A phase I study of Hemay022, an irreversible dual EGFR/HER2 tyrosine kinase inhibitor in Chinese patients with HER2-positive advanced breast cancer.

Objective: Hemay022 is a novel small-molecule and an irreversible tyrosine kinase inhibitor with the target of epidermal growth factor receptor (EGFR)/human epidermal growth factor receptor 2 (HER2), which demonstrated anti-tumor activity in preclinical studies. This first-in-human study evaluated the safety, pharmacokinetics, tolerability and preliminary anti-tumor activity of Hemay022 in HER2-positive advanced breast cancer patients. Methods: Heavily pretreated patients with HER2-positive advanced breast cancer were assigned to eight dose cohorts in a 3+3 dose-escalation pattern at doses of 50-600 mg QD and 300 mg BID. Eligible patients were given a single dose of Hemay022 on d 1 in week 0, followed by once daily continuous doses for four weeks in 28-day cycles. Pharmacokinetic samples were obtained on d 1 and d 28. Clinical responses were assessed every eight weeks. Results: Twenty-eight patients with advanced breast cancer were treated with Hemay022. The most frequently reported drug-related adverse events were diarrhoea (85.7%), vomiting (28.6%), nausea (25.0%) and decreased appetite (17.9%). No grade 4 drug-related adverse events were reported. At 50-600 mg doses, steady state areas under the concentration-time curve and peak concentrations increased with doses. One patient achieved complete response (CR), and three achieved partial response (PR). The objective response rate (ORR) and disease control rate (DCR) were 14.3% and 46.4% in 28 patients, respectively. The median progression-free survival (PFS) was 3.98 months. Conclusions: Hemay022 at the dose of 500 mg once daily was well tolerated. The pharmacokinetic properties and encouraging anti-tumor activities of Hemay022 in advanced breast cancer patients warranted further evaluation of Hemay022 for treating breast cancer patients in the current phase III trial (No. NCT05122494).

The potential neurological effect of the COVID-19 vaccines: A review.

The coronavirus disease 2019 caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has become a pandemic with people infected in almost all countries. The most efficient solution to end this pandemic is a safe and efficient vaccine. Classic platforms are used to develop vaccines including live-attenuated vaccine, inactivated vaccine, protein subunit vaccine, and viral vector. Nucleic acid vaccine uses next-generation platforms for their development. Vaccines are now rushing to the market. Eleven candidates are in advance development. These comprise inactivated vaccines, viral vector vaccine, nucleic acid vaccine, and the protein subunit vaccine platform, which are now quite advanced in trials in various geographic and ethnic populations. The reported severe adverse effects raised the worries about their safety. It becomes critical to know whether these vaccines will cause neurologic disorders like previously recognized vaccine-related demyelinating diseases, fever-induced seizure, and other possible deficits. We reviewed the most promising COVID-2 vaccines with a particular interest in mechanism(s) and adverse effect(s). We exemplify potential neurological problems these vaccines could cause by looking at previous studies. The current evidence indicated a minor risk of the acute neurological disorders after the application. The observation of the long-time effect is still needed.

New onset acute symptomatic seizure and risk factors in coronavirus disease 2019: A retrospective multicenter study.

Our aim was to clarify the incidence and risk of acute symptomatic seizures in people with coronavirus disease 2019 (COVID-19). This multicenter retrospective study enrolled people with COVID-19 from January 18 to February 18, 2020 at 42 government-designated hospitals in Hubei province, the epicenter of the epidemic in China; Sichuan province; and Chongqing municipality. Data were collected from medical records by 11 neurologists using a standard case report form. A total of 304 people were enrolled, of whom 108 had a severe condition. None in this cohort had a known history of epilepsy. Neither acute symptomatic seizures nor status epilepticus was observed. Two people had seizurelike symptoms during hospitalization due to acute stress reaction and hypocalcemia, and 84 (27%) had brain insults or metabolic imbalances during the disease course known to increase the risk of seizures. There was no evidence suggesting an additional risk of acute symptomatic seizures in people with COVID-19. Neither the virus nor potential risk factors for seizures seem to be significant risks for the occurrence of acute symptomatic seizures in COVID-19.

Uncoupling transcription from covalent histone modification.

