Poly(ADP-ribose) polymerase 1 protein (PARP1) mediates chromatin loosening and activates the transcription of inducible genes, but the mechanism of PARP1 regulation in chromatin is poorly understood. We have found that PARP1 interaction with chromatin is dynamic and that PARP1 is exchanged continuously between chromatin and nucleoplasm, as well as between chromatin domains. Specifically, the PARP1 protein preferentially interacts with nucleosomal particles, and although the nucleosomal linker DNA is not necessary for this interaction, we have shown that the core histones, H3 and H4, are critical for PARP1 binding. We have also demonstrated that the histones H3 and H4 interact preferentially with the C-terminal portion of PARP1 protein and that the N-terminal domain of PARP1 negatively regulates these interactions. Finally, we have found that interaction with the N-terminal tail of the H4 histone triggers PARP1 enzymatic activity. Therefore, our data collectively suggests a model in which both the regulation of PARP1 protein binding to chromatin and the enzymatic activation of PARP1 protein depend on the dynamics of nucleosomal core histone mediation.Eukaryotic chromatin organization involves the fundamental nucleosomal unit, which consists of four core histones plus a linker histone (1). Recently, it has been shown that the activity of transcription complexes at nucleosomes is regulated by the PARP1 3 protein (2, 3). Notwithstanding these findings, major gaps in our present understanding exist that involve the mechanism by which the PARP1 protein binds to specific chromatin domains and the mechanism by which the local PARP1 protein is activated in response to developmental and environmental stimuli.After histones, PARP1 is the most abundant nuclear protein (4). The distribution of PARP1 in chromatin is broad and occurs in regions characterized by distinct cell types (2, 3, 5). Nevertheless, exactly how the PARP1 enzyme interacts with chromatin in vivo has not been thoroughly investigated, and the molecular basis for PARP1 binding to chromatin remains poorly understood. Although zinc fingers within the PARP1 protein contribute to DNA binding in vitro, they specifically recognize damaged DNA (6) and therefore do not contribute to the association of PARP1 with intact chromatin. Moreover, a PARP1 paralog, PARP2, that has no zinc fingers and no direct DNA binding capability, nevertheless exhibits a pattern of chromatin association similar to PARP1 and is able to partially complement PARP1 functions in a PARP1 null mutant (7-9). This suggests that PARP1 and PARP2 both bind chromatin indirectly, through an interaction with one or more DNA-binding proteins.A key aim of this study is to determine the specific mechanisms by which PARP1 protein associates with chromatin in vivo. Considerable evidence now suggests that PARP1 interacts with chromatin by binding to histones (10). For example, histones H1, H2A, and H2B are efficient targets for PARP1 binding in vitro (11) and are enzymatically modified by . This idea is, howev...

The mammalian cell nucleus displays a remarkable spatial segregation of active euchromatic from inactive heterochromatic genomic regions. In conventional nuclei, euchromatin is localized in the nuclear interior and heterochromatin at the nuclear periphery. In contrast, rod photoreceptors in nocturnal mammals have inverted nuclei, with a dense heterochromatic core and a thin euchromatic outer shell. This inverted architecture likely converts rod nuclei into microlenses to facilitate nocturnal vision, and may relate to the absence of particular proteins that tether heterochromatin to the lamina. However, both the mechanism of inversion and the role of interactions between different types of chromatin and the lamina in nuclear organization remain unknown. To elucidate this mechanism we performed Hi-C and microscopy on cells with inverted nuclei and their conventional counterparts. Strikingly, despite the inversion evident in microscopy, both types of nuclei display similar Hi-C maps. To resolve this paradox we developed a polymer model of chromosomes and found a universal mechanism that reconciles Hi-C and microscopy for both inverted and conventional nuclei. Based solely on attraction between heterochromatic regions, this mechanism is sufficient to drive phase separation of euchromatin and heterochromatin and faithfully reproduces the 3D organization of inverted nuclei. When interactions between heterochromatin and the lamina are added, the same 1 . CC-BY-NC-ND 4.0 International license It is made available under a was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.The copyright holder for this preprint (which . http://dx.doi.org/10.1101/244038 doi: bioRxiv preprint first posted online Jan. 9, 2018; model recreates the conventional nuclear organization. To further test our models, we eliminated lamina interactions in models of conventional nuclei and found that this triggers a spontaneous process of inversion that qualitatively reproduces the pathway of morphological changes during nuclear inversion in vivo . Together, our experiments and modeling suggest that interactions among heterochromatic regions are central to phase separation of the active and inactive genome in inverted and conventional nuclei, while interactions with the lamina are essential for building the conventional architecture from these segregated phases. Ultimately our data suggest that an inverted organization constitutes the default state of nuclear architecture.Mammalian interphase chromosomes are spatially organized with distinct features ranging from chromosome territories, to active and inactive A/B compartments and to TADs 1,2 . Emerging work argues that these features reflect different underlying mechanisms 3 . Of much recent interest [4][5][6][7][8] , TAD formation appears to result from a cohesin-mediated mechanism of loop extrusion. Compartments are increasingly appreciated as distinct from TADs: compartments both persist when TADs are experimentally disrupted 5,6,8,...