No abstract

Context. By providing information about the location of scattering material along the line of sight (LoS) to pulsars, scintillation arcs are a powerful tool for exploring the distribution of ionized material in the interstellar medium (ISM). Here, we present observations that probe the ionized ISM on scales of ∼0.001–30 au. Aims. We have surveyed pulsars for scintillation arcs in a relatively unbiased sample with DM < 100 pc cm−3. We present multifrequency observations of 22 low to moderate DM pulsars. Many of the 54 observations were also observed at another frequency within a few days. Methods. For all observations, we present dynamic spectra, autocorrelation functions, and secondary spectra. We analyze these data products to obtain scintillation bandwidths, pulse broadening times, and arc curvatures. Results. We detect definite or probable scintillation arcs in 19 of the 22 pulsars and 34 of the 54 observations, showing that scintillation arcs are a prevalent phenomenon. The arcs are better defined in low DM pulsars. We show that well-defined arcs do not directly imply anisotropy of scattering. Only the presence of reverse arclets and a deep valley along the delay axis, which occurs in about 20% of the pulsars in the sample, indicates substantial anisotropy of scattering. Conclusions. The survey demonstrates substantial patchiness of the ionized ISM on both astronomical-unit-size scales transverse to the LoS and on ∼100 pc scales along it. We see little evidence for distributed scattering along most lines of sight in the survey.

Multiplexed fluorescence in situ hybridization (FISH) is a widely used approach for analyzing three-dimensional genome organization, but it is challenging to derive chromosomal conformations from noisy fluorescence signals, and tracing chromatin is not straightforward. Here we report a spatial genome aligner that parses true chromatin signal from noise by aligning signals to a DNA polymer model. Using genomic distances separating imaged loci, our aligner estimates spatial distances expected to separate loci on a polymer in three-dimensional space. Our aligner then evaluates the physical probability observed signals belonging to these loci are connected, thereby tracing chromatin structures. We demonstrate that this spatial genome aligner can efficiently model chromosome architectures from DNA FISH data across multiple scales and be used to predict chromosome ploidies de novo in interphase cells. Reprocessing of previous whole-genome chromosome tracing data with this method indicates the spatial aggregation of sister chromatids in S/G2 phase cells in asynchronous mouse embryonic stem cells and provides evidence for extranumerary chromosomes that remain tightly paired in postmitotic neurons of the adult mouse cortex.

AbstractInsulators play a critical role in spatiotemporal gene expression in metazoans by separating active and repressive chromatin domains and preventing inappropriate enhancer-promoter contacts. The evolutionarily conserved CCCTC-binding factor (CTCF) is required for insulator function in mammals, but not all of its binding sites act as insulators. Here, we explore the sequence requirements of CTCF-mediated transcriptional insulation with the use of a sensitive insulator reporter assay in mouse embryonic stem cells. We find that insulation potency depends on the number of CTCF binding sites in tandem. Furthermore, CTCF-mediated insulation is dependent on DNA sequences flanking its core binding motifs, and CTCF binding sites at topologically associating domain(TAD) boundaries are more likely to function as insulators than those outside TAD boundaries, independent of binding strength. Using chromosomal conformation capture assays and high-resolution chromatin imaging techniques, we demonstrate that insulators form local chromatin domain boundaries and reduce enhancer-promoter contacts. Taken together, our results provide strong genetic, molecular, and structural evidence connecting chromatin topology to the action of insulators in the mammalian genome.

Context: By providing information about the location of scattering material along the line of sight (LoS) to pulsars, scintillation arcs are a powerful tool for exploring the distribution of ionized material in the interstellar medium. Here, we present observations that probe the ionized ISM on scales of ∼ 0.001 -30 au. Aims: We have surveyed pulsars for scintillation arcs in a relatively unbiased sample with DM < 100 pc cm −3 . We present multi-frequency observations of 22 low to moderate DM pulsars. Many of the 54 observations were also observed at another frequency within a few days. Methods: For all observations we present dynamic spectra, autocorrelation functions, and secondary spectra. We analyze these data products to obtain scintillation bandwidths, pulse broadening times, and arc curvatures. Results: We detect definite or probable scintillation arcs in 19 of the 22 pulsars and 34 of the 54 observations, showing that scintillation arcs are a prevalent phenomenon. The arcs are better defined in low DM pulsars. We show that well-defined arcs do not directly imply anisotropy of scattering. Only the presence of reverse arclets and a deep valley along the delay axis, which occurs in about 20% of the pulsars in the sample, indicates substantial anisotropy of scattering. Conclusions: The survey demonstrates substantial patchiness of the ionized ISM on both au size scales transverse to the line of sight and on ∼ 100 pc scales along it. We see little evidence for distributed scattering along most lines of sight in the survey.

Multiplexed DNA fluorescence in situ hybridization (FISH) imaging technologies have been developed to map the folding of chromatin fibers at tens of nanometer and tens of kilobase resolution in single cells. However, computational methods to reliably identify chromatin loops from such imaging datasets are still lacking. Here we present a Single-Nucleus Analysis Pipeline for multiplexed DNA FISH (SnapFISH), to process the multiplexed DNA FISH data and identify chromatin loops. SnapFISH can identify known chromatin loops from mouse embryonic stem cells with high sensitivity and accuracy. In addition, SnapFISH obtained comparable results of chromatin loops across datasets generated from diverse imaging technologies.

Multiplexed fluorescence in situ hybridization (FISH) has emerged as a powerful approach for analyzing 3D genome organization, but it is eminently challenging to derive chromosomal conformations from noisy fluorescence signals. Tracing chromatin is not straightforward as chromosomes lack conserved shapes for reference checking whether an observed fluorescence signal belongs to a chromatin fiber or not. Here we report a spatial genome aligner that parses true chromatin signal from noise by aligning signals to a DNA polymer model. We demonstrate that this spatial genome aligner can efficiently reconstruct chromosome architectures from DNA-FISH data across multiple scales and determine chromosome ploidies de novo in interphase cells. Reprocessing of previous whole-genome chromosome tracing data with this method revealed the spatial aggregation of sister chromatids in S/G2 phase cells in asynchronous mouse embryonic stem cells, and uncovered extranumerary chromosomes that remain tightly paired in post-mitotic neurons of the adult mouse cortex. Our spatial genome aligner may facilitate the adaption of multiplexed DNA-FISH by the community.

In the version of this article initially published, the 4D Nucleome Web Portal accession number (4DNESU4Y9CBF) provided in the Data availability section was incorrect and has been replaced with accession numbers 4DNESIGBIXQS, 4DNESC5PKTQ9, 4DNES51KSIZ9, 4DNESNEKOCAP and 4DNESOXQX1JT in the HTML and PDF versions of the article.