ABSTRACT
Here we provide a brief review of relevant background before presenting results of our investigation into the interplay between scaffold attachment factor A (SAF-A), chromatin-associated RNAs, and DNA condensation. SAF-A, also termed heterogenous nuclear protein U (hnRNP U), is a ubiquitous nuclear scaffold protein that was implicated in XIST RNA localization to the inactive X-chromosome (Xi) but also reported to maintain open DNA packaging in euchromatin. Here we use several means to perturb SAF-A and examine potential impacts on the broad association of RNAs on euchromatin, and on chromatin compaction. SAF-A has an N-terminal DNA binding domain and C-terminal RNA binding domain, and a prominent model has been that the protein provides a single-molecule bridge between XIST RNA and chromatin. Here analysis of the impact of SAF-A on broad RNA-chromatin interactions indicate greater biological complexity. We focus on SAF-A's role with repeat-rich C0T-1 hnRNA (repeat-rich heterogeneous nuclear RNA), shown recently to comprise mostly intronic sequences of pre-mRNAs and diverse long non-coding RNAs (lncRNAs). Our results show that SAF-A mutants cause dramatic changes to cytological chromatin condensation through dominant negative effects on C0T-1 RNA's association with euchromatin, and likely other nuclear scaffold factors. In contrast, depletion of SAF-A by RNA interference (RNAi) had no discernible impact on C0T-1 RNA, nor did it cause similarly marked chromatin changes as did three different SAF-A mutations. Overall results support the concept that repeat-rich, chromatin-associated RNAs interact with multiple RNA binding proteins (RBPs) in a complex dynamic meshwork that is integral to larger-scale chromatin architecture and collectively influences cytological-scale DNA condensation.
Subject(s)
Chromatin , RNA, Long Noncoding , Chromatin/genetics , Euchromatin , Nuclear Proteins/genetics , RNA, Long Noncoding/genetics , X ChromosomeABSTRACT
In this issue of Molecular Cell, Ishida et al. (2012) and Keller et al. (2012) show distinct outcomes for heterochromatic RNAs that bind different chromodomain proteins; Chp1 tethers transcripts to centromeres, whereas Swi6(HP1)-bound transcripts are evicted from chromatin and destroyed.
ABSTRACT
Maintenance of the correct level and organisation of nucleosomes is crucial for genome function. Here, we uncover a role for a conserved bromodomain AAA-ATPase, Abo1, in the maintenance of nucleosome architecture in fission yeast. Cells lacking abo1(+) experience both a reduction and mis-positioning of nucleosomes at transcribed sequences in addition to increased intragenic transcription, phenotypes that are hallmarks of defective chromatin re-establishment behind RNA polymerase II. Abo1 is recruited to gene sequences and associates with histone H3 and the histone chaperone FACT. Furthermore, the distribution of Abo1 on chromatin is disturbed by impaired FACT function. The role of Abo1 extends to some promoters and also to silent heterochromatin. Abo1 is recruited to pericentromeric heterochromatin independently of the HP1 ortholog, Swi6, where it enforces proper nucleosome occupancy. Consequently, loss of Abo1 alleviates silencing and causes elevated chromosome mis-segregation. We suggest that Abo1 provides a histone chaperone function that maintains nucleosome architecture genome-wide.
