Organization, stability, and expression of the genome

Abstract

At this year's ASCB meeting, the dynamic genome took center stage. Three Minisymposia carried this thread from start to finish, revealing the impacts of cell biology on all aspects of the genome. New concepts about the physical nature and organization of chromatin were presented, highlighting cutting-edge techniques such as high-throughput chromosome conformation capture (Hi-C) and biophysical approaches to assess the mechanical properties of chromosomes. The intimate connection between transcription and the building of nuclear bodies took on new importance as both cause and consequence of cellular transformation. Several presentations focused on how the physical state of chromatin can be transduced into biochemical signals to support homeostasis, an emerging theme in nuclear cell biology. Four of the talks are highlighted here. Pol I and Pol III in nuclear architecture and cancer Sui Huang (Northwestern University) presented evidence of a functional connection between perinucleolar compartment (PNC) formation and cancer metastasis. Using loss of the PNC as a readout to screen chemical compounds, Huang's team identified a lead molecule that remarkably inhibited metastasis in an animal model without displaying cytotoxicity. The compound altered nucleolar structure and selectively decreased Pol I and Pol III, but not Pol II, activity. The success of this chemical biology approach highlights a new way to probe the mechanistic connection between nuclear architecture and cancer. Together, insulator proteins hold all the ACEs In addition to their transcriptional roles, the transcription factor TFIIIC and pol III have been implicated in contributing to chromatin boundary activity. Kevin Van Bortle (Victor Corces’ laboratory, Emory University) presented evidence that topologically associated domains (TADs) are defined by architectural clustering elements (ACEs)—sites associated with multiple insulator proteins, including TFIIIC, CTCF, PRDM5, and the SMC complexes cohesin and condensin (see Figure 1). Thus, these protein complexes likely carry out both unique functions at distinct, nonboundary sites while working cooperatively at common sites to define boundaries, thereby separating TADs. FIGURE 1: Combinatorial binding of insulator proteins at ACEs shapes TAD structure and regulatory function. Chromatin immunoprecipitation followed by high-throughput sequencing reveals that insulators form dense clusters and that TAD border strengths identified ... SMC proteins stiffen mitotic chromosomes Mingxuan Sun (John Marko's laboratory, Northwestern University) presented work demonstrating that condensins do double duty by contributing to the physical properties of metaphase chromatin. After individual mitotic chromosomes were mechanically removed from cells, glass pipettes were used to probe the mechanical properties of the chromosomes. While the DNA polymer makes the largest contribution to chromosome structure (digestion with nucleases can “liquefy” the chromosomes), both condensin I and more prominently condensin II contribute to chromosome stiffness. Provocatively, threads of DNA between individual chromosomes were also detected using this approach, raising interesting questions about the biological context for these connections and the mechanisms of their resolution. Tel1 tells short telomeres to get replicating Investigating how telomere length can be sensed and communicated to the replication machinery, Akila Sridhar (Anne Donaldson's laboratory, University of Aberdeen) uncovered an essential role for the Tel1 kinase (the budding yeast ATM homologue) in shifting the timing of telomere replication earlier in response to a “short telomere” signal. Normally, the telomere-binding factor Rif1 attenuates this Tel1 cascade, but Tel1 can override this blockade at short telomeres. Sridhar found that Rif1 becomes a substrate for Tel1 in response to short telomeres, suggesting that Rif1 phosphorylation may contribute to this change in state. However, the minor effect of mutating the Rif1 phosphorylation sites on replication timing suggests additional inputs remain to be uncovered.