It is widely accepted that transcriptional regulation of eukaryotic genes is intimately coupled to covalent modifications of the underlying chromatin template, and in certain cases the functional consequences of these modifications have been characterized. Here we present evidence that gene activation in the silent heterochromatin of the yeast Saccharomyces cerevisiae can occur in the context of little, if any, covalent histone modification. Using a SIR-regulated heat shock-inducible transgene, hsp82-2001, and a natural drug-inducible subtelomeric gene, YFR057w, as models we demonstrate that substantial transcriptional induction (>200-fold) can occur in the context of restricted histone loss and negligible levels of H3K4 trimethylation, H3K36 trimethylation and H3K79 dimethylation, modifications commonly linked to transcription initiation and elongation. Heterochromatic gene activation can also occur with minimal H3 and H4 lysine acetylation and without replacement of H2A with the transcription-linked variant H2A.Z. Importantly, absence of histone modification does not stem from reduced transcriptional output, since hsp82-ΔTATA, a euchromatic promoter mutant lacking a TATA box and with threefold lower induced transcription than heterochromatic hsp82-2001, is strongly hyperacetylated in response to heat shock. Consistent with negligible H3K79 dimethylation, dot1Δ cells lacking H3K79 methylase activity show unimpeded occupancy of RNA polymerase II within activated heterochromatic promoter and coding regions. Our results indicate that large increases in transcription can be observed in the virtual absence of histone modifications often thought necessary for gene activation.

A critical role for Pol II CTD phosphorylation in heterochromatic gene activation.

How gene activation works in heterochromatin, and how the mechanism might differ from the one used in euchromatin, has been largely unexplored. Previous work has shown that in SIR-regulated heterochromatin of Saccharomyces cerevisiae, gene activation occurs in the absence of covalent histone modifications and other alterations of chromatin commonly associated with transcription.Here we demonstrate that such activation occurs in a substantial fraction of cells, consistent with frequent transcriptional bursting, and this raises the possibility that an alternative activation pathway might be used. We address one such possibility, Pol II CTD phosphorylation, and explore this idea using a natural telomere-linked gene, YFR057w, as a model. Unlike covalent histone modifications, we find that Ser2, Ser5 and Ser7 CTD phosphorylated Pol II is prevalent at the drug-induced heterochromatic gene. Particularly enriched relative to the euchromatic state is Ser2 phosphorylation. Consistent with a functional role for Ser2P, YFR057w is negligibly activated in cells deficient in the Ser2 CTD kinases Ctk1 and Bur1 even though the gene is strongly stimulated when it is placed in a euchromatic context. Collectively, our results are consistent with a critical role for Ser2 CTD phosphorylation in driving Pol II recruitment and transcription of a natural heterochromatic gene - an activity that may supplant the need for histone epigenetic modifications.

Efficacy and safety of add-on antiseizure medications for focal epilepsy: A network meta-analysis.

OBJECTIVE: Several antiseizure medications (ASMs) have been approved for the treatment of focal epilepsy. However, there is a paucity of evidence on direct comparison of ASMs. We evaluated the comparative efficacy and safety of all approved add-on ASMs for the treatment of focal epilepsy using network meta-analysis. METHODS: Data through extensive literature search was retrieved from PubMed, Embase, Cochrane, and ClinicalTrial.gov databases using predefined search terms from inception through March 2023. PRISMA reporting guidelines (CRD42023403450) were followed in this study. Efficacy outcomes assessed were ≥50%, ≥75%, and 100% responder rates. Patient retention rate and safety outcomes such as overall treatment-emergent adverse events (TEAEs) and individual TEAEs were assessed. "Gemtc" 4.0.4 package was used to perform Bayesian analysis. Outcomes are reported as relative risks (RRs) and 95% confidence interval (CI). RESULTS: Literature search retrieved 5807 studies of which, 75 studies were included in the analysis. All ASMs showed significantly higher ≥50% responder rate compared with placebo. Except the ≥75% seizure frequency reduction for zonisamide (2.23; 95% CI: 1.00-5.70) and 100% for rufinamide (2.03; 95% CI: 0.54-11.00), all other interventions showed significantly higher ≥75% and 100% responder rates compared with placebo. Among treatments, significantly higher 100% responder rate was observed with cenobamate compared to eslicarbazepine (10.71; 95% CI: 1.56-323.9) and zonisamide (10.63; 95% CI: 1.37-261.2). All ASMs showed a lower patient retention rate compared to placebo, with the least significant value observed for oxcarbazepine (0.77; 95% CI: 0.7-0.84). Levetiracetam showed a lower risk of incidence (1.0; 95%CI: 0.94-1.1; SUCRA: 0.885067) for overall TEAE compared with other medications. SIGNIFICANCE: All approved ASMs were effective as add-on treatment for focal epilepsy. Of the ASMs included, cenobamate had the greatest likelihood of allowing patients to attain seizure freedom. PLAIN LANGUAGE SUMMARY: This article compares the efficacy and safety of antiseizure medications (ASMs) currently available to neurologists in the treatment of epileptic patients. Several newer generation ASMs that have been developed may be as effective or better than the older medications. We included 75 studies in the analysis. In comparison, all drugs improved ≥50%, ≥75% and 100% responder rates compared to control, except for Zonisamide and Rufinamide in the ≥75% and 100% responder rate categories. Retention of patients undergoing treatment was lower in drugs than placebo. All drugs were tolerated, the levetiracetam showed the best tolerability. Cenobamate more likely help completely to reduce seizures.

