CTCF is an architectural protein with a critical role in connecting higher-order chromatin folding in pluripotent stem cells. Recent reports have suggested that CTCF binding is more dynamic during ...development than previously appreciated. Here, we set out to understand the extent to which shifts in genome-wide CTCF occupancy contribute to the 3D reconfiguration of fine-scale chromatin folding during early neural lineage commitment. Unexpectedly, we observe a sharp decrease in CTCF occupancy during the transition from naïve/primed pluripotency to multipotent primary neural progenitor cells (NPCs). Many pluripotency gene-enhancer interactions are anchored by CTCF, and its occupancy is lost in parallel with loop decommissioning during differentiation. Conversely, CTCF binding sites in NPCs are largely preexisting in pluripotent stem cells. Only a small number of CTCF sites arise de novo in NPCs. We identify another zinc finger protein, Yin Yang 1 (YY1), at the base of looping interactions between NPC-specific genes and enhancers. Putative NPC-specific enhancers exhibit strong YY1 signal when engaged in 3D contacts and negligible YY1 signal when not in loops. Moreover, siRNA knockdown of
specifically disrupts interactions between key NPC enhancers and their target genes. YY1-mediated interactions between NPC regulatory elements are often nested within constitutive loops anchored by CTCF. Together, our results support a model in which YY1 acts as an architectural protein to connect developmentally regulated looping interactions; the location of YY1-mediated interactions may be demarcated in development by a preexisting topological framework created by constitutive CTCF-mediated interactions.
Features of higher-order chromatin organization-such as A/B compartments, topologically associating domains and chromatin loops-are temporarily disrupted during mitosis
. Because these structures are ...thought to influence gene regulation, it is important to understand how they are re-established after mitosis. Here we examine the dynamics of chromosome reorganization by Hi-C after mitosis in highly purified, synchronous mouse erythroid cell populations. We observed rapid establishment of A/B compartments, followed by their gradual intensification and expansion. Contact domains form from the 'bottom up'-smaller subTADs are formed initially, followed by convergence into multi-domain TAD structures. CTCF is partially retained on mitotic chromosomes and immediately resumes full binding in ana/telophase. By contrast, cohesin is completely evicted from mitotic chromosomes and regains focal binding at a slower rate. The formation of CTCF/cohesin co-anchored structural loops follows the kinetics of cohesin positioning. Stripe-shaped contact patterns-anchored by CTCF-grow in length, which is consistent with a loop-extrusion process after mitosis. Interactions between cis-regulatory elements can form rapidly, with rates exceeding those of CTCF/cohesin-anchored contacts. Notably, we identified a group of rapidly emerging transient contacts between cis-regulatory elements in ana/telophase that are dissolved upon G1 entry, co-incident with the establishment of inner boundaries or nearby interfering chromatin loops. We also describe the relationship between transcription reactivation and architectural features. Our findings indicate that distinct but mutually influential forces drive post-mitotic chromatin reconfiguration.
Mammalian genomes are folded into tens of thousands of long-range looping interactions. The cause-and-effect relationship between looping and genome function is poorly understood, and the extent to ...which loops are dynamic on short time scales remains an unanswered question. Here, we engineer a new class of synthetic architectural proteins for directed rearrangement of the three-dimensional genome using blue light. We target our light-activated-dynamic-looping (LADL) system to two genomic anchors with CRISPR guide RNAs and induce their spatial colocalization via light-induced heterodimerization of cryptochrome 2 and a dCas9-CIBN fusion protein. We apply LADL to redirect a stretch enhancer (SE) away from its endogenous Klf4 target gene and to the Zfp462 promoter. Using single-molecule RNA-FISH, we demonstrate that de novo formation of the Zfp462-SE loop correlates with a modest increase in Zfp462 expression. LADL facilitates colocalization of genomic loci without exogenous chemical cofactors and will enable future efforts to engineer reversible and oscillatory loops on short time scales.
