A common transcriptional mechanism involving R-loop and RNA abasic site regulates an enhancer RNA of APOE.

RNA is modified by hundreds of chemical reactions and folds into innumerable shapes. However, the regulatory role of RNA sequence and structure and how dysregulation leads to diseases remain largely unknown. Here, we uncovered a mechanism where RNA abasic sites in R-loops regulate transcription by pausing RNA polymerase II. We found an enhancer RNA, AANCR, that regulates the transcription and expression of apolipoprotein E (APOE). In some human cells such as fibroblasts, AANCR is folded into an R-loop and modified by N-glycosidic cleavage; in this form, AANCR is a partially transcribed nonfunctional enhancer and APOE is not expressed. In contrast, in other cell types including hepatocytes and under stress, AANCR does not form a stable R-loop as its sequence is not modified, so it is transcribed into a full-length enhancer that promotes APOE expression. DNA sequence variants in AANCR are associated significantly with APOE expression and Alzheimer's Disease, thus AANCR is a modifier of Alzheimer's Disease. Besides AANCR, thousands of noncoding RNAs are regulated by abasic sites in R-loops. Together our data reveal the essentiality of the folding and modification of RNA in cellular regulation and demonstrate that dysregulation underlies common complex diseases such as Alzheimer's disease.

RNA abasic sites in yeast and human cells.

RNA abasic sites and the mechanisms involved in their regulation are mostly unknown; in contrast, DNA abasic sites are well-studied. We found surprisingly that, in yeast and human cells, RNA abasic sites are prevalent. When a base is lost from RNA, the remaining ribose is found as a closed-ring or an open-ring sugar with a reactive C1' aldehyde group. Using primary amine-based reagents that react with the aldehyde group, we uncovered evidence for abasic sites in nascent RNA, messenger RNA, and ribosomal RNA from yeast and human cells. Mass spectroscopic analysis confirmed the presence of RNA abasic sites. The RNA abasic sites were found to be coupled to R-loops. We show that human methylpurine DNA glycosylase cleaves N-glycosidic bonds on RNA and that human apurinic/apyrimidinic endonuclease 1 incises RNA abasic sites in RNA-DNA hybrids. Our results reveal that, in yeast and human cells, there are RNA abasic sites, and we identify a glycosylase that generates these sites and an AP endonuclease that processes them.

Histone H3 Lysine 56 Acetylation Enhances AP Endonuclease 1-Mediated Repair of AP Sites in Nucleosome Core Particles.

Deciphering factors modulating DNA repair in chromatin is of great interest because nucleosomal positioning influences mutation rates. H3K56 acetylation (Ac) is implicated in chromatin landscape regulation, impacting genomic stability, yet the effect of H3K56Ac on DNA base excision repair (BER) remains unclear. We determined whether H3K56Ac plays a role in regulating AP site incision by AP endonuclease 1 (APE1), an early step in BER. Our in vitro studies of acetylated, well-positioned nucleosome core particles (H3K56Ac-601-NCPs) demonstrate APE1 strand incision is enhanced compared with that of unacetylated WT-601-NCPs. The high-mobility group box 1 protein enhances APE1 activity in WT-601-NCPs, but this effect is not observed in H3K56Ac-601-NCPs. Therefore, our results suggest APE1 activity on NCPs can be modulated by H3K56Ac.

A cassette of basic amino acids in histone H2B regulates nucleosome dynamics and access to DNA damage.

