Many aspects of behavior and physiology, including sleep/ awake cycles and hormone levels, keep a rhythm with about a 24-h period, even under constant conditions without any external time cues (1). Circadian rhythms are generated by a self-sustaining time-measuring system called the circadian clock. In mammals, the hypothalamic suprachiasmatic nucleus (SCN) functions as the master clock, and circadian clocks are also located in peripheral tissues such as the liver (2-5). In individual cells, clock genes and their products form transcriptional/translational feedback loops (6). The basic helix-loop-helix (bHLH)-PAS transcription factors CLOCK and BMAL1 play a role as positive factors in the loops, and the heterodimer of these proteins binds to the CACGTG E-box or related E-box-like sequences to transactivate a wide range of target genes, including Per and Cry (7-10). Translated PER and CRY proteins then bind to the CLOCK-BMAL1 complex, leading to the suppression of E-box-dependent transactivation. This negative-feedback mechanism forms a molecular clock generating circadian rhythms. In addition to the Ebox element, the D-box element and the REV-ERB/ROR-binding element (RRE) form a regulatory network of gene expression, governing coordinately circadian transcriptional oscillations (11,12). The D-box element is activated and repressed by DBP and E4BP4, respectively, while RRE is activated and repressed by RORs and REV-ERBs, respectively.During the circadian cycling of the transcriptional/translational steps, posttranslational modifications, such as phosphorylation, regulate the clock proteins, in terms of activity, stability, localization, and interaction (13). It was reported previously that CLOCK and BMAL1 are phosphorylated in a time-of-day-dependent manner (14)(15)(16)(17). CLOCK phosphorylation at its DNA-binding domain (16, 18) may be important for rhythmic inhibition of the ability of the CLOCK-BMAL1 complex to bind to the E-box element. This is consistent with the observation that the CLOCK-BMAL1 complex rhythmically dissociates from the E-box in the locus of the Dbp gene (19). Here we found in vivo binding sites of CLOCK protein in the mouse liver in a genome-wide manner by chromatin immunoprecipitation-sequencing (ChIP-Seq) analysis. Previous ChIP-Seq studies of circadian clocks confirmed CLOCK-BMAL1 binding to canonical motifs instead of finding all potential binding motifs (20)(21)(22)(23). In this study, significant CLOCK-binding motifs were comprehensively examined by developing a bioinformatics method, MOCCS (motif centrality analysis of ChIP-Seq), which analyzes the frequency distribution of DNA sequences centered at DNA-binding sites found by ChIPSeq analyses. In parallel, all the rhythmic transcripts in the liver were identified by circadian deep-sequencing analysis of poly(A)-tailed RNA and small RNA. Based on these data, we demonstrate the functional importance of rhythmic posttranscriptional regulations, such as microRNA (miRNA)-mediated gene silencing, in dynamic circadian RNA rhythms.

Despite their central role in multicellular organization, navigation rules that dictate cell rearrangement remain largely undefined. Contact between neighboring cells and diffusive attractant molecules are two of the major determinants of tissue-level patterning; however, in most cases, molecular and developmental complexity hinders one from decoding the exact governing rules of individual cell movement. A primordial example of tissue patterning by cell rearrangement is found in the social amoebaDictyostelium discoideumwhere the organizing center or the “tip” self-organizes as a result of sorting of differentiating prestalk and prespore cells. By employing microfluidics and microsphere-based manipulation of navigational cues at the single-cell level, here we uncovered a previously overlooked mode ofDictyosteliumcell migration that is strictly directed by cell–cell contact. The cell–cell contact signal is mediated by E-set Ig-like domain-containing heterophilic adhesion molecules TgrB1/TgrC1 that act in trans to induce plasma membrane recruitment of the SCAR complex and formation of dendritic actin networks, and the resulting cell protrusion competes with those induced by chemoattractant cAMP. Furthermore, we demonstrate that both prestalk and prespore cells can protrude toward the contact signal as well as to chemotax toward cAMP; however, when given both signals, prestalk cells orient toward the chemoattractant, whereas prespore cells choose the contact signal. These data suggest a model of cell sorting by competing juxtacrine and diffusive cues, each with potential to drive its own mode of collective cell migration.

Targeting chromatin regulators to specific genomic locations for gene control is emerging as a powerful method in basic research and synthetic biology. However, many chromatin regulators are large, making them difficult to deliver and combine in mammalian cells. Here, we develop a strategy for gene control using small nanobodies that bind and recruit endogenous chromatin regulators to a gene. We show that an antiGFP nanobody can be used to simultaneously visualize GFP-tagged chromatin regulators and control gene expression, and that nanobodies against HP1 and DNMT1 can silence a reporter gene. Moreover, combining nanobodies together or with other regulators, such as DNMT3A or KRAB, can enhance silencing speed and epigenetic memory. Finally, we use the slow silencing speed and high memory of antiDNMT1 to build a signal duration timer and recorder. These results set the basis for using nanobodies against chromatin regulators for controlling gene expression and epigenetic memory.

In mammalian cells genes that are in close proximity can be transcriptionally coupled: silencing or activating one gene can affect its neighbors. Understanding these dynamics is important for natural processes, such as heterochromatin spreading during development and aging, and when designing synthetic gene regulation circuits. Here, we systematically dissect this process in single cells by recruiting and releasing repressive chromatin regulators at dual-gene synthetic reporters, and measuring how fast gene silencing and reactivation spread as a function of intergenic distance and configuration of insulator elements. We find that silencing by KRAB, associated with histone methylation, spreads between two genes within hours, with a time delay that increases with distance. This fast KRAB-mediated spreading is not blocked by the classical cHS4 insulators. Silencing by histone deacetylase HDAC4 of the upstream gene can also facilitate background silencing of the downstream gene by PRC2, but with a days-long delay that does not change with distance. This slower silencing can sometimes be stopped by insulators. Gene reactivation of neighboring genes is also coupled, with strong promoters and insulators determining the order of reactivation. Our data can be described by a model of multi-gene regulation that builds upon previous knowledge of heterochromatin spreading, where both gene silencing and gene reactivation can act at a distance, allowing for coordinated dynamics via chromatin regulator recruitment.