Subject(s)
Adenosine Triphosphatases/metabolism , Chromatin/genetics , Chromatin/metabolism , Nucleosomes/metabolism , Schizosaccharomyces pombe Proteins/metabolism , Schizosaccharomyces/genetics , Schizosaccharomyces/metabolism , Adenosine Triphosphatases/chemistry , Adenosine Triphosphatases/genetics , Chromatin Assembly and Disassembly , Chromosomal Proteins, Non-Histone/metabolism , Chromosome Segregation , DNA, Intergenic , Gene Silencing , Histone Chaperones/genetics , Histone Chaperones/metabolism , Histones/genetics , Histones/metabolism , Nucleosomes/genetics , Promoter Regions, Genetic , RNA Polymerase II/genetics , Schizosaccharomyces pombe Proteins/chemistry , Schizosaccharomyces pombe Proteins/genetics , Transcription Factors/metabolism , Transcription, GeneticABSTRACT
The linear DNA sequence of mammalian chromosomes is organized in large blocks of DNA with similar sequence properties, producing a pattern of dark and light staining bands on mitotic chromosomes. Cytogenetic banding is essentially invariant between people and cell-types and thus may be assumed unrelated to genome regulation. We investigate whether large blocks of Alu-rich R-bands and L1-rich G-bands provide a framework upon which functional genome architecture is built. We examine two models of large-scale chromatin condensation: X-chromosome inactivation and formation of senescence-associated heterochromatin foci (SAHFs). XIST RNA triggers gene silencing but also formation of the condensed Barr Body (BB), thought to reflect cumulative gene silencing. However, we find Alu-rich regions are depleted from the L1-rich BB, supporting it is a dense core but not the entire chromosome. Alu-rich bands are also gene-rich, affirming our earlier findings that genes localize at the outer periphery of the BB. SAHFs similarly form within each territory by coalescence of syntenic L1 regions depleted for highly Alu-rich DNA. Analysis of senescent cell Hi-C data also shows large contiguous blocks of G-band and R-band DNA remodel as a segmental unit. Entire dark-bands gain distal intrachromosomal interactions as L1-rich regions form the SAHF. Most striking is that sharp Alu peaks within R-bands resist these changes in condensation. We further show that Chr19, which is exceptionally Alu rich, fails to form a SAHF. Collective results show regulation of genome architecture corresponding to large blocks of DNA and demonstrate resistance of segments with high Alu to chromosome condensation.
ABSTRACT
Formation of centromeric heterochromatin in fission yeast requires the combined action of chromatin modifying enzymes and small RNAs derived from centromeric transcripts. Positive feedback mechanisms that link the RNAi pathway and the Clr4/Suv39h1 histone H3K9 methyltransferase complex (Clr-C) result in requirements for H3K9 methylation for full siRNA production and for siRNA production to achieve full histone methylation. Nonetheless, it has been proposed that the Argonaute protein, Ago1, is the key initial trigger for heterochromatin assembly via its association with Dicer-independent "priRNAs." The RITS complex physically links Ago1 and the H3-K9me binding protein Chp1. Here we exploit an assay for heterochromatin assembly in which loss of silencing by deletion of RNAi or Clr-C components can be reversed by re-introduction of the deleted gene. We showed previously that a mutant version of the RITS complex (Tas3(WG)) that biochemically separates Ago1 from Chp1 and Tas3 proteins permits maintenance of heterochromatin, but prevents its formation when Clr4 is removed and re-introduced. Here we show that the block occurs with mutants in Clr-C, but not mutants in the RNAi pathway. Thus, Clr-C components, but not RNAi factors, play a more critical role in assembly when the integrity of RITS is disrupted. Consistent with previous reports, cells lacking Clr-C components completely lack H3K9me2 on centromeric DNA repeats, whereas RNAi pathway mutants accumulate low levels of H3K9me2. Further supporting the existence of RNAi-independent mechanisms for establishment of centromeric heterochromatin, overexpression of clr4(+) in clr4Δago1Δ cells results in some de novo H3K9me2 accumulation at centromeres. These findings and our observation that ago1Δ and dcr1Δ mutants display indistinguishable low levels of H3K9me2 (in contrast to a previous report) challenge the model that priRNAs trigger heterochromatin formation. Instead, our results indicate that RNAi cooperates with RNAi-independent factors in the assembly of heterochromatin.
