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Abstract Background Topologically associating domains (TADs) are important building blocks of three-dimensional genome architectures. The formation of TADs has been shown to depend on cohesin in a loop-extrusion mechanism. Recently, advances in an image-based spatial genomics technique known as chromatin tracing lead to the discovery of cohesin-independent TAD-like structures, also known as single-cell domains, which are highly variant self-interacting chromatin domains with boundaries that occasionally overlap with TAD boundaries but tend to differ among single cells and among single chromosome copies. Recent computational modeling studies suggest that epigenetic interactions may underlie the formation of the single-cell domains. Results Here we use chromatin tracing to visualize in female human cells the fine-scale chromatin folding of inactive and active X chromosomes, which are known to have distinct global epigenetic landscapes and distinct population-averaged TAD profiles, with inactive X chromosomes largely devoid of TADs and cohesin. We show that both inactive and active X chromosomes possess highly variant single-cell domains across the same genomic region despite the fact that only active X chromosomes show clear TAD structures at the population level. These X chromosome single-cell domains exist in distinct cell lines. Perturbations of major epigenetic components and transcription mostly do not affect the frequency or strength of the single-cell domains. Increased chromatin compaction of inactive X chromosomes occurs at a length scale above that of the single-cell domains. Conclusions In sum, this study suggests that single-cell domains are genome architecture building blocks independent of the tested major epigenetic components.

Abstract Fluorescence in situ hybridization (FISH) is a powerful method to visualize the spatial positions of specific genomic loci and RNA species. Recent technological advances have leveraged FISH to visualize these features in a highly multiplexed manner. Notable examples include chromatin tracing, RNA multiplexed error-robust FISH (MERFISH), multiplexed imaging of nucleome architectures (MINA), and sequential single-molecule RNA FISH. However, one obstacle to the broad adoption of these methods is the complexity of the multiplexed FISH probe design. In this paper, we introduce an easy-to-use, versatile, and all-in-one application called ProbeDealer to design probes for a variety of multiplexed FISH techniques and their combinations. ProbeDealer offers a one-stop shop for multiplexed FISH design needs of the research community.

Faithful chromosome segregation during mitosis is critical for maintaining genome integrity in cell progeny and relies on accurate and robust kinetochore-microtubule attachments. The NDC80 complex, a tetramer comprising kinetochore protein HEC1 (HEC1), NDC80 kinetochore complex component NUF2 (NUF2), NDC80 kinetochore complex component SPC24 (SPC24), and SPC25, plays a critical role in kinetochore-microtubule attachment. Mounting evidence indicates that phosphorylation of HEC1 is important for regulating the binding of the NDC80 complex to microtubules. However, it remains unclear whether other post-translational modifications, such as acetylation, regulate NDC80-microtubule attachment during mitosis. Here, using pulldown assays with HeLa cell lysates and site-directed mutagenesis, we show that HEC1 is a bona fide substrate of the lysine acetyltransferase Tat-interacting protein, 60 kDa (TIP60) and that TIP60-mediated acetylation of HEC1is essential for accurate chromosome segregation in mitosis. We demonstrate that TIP60 regulates the dynamic interactions between NDC80 and spindle microtubules during mitosis and observed that TIP60 acetylates HEC1 at two evolutionarily conserved residues, Lys-53 and Lys-59. Importantly, this acetylation weakened the phosphorylation of the N-terminal HEC1(1-80) region at Ser-55 and Ser-62, which is governed by Aurora B and regulates NDC80-microtubule dynamics, indicating functional cross-talk between these two post-translation modifications of HEC1. Moreover, the TIP60-mediated acetylation was specifically reversed by sirtuin 1 (SIRT1). Taken together, our results define a conserved signaling hierarchy, involving HEC1, TIP60, Aurora B, and SIRT1, that integrates dynamic HEC1 acetylation and phosphorylation for accurate kinetochore-microtubule attachment in the maintenance of genomic stability during mitosis. [ABSTRACT FROM AUTHOR]

Ghost imaging is an indirect system that allows the imaging of an object without directly seeing the object. The speckle pattern that contains the information about light and objects has increasingly become a popular topic in pseudothermal light ghost imaging. However, existing research still has encountered problems of poor imaging quality and slow sampling speeds. We propose a ghost imaging method based on N-order speckle patterns to recover the object (NSGI). The N-order speckle patterns combine N independent laser speckles individually produced by passing an expanded and collimated He–Ne laser through a digital micromirror device (DMD). The sampling frequency can be improved by controlling the trigger signals of different DMDs. The results of the simulation and experiment have verified that our method can increase sampling speed and reconstruction accuracy. In addition, NSGI can be applied to more applications by designing multiple independent speckles with different properties. [ABSTRACT FROM AUTHOR]

Gradient ghost imaging (GGI) is a new imaging method that can directly extract the edge of a target from the correlation of light intensity fluctuations. However, there are problems of poor image quality and practicability in GGI. The corner point is an important target feature and has important applications in the fields of image processing and machine vision. In this paper, we propose a corner detection scheme that combines a corner detection algorithm based on curvature scale space with a GGI system, which can directly extract corner points from the reconstruction results of ghost imaging. A simulation and experimental results show that our method can acquire precise and robust corner information of an unknown target in undersampled cases, which promotes the practical development of ghost imaging. [ABSTRACT FROM AUTHOR]

In order to improve the imaging quality of ghost imaging and solve the problem of high distortion at a low sampling rate, the compressive sensing ghost imaging based on image gradient (IGGI) is proposed. The image gradient can reflect the changes of optical characteristics and carry the edge information of object. In this paper, the principle of compressive sensing ghost imaging is analyzed. And the total variation, the integral of image gradient, is used to optimize the reconstruction process. Simultaneously, the threshold of matching degree is set up to reduce computation load and improve imaging speed. The results of simulation and experiments show that compared with traditional ghost imaging, the IGGI can achieve high-quality images and obtain the edge information of targets at a low sampling rate, which further facilitate the practical application of ghost imaging. [ABSTRACT FROM AUTHOR]