Rbfox2 controls autoregulation in RNA-binding protein networks

The tight regulation of splicing networks is critical for organismal development. To maintain robust splicing patterns, many splicing factors autoregulate their expression through alternative splicing-coupled nonsense-mediated decay (AS-NMD). However, as negative autoregulation results in a self-limiting window of splicing factor expression, it is unknown how variations in steady-state protein levels can arise in different physiological contexts. Here, we demonstrate that Rbfox2 cross-regulates AS-NMD events within RNA-binding proteins to alter their expression. Using individual nucleotide-resolution cross-linking immunoprecipitation coupled to high-throughput sequencing (iCLIP) and mRNA sequencing, we identified >200 AS-NMD splicing events that are bound by Rbfox2 in mouse embryonic stem cells. These “silent” events are characterized by minimal apparent splicing changes but appreciable changes in gene expression upon Rbfox2 knockdown due to degradation of the NMD-inducing isoform. Nearly 70 of these AS-NMD events fall within genes encoding RNA-binding proteins, many of which are autoregulated. As with the coding splicing events that we found to be regulated by Rbfox2, silent splicing events are evolutionarily conserved and frequently contain the Rbfox2 consensus UGCAUG. Our findings uncover an unexpectedly broad and multilayer regulatory network controlled by Rbfox2 and offer an explanation for how autoregulatory splicing networks are tuned.United States. Public Health Service (RO1-GM34277)National Cancer Institute (U.S.). Integrative Cancer Biology Program (Grant CA112967)National Cancer Institute (U.S.) (Koch Institute Support (Core) Grant P30-CA14051)David H. Koch Graduate Fellowshi

Detained introns are a novel, widespread class of post-transcriptionally spliced introns

Deep sequencing of embryonic stem cell RNA revealed many specific internal introns that are significantly more abundant than the other introns within polyadenylated transcripts; we classified these as “detained” introns (DIs). We identified thousands of DIs, many of which are evolutionarily conserved, in human and mouse cell lines as well as the adult mouse liver. DIs can have half-lives of over an hour yet remain in the nucleus and are not subject to nonsense-mediated decay (NMD). Drug inhibition of Clk, a stress-responsive kinase, triggered rapid splicing changes for a specific subset of DIs; half showed increased splicing, and half showed increased intron detention, altering transcript pools of >300 genes. Srsf4, which undergoes a dramatic phosphorylation shift in response to Clk kinase inhibition, regulates the splicing of some DIs, particularly in genes encoding RNA processing and splicing factors. The splicing of some DIs—including those in Mdm4, a negative regulator of p53—was also altered following DNA damage. After 4 h of Clk inhibition, the expression of >400 genes changed significantly, and almost one-third of these are p53 transcriptional targets. These data suggest a widespread mechanism by which the rate of splicing of DIs contributes to the level of gene expression.National Institutes of Health (U.S.) (Grant R01 GM34277-23)American Cancer Society (Novartis Institutes of Biomedical Research Postdoctoral Research Fellowship)National Cancer Institute (U.S.) (Koch Institute Support (Core) Grant P30-CA14051

Gene Loss and Adaptation to Hominids Underlie the Ancient Origin of HIV-1

SummaryHIV-1 resulted from cross-species transmission of SIVcpz, a simian immunodeficiency virus that naturally infects chimpanzees. SIVcpz, in turn, is a recombinant between two SIV lineages from Old World monkeys. Lentiviral interspecies transmissions are partly driven by the evolution and capacity of viral accessory genes, such as vpx, vpr, and vif, to antagonize host antiviral factors, such as SAMHD1 and the APOBEC3 proteins. We show that vpx, which in other lentiviruses antagonizes SAMHD1, was deleted during the creation of SIVcpz. This genomic deletion resulted in the reconstruction of the overlapping vif gene by “overprinting,” creating a unique vif that overlaps in its 3′ end with the vpr gene and can antagonize hominid APOBEC3s. Moreover, passage of SIVs through chimpanzees facilitated the subsequent adaptation of HIV-1 to humans. Thus, HIV-1 originated through a series of gene loss and adaptation events that generated its chimpanzee precursor and lowered the species barrier to human infection

An analytic toy model for relativistic accretion in Kerr spacetime

We present a relativistic model for the stationary axisymmetric accretion flow of a rotating cloud of non-interacting particles falling onto a Kerr black hole. Based on a ballistic approximation, streamlines are described analytically in terms of timelike geodesics, while a simple numerical scheme is introduced for calculating the density field. A novel approach is presented for describing all of the possible types of orbit by means of a single analytic expression. This model is a useful tool for highlighting purely relativistic signatures in the accretion flow dynamics coming from a strong gravitational field with frame-dragging. In particular, we explore the coupling due to this between the spin of the black hole and the angular momentum of the infalling matter. Moreover, we demonstrate how this analytic solution may be used for benchmarking general relativistic numerical hydrodynamics codes by comparing it against results of smoothed particle hydrodynamics simulations for a collapsar-like setup. These simulations are performed first for a ballistic flow (with zero pressure) and then for a hydrodynamical one where we measure the effects of pressure gradients on the infall, thus exploring the extent of applicability of the ballistic approximation.Comment: 15 pages, 8 figures, references and minor changes added to match version accepted for publication in MNRA

Racial and Ethnic Differences in Serum Cotinine Levels of Cigarette Smokers Third National Health and Nutrition Examination Survey, 1988-1991

Context.— Cotinine, a metabolite of nicotine, is a marker of exposure to tobacco smoke. Previous studies suggest that non-Hispanic blacks have higher levels of serum cotinine than non-Hispanic whites who report similar levels of cigarette smoking. Objective.— To investigate differences in levels of serum cotinine in black, white, and Mexican American cigarette smokers in the US adult population. Design.— Third National Health and Nutrition Examination Survey, 1988-1991. Participants.— A nationally representative sample of persons aged 17 years or older who participated in the survey. Outcome Measures.— Serum cotinine levels by reported number of cigarettes smoked per day and by race and ethnicity. Results.— A total of 7182 subjects were involved in the study; 2136 subjects reported smoking at least 1 cigarette in the last 5 days. Black smokers had cotinine concentrations substantially higher at all levels of cigarette smoking than did white or Mexican American smokers (P\u3c.001). Serum cotinine levels for blacks were 125 nmol/L (22 ng/mL) (95% confidence interval [CI], 79-176 nmol/L [14-31 ng/mL]) to 539 nmol/L (95 ng/mL) (95% CI, 289-630 nmol/L [51-111 ng/mL]) higher than for whites and 136 nmol/L (24 ng/mL) (95% CI, 85-182 nmol/L [15-32 ng/mL]) to 641 nmol/L (113 ng/mL) (95% CI, 386-897 nmol/L [68-158 ng/mL]) higher than for Mexican Americans. These differences do not appear to be attributable to differences in environmental tobacco smoke exposure or in number of cigarettes smoked. Conclusions.— To our knowledge, this study provides the first evidence from a national study that serum cotinine levels are higher among black smokers than among white or Mexican American smokers. If higher cotinine levels among blacks indicate higher nicotine intake or differential pharmacokinetics and possibly serve as a marker of higher exposure to cigarette carcinogenic components, they may help explain why blacks find it harder to quit and are more likely to experience higher rates of lung cancer than white smokers