Automated tracking of animal movement allows analyses that would not otherwise be possible by providing great quantities of data. The additional capability of tracking in real time—with minimal ...latency—opens up the experimental possibility of manipulating sensory feedback, thus allowing detailed explorations of the neural basis for control of behaviour. Here, we describe a system capable of tracking the three-dimensional position and body orientation of animals such as flies and birds. The system operates with less than 40 ms latency and can track multiple animals simultaneously. To achieve these results, a multi-target tracking algorithm was developed based on the extended Kalman filter and the nearest neighbour standard filter data association algorithm. In one implementation, an 11-camera system is capable of tracking three flies simultaneously at 60 frames per second using a gigabit network of nine standard Intel Pentium 4 and Core 2 Duo computers. This manuscript presents the rationale and details of the algorithms employed and shows three implementations of the system. An experiment was performed using the tracking system to measure the effect of visual contrast on the flight speed of Drosophila melanogaster. At low contrasts, speed is more variable and faster on average than at high contrasts. Thus, the system is already a useful tool to study the neurobiology and behaviour of freely flying animals. If combined with other techniques, such as ‘virtual reality’-type computer graphics or genetic manipulation, the tracking system would offer a powerful new way to investigate the biology of flying animals.
DNA replication occurs through an intricately regulated series of molecular events and is fundamental for genome stability
. At present, it is unknown how the locations of replication origins are ...determined in the human genome. Here we dissect the role of topologically associating domains (TADs)
, subTADs
and loops
in the positioning of replication initiation zones (IZs). We stratify TADs and subTADs by the presence of corner-dots indicative of loops and the orientation of CTCF motifs. We find that high-efficiency, early replicating IZs localize to boundaries between adjacent corner-dot TADs anchored by high-density arrays of divergently and convergently oriented CTCF motifs. By contrast, low-efficiency IZs localize to weaker dotless boundaries. Following ablation of cohesin-mediated loop extrusion during G1, high-efficiency IZs become diffuse and delocalized at boundaries with complex CTCF motif orientations. Moreover, G1 knockdown of the cohesin unloading factor WAPL results in gained long-range loops and narrowed localization of IZs at the same boundaries. Finally, targeted deletion or insertion of specific boundaries causes local replication timing shifts consistent with IZ loss or gain, respectively. Our data support a model in which cohesin-mediated loop extrusion and stalling at a subset of genetically encoded TAD and subTAD boundaries is an essential determinant of the locations of replication origins in human S phase.
The class IV homeodomain leucine zipper transcription factor GLABRA2 (GL2) acts in a complex regulatory circuit that regulates the differentiation of trichomes in Arabidopsis thaliana. We describe a ...genetic interaction with HOMEODOMAIN GLABROUS11 (HDG11), previously identified as a negative regulator of trichome branching. gl2 hdg11 double mutants display enhanced trichome cell-type differentiation defects. Transgenic expression of HDG11 using the GL2 promoter partially suppresses gl2 trichome phenotypes. Vice versa, expression of GL2 under the control of its native promoter partially complements hdg11 ectopie branching. Since gl2 hdg11 and gl2 myb23 double mutants and the triple mutant display similar trichome differentiation defects, we investigated a connection to the R2R3-MYB transcription factor MYB23. We show that MYB23 transcript levels are significantly reduced in shoots from gl2 mutants and that GL2 can drive the expression of a MYB23-promoter fusion to green fluorescent protein. Yeast one-hybrid, chromatin immunoprecipitation, and in planta reporter gene experiments indicate that an L1-box in the MYB23 promoter acts as a GL2 binding site. Taken together, our findings reveal a functional redundancy between GL2 and HDG11, two homeodomain leucine zipper transcription factors previously thought to mediate opposing functions in trichome morphogenesis. A model is proposed in which GL2 transcript levels are maintained through a positive feedback loop involving GL2 activation of MYB23.
Long-term sperm storage by females in various regions of the oviduct is documented across many invertebrate and vertebrate species. Although, many reports emphasize on the histology, histochemistry ...and ultrastructural features of sperm storage, very little is known about the mechanisms underlying the sperm storage. The current review documents the occurrence of sperm storage by females in a wide array of invertebrate and vertebrate species. This review also provides an insight on the presence of various molecular factors of the sperm storage tubules presumably responsible for the prolonged sperm storage with an emphasis on a model reptile, the Indian garden lizard, Calotes versicolor which contains a unique approximately 55-kDa protein in its utero-vaginal lavage and found to inhibit washed epididymal sperm motility in a concentration and time-dependent manner in a reversible fashion.
At the beginning of the COVID-19 pandemic in the United States in the spring of 2020, many Americans avoided the healthcare system, while those with COVID-19 symptoms were faced with decisions about ...seeking healthcare services for this novel virus.