Nucleosome dynamics, such as spontaneous DNA unwrapping, are postulated to have a critical role in regulating the access of DNA repair machinery to DNA lesions within nucleosomes. However, the specific histone domains that regulate nucleosome dynamics and the impact of such changes in intrinsic nucleosome dynamics on DNA repair are not well understood. Previous studies identified a highly conserved region in the N-terminal tail of histone H2B known as the histone H2Brepression (or HBR) domain, which has a significant influence on gene expression, chromatin assembly, and DNA damage formation and repair. However, the molecular mechanism(s) that may account for these observations are limited. In this study, we characterized the stability and dynamics of ΔHBR mutant nucleosome core particles (NCPs) in vitro by restriction enzyme accessibility (REA), FRET, and temperature-induced sliding of histone octamers. Our results indicate that ΔHBR-NCPs are more dynamic, with a larger steady-state fraction of the NCP population occupying the unwrapped state than for WT-NCPs. Additionally, ΔHBR-histone octamers are more susceptible to temperature-induced sliding on DNA than WT histone octamers. Furthermore, we show that the activity of base excision repair enzymes at uracil lesions and single nucleotide gaps is enhanced in a site-specific manner in ΔHBR-NCPs. This enhanced activity correlates well with regions exhibiting increased DNA unwrapping. Finally, removal of the HBR domain is not sufficient to completely alleviate the structural constraints imposed by histone octamers on the activity of base excision repair enzymes.

DNA polymerase ß uses its lyase domain in a processive search for DNA damage.

DNA polymerase (Pol) ß maintains genome fidelity by catalyzing DNA synthesis and removal of a reactive DNA repair intermediate during base excision repair (BER). Situated within the middle of the BER pathway, Pol ß must efficiently locate its substrates before damage is exacerbated. The mechanisms of damage search and location by Pol ß are largely unknown, but are critical for understanding the fundamental features of the BER pathway. We developed a processive search assay to determine if Pol ß has evolved a mechanism for efficient DNA damage location. These assays revealed that Pol ß scans DNA using a processive hopping mechanism and has a mean search footprint of ∼24 bp at predicted physiological ionic strength. Lysines within the lyase domain are required for processive searching, revealing a novel function for the lyase domain of Pol ß. Application of our processive search assay into nucleosome core particles revealed that Pol ß is not processive in the context of a nucleosome, and its single-turnover activity is reduced ∼500-fold, as compared to free DNA. These data suggest that the repair footprint of Pol ß mainly resides within accessible regions of the genome and that these regions can be scanned for damage by Pol ß.

Unencumbered Pol ß lyase activity in nucleosome core particles.

Packaging of DNA into the nucleosome core particle (NCP) is considered to exert constraints to all DNA-templated processes, including base excision repair where Pol ß catalyzes two key enzymatic steps: 5'-dRP lyase gap trimming and template-directed DNA synthesis. Despite its biological significance, knowledge of Pol ß activities on NCPs is still limited. Here, we show that removal of the 5'-dRP block by Pol ß is unaffected by NCP constraints at all sites tested and is even enhanced near the DNA ends. In contrast, strong inhibition of DNA synthesis is observed. These results indicate 5'-dRP gap trimming proceeds unperturbed within the NCP; whereas, gap filling is strongly limited. In the absence of additional factors, base excision repair in NCPs will stall at the gap-filling step.

Site-specific Acetylation of Histone H3 Decreases Polymerase ß Activity on Nucleosome Core Particles in Vitro.

Histone posttranslational modifications have been associated with changes in chromatin structure necessary for transcription, replication, and DNA repair. Acetylation is one of the most studied and best characterized histone posttranslational modifications, but it is not known if histone acetylation modulates base excision repair of DNA lesions in chromatin. To address this question, we generated nucleosome core particles (NCPs) containing site-specifically acetylated H3K14 or H3K56 and measured repair of uracil and single-nucleotide gaps. We find that H3K56Ac and H3K14Ac do not significantly contribute to removal of uracils by uracil DNA glycosylase regardless of the translational or rotational position of the lesions within NCPs. In repair of single-nucleotide gaps, however, the presence of H3K56Ac or H3K14Ac in NCPs decreases the gap-filling activity of DNA polymerase ß near the dyad center, with H3K14Ac exhibiting stronger inhibition. To a lesser extent, H3K56Ac induces a similar effect near the DNA ends. Moreover, using restriction enzyme accessibility, we detect no changes in NCP structure or dynamics between H3K14Ac-NCPs and WT-NCPs containing single-nucleotide gaps. Thus, acetylation at H3K56 and H3K14 in nucleosomes may promote alternative gap-filling pathways by inhibiting DNA polymerase ß activity.