Localized activity alternations in periventricular nodular heterotopia-related epilepsy.

OBJECTIVE: Periventricular nodular heterotopia (PNH) is a common type of heterotopia usually characterized by epilepsy. Previous studies have identified alterations in structural and functional connectivity related to this disorder, but its local functional neural basis has received less attention. The purpose of this study was to combine univariate analysis and a Gaussian process classifier (GPC) to assess local activity and further explore neuropathological mechanisms in PNH-related epilepsy. METHODS: We used a 3.0-T scanner to acquire resting-state data and measure local regional homogeneity (ReHo) alterations in 38 patients with PNH-related epilepsy and 38 healthy controls (HCs). We first assessed ReHo alterations by comparing the PNH group to the HC group using traditional univariate analysis. Next, we applied a GPC to explore whether ReHo could be used to differentiate PNH patients from healthy patients at an individual level. RESULTS: Compared to HCs, PNH-related epilepsy patients exhibited lower ReHo in the left insula extending to the putamen as well as in the subgenual anterior cingulate cortex (sgACC) extending to the orbitofrontal cortex (OFC) [p < 0.05, family-wise error corrected]. Both of these regions were also correlated with epilepsy duration. Furthermore, the ReHo GPC classification yielded a 76.32% accuracy (sensitivity = 71.05% and specificity = 81.58%) with p < 0.001 after permutation testing. INTERPRETATION: Using the resting-state approach, we identified localized activity alterations in the left insula extending to the putamen and the sgACC extending to the OFC, providing pathophysiological evidence of PNH. These local connectivity patterns may provide a means to differentiate PNH patients from HCs.

First add-on lacosamide treatment in children with focal epilepsy in China: A multi-centre real-life cohort study.

AIM: To assess the effectiveness and safety of lacosamide (LCM) as the first add-on therapy for children with focal epilepsy at multiple centres in China. METHOD: Children aged 4-16 years with focal epilepsy from 13 epilepsy centres were included in this study. All patients were treated with LCM as the first add-on treatment and followed up for 26 weeks. The seizure frequency, seizure-free rate, ≥50% response rate, retention rate, and incidence of adverse drug reactions after the addition of LCM were analysed. RESULTS: Ninety-nine children (58 males; aged 4-16 years; mean age 8.51 ± 2.95 years) were enroled. The mean age at first seizure was 5.74 ± 3.12 years. All patients were administered LCM as the first add-on treatment for focal epilepsy. Twenty-eight patients (28/99, 28.28%) did not experience seizures during the follow-up period. The ≥50% response rates were 80.81% (80/99), 93.88% (92/98), 98.98% (97/98), and 100.0% (98/98) at 6 weeks (visit two), 10 weeks (visit three), 18 weeks (visit four), and 26 weeks (visit five), respectively, compared to that at baseline (visit one). The intelligence scores decreased in 12 participants, remained unchanged in 64, and increased in 16. Adverse events occurred in three participants during the trial, all of which were mild. INTERPRETATION: LCM was effective as the first add-on therapy in this real-life multi-centre study of a paediatric population with focal epilepsy. Further prospective studies with long-term follow-up periods are needed to confirm the effectiveness and tolerability of LCM.

Lacosamide as the first add-on therapy in adult patients with focal epilepsy: A multicenter real-world study.

