Comparative Genomics Reveals Chd1 as a Determinant of Nucleosome Spacing in Vivo

Packaging of genomic DNA into nucleosomes is nearly universally conserved in eukaryotes, and many features of the nucleosome landscape are quite conserved. Nonetheless, quantitative aspects of nucleosome packaging differ between species because, for example, the average length of linker DNA between nucleosomes can differ significantly even between closely related species. We recently showed that the difference in nucleosome spacing between two Hemiascomycete species-Saccharomyces cerevisiae and Kluyveromyces lactis-is established by trans-acting factors rather than being encoded in cis in the DNA sequence. Here, we generated several S. cerevisiae strains in which endogenous copies of candidate nucleosome spacing factors are deleted and replaced with the orthologous factors from K. lactis. We find no change in nucleosome spacing in such strains in which H1 or Isw1 complexes are swapped. In contrast, the K. lactis gene encoding the ATP-dependent remodeler Chd1 was found to direct longer internucleosomal spacing in S. cerevisiae, establishing that this remodeler is partially responsible for the relatively long internucleosomal spacing observed in K. lactis. By analyzing several chimeric proteins, we find that sequence differences that contribute to the spacing activity of this remodeler are dispersed throughout the coding sequence, but that the strongest spacing effect is linked to the understudied N-terminal end of Chd1. Taken together, our data find a role for sequence evolution of a chromatin remodeler in establishing quantitative aspects of the chromatin landscape in a species-specific manner

Chromatin \u27programming\u27 by sequence - is there more to the nucleosome code than %GC

The role of genomic sequence in directing the packaging of eukaryotic genomes into chromatin has been the subject of considerable recent debate. A new paper from Tillo and Hughes shows that the intrinsic thermodynamic preference of a given sequence in the yeast genome for the histone octamer can largely be captured with a simple model, and in fact is mostly explained by %GC. Thus, the rules for predicting nucleosome occupancy from genomic sequence are much less complicated than has been claimed

Ultraluminous infrared galaxies: mergers of sub-L* galaxies?

A sample of 27 low-redshift, mostly cool, ultraluminous infrared galaxies (ULIRGs) has been imaged at 1.6 μm with the Hubble Space Telescope (HST) Near-Infrared Camera and Multi-Object Spectrometer (NICMOS). The majority (67%) of the sample's galaxies are multiple-nucleus galaxies with projected separations of up to 17 kpc, and the rest of the sample (33%) are single-nucleus galaxies, as determined by the NICMOS angular resolution limit. The average observed, integrated (host+nucleus) H magnitude of our HST H sample ULIRGs is -24.3, slightly above that of an L* galaxy (MH = -24.2), and 52% of the sample's galaxies have sub-L* luminosities. The ULIRGs in the HST H sample are not generated as a result of the merging of two luminous (i.e., ≥L*) spiral galaxies. Instead, the interactions and mergers occur in general between two, or in some cases more, less massive sub-L* (0.3-0.5L*) galaxies. Only one out of the 49 nuclei identified in the entire HST H sample has the properties of a bright quasar-like nucleus. On average, the brightest nuclei in the HST H sample galaxies (i.e., cool ULIRGs) are 1.2 mag fainter than warm ULIRGs and low-luminosity Bright Quasar Survey quasars (BQS QSOs) and 2.6 mag fainter than high-luminosity BQS QSOs. Since the progenitor galaxies involved in the merger are sub-L* galaxies, the mass of the central black hole in these ULIRGs would be only about (1-2) × 107 M☉, if the bulge-to-black hole mass ratio of nearby galaxies holds for ULIRGs. The estimated mass of the central black hole is similar to that of nearby Seyfert 2 galaxies but at least 1 order of magnitude lower than the massive black holes thought to be located at the center of high-luminosity QSOs. Massive nuclear starbursts with constant star formation rates of 10-40 M☉ yr-1 could contribute significantly to the nuclear H-band flux and are consistent with the observed nuclear H-band magnitudes of the ULIRGs in the HST H sample. An evolutionary merging scenario is proposed for the generation of the different types of ULIRGs and QSOs on the basis of the masses of the progenitors involved in the merging process. According to this scenario, cool ULIRGs would be the end product of the merging of two or more low-mass (0.3L*-0.5L*) disk galaxies. Warm ULIRGs and low-luminosity QSOs would be generated by a merger involving intermediate-mass (0.5 L*) disk galaxies. Under this scenario, warm ULIRGs could still be the dust-enshrouded phases of UV-bright low-luminosity QSOs, but cool ULIRGs, which are most ULIRGs, would not evolve into QSOs