Impact of Ribonucleotide Backbone on Translesion Synthesis and Repair of 7,8-Dihydro-8-oxoguanine.

Numerous ribonucleotides are incorporated into the genome during DNA replication. Oxidized ribonucleotides can also be erroneously incorporated into DNA. Embedded ribonucleotides destabilize the structure of DNA and retard DNA synthesis by DNA polymerases (pols), leading to genomic instability. Mammalian cells possess translesion DNA synthesis (TLS) pols that bypass DNA damage. The mechanism of TLS and repair of oxidized ribonucleotides remains to be elucidated. To address this, we analyzed the miscoding properties of the ribonucleotides riboguanosine (rG) and 7,8-dihydro-8-oxo-riboguanosine (8-oxo-rG) during TLS catalyzed by the human TLS pols κ and η in vitro The primer extension reaction catalyzed by human replicative pol α was strongly blocked by 8-oxo-rG. pol κ inefficiently bypassed rG and 8-oxo-rG compared with dG and 7,8-dihydro-8-oxo-2'-deoxyguanosine (8-oxo-dG), whereas pol η easily bypassed the ribonucleotides. pol α exclusively inserted dAMP opposite 8-oxo-rG. Interestingly, pol κ preferentially inserted dCMP opposite 8-oxo-rG, whereas the insertion of dAMP was favored opposite 8-oxo-dG. In addition, pol η accurately bypassed 8-oxo-rG. Furthermore, we examined the activity of the base excision repair (BER) enzymes 8-oxoguanine DNA glycosylase (OGG1) and apurinic/apyrimidinic endonuclease 1 on the substrates, including rG and 8-oxo-rG. Both BER enzymes were completely inactive against 8-oxo-rG in DNA. However, OGG1 suppressed 8-oxo-rG excision by RNase H2, which is involved in the removal of ribonucleotides from DNA. These results suggest that the different sugar backbones between 8-oxo-rG and 8-oxo-dG alter the capacity of TLS and repair of 8-oxoguanine.

The structural location of DNA lesions in nucleosome core particles determines accessibility by base excision repair enzymes.

BACKGROUND: Base excision repair is hindered by nucleosomes. RESULTS: Outwardly oriented uracils near the nucleosome center are efficiently cleaved; however, polymerase ß is strongly inhibited at these sites. CONCLUSION: The histone octamer presents different levels of constraints on BER, dependent on the structural requirements for enzyme activity. SIGNIFICANCE: Chromatin remodeling is necessary to prevent accumulation of aborted intermediates in nucleosomes. Packaging of DNA into chromatin affects accessibility of DNA regulatory factors involved in transcription, replication, and repair. Evidence suggests that even in the nucleosome core particle (NCP), accessibility to damaged DNA is hindered by the presence of the histone octamer. Base excision repair is the major pathway in mammalian cells responsible for correcting a large number of chemically modified bases. We have measured the repair of site-specific uracil and single nucleotide gaps along the surface of the NCP. Our results indicate that removal of DNA lesions is greatly dependent on their rotational and translational positioning in NCPs. Significantly, the rate of uracil removal with outwardly oriented DNA backbones is 2-10-fold higher than those with inwardly oriented backbones. In general, uracils with inwardly oriented backbones farther away from the dyad center of the NCP are more accessible than those near the dyad. The translational positioning of outwardly oriented gaps is the key factor driving gap filling activity. An outwardly oriented gap near the DNA ends exhibits a 3-fold increase in gap filling activity as compared with one near the dyad with the same rotational orientation. Near the dyad, uracil DNA glycosylase/APE1 removes an outwardly oriented uracil efficiently; however, polymerase ß activity is significantly inhibited at this site. These data suggest that the hindrance presented by the location of a DNA lesion is dependent on the structural requirements for enzyme catalysis. Therefore, remodeling at DNA damage sites in NCPs is critical for preventing accumulation of aborted intermediates and ensuring completion of base excision repair.

