Sequence, Chromatin and Evolution of Satellite DNA

Satellite DNA consists of abundant tandem repeats that play important roles in cellular processes, including chromosome segregation, genome organization and chromosome end protection. Most satellite DNA repeat units are either of nucleosomal length or 5–10 bp long and occupy centromeric, pericentromeric or telomeric regions. Due to high repetitiveness, satellite DNA sequences have largely been absent from genome assemblies. Although few conserved satellite-specific sequence motifs have been identified, DNA curvature, dyad symmetries and inverted repeats are features of various satellite DNAs in several organisms. Satellite DNA sequences are either embedded in highly compact gene-poor heterochromatin or specialized chromatin that is distinct from euchromatin. Nevertheless, some satellite DNAs are transcribed into non-coding RNAs that may play important roles in satellite DNA function. Intriguingly, satellite DNAs are among the most rapidly evolving genomic elements, such that a large fraction is species-specific in most organisms. Here we describe the different classes of satellite DNA sequences, their satellite-specific chromatin features, and how these features may contribute to satellite DNA biology and evolution. We also discuss how the evolution of functional satellite DNA classes may contribute to speciation in plants and animals.

A unique chromatin complex occupies young α-satellite arrays of human centromeres

The intractability of homogeneous α-satellite arrays has impeded understanding of human centromeres. Artificial centromeres are produced from higher-order repeats (HORs) present at centromere edges, although the exact sequences and chromatin conformations of centromere cores remain unknown. We use high-resolution chromatin immunoprecipitation (ChIP) of centromere components followed by clustering of sequence data as an unbiased approach to identify functional centromere sequences. We find that specific dimeric α-satellite units shared by multiple individuals dominate functional human centromeres. We identify two recently homogenized α-satellite dimers that are occupied by precisely positioned CENP-A (cenH3) nucleosomes with two ~100-base pair (bp) DNA wraps in tandem separated by a CENP-B/CENP-C-containing linker, whereas pericentromeric HORs show diffuse positioning. Precise positioning is largely maintained, whereas abundance decreases exponentially with divergence, which suggests that young α-satellite dimers with paired ~100-bp particles mediate evolution of functional human centromeres. Our unbiased strategy for identifying functional centromeric sequences should be generally applicable to tandem repeat arrays that dominate the centromeres of most eukaryotes.

Paediatric cataract blindness in the developing world: surgical techniques and intraocular lenses in the new millennium

Paediatric cataract blindness presents an enormous problem to developing countries in terms of human morbidity, economic loss, and social burden. Managing cataracts in children remains a challenge: treatment is often difficult, tedious, and requires a dedicated team effort. To assure the best long term outcome for cataract blind children, appropriate paediatric surgical techniques need to be defined and adopted by ophthalmic surgeons of developing countries. The high cost of operative equipment and the uneven world distribution of ophthalmologists, paediatricians, and anaesthetists create unique challenges. This review focuses on issues related to paediatric cataract management that are appropriate and suitable for ophthalmic surgeons in the developing world. Practical guidelines and recommendations have also been provided for ophthalmic surgeons and health planners dealing with childhood cataract management in the developing world.

Efficient neocentromere formation is suppressed by gene conversion to maintain centromere function at native physical chromosomal loci in Candida albicans

CENPA/Cse4 assembles centromeric chromatin on diverse DNA. CENPA chromatin is epigenetically propagated on unique and different centromere DNA sequences in a pathogenic yeast Candida albicans. Formation of neocentromeres on DNA, nonhomologous to native centromeres, indicates a role of non-DNA sequence determinants in CENPA deposition. Neocentromeres have been shown to form at multiple loci in C. albicans when a native centromere was deleted. However, the process of site selection for CENPA deposition on native or neocentromeres in the absence of defined DNA sequences remains elusive. By systematic deletion of CENPA chromatin-containing regions of variable length of different chromosomes, followed by mapping of neocentromere loci in C. albicans and its related species Candida dubliniensis, which share similar centromere properties, we demonstrate that the chromosomal location is an evolutionarily conserved primary determinant of CENPA deposition. Neocentromeres on the altered chromosome are always formed close to the site which was once occupied by the native centromere. Interestingly, repositioning of CENPA chromatin from the neocentromere to the native centromere occurs by gene conversion in C. albicans.