Rights, not rescue: trafficking (in)securities at the sport mega-event

We examine the impact of fantasies used in the redevelopment of sport mega-event cities on host communities; particularly as related to the male-dominated FIFA World Cup and forced prostitution. We start with a discussion of event fantasies, particularly those that circulate in relation to humanitarian aid and the alleged involvement of women and children in forced labour and sexual exploitation. We trace these fantasies across several FIFA host cities since the 2006 FIFA World Cup, hosted in Germany, to leverage continual and perpetuate attention (and profit) through the non-profit industrial complex. These fantasies have facilitated and coordinated collaborative consensus amongst state authorities and allies to act in a meaningful manner even as the evidence of forced prostitution is still scant—while the realities of people that continue to be subjected to violent and exploitative labour in the construction of stadia, athlete recruitment, or equipment and apparel industries are seldom addressed. We do this to question the lived impact of policies and personalities of rescue on people engaged, consensually, in erotic labour within host cities, that are often made target of rescue intervention. The figure of the proverbial sex slave, as a highly racialized and hypersexualized trope, is mobilized through the sport mega-event to further police the bodies of all women in labour and migration. We end with a cautious message to future host cities, particularly cities implicated in the 2026 FIFA World Cup within Mexico, Canada, and the United States, of the highly-profitable and politically-advantageous rhetoric of damsel in distress

Histone exchange is associated with activator function at transcribed promoters and with repression at histone loci

Transcription in eukaryotes correlates with major chromatin changes, including the replacement of old nucleosomal histones by new histones at the promoters of genes. The role of these histone exchange events in transcription remains unclear. In particular, the causal relationship between histone exchange and activator binding, preinitiation complex (PIC) assembly, and/or subsequent transcription remains unclear. Here, we provide evidence that histone exchange at gene promoters is not simply a consequence of PIC assembly or transcription but instead is mediated by activators. We further show that not all activators up-regulate gene expression by inducing histone turnover. Thus, histone exchange does not simply correlate with transcriptional activity, but instead reflects the mode of action of the activator. Last, we show that histone turnover is not only associated with activator function but also plays a role in transcriptional repression at the histone loci

Genome-wide histone modification patterns in Kluyveromyces Lactis reveal evolutionary adaptation of a heterochromatin-associated mark [preprint]

The packaging of eukaryotic genomes into nucleosomes plays critical roles in all DNA-templated processes, and chromatin structure has been implicated as a key factor in the evolution of gene regulatory programs. While the functions of many histone modifications appear to be highly conserved throughout evolution, some well-studied modifications such as H3K9 and H3K27 methylation are not found in major model organisms such as Saccharomyces cerevisiae, while other modifications gain/lose regulatory functions during evolution. To study such a transition we focused on H3K9 methylation, a heterochromatin mark found in metazoans and in the fission yeast S. pombe, but which has been lost in the lineage leading to the model budding yeast S. cerevisiae. We show that this mark is present in the relatively understudied yeast Kluyveromyces lactis, a Hemiascomycete that diverged from S. cerevisiae prior to the whole-genome duplication event that played a key role in the evolution of a primarily fermentative lifestyle. We mapped genome-wide patterns of H3K9 methylation as well as several conserved modifications. We find that well-studied modifications such as H3K4me3, H3K36me3, and H3S10ph exhibit generally conserved localization patterns. Interestingly, we show H3K9 methylation in K. lactis primarily occurs over highly-transcribed regions, including both Pol2 and Pol3 transcription units. We identified the H3K9 methylase as the ortholog of Set6, whose function in S. cerevisiae is obscure. Functionally, we show that deletion of KlSet6 does not affect highly H3K9me3-marked genes, providing another example of a major disconnect between histone mark localization and function. Together, these results shed light on surprising plasticity in the function of a widespread chromatin mark

Corticosterone Acts in the Nucleus Accumbens to Enhance Dopamine Signaling and Potentiate Reinstatement of Cocaine Seeking