Subject(s)
Cell Cycle Proteins/genetics , Heterochromatin/genetics , Methyltransferases/genetics , RNA Interference , Schizosaccharomyces pombe Proteins/genetics , Schizosaccharomyces/genetics , Argonaute Proteins , Carrier Proteins/genetics , Carrier Proteins/metabolism , Cell Cycle Proteins/metabolism , Centromere/genetics , Chromatin Immunoprecipitation , Chromosomal Proteins, Non-Histone/genetics , Chromosomal Proteins, Non-Histone/metabolism , Cullin Proteins/genetics , Cullin Proteins/metabolism , Heterochromatin/metabolism , Histone-Lysine N-Methyltransferase , Histones/metabolism , Lysine/metabolism , Methylation , Methyltransferases/metabolism , Mutation , RNA-Binding Proteins/genetics , RNA-Binding Proteins/metabolism , Schizosaccharomyces/metabolism , Schizosaccharomyces pombe Proteins/metabolismABSTRACT
Repetitive sequences including transposable elements and transposon-derived fragments account for nearly half of the human genome. While transposition-competent transposable elements must be repressed to maintain genomic stability, mutated and fragmented transposable elements comprising the bulk of repetitive sequences can also contribute to regulation of host gene expression and broader genome organization. Here, we analyzed published ChIP-seq data sets to identify proteins broadly enriched on transposable elements in the human genome. We show 2 of the proteins identified, C2H2 zinc finger-containing proteins ZNF146 (also known as OZF) and ZNF507, are targeted to distinct sites within LINE-1 ORF2 at thousands of locations in the genome. ZNF146 binding sites are found at old and young LINE-1 elements. In contrast, ZNF507 preferentially binds at young LINE-1 sequences correlated to sequence changes in LINE-1 elements at ZNF507's binding site. To gain further insight into ZNF146 and ZNF507 function, we disrupt their expression in HEK293 cells using CRISPR/Cas9 and perform RNA sequencing, finding modest gene expression changes in cells where ZNF507 has been disrupted. We further identify a physical interaction between ZNF507 and PRMT5, suggesting ZNF507 may target arginine methylation activity to LINE-1 sequences.
Subject(s)
Kruppel-Like Transcription Factors , Long Interspersed Nucleotide Elements , RNA-Binding Proteins , Binding Sites , DNA Transposable Elements , Genome, Human/genetics , HEK293 Cells , Humans , Kruppel-Like Transcription Factors/genetics , Kruppel-Like Transcription Factors/metabolism , Protein-Arginine N-Methyltransferases/metabolism , RNA-Binding Proteins/genetics , RNA-Binding Proteins/metabolismABSTRACT
INTRODUCTION: The authors compared pediatric thoracic patients in the Joint Theatre Trauma Registry (JTTR) to those in the National Trauma Data Bank (NTDB) to assess differences in patient mortality rates and mortality risk accounting for age, injury patterns, and injury severity. MATERIALS AND METHODS: Patients less than 19 years of age with thoracic trauma were identified in both the JTTR and NTDB. Multiple logistic regression, χ2, Student's t-test, or Mann-Whitney U test were used as indicated to compare the two groups. RESULTS: Pediatric thoracic trauma patients seen in Iraq and Afghanistan (n = 955) had a significantly higher mortality rate (15.1 vs. 6.0%, P <.01) than those in the NTDB (n = 9085). After controlling for covariates between the JTTR and the NTDB, there was no difference in mortality (odds ratio for mortality for U.S. patients was 0.74, 95% CI 0.52-1.06, P = .10). The patients seen in Iraq or Afghanistan were significantly younger (8 years old, interquartile ratio (IQR) 2-13 vs. 15, IQR 10-17, P <.01) had greater severity of injuries (injury severity score 17, IQR 12-26 vs. 12, IQR 8-22, P <.01), had significantly more head injuries (29 vs. 14%, P <.01), and over half were exposed to a blast. DISCUSSION: Pediatric patients with thoracic trauma in Iraq and Afghanistan in the JTTR had similar mortality rates compared to the civilian population in the NTDB after accounting for confounding covariates. These findings indicate that deployed military medical professionals are providing comparable quality of care in extremely challenging circumstances. This information has important implications for military preparedness, medical training, and casualty care.