Using a probability sample (n = 1088) from the Michigan adult population of PCR-confirmed COVID-19 cases who were diagnosed prior to July 31, 2020, we used logistic regression to examine sociodemographic and symptom severity predictors of care-seeking behaviors. The analyses examined three different outcomes: (1) whether respondents sought care and, among those who sought care, whether they sought care from (2) a primary care provider or (3) an emergency room. Final models were adjusted for sex, age, race and ethnicity, income, education, marital status, living arrangement, health insurance, and self-reported symptom severity.
We found that participants ages 65 and older had 4.00 times higher odds of seeking care than 18-34-year-olds (95% CI: 2.21, 7.24), while adults reporting very severe symptoms had roughly 15 times higher odds of seeking care than those with mild symptoms (95% CI: 7.73, 27.01). Adults who were non-Hispanic Black or were uninsured had lower odds of seeking care from a primary care physician versus seeking care from other locations in comparison to adults who were non-Hispanic White or were privately insured, respectively (non-Hispanic Black: aOR = 0.27, 95% CI: 0.16, 0.44; Uninsured: aOR = 0.19, 95% CI: 0.09, 0.42). Conversely, adults who were older or reported more severe symptoms had higher odds of seeking care from an emergency room versus other locations in comparison to adults who were younger or reported less severe symptoms (Age 65+: aOR = 2.96, 95% CI: 1.40, 6.28; Very Severe Symptoms: aOR = 6.63, 95% CI: 3.33, 13.20).
Our results suggest differential utilization of healthcare services early in the COVID-19 pandemic. Further analyses are needed to examine the reasons for these differences.
Liquid-liquid phase separation underlies the formation of membrane-less organelles inside living cells. The mechanism of this process can be examined using simple aqueous mixtures of two or more ...solutes, which are able to phase separate at specific concentration thresholds. This work presents the first experimental evidence that mesoscopic changes precede visually detected macroscopic phase separation in aqueous mixtures of two polymers and a single polymer and salt. Dynamic light scattering (DLS) analysis indicates the formation of mesoscopic polymer agglomerates in these systems. These agglomerates increase in size with increasing polymer concentrations prior to visual phase separation. Such mesoscopic changes are paralleled by changes in water structure as evidenced by Attenuated Total Reflection-Fourier Transform Infrared (ATR-FTIR) spectroscopic analysis of OH-stretch bands. Through OH-stretch band analysis, we obtain quantitative estimates of the relative fractions of four subpopulations of water structures coexisting in aqueous solutions. These estimates indicate that abrupt changes in hydrogen bond arrangement take place at concentrations below the threshold of macroscopic phase separation. We used these experimental observations to develop a model of phase separation in aqueous media.
Females have historically lower rates of cardiovascular testing when compared to males. Clinical decision pathways (CDP) that utilize standardized risk-stratification methods may balance this ...disparity. We sought to determine whether clinical decision pathways could minimize sex-based differences in the non-invasive workup of chest pain in the emergency department (ED). Moreover, we evaluated whether the HEART score would minimize sex-based differences in risk-stratification.
We conducted a retrospective cohort review of adult ED encounters for chest pain where CDP was employed. Primary outcome was any occurrence of non-invasive imaging (coronary CTA, stress imaging), invasive testing, intervention (PCI or CABG), or death. Secondary outcomes were 30-day major adverse cardiac events (MACE). We stratified HEART scores and primary/secondary outcomes by sex.
A total of 1078 charts met criteria for review. Mean age at presentation was 59 years. Females represented 47% of the population. Low, intermediate, and high-risk patients as determined by the HEART score were 17%, 65%, and 18% of the population, respectively, without any significant differences between males and females. Non-invasive testing was similar between males and females when stratified by risk. Males categorized as high risk underwent more coronary angiogram (33% vs. 16%, p = 0.01) and PCI (18% vs. 8%, p = 0.04) than high risk females, but this was not seen in patients categorized as low or intermediate risk. Males experienced more MACE than females (8% vs. 3%, p = 0.001).
We identified no sex-based differences in risk-stratification or non-invasive testing when the CDP was used. High risk males, however, underwent more coronary angiogram and PCI than high risk females, and consequently males experienced more overall MACE than females. This disparity may be explained by sex-based differences in the pathophysiology driving each patient's presentation.
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