Molecular Complexes at Euchromatin, Heterochromatin and Centromeric Chromatin

Chromatin consists of a complex of DNA and histone proteins as its core components and plays an important role in both packaging DNA and regulating DNA metabolic pathways such as DNA replication, transcription, recombination, and chromosome segregation. Proper functioning of chromatin further involves a network of interactions among molecular complexes that modify chromatin structure and organization to affect the accessibility of DNA to transcription factors leading to the activation or repression of the transcription of target DNA loci. Based on its structure and compaction state, chromatin is categorized into euchromatin, heterochromatin, and centromeric chromatin. In this review, we discuss distinct chromatin factors and molecular complexes that constitute euchromatin-open chromatin structure associated with active transcription; heterochromatin-less accessible chromatin associated with silencing; centromeric chromatin-the site of spindle binding in chromosome segregation.

A coordinated interdependent protein circuitry stabilizes the kinetochore ensemble to protect CENP-A in the human pathogenic yeast Candida albicans

Unlike most eukaryotes, a kinetochore is fully assembled early in the cell cycle in budding yeasts Saccharomyces cerevisiae and Candida albicans. These kinetochores are clustered together throughout the cell cycle. Kinetochore assembly on point centromeres of S. cerevisiae is considered to be a step-wise process that initiates with binding of inner kinetochore proteins on specific centromere DNA sequence motifs. In contrast, kinetochore formation in C. albicans, that carries regional centromeres of 3-5 kb long, has been shown to be a sequence independent but an epigenetically regulated event. In this study, we investigated the process of kinetochore assembly/disassembly in C. albicans. Localization dependence of various kinetochore proteins studied by confocal microscopy and chromatin immunoprecipitation (ChIP) assays revealed that assembly of a kinetochore is a highly coordinated and interdependent event. Partial depletion of an essential kinetochore protein affects integrity of the kinetochore cluster. Further protein depletion results in complete collapse of the kinetochore architecture. In addition, GFP-tagged kinetochore proteins confirmed similar time-dependent disintegration upon gradual depletion of an outer kinetochore protein (Dam1). The loss of integrity of a kinetochore formed on centromeric chromatin was demonstrated by reduced binding of CENP-A and CENP-C at the centromeres. Most strikingly, Western blot analysis revealed that gradual depletion of any of these essential kinetochore proteins results in concomitant reduction in cellular protein levels of CENP-A. We further demonstrated that centromere bound CENP-A is protected from the proteosomal mediated degradation. Based on these results, we propose that a coordinated interdependent circuitry of several evolutionarily conserved essential kinetochore proteins ensures integrity of a kinetochore formed on the foundation of CENP-A containing centromeric chromatin.

Architectural RNA in chromatin organization

RNA plays a well-established architectural role in the formation of membraneless interchromatin nuclear bodies. However, a less well-known role of RNA is in organizing chromatin, whereby specific RNAs have been found to recruit chromatin modifier proteins. Whether or not RNA can act as an architectural molecule for chromatin remains unclear, partly because dissecting the architectural role of RNA from its regulatory role remains challenging. Studies that have addressed RNA's architectural role in chromatin organization rely on in situ RNA depletion using Ribonuclease A (RNase A) and suggest that RNA plays a major direct architectural role in chromatin organization. In this review, we will discuss these findings, candidate chromatin architectural long non-coding RNAs and possible mechanisms by which RNA, along with RNA binding proteins might be mediating chromatin organization.