Rotational dynamics of DNA on the nucleosome surface markedly impact accessibility to a DNA repair enzyme.

Histones play a crucial role in the organization of DNA in the nucleus, but their presence can prevent interactions with DNA binding proteins responsible for repair of DNA damage. Uracil is an abundant mutagenic lesion recognized by uracil DNA glycosylase (UDG) in the first step of base excision repair (BER). In nucleosome core particles (NCPs), we find substantial differences in UDG-directed cleavage at uracils rotationally positioned toward (U-In) or away from (U-Out) the histone core, or midway between these orientations (U-Mid). Whereas U-Out NCPs show a cleavage rate just below that of naked DNA, U-In and U-Mid NCPs have markedly slower rates of cleavage. Crosslinking of U-In DNA to histones in NCPs yields a greater reduction in cleavage rate but, surprisingly, yields a higher rate of cleavage in U-Out NCPs compared with uncrosslinked NCPs. Moreover, the next enzyme in BER, APE1, stimulates the activity of human UDG in U-Out NCPs, suggesting these enzymes interact on the surface of histones in orientations accessible to UDG. These data indicate that the activity of UDG likely requires "trapping" transiently exposed states arising from the rotational dynamics of DNA on histones.

Preparation of Nucleosome Core Particles Complexed with DNA Repair Factors for Cryo-Electron Microscopy Structural Determination.

DNA repair in the context of chromatin is poorly understood. Biochemical studies using nucleosome core particles, the fundamental repeating unit of chromatin, show most DNA repair enzymes remove DNA damage at reduced rates as compared to free DNA. The molecular details on how base excision repair (BER) enzymes recognize and remove DNA damage in nucleosomes have not been elucidated. However, biochemical BER data of nucleosomal substrates suggest the nucleosome presents different structural barriers dependent on the location of the DNA lesion and the enzyme. This indicates the mechanisms employed by these enzymes to remove DNA damage in free DNA may be different than those employed in nucleosomes. Given that the majority of genomic DNA is assembled into nucleosomes, structural information of these complexes is needed. To date, the scientific community lacks detailed protocols to perform technically feasible structural studies of these complexes. Here, we provide two methods to prepare a complex of two genetically fused BER enzymes (Polymerase ß and AP Endonuclease1) bound to a single-nucleotide gap near the entry-exit of the nucleosome for cryo-electron microscopy (cryo-EM) structural determination. Both methods of sample preparation are compatible for vitrifying quality grids via plunge freezing. This protocol can be used as a starting point to prepare other nucleosomal complexes with different BER factors, pioneer transcription factors, and chromatin-modifying enzymes.

Individual and population effects of eugregarine, Gregarina niphandrodes (Eugregarinida: Gregarinidae), on Tenebrio molitor (Coleoptera: Tenebrionidae).

Gregarines are single-celled parasites in the phylum Apicomplexa that infect invertebrates. They are highly abundant on three levels: among a large diversity of invertebrates, in the proportion of population of organisms they infect, and within individually infected organisms. Because of their remarkable prevalence, we hypothesize that they play an important role in support of their hosts. However, studies done to date on the impact of gregarines on their host are conflicting. Therefore, we studied the impact of gregarines on their host using a model Gregarina niphandrodes infection in Tenebrio molitor. The impact of infection was measured by comparing beetles with no or low infection to those with artificially induced high infection. The numbers of individuals in each of the three easily visible developmental stages of the T. molitor (larva, pupa, and adult) were censused weekly. From these observations, fertilities and probabilities of survival with transition between stages were estimated. These estimated vital rates were used to construct a stage-classified projection matrix model. We also measured the longevity of individual beetles with low and high infection that were grown in isolation. The results indicate that there is no significant difference in the population dynamics of beetles with low and high infection. However, the longevity was significantly different between beetles with low infection than the deliberately highly infected group.