Subject(s)
Military Personnel , Thoracic Injuries , Afghan Campaign 2001- , Afghanistan/epidemiology , Child , Humans , Iraq/epidemiology , Iraq War, 2003-2011 , Registries , Retrospective Studies , Thoracic Injuries/epidemiology , United States/epidemiologyABSTRACT
Introduction Pediatric hospitalists are expected to lead resuscitative efforts for cardiopulmonary arrests, but the infrequency of these events and pediatric advanced life support (PALS) re-certifications are insufficient to maintain skill proficiency.We created a novel resuscitation refresher curriculum for pediatric hospitalists with strategic pauses during simulations for expert and peer coaching of procedural skills. Methods In a tertiary care academic pediatric hospital between September 2018 to June 2019, pediatric hospitalists and fellows voluntarily participated in a series of three quarterly two-hour training sessions taught by expert peer facilitators. Sessions focused on the thirty-second rapid cardiopulmonary assessment and each of the pediatric advanced life support (PALS) algorithms. Scenarios were strategically paused to practice critical hands-on skills. Cases centered on the themes of shock, respiratory, and cardiac emergencies and took place in a high-fidelity simulation lab requiring a technician and expert peer facilitator. Participants anonymously completed Likert scale-based evaluations after each session and again at the end of the year that focused on participants' own perceived change in their comfort levels in performing various resuscitation skills and in knowing basic resuscitation steps. As part of our institutional and personal assessment of the curriculum, an end-of-year survey additionally asked participants to reflect on the overall simulation curriculum and resultant changes in their clinical practice. Results Comfort in all skills practiced across the three sessions increased. The end-of-year survey showed a significant rise in comfort above baseline but some decrements when compared to that immediately post-training. Ninety-six percent of pediatric hospitalists rated the overall quality of the training "better" or "much better" than other resuscitation training (including PALS classes and traditional simulations with skills training after the scenario). The overall effect of the curriculum on perceived knowledge, skills, and confidence levels was significant (p <0.0001). Conclusion Serial resuscitation skills refreshers with expert peer coaching and strategic pauses for hands-on skills practice can result in significant improvements in perceived knowledge and comfort with skill performance as well as the leadership role among pediatric hospitalists.
ABSTRACT
A 2-week-old infant developed respiratory failure due to a mediastinal Kaposiform hemangioendothelioma that was complicated by thrombocytopenia and consumptive coagulopathy. Initial surgery was unsuccessful at removing the tumorous infiltration of mediastinal structures. Multiple transfusions with fresh frozen plasma, platelets, and red blood cells were needed for the consumptive coagulopathy, and ventilatory support was required for 5 months. Therapy for the tumor included methylprednisolone, aminocaproic acid, and vincristine, but a sustained response was achieved only after the initiation of alpha interferon. The patient was monitored closely and did not develop neurologic toxicity. This case demonstrates that interferon can be used to treat infants with Kaposiform hemangioendothelioma in life-threatening situations that do not respond to other forms of treatment.
Subject(s)
Anemia, Hemolytic/etiology , Antineoplastic Combined Chemotherapy Protocols/therapeutic use , Disseminated Intravascular Coagulation/etiology , Hemangioendothelioma/complications , Interferon-alpha/therapeutic use , Mediastinal Neoplasms/complications , Respiratory Insufficiency/etiology , Thrombocytopenia/etiology , Aminocaproates/administration & dosage , Anemia, Hemolytic/therapy , Blood Component Transfusion , Combined Modality Therapy , Disseminated Intravascular Coagulation/therapy , Female , Hemangioendothelioma/drug therapy , Hemangioendothelioma/surgery , Humans , Infant, Newborn , Mediastinal Neoplasms/drug therapy , Mediastinal Neoplasms/surgery , Methylprednisolone/administration & dosage , Plasma , Respiration, Artificial , Respiratory Insufficiency/therapy , Syndrome , Thoracotomy , Thrombocytopenia/therapy , Thymectomy , Vincristine/administration & dosageABSTRACT
BACKGROUND: Humanitarian and civilian emergency care accounts for up to one-third of US military combat support hospital (CSH) admissions. Almost half of these admissions are children. The purpose of this study is to describe the features of pediatric wartime admissions to deployed CSHs in Iraq and Afghanistan. METHODS: A retrospective database review was conducted using the Patient Administration Systems and Biostatistics Activity. Details of 2,060 pediatric admissions to deployed CSHs were analyzed. RESULTS: Nontraumatic diagnoses were responsible for 25% of all pediatric admissions. Penetrating injuries (76.3%) dominate the trauma admissions. The primary mechanisms of injury were gunshot wound (39%) followed by explosive injuries (32%). Categorizing the injuries by location revealed 38.3% extremity wounds, 23.6% torso injuries, 23.5% head, face, and neck injuries, and 13.3% burns. More than half of the children required two or more invasive or surgical procedures, 19.8% needed a transfusion, and 5.6% required mechanical ventilation. The mortality rate was 6.9%. The primary cause of death involved head trauma (29.5%) and burns (27.3%), followed by infectious diagnoses (7.2%). The case fatality rate for head injury and burn patients was 20.1% and 15.9%, respectively, in contrast to the fatality rate for all other diagnoses at 3.8% (p < 0.01). Excluding emergency department deaths, mortality rates for Afghanistan (6.2%) and Iraq (3.9%) significantly differ (p < 0.02). CONCLUSION: Pediatric patients account for approximately 10% of all CSH admissions in Afghanistan and Iraq. Burns and penetrating head injury account for the majority of pediatric mortality at the CSH.