Willingness to pay for cataract surgery in Kathmandu valley

AIM

A cross sectional study was carried out on 78 screened cataract patients of two screening camps in Kathmandu valley, Nepal, to assess the willingness to pay for cataract surgery.

METHODS

A non-probability sampling technique with open ended and close ended questionnaires was used.

RESULTS

The average age of patients was 68.8 years. The ratio of men and women was 0.9:1. 42.3% (33) of patients were willing to pay for cataract surgery. Among them 48.5% (16) of people were willing to pay less than dollars 13 and 51.5% (17) were willing to pay more than dollars 13. The mean was dollars 2.3 (SD dollars 15.5) per case. Patients with bilateral cataract were more willing to pay than unilateral cases. Poverty (44.4%, 20) was the main barrier for unwillingness to pay for cataract surgery. Other reasons were the lack of family support (28.9%, 13), lack of knowledge of surgery and belief that it was an unnecessary procedure (15.6%, seven), and waiting for a free surgical service (11.1%, five).

CONCLUSION

This study clearly indicates that although there was awareness of the availability of treatment and services provided within the reach, people are not willing to pay for the surgery and use the facility primarily because of poverty. Hence, to change patients' attitudes, a more holistic approach is needed, keeping in view the cultural, social, and economic background of the society.

CENPT bridges adjacent CENPA nucleosomes on young human α-satellite dimers

Nucleosomes containing the CenH3 (CENPA or CENP-A) histone variant replace H3 nucleosomes at centromeres to provide a foundation for kinetochore assembly. CENPA nucleosomes are part of the constitutive centromere associated network (CCAN) that forms the inner kinetochore on which outer kinetochore proteins assemble. Two components of the CCAN, CENPC and the histone-fold protein CENPT, provide independent connections from the ∼171-bp centromeric α-satellite repeat units to the outer kinetochore. However, the spatial relationship between CENPA nucleosomes and these two branches remains unclear. To address this issue, we use a base-pair resolution genomic readout of protein-protein interactions, comparative chromatin immunoprecipitation (ChIP) with sequencing, together with sequential ChIP, to infer the in vivo molecular architecture of the human CCAN. In contrast to the currently accepted model in which CENPT associates with H3 nucleosomes, we find that CENPT is centered over the CENPB box between two well-positioned CENPA nucleosomes on the most abundant centromeric young α-satellite dimers and interacts with the CENPB/CENPC complex. Upon cross-linking, the entire CENPA/CENPB/CENPC/CENPT complex is nuclease-protected over an α-satellite dimer that comprises the fundamental unit of centromeric chromatin. We conclude that CENPA/CENPC and CENPT pathways for kinetochore assembly are physically integrated over young α-satellite dimers.

Trans- and cis-acting effects of Firre on epigenetic features of the inactive X chromosome

Firre encodes a lncRNA involved in nuclear organization. Here, we show that Firre RNA expressed from the active X chromosome maintains histone H3K27me3 enrichment on the inactive X chromosome (Xi) in somatic cells. This trans-acting effect involves SUZ12, reflecting interactions between Firre RNA and components of the Polycomb repressive complexes. Without Firre RNA, H3K27me3 decreases on the Xi and the Xi-perinucleolar location is disrupted, possibly due to decreased CTCF binding on the Xi. We also observe widespread gene dysregulation, but not on the Xi. These effects are measurably rescued by ectopic expression of mouse or human Firre/FIRRE transgenes, supporting conserved trans-acting roles. We also find that the compact 3D structure of the Xi partly depends on the Firre locus and its RNA. In common lymphoid progenitors and T-cells Firre exerts a cis-acting effect on maintenance of H3K27me3 in a 26 Mb region around the locus, demonstrating cell type-specific trans- and cis-acting roles of this lncRNA.

