechanisms underlying human disease .