research highlights

imaging A brief history of nuclear organization

By marking -DNA interactions in in new work, Kind and colleagues fused matin that repress expression, but the real time, scientists track chromosomal the m6A-recognition domain from DpnI researchers learned that NL-interacting rearrangements in the nuclei of living to enhanced green fluorescent protein LADs are also especially prone to feature cells. (EGFP), thereby devis- the repressive 3 Eukaryotic nuclei are not merely hap- ing a genetically encod- lysine 9 dimethylation hazard jumbles of , like ed “m6A-Tracer” that (H3K9me2) pattern. some neglected storage drawer full of detects these marks in They fused m6A-Tracer cables. Instead, the nucleus maintains living cells. to a viral protein that three-dimensional organization via asso- Kind and van Steensel disrupts heterochroma- ciations between an inner layer called the generated lines that tin, thereby specifically nuclear lamina (NL), composed of lamins express lamin B1 fused targeting NL-interacting and other , and lamina-associated to the DNA-labeling LADs. This resulted domains (LADs) sprinkled liberally enzyme and m6A-Trac- in reduced levels of throughout each . er. Each of these was H3K9me2 at these sites Bas van Steensel’s team at the regulated by a distinct Lamina-associated domains (green) and a greater overall Netherlands Cancer Institute in conditional expres- charted during . Reprinted from tendency for LADs to Amsterdam has previously conducted sion system so that Cell with permission from Elsevier. ‘wander away’ from the thorough surveys of LADs in diverse cell the researchers could NL. This suggests a close types. “They always comprise 30%–40% tightly control the timing and dura- connection between the presence of this of the whole , even across differ- tion of labeling and tracing. This repressive modification and LAD anchor- ent organisms,” explains Jop Kind, a post- technique thus provided molecular- ing at the nuclear periphery, although the doc in van Steensel’s group, “and they look scale insight into lamin-chromosome nature of this relationship remains unclear. pretty much the same in all the cells we’ve interactions. “We know that a piece of Kind believes single-cell studies will

© 2013 Nature America, Inc. All rights reserved. America, Inc. © 2013 Nature looked at so far.” However, many questions DNA must have been within nanometer help address this and other unanswered remain about the LADs’ dynamic behav- distance from lamin B1 to establish that questions. For example, this study focused ior. Not all LADs are engaged with the print,” says Kind. Equally importantly, this on lamin B1, but there are other lamin

npg NL simultaneously, and some studies hint approach tracks interaction history such proteins—including lamin A, which is that there may be a heritable component that a given LAD will retain the signature found throughout the nuclear interior. wherein mitotic cells pass along aspects of of its interaction with the NL even if it Because all lamins appear to show the their nuclear organization to their ‘daugh- subsequently shifts further into the nucle- same chromosomal binding preferences, ters’. us. This proved useful, as many tagged this could explain why so many LADs lie Kind, van Steensel and their colleagues LADs were observed at distances up to a deeper within the nucleus than expected. therefore devised a minimally intrusive micrometer from the NL, which indicated “We think that lamin A specifically inter- system for charting DNA-protein inter- clear reorganization over the course of acts with LADs in the middle of the cell,” actions in living cells. In earlier work, the experiment. When they labeled cells says Kind, “but this is pure speculation at the researchers devised a method called undergoing mitosis, the researchers were this point.” He also sees the potential to DamID, in which they fused a protein of surprised to note that the majority of the conduct similar live-cell labeling experi- interest to a bacterial enzyme that intro- NL-interacting sites from the premitotic ments to track the dynamics of chromo- duces an adenine-6-methylation (m6A) cell were situated deeper in the nuclear somal interactions with the nucleolus or modification to any DNA sites with which interior in the daughter cells, some dis- large multiprotein regulatory complexes it comes in contact. “This print is absent tance away from the NL. “I had expected with this method, offering scientists a in higher eukaryotes, so you won’t find it some mobility of LADs, but that they were helpful tool to assign meaning to the unless you express this protein,” says Kind. completely rearranged—stochastically, it seeming chaos of the nucleus. The original DamID method involved seems, as we couldn’t find any heritable Michael Eisenstein breaking open cells and treating them patterns,” says Kind. RESEARCH PAPERS with DpnI, an enzyme that selectively They also observed striking patterns of Kind, J. et al. Single-cell dynamics of genome- cuts DNA at m6A marks, to map modified distribution. LADs are known nuclear lamina interactions. Cell 153, 178–192 genomic sites. Building on this approach to reside in dense regions of heterochro- (2013).

nature methods | VOL.10 NO.5 | MAY 2013 | 379