Accessing DNA damage in chromatin: Preparing the chromatin landscape for base excision repair.

DNA damage in chromatin comes in many forms, including single base lesions that induce base excision repair (BER). We and others have shown that the structural location of DNA lesions within nucleosomes greatly influences their accessibility to repair enzymes. Indeed, a difference in the location of uracil as small as one-half turn of the DNA backbone on the histone surface can result in a 10-fold difference in the time course of its removal in vitro. In addition, the cell has evolved several interdependent processes capable of enhancing the accessibility of excision repair enzymes to DNA lesions in nucleosomes, including post-translational modification of histones, ATP-dependent chromatin remodeling and interchange of histone variants in nucleosomes. In this review, we focus on different factors that affect accessibility of BER enzymes to nucleosomal DNA.

Ataxias cerebelosas hereditarias: principales avances neurofisiológicos, clínicos y genéticos / Main neurophysiological, clinical and genetics advances on Hereditary cerebellar ataxias

RESUMEN El término ataxias cerebelosas hereditarias comprende un amplio espectro de trastornos neurológicos en los cuales la ataxia es el síntoma principal. Conforman un complejo grupo de entidades cuyo reconocimiento es esencial para el correcto asesoramiento genético, el adecuado control clínico y, en algunos casos, el apropiado abordaje terapéutico. La riqueza clínico-semiológica y los avances en la biología molecular han convertido a las ataxias hereditarias en uno de los temas más apasionantes de la neurología. El diagnóstico clínico de los subtipos de ataxias es complicado, por la prominente superposición de fenotipos entre los subtipos genéticos. En este artículo abordamos los principales avances neurofisiológicos, clínicos y genéticos de las ataxias cerebelosas hereditarias.

ABSTRACT The term "Hereditary cerebellar ataxia" comprises a wide spectrum of neurological disorders where ataxia is the main symptom. Hereditary ataxias are a complex group of entities, in which detection is essential for an adequate genetic assessment, satisfactory clinical control and in some cases, a suitable therapeutic approach. Clinical semiology variety and molecular biology advanceshave become hereditary ataxias one of the most interesting subjects inside neurology. Subtypes clinical diagnosis of ataxias is complicated by the salient overlap of phenotypes between genetic subtypes. In this article, we refer to the most important neurophysiological, clinical and genetics advances of hereditary cerebellar ataxias.

Principales aspectos neurofisiológicos, clínicos, y genéticos, en una recién nacida con Síndrome de Cayler / Clinical, genetic, and neurophysiological main features in a newborn girl with Cayler Syndrome

En los neonatos, la hipoplasia o agenesia congénita del músculo depresor del ángulo de la boca (depresor anguli oris), es la causa de la asimetría facial durante el llanto. Los pacientes con esta anomalía, presentan caída de la comisura labial del lado intacto a diferencia de la parálisis facial de origen traumático o congénito, y su diagnóstico se obtiene fácilmente, mediante el examen físico. Esta anomalía está asociada con otras de origen congénito, sobre todo los defectos cardíacos, por lo que se nombra síndrome cardiofacial de Cayler. Se presenta una niña, recién nacida de 56 horas, atendida en el servicio de Neonatología del Hospital Pediátrico "Octavio de la Concepción de la Pedraja" de Holguín, Cuba. La paciente egresa con diagnóstico de síndrome de Cayler, al presentar asimetría facial durante el llanto, y tetralogía de Fallot. Se realizan estudios neurofisiológicos como: electroneurografía del nervio facial y electromiograma de los músculos depresores del labio.