Subject(s)
Hospitalization/statistics & numerical data , Hospitals, Military/statistics & numerical data , Wounds and Injuries/epidemiology , Afghan Campaign 2001- , Child , Craniocerebral Trauma/mortality , Humans , Iraq War, 2003-2011 , Length of Stay , Retrospective Studies , United States , Wounds, Penetrating/epidemiologyABSTRACT
PURPOSE: Over 3,500 infants and children, many critically ill and injured, have been admitted to military combat support hospitals (CSH) in Afghanistan and Iraq, which are not doctrinally staffed or equipped to provide their care. This report details how the military medical system is adapting to create a data driven and comprehensive response to optimize the medical and surgical pediatric care being provided. METHODS: Information from multiple sources was used over time to craft the military medical response to the pediatric wartime mission. Pediatric data from both the Joint Theater Trauma Registry (JTTR) and the Patient Administration Systems and Biostatistics Activity (PASBA) database were utilized extensively. The resulting educational, supply, and personnel adaptations implemented by the U.S. military will be highlighted, and innovations currently under development will also be described on the basis of this demonstrated need. RESULTS: This information helped drive pediatric-specific, just-in-time education for CSH personnel, modified CSH equipment and supply lists, inspired the 24/7 pediatric critical care teleconsultation service, and resulted in new initiatives in the predeployment training for CSH personnel. CONCLUSION: Military physicians are routinely asked to perform outside their traditional scopes of practice while deployed. Given this reality, military pediatric specialists in medicine and surgery have initiated several successful multidisciplinary programs designed to improve in-theater care of injured children. These innovative efforts include drafting a pediatric addendum to the Army's "Emergency War Surgery" manual, development of instructional compact discs, augmenting and refining the pediatric portion of the Joint Forces Combat Trauma Management course, formation of a pediatric augmentation team to the CSH, and a comprehensive hyperlinked Web-based pediatric critical care and trauma educational platform.