Background: Prospective observations on the effectiveness, safety, tolerance, and influence of comorbidity of add-on lacosamide (LCM) therapy are still lacking, especially for domestic generic LCM in China. Objective: In this multicenter real-world study, we aimed to evaluate lacosamide (LCM) as the first add-on therapy in adult Chinese patients with focal epilepsy that had initially been treated with monotherapy. Methods: A cohort of consecutive focal epilepsy patients aged over 16 years were enrolled and followed at the multi-epilepsy centers in China. LCM was prescribed as the first add-on therapy. The main outcome measures included seizure frequency and response rate. Data on seizure-free rate, retention rate, scales of depression and anxiety, and adverse events were also collected as additional outcome measures. Results: A total number of 107 adult subjects (60 men, 56.07%) were enrolled. The mean age was 37.16 ± 15.01 years, and the mean age at seizure onset was 312.35 ± 199.97 months. After the LCM add-on therapy, the ≥50% response rates were 76.19, 81.73, 94.12, and 95.79% at the visit at 4 weeks (visit 2), 8 weeks (visit 3), 16 weeks (visit 4), and 24 weeks (visit 5), respectively, compared to the baseline (visit 1). A total of 34 patients (31.78%) had no seizures during the whole follow-up period. The posttreatment emotional performance of the 97 subjects, defined as generalized anxiety disorder (GAD) and Neurological Disorders Depression Inventory (NDDI) scores, was significantly better than the baseline one. Only one patient suffered from mild dizziness. Conclusion: LCM as the first add-on therapy in adult focal epilepsy in China was effective and safe. Further prospective studies with long-term follow-up periods are needed to confirm our present findings. Clinical trial registration: http://www.chictr.org.cn, ChiCTR2100042485.

Up-regulation of cholesterol synthesis pathways and limited neurodegeneration in a knock-in Sod1 mutant mouse model of ALS.

Amyotrophic lateral sclerosis (ALS) is a severe neurodegenerative disorder affecting brain and spinal cord motor neurons. Mutations in the copper/zinc superoxide dismutase gene ( SOD1 ) are associated with ∼20% of inherited and 1-2% of sporadic ALS cases. Much has been learned from mice expressing transgenic copies of mutant SOD1, which typically involve high-level transgene expression, thereby differing from ALS patients expressing one mutant gene copy. To generate a model that more closely represents patient gene expression, we created a knock-in point mutation (G85R, a human ALS-causing mutation) in the endogenous mouse Sod1 gene, leading to mutant SOD1 G85R protein expression. Heterozygous Sod1 G85R mutant mice resemble wild type, whereas homozygous mutants have reduced body weight and lifespan, a mild neurodegenerative phenotype, and express very low mutant SOD1 protein levels with no detectable SOD1 activity. Homozygous mutants exhibit partial neuromuscular junction denervation at 3-4 months of age. Spinal cord motor neuron transcriptome analyses of homozygous Sod1 G85R mice revealed up-regulation of cholesterol synthesis pathway genes compared to wild type. Transcriptome and phenotypic features of these mice are similar to Sod1 knock-out mice, suggesting the Sod1 G85R phenotype is largely driven by loss of SOD1 function. By contrast, cholesterol synthesis genes are down-regulated in severely affected human TgSOD1 G93A transgenic mice at 4 months. Our analyses implicate dysregulation of cholesterol or related lipid pathway genes in ALS pathogenesis. The Sod1 G85R knock-in mouse is a useful ALS model to examine the importance of SOD1 activity in control of cholesterol homeostasis and motor neuron survival. SIGNIFICANCE STATEMENT: Amyotrophic lateral sclerosis is a devastating disease involving the progressive loss of motor neurons and motor function for which there is currently no cure. Understanding biological mechanisms leading to motor neuron death is critical for developing new treatments. Using a new knock-in mutant mouse model carrying a Sod1 mutation that causes ALS in patients, and in the mouse, causes a limited neurodegenerative phenotype similar to Sod1 loss-of-function, we show that cholesterol synthesis pathway genes are up-regulated in mutant motor neurons, whereas the same genes are down-regulated in transgenic SOD1 mice with a severe phenotype. Our data implicate dysregulation of cholesterol or other related lipid genes in ALS pathogenesis and provide new insights that could contribute to strategies for disease intervention.

Long-Term Prognosis of Patients With Anti-N-Methyl-D-Aspartate Receptor Encephalitis Who Underwent Teratoma Removal: An Observational Study.

