Beyond A and B Compartments: how major nuclear locales define nuclear genome organization and function.

Models of nuclear genome organization often propose a binary division into active versus inactive compartments, yet they overlook nuclear bodies. Here we integrated analysis of sequencing and image-based data to compare genome organization in four human cell types relative to three different nuclear locales: the nuclear lamina, nuclear speckles, and nucleoli. Whereas gene expression correlates mostly with nuclear speckle proximity, DNA replication timing correlates with proximity to multiple nuclear locales. Speckle attachment regions emerge as DNA replication initiation zones whose replication timing and gene composition vary with their attachment frequency. Most facultative LADs retain a partially repressed state as iLADs, despite their positioning in the nuclear interior. Knock out of two lamina proteins, Lamin A and LBR, causes a shift of H3K9me3-enriched LADs from lamina to nucleolus, and a reciprocal relocation of H3K27me3-enriched partially repressed iLADs from nucleolus to lamina. Thus, these partially repressed iLADs appear to compete with LADs for nuclear lamina attachment with consequences for replication timing. The nuclear organization in adherent cells is polarized with nuclear bodies and genomic regions segregating both radially and relative to the equatorial plane. Together, our results underscore the importance of considering genome organization relative to nuclear locales for a more complete understanding of the spatial and functional organization of the human genome.

Retrospective evaluation of wobbly hedgehog syndrome in 49 African pygmy hedgehogs (Atelerix albiventris): 2000-2020.

OBJECTIVE: To retrospectively evaluate the prevalence and clinical progression of wobbly hedgehog syndrome (WHS) and concurrent incidence of neoplasia in a cohort of African pygmy hedgehogs (Atelerix albiventris). ANIMALS: 49 hedgehogs. CLINICAL PRESENTATION AND PROCEDURES: Medical records of hedgehogs from 7 institutions across the US over a 20-year period (2000 to 2020) were retrospectively reviewed. Inclusion criteria were hedgehogs of any sex or age with postmortem CNS histopathology consistent with WHS. Collected data included sex, age at onset and euthanasia, major histopathologic findings, reported neurologic clinical signs, and treatments administered. RESULTS: 24 males and 25 females were included. Fifteen of 49 (31%) individuals had subclinical WHS with no reported antemortem neurologic clinical signs. In neurologically affected (clinical) hedgehogs (n = 34), the mean ± SD age at onset was 3.3 ± 1.5 years with a median (range) time from onset to euthanasia of 51 days (1 to 319 days). In neurologically affected hedgehogs, the most commonly reported clinical signs were ataxia (n = 21) and pelvic limb paresis (16) and the most commonly administered treatment was meloxicam (13). Overall, 31 of 49 (63%) hedgehogs had a concurrent histopathologic diagnosis of neoplasia outside of the CNS. CLINICAL RELEVANCE: The prognosis for hedgehogs with WHS is poor. No treatment had a significant effect on survival time, and neoplasia was a common comorbidity in the current cohort. A small but clinically relevant subset of neurologically normal hedgehogs had a histopathologic diagnosis of WHS.

Imaging Method Using CRISPR/dCas9 and Engineered gRNA Scaffolds Can Perturb Replication Timing at the HSPA1 Locus.

Fluorescence microscopy imaging of specific chromosomal sites is essential for genome architecture research. To enable visualization of endogenous loci in mammalian cells, programmable DNA-binding proteins such as TAL effectors and CRISPR/dCas9 are commonly utilized. In addition, site-specific insertion of a TetO repeat array, coupled with TetR-enhanced green fluorescent protein fusion protein expression, can be used for labeling nonrepetitive endogenous loci. Here, we performed a comparison of several live-cell chromosome tagging methods, including their effect on subnuclear positioning, expression of adjacent genes, and DNA replication timing. Our results showed that the CRISPR-based imaging method can delay DNA replication timing and sister chromatid resolution at certain region. However, subnuclear localization of the labeled locus and gene expression from adjacent loci were unaffected by either TetO/TetR or CRISPR-based methods, suggesting that CRISPR-based imaging could be used for applications that do not require DNA replication analysis.