Subject(s)
General Surgery/organization & administration , Hospitals, Military/organization & administration , Military Medicine/organization & administration , Pediatrics/organization & administration , Wounds and Injuries/therapy , Adolescent , Afghan Campaign 2001- , Child , Child, Preschool , Health Services Needs and Demand , Humans , Infant , Infant, Newborn , Iraq War, 2003-2011 , United States , WorkforceABSTRACT
Introduction: The objective of this study is to review available data on pediatric thoracic trauma seen at U.S. military treatment facilities in Iraq and Afghanistan and describe the scope of injuries, patterns seen, and associated mortality. The results were compared with adults injured in Iraq and Afghanistan and other reports of pediatric thoracic trauma in the literature. Materials and Methods: The investigators received approval from the Uniformed Services University of the Health Sciences' institutional review board before the study. The Joint Theatre Trauma Registry was queried for all patients with an ICD-9 code for thoracic trauma. Two-tailed Student's t-test, Mann-Whitney rank sum, χ2, ANOVA, or multiple logistic regression was used as indicated. Results: There were 955 patients under the age of 18 yr, just over 12% of all thoracic trauma. Penetrating injuries were common (73.6%), including gunshot wounds. The most common pediatric diagnoses were contusions (45%), pneumothorax (40%), and rib and/or sternal fractures (18%). The overall mortality for children was 15.2% compared with 13.8% and 9% for civilian adults and Coalition members with thoracic trauma, respectively. Mortality was inversely related to age among pediatric patients. Children under 2 yr of age had the highest mortality (25.1%). Patients under 12 yr of age were more likely to die than those between 12 and 18 (OR 2.02, 95% CI 1.27-3.22) yr. Thoracic vascular injuries and cardiac injuries resulted in the highest mortality among pediatric patients. The presence of a hemothorax was independently associated with an increased risk for mortality (OR 1.78, 95% CI 1.06-2.99) as was a concomitant head injury (OR 2.17, 95% CI 1.33-3.54). There was a 2.7% incidence of burns among pediatric patients with a high associated mortality (46.2%). Nearly one-half of all the children identified required a transfusion (47%). Conclusion: Penetrating injuries predominated and these children commonly required a transfusion. Mortality was inversely related to age. Children with a hemothorax or a concomitant head injury had significant increases in mortality. Children with thoracic injury as the result of a burn suffered the highest mortality.
Subject(s)
Thoracic Injuries/complications , Adolescent , Afghan Campaign 2001- , Afghanistan/epidemiology , Afghanistan/ethnology , Child , Child, Preschool , Female , Hospitals, Military/organization & administration , Hospitals, Military/statistics & numerical data , Humans , Incidence , Infant , Iraq/epidemiology , Iraq/ethnology , Iraq War, 2003-2011 , Male , Pediatrics/statistics & numerical data , Retrospective Studies , Thoracic Injuries/epidemiology , Thoracic Injuries/ethnologyABSTRACT
This single blinded observational study compared the bispectral index (BIS) monitor with a validated pediatric sedation scale, the University of Michigan Sedation Scale (UMSS), to evaluate whether the BIS score can be used to judge the depth of sedation in pediatric outpatients. Thirty-eight children, with a mean age of 5.8 years, undergoing routine sedation for both noninvasive and gastrointestinal procedures, had simultaneous BIS and UMSS scores recorded. Sedation categories were defined as light, moderate, and deep for both UMSS and BIS. There was a moderate correlation between BIS and the UMSS, Spearman's r < -0.499. The correlation was poor for children receiving chloral hydrate, r < -0.213. The BIS score was not predictive of any specific UMSS score. The UMSS and BIS categories of sedation matched only 36% of the time. BIS underestimated the clinical level of sedation.
Subject(s)
Chloral Hydrate , Conscious Sedation/classification , Hypnotics and Sedatives , Midazolam , Pentobarbital , Child , Child, Preschool , Humans , PediatricsABSTRACT
BACKGROUND: Component balanced resuscitation and avoidance of crystalloids in traumatically injured adults requiring massive transfusion are beneficial. Evidence for children is lacking. METHODS: After institutional review board approval was obtained, the Department of Defense Trauma Database identified 1,311 injured children 14 years or younger requiring transfusion after an injury and admitted to a deployed US military hospital from 2002 to 2012. Logistic regression determined risk factors for high-volume (≥40 mL/kg) or massive (≥70 mL/kg) transfusions. The effects of crystalloid and balanced component resuscitation in the first 24 hours were assessed. RESULTS: Nine hundred seven patients had recorded data sufficient for analysis. Two hundred twenty-four children received high-volume transfusion, and 77 received massive transfusions. Mortality was significantly higher for massive transfusions and high-volume transfusions than others (25% vs. 10% and 19% vs. 9%, respectively). Age of less than 4 years, penetrating injury, and Injury Severity Score (ISS) greater than 15 were associated with high-volume transfusions; an ISS greater than 15 and penetrating injury were associated with massive transfusions. Increased crystalloid administration showed a significant positive association with hospital days and intensive care unit days for both massive and high-volume transfusions, as well as a significant positive association with increased ventilator days in patients with high-volume transfusions. Balanced component resuscitation was not associated with improved measured outcomes and was independently associated with a higher mortality when all transfused patients were considered. CONCLUSION: In this cohort, heavy reliance on crystalloid for resuscitation had an adverse effect on outcomes. Balanced component resuscitation did not improve outcomes and was associated with higher mortality when all transfused patients were considered. Further study is needed regarding efficacy and clinical triggers for the implementation of massive transfusion in children. LEVEL OF EVIDENCE: Prognostic study, level IV.