Objective: This study aimed to evaluate the clinical characteristics and long-term surgical outcomes of patients with anti-N-methyl-D-aspartate receptor (NMDAR) encephalitis with teratoma. Methods: Patients who were admitted to West China Hospital from June 2012 to June 2019 and diagnosed with anti-NMDAR encephalitis were enrolled in the study. Medical records were reviewed prospectively to gather clinical characteristic data. Patients were followed up at long-term every 3 months. Results: This study included 192 patients, among whom 21 (10.9%) were detected with having a teratoma. Patients included 20 women, with a mean age of 24.62 ± 7.61 years. Seizure and psychiatric symptoms were the most dominant symptoms in both groups, followed by memory deficits. Central hypoventilation (52.4 vs. 17%, p < 0.001) and decreased consciousness (71.4 vs. 31.3%, p = 0.002) were significantly more frequent in patients with teratoma than in those without. Moreover, the anti-NMDAR antibody titer was higher (p = 0.021) and the baseline modified Rankin scale score was lower (p = 0.004) in patients with teratoma than in those without. First-line immunotherapy was performed in 21 (100%) patients with teratoma and 167 (97.7%) patients without teratoma. All patients with teratoma had the tumor removed. During follow-up, two (9.5%) patients with teratoma and 11 (6.4%) patients without teratoma died, whereas 1 (4.8%) patient with teratoma and 37 (21.6%) patients without teratoma had relapses. Overall, 19 (90.5%) patients with teratoma and 151 (88.3%) patients without teratoma achieved favorable clinical outcomes at the final follow-up. Conclusions: With early detection and removal of teratoma, most patients with anti-NMDAR encephalitis and teratoma achieved a favorable long-term prognosis.

Stable and orally bio-available pro-drugs of CPS11.

Stable and orally bio-available pro-drugs of CPS11 were synthesized. They are active on human umbilical vein endothelial cell proliferation assay and tube formation assay. The therapeutic efficacy and safety of 4 as a single agent or combined with Taxol in the treatment of MX-1 human breast cancer xenograft were evaluated. Compound 4 as a single agent failed to produce an anti-tumor activity, while it significantly enhanced antitumor potency of Taxol.

A Convolutional Neural Network Combined With Prototype Learning Framework for Brain Functional Network Classification of Autism Spectrum Disorder.

The application of deep learning methods in brain disease diagnosis is becoming a new research hotspot. This study constructed brain functional networks based on the functional magnetic resonance imaging (fMRI) data, and proposed a novel convolutional neural network combined with a prototype learning (CNNPL) framework to classify brain functional networks for the diagnosis of autism spectrum disorder (ASD). At the bottom of CNNPL, traditional CNN was employed as the basic feature extractor, while at the top of CNNPL multiple prototypes were automatically learnt on the features to represent different categories. A generalized prototype loss based on distance cross-entropy was proposed to jointly learn the parameters of the CNN feature extractor and the prototypes. The classification was implemented with prototype matching. A transfer learning strategy was introduced to our CNNPL for weight initialization in the subsequent fine-tuning phase to promote model training. We conducted systematic experiments on the aggregate multi-sites ASD dataset. Experimental results revealed that our model outperforms the current state-of-the-art methods in ASD classification and can reliably learn inter-site biomarkers, indicating the robustness of our model on large-scale dataset with inter-site variability. Furthermore, our model demonstrated robust learning capability for high-level organization of brain functionality. Our study also identified important brain regions as biomarkers associated with ASD classification. Together, our proposed model provides a promising solution for learning and classifying brain functional networks, and thus contributes to the biomarker extraction and imaging diagnosis of ASD.

New onset neurologic events in people with COVID-19 in 3 regions in China.