Asymmetrical Crying Facies Syndrome, is caused by congenital hypolapsia or anguli oris agenesis. Patients usually present drop of the intact corner of their mouths while crying. Though it is easily diagnosed, it must be differentiated from traumatic or congenital facial palsies. This condition has been associated with several other anomalies, especially with heart issues. That´s why it is called Cayler Cardiofacial Syndrome. We have reported a case of a 56 hours newborn girl. She shows facial asymmetry as a valuable sign for suspecting other congenital anomalies. Clinical evaluation, including facial nerve electroneurography and electromyography, were performed.

Hipertensión intracraneal idiopática: principales aspectos neurofisiológicos, diagnósticos y terapéuticos / Idiopathic Intracranial Hypertension: Main Neurophysiological, Diagnosis and Therapeutic Features

La hipertensión intracraneal idiopática, también conocida como pseudotumor cerebral, es una enfermedad caracterizada por un incremento de la presión intracraneal no atribuible a masas cerebrales o a alteraciones estructurales focales, con composición normal del líquido cefalorraquídeo. En estudios imagenológicos pueden observarse ventrículos normales o pequeños. Se desconoce su etiología y patogenia. Es causa eludible de pérdida de la visión, tanto en adultos como en niños. El tratamiento es con frecuencia efectivo y la mayoría de los pacientes experimentan una resolución completa de los síntomas sin persistencia de déficits.

Idiopathic intracranial hypertension, also known as pseudotumor cerebri is a condition characterized by increased intracranial pressure, not caused to mass lesions or focal structural abnormalities, or with normal composition of the cerebrospinal fluid. Ventricles can be observed normal or small in imaging studies. Its etiology and pathogenesis are unknown. Idiopathic intracranial hypertension is an avoidable cause of visual loss, in both adults and children. Treatment is usually effective, and most patients have observed complete resolution of symptoms without persistent deficits.

Actualización en enfermedad de Parkinson idiopática / Update on Idiopathic Parkinson’s disease

Se realizó una revisión general del estado actual de conocimiento de la enfermedad de Parkinson idiopática, se incluyeron aspectos etiopatogénicos, clínicos, de metodología diagnóstica y opciones terapéuticas. El diagnóstico de la enfermedad de Parkinson es uno de los retos actuales en el campo neurológico. En los últimos años se han producido avances significativos, fundamentalmente en el campo de la neuroimagen, que abren nuevas rutas en la investigación y sirven al médico como apoyo diagnóstico. A pesar de ello, es un proceso clínico que se cuestiona en cada momento.

A review on the current knowledge of idiopathic Parkinson's disease was carried out. Etiopathogenic, clinical, diagnostic methods and treatment options were included. The diagnosis of Parkinson's disease is one of the current challenges in the neurological field. In recent years significant progress has been made, mainly in the field of neuroimaging, which open new routes in scientific investfgation and medical diagnostic support. Nonetheless, it is a clinical process at issue in every moment.

Actualización en enfermedad de Huntington / Update on Huntington Disease

La enfermedad de Huntington es un trastorno neurodegenerativo trasmitido con rasgo autosómico dominante. La pérdida neuronal selectiva en el estriado produce corea y deterioro cognitivo. Se trata de una enfermedad progresiva que comienza en la mitad de la vida adulta, evoluciona de manera crónica durante muchos años y para la que no existe en la actualidad un tratamiento curativo. Se realizó una revisión general del estado actual de conocimiento de la enfermedad de Huntington, se incluyeron aspectos etiopatogénicos, clínicos, de metodología diagnóstica y opciones terapéuticas.

Huntington Disease is a neurodegenerative disorder transmitted as an autosomal dominant trait. Selective neuronal loss in the striatum leads to chorea and cognitive impairment. It is a progressive disease with onset in midlife, which chronically evolves over many years and for which no curative treatment is available today. A review on the current knowledge of Huntington Disease was carried out. Etiopathogenic, clinical, diagnostic methods and treatment options were included.