No abstract

Gene loops are formed by the interaction of initiation and termination factors occupying the distal ends of a gene during transcription. RNAPII is believed to affect gene looping indirectly owing to its essential role in transcription. The results presented here, however, demonstrate a direct role of RNAPII in gene looping through the Rpb4 subunit. 3C analysis revealed that gene looping is abolished in the rpb4Δ mutant. In contrast to the other looping-defective mutants, rpb4Δ cells do not exhibit a transcription termination defect. RPB4 overexpression, however, rescued the transcription termination and gene looping defect of sua7-1, a mutant of TFIIB. Furthermore, RPB4 overexpression rescued the ssu72-2 gene looping defect, while SSU72 overexpression restored the formation of gene loops in rpb4Δ cells. Interestingly, the interaction of TFIIB with Ssu72 is compromised in rpb4Δ cells. These results suggest that the TFIIB–Ssu72 interaction, which is critical for gene loop formation, is facilitated by Rpb4. We propose that Rpb4 is promoting the transfer of RNAPII from the terminator to the promoter for reinitiation of transcription through TFIIB–Ssu72 mediated gene looping.

Abstract. The large number of tweets generated daily is providing decision makers with means to obtain insights into recent events around the globe in near real-time. The main barrier for extracting such insights is the impossibility of manual inspection of a diverse and dynamic amount of information. This problem has attracted the attention of industry and research communities, resulting in algorithms for the automatic extraction of semantics in tweets and linking them to machine readable resources. While a tweet is shallowly comparable to any other textual content, it hides a complex and challenging structure that requires domainspecific computational approaches for mining semantics from it. The NEEL challenge series, established in 2013, has contributed to the collection of emerging trends in the field and definition of standardised benchmark corpora for entity recognition and linking in tweets, ensuring high quality labelled data that facilitates comparisons between different approaches. This article reports the findings and lessons learnt through an analysis of specific characteristics of the created corpora, limitations, lessons learnt from the different participants and pointers for furthering the field of entity recognition and linking in tweets.

the widely used mood stabilizer valproate (VpA) causes perturbation of energy metabolism, which is implicated in both the therapeutic mechanism of action of the drug as well as drug toxicity. to gain insight into these mechanisms, we determined the effects of VPA on energy metabolism in yeast. VpA treatment increased levels of glycolytic intermediates, increased expression of glycolysis genes, and increased ethanol production. increased glycolysis was likely a response to perturbation of mitochondrial function, as reflected in decreased membrane potential and oxygen consumption. interestingly, yeast, mouse liver, and isolated bovine cytochrome c oxidase were directly inhibited by the drug, while activities of other oxidative phosphorylation complexes (III and V) were not affected. These findings have implications for mechanisms of therapeutic action and toxicity. Bipolar disorder (BD) is a severe psychiatric illness characterized by shifts in mood, ranging from mania to depression. It affects at least 1% of the population and leads to suicide in 15% of cases 1. BD patients exhibit a higher prevalence of obesity, cardiovascular disease, and diabetes than the general population 2,3. Many studies have shown that the pathophysiology of BD involves altered energy metabolism 4-8. While most of the metabolic markers measured indicate mitochondrial dysfunction in BD 9-12 , some studies have suggested the presence of increased mitochondrial activity in the manic phase of BD 13 , including increased energy generation 14 , basal metabolic rate 15 , uric acid 16 , and calcium ions 17. Valproate (VPA) is one of several mood stabilizers approved by the FDA for the treatment of BD 18,19 , epilepsy 20,21 , and migraine 22. The mechanism of action of VPA is not understood 23. VPA is effective in only 40-60% of cases and can cause serious side effects, including hepatotoxicity and teratogenicity 24. Hepatotoxicity can be life-threatening 25,26 and may occur even at therapeutic doses 27. Although rare, lethal hepatotoxicity associated with VPA has been described in both children 28 and adults 29. The prominent feature of this type of hepatotoxicity is microvesicular steatosis 30 , consistent with mitochondrial dysfunction 31. In agreement with this, patients with congenital defects in mitochondrial metabolism are at a higher risk for susceptibility to VPA toxicity 32-34. VPA exerts numerous documented effects on mitochondrial metabolism. It is metabolized by and inhibits ß-oxidation through several mechanisms 35. VPA and its metabolites sequester coenzyme A (CoA), depleting mitochondrial CoA 36. Furthermore, studies suggest that both unesterified VPA as well as VPA acyl-CoA esters inhibit fatty acid oxidation enzymes 37,38. In addition to affecting ß-oxidation, VPA inhibits α-ketoglutarate dehydrogenase, a key enzyme of the tricarboxylic acid (TCA) cycle 39,40. Inhibition of this enzyme is a proposed mechanism underlying decreased TCA cycle flux in the presence of VPA 41. VPA also decreases levels of carnitine 42,43 , which transpo...

words)Gene loops are formed by the interaction of initiation and termination factors occupying the distal ends of a gene during transcription. RNAPII is believed to affect gene looping indirectly owing to its essential role in transcription. The results presented here, however, demonstrate a direct role of RNAPII in gene looping through the Rpb4 subunit. 3C analysis revealed that gene looping is abolished in the rpb4∆ mutant. In contrast to the other looping-defective mutants, rpb4∆ cells do not exhibit a transcription termination defect. RPB4 overexpression, however, rescued the transcription termination and gene looping defect of sua7-1, a mutant of TFIIB. Furthermore, RPB4 overexpression rescued the ssu72-2 gene looping defect, while SSU72 overexpression restored the formation of gene loops in rpb4∆ cells. Interestingly, the interaction of TFIIB with Ssu72 is compromised in rpb4∆ cells. These results suggest that the TFIIB-Ssu72 interaction, which is critical for gene loop formation, is facilitated by Rpb4. We propose that Rpb4 is promoting the transfer of RNAPII from the terminator to the promoter for reinitiation of transcription through TFIIB-Ssu72 mediated gene looping.[14]. Besides activators and TFIIB, TFIIH and Mediator complex also play a critical role in gene loop formation by directly interacting with the CF1 and CPF 3'-end processing/termination factors [12,16]. It is generally believed that RNAPII is not directly involved in formation of gene loops, but is a rather passive player in the process. Since gene looping is a transcription-dependent process, it has been presumed that all mutations that affect transcription will also alter gene looping. Accordingly, gene looping was completely abolished in the rpb1-1 mutant [17].The structure of RNAPII is highly conserved among eukaryotes. In all eukaryotes from yeast to humans, RNAPII is composed of 12 subunits. Only Saccharomyces cerevisiae RNAPII exists in a 10-subunit core and a dissociable subcomplex formed by Rpb4 and Rpb7 [18,19].The 12 subunits of RNAPII have been implicated in different functions during the process of transcription. The two largest subunits, Rpb1 and Rpb2, are required for binding to the DNA template. Rpb1 contains a groove for the entry of deoxyribonucleotides. Rpb7 has two RNA binding domains and plays a pivotal role in mRNA decay [20]. Rpb9 has been implicated in start-site selection, but is dispensable for assembly of the 10-subunit enzyme (Hull et al., 1995). While the two largest subunits, Rpb1 and Rpb2, have well-established roles in the initiation of transcription, a few published reports suggest that some of the RNAPII subunits function in the termination of transcription. The CTD of the largest subunit Rpb1 consists of multiple repeats of the heptapeptide sequence (YSPTSPS). The phosphorylation of Ser2 of the CTD is critical for the recruitment of 3'-end processing factors and for termination of transcription [21,22]. In the crystal structure, the Rpb3/Rpb11 heterodimer lies in close proximity of the RNA exit channel [...