OBJECTIVE: To investigate new-onset neurologic impairments associated with coronavirus disease 2019 (COVID-19). METHODS: A retrospective multicenter cohort study was conducted between January 18 and March 20, 2020, including people with confirmed COVID-19 from 56 hospitals officially designated in 3 Chinese regions; data were extracted from medical records. New-onset neurologic events as assessed by neurology consultants based on manifestations, clinical examination, and investigations were noted, in which critical events included disorders of consciousness, stroke, CNS infection, seizures, and status epilepticus. RESULTS: We enrolled 917 people with average age 48.7 years and 55% were male. The frequency of new-onset critical neurologic events was 3.5% (32/917) overall and 9.4% (30/319) among those with severe or critical COVID-19. These were impaired consciousness (n = 25) or stroke (n = 10). The risk of critical neurologic events was highly associated with age above 60 years and previous history of neurologic conditions. Noncritical events were seen in fewer than 1% (7/917), including muscle cramp, unexplained headache, occipital neuralgia, tic, and tremor. Brain CT in 28 people led to new findings in 9. Findings from lumbar puncture in 3 with suspected CNS infection, unexplained headache, or severe occipital neuralgia were unremarkable. CONCLUSIONS: People with COVID-19 aged over 60 and with neurologic comorbidities were at higher risk of developing critical neurologic impairment, mainly impaired consciousness and cerebrovascular accidents. Brain CT should be considered when new-onset brain injury is suspected, especially in people under sedation or showing an unexplained decline in consciousness. Evidence of direct acute insult of severe acute respiratory syndrome coronavirus 2 to the CNS is lacking.

[Detection of interleukin-10 in alveolar macrophage and peripheral blood monocyte from lung cancer patients and its clinical significance].

BACKGROUND: To investigate the ability of alveolar macrophage (AM) and peripheral blood monocyte (PBMC) from lung cancer patients to produce Interleukin-10 (IL-10) and to evaluate the local and general cellular immune state of lung cancer patients. METHODS: AM and PBMC were obtained from 57 patients with lung cancer, 33 patients with benign pulmonary diseases and 12 healthy volunteers. IL-10 in the culture supernatants was measured quantitatively by ELISA. RESULTS: (1) Elevated levels of IL-10 produced by PBMC were found in lung cancer group with respect to healthy volunteers and patients with benign pulmonary diseases (148.60±35.56 vs 93.83±9.22 and 108.91±15.95 ng×L⁻¹ respectively) (P < 0.001). The level of IL-10 by AM from lung cancer patients was 132.06±30.42 ng×L⁻¹, which was remarkably higher than that of healthy volunteers (92.67±11.22 ng×L⁻¹) and benign pulmonary diseases (94.39±10.04 ng×L⁻¹) (P < 0.001). (2) The level of IL-10 produced by PBMC from lung cancer group of stage IV was significantly higher than that of stage I+II (178.33±13.52 vs 131.57±25.35 ng×L⁻¹) (P < 0.001). AM from lung cancer patients of stage III and IV produced more IL-10 than that of stage I+II did (150.13±15.57 and 160.50± 18.75 vs 117.05±28.12 ng×L⁻¹ respectively) (P < 0.001); PBMC from small cell lung cancer patients produced higher level of IL-10 than squamous cell carcinoma and adenocarcinoma did (194.83±23.88 vs 140.37± 27.00 ng×L⁻¹ and 136.50±27.39 ng×L⁻¹ respectively) (P < 0.01). AM from small cell lung cancer patients produced higher levels of IL-10 than squamous cell carcinoma and adenocarcinoma did (165.33±23.78 vs 127.74±26.19 ng×L⁻¹ and 120.30±29.66 ng×L⁻¹ respectively) (P < 0.01); Size of mass and performance status greatly affected the level of IL-10; IL-10 level of lung cancer patients with survival time more than 2 years was remarkably lower than that of patients with survival time less than 2 years (P < 0.01). CONCLUSIONS: Higher level of IL-10 presents both in local and general body of lung cancer patients. IL-10 may play an important role in deterioration of lung cancer. Detection of IL-10 level may be helpful to evaluate cellular immunity and predict prognosis of lung cancer patients.

A novel mechanism of antagonism between ATP-dependent chromatin remodeling complexes regulates RNR3 expression.