Subject(s)
Blood Component Transfusion/methods , Isotonic Solutions/therapeutic use , Resuscitation/methods , Wounds and Injuries/therapy , Adolescent , Afghanistan/epidemiology , Child , Child, Preschool , Critical Care/statistics & numerical data , Crystalloid Solutions , Female , Hospital Mortality , Hospitals, Military , Humans , Infant , Infant, Newborn , Iraq/epidemiology , Length of Stay/statistics & numerical data , Respiration, Artificial/statistics & numerical data , Retrospective Studies , Treatment Outcome , United States , Wounds and Injuries/mortalityABSTRACT
Mit1 is the putative chromatin remodeling subunit of the fission yeast Snf2/histone deacetylase (HDAC) repressor complex (SHREC) and is known to repress transcription at regions of heterochromatin. However, how Mit1 modifies chromatin to silence transcription is largely unknown. Here we report that Mit1 mobilizes histone octamers in vitro and requires ATP hydrolysis and conserved chromatin tethering domains, including a previously unrecognized chromodomain, to remodel nucleosomes and silence transcription. Loss of Mit1 remodeling activity results in nucleosome depletion at specific DNA sequences that display low intrinsic affinity for the histone octamer, but its contribution to antagonizing RNA polymerase II (Pol II) access and transcription is not restricted to these sites. Genetic epistasis analyses demonstrate that SHREC subunits and the transcription-coupled Set2 histone methyltransferase, which is involved in suppression of cryptic transcription at actively transcribed regions, cooperate to silence heterochromatic transcripts. In addition, we have demonstrated that Mit1's remodeling activity contributes to SHREC function independently of Clr3's histone deacetylase activity on histone H3 K14. We propose that Mit1 is a chromatin remodeling factor that cooperates with the Clr3 histone deacetylase of SHREC and other chromatin modifiers to stabilize heterochromatin structure and to prevent access to the transcriptional machinery.
Subject(s)
Chromatin Assembly and Disassembly/genetics , Gene Expression Regulation, Fungal , Heterochromatin/genetics , Mi-2 Nucleosome Remodeling and Deacetylase Complex/metabolism , Nucleosomes/genetics , Repressor Proteins/metabolism , Schizosaccharomyces pombe Proteins/metabolism , Schizosaccharomyces/genetics , Schizosaccharomyces/metabolism , Amino Acid Sequence , Cell Cycle Proteins/genetics , Histone-Lysine N-Methyltransferase/genetics , Histones/genetics , Histones/metabolism , Mi-2 Nucleosome Remodeling and Deacetylase Complex/genetics , Molecular Sequence Data , RNA Interference , RNA Polymerase II/antagonists & inhibitors , RNA, Small Interfering , Repressor Proteins/genetics , Schizosaccharomyces pombe Proteins/genetics , Transcription, GeneticABSTRACT
In recent years, a bevy of evidence has been unearthed indicating that 'silent' heterochromatin is not as transcriptionally inert as once thought. In the unicellular yeast Schizosaccharomyces pombe, the processing of transcripts derived from centromeric repeats into homologous short interfering RNA (siRNA) is essential for the formation of centromeric heterochromatin. Deletion of genes required for siRNA biogenesis showed that core components of the canonical RNA interference (RNAi) pathway are essential for centromeric heterochromatin assembly as well as for centromere function. Subsequent purification of the RNA-induced initiation of transcriptional gene silencing (RITS) complex provided the critical link between siRNAs and heterochromatin assembly, with RITS acting as a physical bridge between noncoding RNA scaffolds and chromatin. Here, we review current understanding of how RITS promotes heterochromatin formation and how it participates in transcription-coupled silencing. WIREs RNA 2011 2 632-646 DOI: 10.1002/wrna.80 For further resources related to this article, please visit the WIREs website.