Stressful life events are important contributors to relapse in recovering cocaine addicts, but the mechanisms by which they influence motivational systems are poorly understood. Studies suggest that stress may “set the stage” for relapse by increasing the sensitivity of brain reward circuits to drug-associated stimuli. We examined the effects of stress and corticosterone on behavioral and neurochemical responses of rats to a cocaine prime after cocaine self-administration and extinction. Exposure of rats to acute electric footshock stress did not by itself reinstate drug-seeking behavior but potentiated reinstatement in response to a subthreshold dose of cocaine. This effect of stress was not observed in adrenalectomized animals, and was reproduced in nonstressed animals by administration of corticosterone at a dose that reproduced stress-induced plasma levels. Pretreatment with the glucocorticoid receptor antagonist RU38486 did not block the corticosterone effect. Corticosterone potentiated cocaine-induced increases in extracellular dopamine in the nucleus accumbens (NAc), and pharmacological blockade of NAc dopamine receptors blocked corticosterone-induced potentiation of reinstatement. Intra-accumbens administration of corticosterone reproduced the behavioral effects of stress and systemic corticosterone. Corticosterone treatment acutely decreased NAc dopamine clearance measured by fast-scan cyclic voltammetry, suggesting that inhibition of uptake2-mediated dopamine clearance may underlie corticosterone effects. Consistent with this hypothesis, intra-accumbens administration of the uptake2 inhibitor normetanephrine potentiated cocaine-induced reinstatement. Expression of organic cation transporter 3, a corticosterone-sensitive uptake2 transporter, was detected on NAc neurons. These findings reveal a novel mechanism by which stress hormones can rapidly regulate dopamine signaling and contribute to the impact of stress on drug intake

Am I on Track? Evaluating Patient-Specific Weight Loss After Bariatric Surgery Using an Outcomes Calculator

PURPOSE: Individual weight loss outcomes after bariatric surgery can vary considerably. As a result, identifying and assisting patients who are not on track to reach their weight loss goals can be challenging. MATERIALS AND METHODS: Using a bariatric surgery outcomes calculator, which was formulated using a state-wide bariatric-specific data registry, predicted weight loss at 1 year after surgery was calculated on 658 patients who underwent bariatric surgery at 35 different bariatric surgery programs between 2015 and 2017. Patient characteristics, postoperative complications, and weight loss trajectories were compared between patients who met or exceeded their predicted weight loss calculation to those who did not based on observed to expected weight loss ratio (O:E) at 1 year after surgery. RESULTS: Patients who did not meet their predicted weight loss at 1 year (n = 237, 36%) had a mean O:E of 0.71, while patients who met or exceeded their prediction (n = 421, 63%) had a mean O:E = 1.14. At 6 months, there was a significant difference in the percent of the total amount of predicted weight loss between the groups (88% of total predicted weight loss for those that met their 1-year prediction vs 66% for those who did not, p \u3c 0.0001). Age, gender, procedure type, and risk-adjusted complication rates were similar between groups. CONCLUSION: Using a bariatric outcomes calculator can help set appropriate weight-loss expectations after surgery and also identify patients who may benefit from additional therapy prior to reaching their weight loss nadir

Re-sensitization of Mycobacterium smegmatis to Rifampicin Using CRISPR Interference Demonstrates Its Utility for the Study of Non-essential Drug Resistance Traits

© 2021 Faulkner, Cox, Goh, van Bohemen, Gibson, Liebster, Wren, Willcocks and Kendall. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). https://creativecommons.org/licenses/by/4.0/A greater understanding of the genes involved in antibiotic resistance in Mycobacterium tuberculosis (Mtb) is necessary for the design of improved therapies. Clustered regularly interspaced short palindromic repeat interference (CRISPRi) has been previously utilized in mycobacteria to identify novel drug targets by the demonstration of gene essentiality. The work presented here shows that it can also be usefully applied to the study of non-essential genes involved in antibiotic resistance. The expression of an ADP-ribosyltransferase (Arr) involved in rifampicin resistance in Mycobacterium smegmatis was silenced using CRISPRi and the impact on rifampicin susceptibility was measured. Gene silencing resulted in a decrease in the minimum inhibitory concentration (MIC) similar to that previously reported in an arr deletion mutant. There is contradictory evidence for the toxicity of Streptococcus pyogenes dCas9 (dCas9 Spy) in the literature. In this study the expression of dCas9 Spy in M. smegmatis showed no impact on viability. Silencing was achieved with concentrations of the aTc inducer lower than previously described and with shorter induction times. Finally, designing small guide RNAs (sgRNAs) that target transcription initiation, or the early stages of elongation had the most impact on rifampicin susceptibility. This study demonstrates that CRISPRi based gene silencing can be as impactful as gene deletion for the study of non-essential genes and further contributes to the knowledge on the design and induction of sgRNAs for CRISPRi. This approach can be applied to other non-essential antimicrobial resistance genes such as drug efflux pumps.Peer reviewe