Gene expression depends upon the antagonistic actions of chromatin remodeling complexes. While this has been studied extensively for the enzymes that covalently modify the tails of histones, the mechanism of how ATP-dependent remodeling complexes antagonize each other to maintain the proper level of gene activity is not known. The gene encoding a large subunit of ribonucleotide reductase, RNR3, is regulated by ISW2 and SWI/SNF, complexes that repress and activate transcription, respectively. Here, we studied the functional interactions of these two complexes at RNR3. Deletion of ISW2 causes constitutive recruitment of SWI/SNF, and conditional reexpression of ISW2 causes the repositioning of nucleosomes and reduced SWI/SNF occupancy at RNR3. Thus, ISW2 is required for restriction of access of SWI/SNF to the RNR3 promoter under the uninduced condition. Interestingly, the binding of sequence-specific DNA binding factors and the general transcription machinery are unaffected by the status of ISW2, suggesting that disruption of nucleosome positioning does not cause a nonspecific increase in cross-linking of all factors to RNR3. We provide evidence that ISW2 does not act on SWI/SNF directly but excludes its occupancy by positioning nucleosomes over the promoter. Genetic disruption of nucleosome positioning by other means led to a similar phenotype, linking repressed chromatin structure to SWI/SNF exclusion. Thus, incorporation of promoters into a repressive chromatin structure is essential for prevention of the opportunistic actions of nucleosome-disrupting activities in vivo, providing a novel mechanism for maintaining tight control of gene expression.

Dissection of coactivator requirement at RNR3 reveals unexpected contributions from TFIID and SAGA.

The gene encoding ribonucleotide reductase 3 (RNR3) is strongly induced in response to DNA damage. Its expression is strictly dependent upon the TAF(II) subunits of TFIID, which are required for the recruitment of SWI/SNF and nucleosome remodeling. However, full activation of RNR3 also requires GCN5, the catalytic subunit of the SAGA histone acetyltransferase complex. Thus, RNR3 is dependent upon both TFIID and SAGA, two complexes that deliver TATA-binding protein (TBP) to promoters. Furthermore, unlike the majority of TFIID-dominated genes, RNR3 contains a consensus TATA-box, a feature of SAGA-regulated core promoters. Although a large fraction of the genome can be characterized as either TFIID- or SAGA-dominant, it is expected that many genes utilize both. The mechanism of activation and the relative contributions of SAGA and TFIID at genes regulated by both complexes have not been examined. Here we delineated the role of SAGA in the regulation of RNR3 and contrast it to that of TFIID. We find that SAGA components fulfill distinct functions in the regulation of RNR3. The core promoter of RNR3 is SAGA-dependent, and we provide evidence that SAGA, not TAF(II)s within TFIID, are largely responsible for TBP recruitment. This taken together with our previous work provides evidence that SAGA recruits TBP, whereas TFIID mediates chromatin remodeling. Thus, we described an unexpected shift in the division of labor between these two complexes and provide the first characterization of a gene that requires both SAGA and TFIID.

Isolation of highly purified yeast nuclei for nuclease mapping of chromatin structure.

Probing chromatin structure with nucleases is a well-established method for determining the accessibility of DNA to gene regulatory proteins and measuring competency for transcription. A hallmark of many silent genes is the presence of translationally positioned nucleosomes over their promoter regions, which can be inferred by the sensitivity of the underlying DNA to nucleases, particularly micrococcal nuclease. The quality of this data is highly dependent upon the nuclear preparation, especially if the digestion products are analyzed by high-resolution detection methods such as reiterative primer extension. Here we describe a method to isolate highly purified nuclei from the budding yeast Saccharomyces cerevisiae and the use of micrococcal nuclease to map the positions of nucleosomes at the RNR3 gene. Nuclei isolated by this procedure are competent for many of the commonly used chromatin mapping and detection procedures.

Exposing the core promoter is sufficient to activate transcription and alter coactivator requirement at RNR3.

Chromatin is a formidable barrier to transcription. Nucleosome density is lowest over the regulatory regions of active genes, and many repressed genes have a tightly positioned nucleosome over their core promoter. However, it has not been shown that nucleosome positioning is sufficient for repression or whether disrupting a core promoter nucleosome specifically can activate gene expression in the absence of activating signals. Here we show that disrupting the nucleosome over the core promoter of RNR3 is sufficient to drive preinitiation complex assembly and activate transcription in the absence of activating signals. Remodeling of chromatin over the RNR3 promoter requires the recruitment of the SWI/SNF complex by the general transcription factor TFIID. We found that disrupting the nucleosome over the RNR3 core promoter relieves its dependence on TFIID and SWI/SNF, indicating a functional link between these two complexes. These results suggest that the specific function of TAF(II)s is to direct the chromatin remodeling step through SWI/SNF recruitment, and not core promoter selectivity. Our results indicate that nucleosome placement plays a dominant role in repression and that the ability of the core promoter to position a nucleosome is a major determinant in TAF(II) dependency of genes in vivo.