Subject(s)
Chromatin Assembly and Disassembly , RNA Interference , Schizosaccharomyces/genetics , Schizosaccharomyces/metabolism , Transcription, Genetic , Heterochromatin/genetics , Heterochromatin/metabolism , Models, Biological , RNA, Fungal/genetics , RNA, Fungal/metabolism , RNA, Small Interfering/genetics , RNA, Small Interfering/metabolism , RNA-Induced Silencing Complex/genetics , RNA-Induced Silencing Complex/metabolism , Schizosaccharomyces pombe Proteins/genetics , Schizosaccharomyces pombe Proteins/metabolismABSTRACT
Cdk1 controls many aspects of mitotic chromosome behavior and spindle microtubule (MT) dynamics to ensure accurate chromosome segregation. In this paper, we characterize a new kinetochore substrate of fission yeast Cdk1, Nsk1, which promotes proper kinetochore-MT (k-MT) interactions and chromosome movements in a phosphoregulated manner. Cdk1 phosphorylation of Nsk1 antagonizes Nsk1 kinetochore and spindle localization during early mitosis. A nonphosphorylatable Nsk1 mutant binds prematurely to kinetochores and spindle, cementing improper k-MT attachments and leading to high rates of lagging chromosomes that missegregate. Accordingly, cells lacking nsk1 exhibit synthetic growth defects with mutations that disturb MT dynamics and/or kinetochore structure, and lack of proper phosphoregulation leads to even more severe defects. Intriguingly, Nsk1 is stabilized by binding directly to the dynein light chain Dlc1 independently of the dynein motor, and Nsk1-Dlc1 forms chainlike structures in vitro. Our findings establish new roles for Cdk1 and the Nsk1-Dlc1 complex in regulating the k-MT interface and chromosome segregation.
Subject(s)
CDC2 Protein Kinase/metabolism , Cell Cycle Proteins/metabolism , Chromosome Segregation , Chromosomes, Fungal/metabolism , Kinetochores/metabolism , Saccharomyces cerevisiae Proteins/metabolism , Saccharomyces cerevisiae/metabolism , Dyneins/metabolism , Microtubules/metabolism , Mitosis , Phosphorylation , Saccharomyces cerevisiae/cytology , Spindle Apparatus/metabolismSubject(s)
Attitude of Health Personnel , Cardiopulmonary Resuscitation , Family , Adult , Child , Humans , PediatricsABSTRACT
OBJECTIVE: To develop a pathway to provide safe, effective, and efficient sedation for pediatric diagnostic imaging studies using non-radiology personnel. MATERIALS AND METHODS: A multidisciplinary team considered manpower and training requirements and national sedation standards before designing a sedation pathway, which included scheduling, pre-sedation history and physical, medication protocols, and monitoring. Oral and IV medication protocols were developed based on patient age and weight. Sedation delays were defined as >15 min (IV) or >30 min (PO) from start of sedation to start of imaging. A sedation failure resulted in an incomplete diagnostic imaging study. Failure rates of 124 sedations before and 388 sedations after the pathway were compared. RESULTS: The sedation failure rate for 7 months prior to pathway initiation was 15% (19/124). In the first 25 months after pathway initiation, failures were significantly reduced to 1.5% (6/388) ( P<0.0001). Three (50%) of the six failures after pathway initiation were long examinations (>55 min). Deviation from the recommended medication protocol accounted for most of the 115 delays. Only minor adverse events were seen (12/388, 3.1%). CONCLUSION: Implementing a pediatric sedation pathway significantly decreases the sedation failure rate. Pediatric residents and nurses can safely, effectively and efficiently sedate pediatric patients for routine diagnostic imaging procedures without the need for a radiology department sedation team in a department with a small-to-moderate volume of pediatric patients.