Unexpected conformational variations of the human centromeric chromatin complex

We combined classical salt fractionation with chromatin immunoprecipitation to recover human centromeric chromatin under native conditions. We found that >85% of the total centromeric chromatin is insoluble under conditions typically used for native chromatin extraction. To map both soluble and insoluble chromatin in situ, we combined CUT&RUN (cleavage under targets and release using nuclease), a targeted nuclease method, with salt fractionation. Using this approach, we observed unexpected structural and conformational variations of centromere protein A (CENP-A)-containing complexes on different α-satellite dimeric units within highly homogenous arrays. Our results suggest that slight α-satellite sequence differences control the structure and occupancy of the associated centromeric chromatin complex.

Ketamine anaesthesia for paediatric ophthalmology surgery

AIMS

Children with treatable, vision impairing conditions may not have access to surgical care when they live in regions where anaesthesia is unavailable. The use of ketamine anaesthesia in a developing region was studied to determine its safety and effectiveness.

METHODS

This is a consecutive series of 679 children who had a variety of paediatric eye disorders necessitating a short general anaesthesia. Ketamine was administered intravenously by a paediatrician with training in paediatric resuscitation procedures. Both intraocular and extraocular procedures were performed. The location of treatment was the Tilganga Eye Hospital in Kathmandu, Nepal, a developing region of the world. The study took place over a 5 year period.

RESULTS

All procedures were performed without any anaesthetic complications. No child required unanticipated resuscitation or laryngeal intubation. Postoperative dysphoria occurred occasionally and was difficult to measure quantitatively. This side effect of ketamine resolved by the first postoperative day.

CONCLUSION

Ketamine is an effective agent for both intraocular and extraocular surgery in the paediatric age group. None of the children in this series needed resuscitation or intubations, and the ophthalmic surgery was carried out safely. Ketamine can be used safely in any ophthalmic procedure of short duration by a person having some training in anaesthetic resuscitation procedures. Because of its simplicity and safety, ketamine may be useful in a simple ophthalmic setup in the developing word.

The surgical challenge of ossified ventrolateral spinal meningiomas: tricks and pearls for managing large ossified meningiomas of the thoracic spine

The authors present an illustrative technical note on microsurgical resection of ventrolateral completely ossified spinal meningiomas (OSMs) and a literature review of the surgical management of calcified spinal meningiomas or OSMs. These tumors are surgically demanding due to their solid consistency, especially when in a ventrolateral location with dislocation of the spinal cord. A challenging case with significant thoracic cord compression and displacement is described. Due to the firm consistency and the ventrolateral localization of the meningioma, a piecemeal resection was necessary. This could have resulted in a free-floating tumor remnant adherent to the spinal cord, impeding safe tumor resection. To avoid such a remnant, an anchoring burr hole was drilled at the border between the spinal cord and the adamantine tumor mass. Then, a microdissector was placed within the anchoring burr hole and the tumor was gently pulled laterally while drilling away the medial parts of the ossified tumor. This procedure was repeated until separation of the tumor from the spinal cord was possible and a gross-total resection (Simpson grade II) was manageable. Throughout the procedure, continuous intraoperative neurophysiological monitoring was performed.

Remarkable Evolutionary Plasticity of Centromeric Chromatin

Centromeres were familiar to cell biologists in the late 19th century, but for most eukaryotes the basis for centromere specification has remained enigmatic. Much attention has been focused on the cenH3 (CENP-A) histone variant, which forms the foundation of the centromere. To investigate the DNA sequence requirements for centromere specification, we applied a variety of epigenomic approaches, which have revealed surprising diversity in centromeric chromatin properties. Whereas each point centromere of budding yeast is occupied by a single precisely positioned tetrameric nucleosome with one cenH3 molecule, the "regional" centromeres of fission yeast contain unphased presumably octameric nucleosomes with two cenH3s. In Caenorhabditis elegans, kinetochores assemble all along the chromosome at sites of cenH3 nucleosomes that resemble budding yeast point centromeres, whereas holocentric insects lack cenH3 entirely. The "satellite" centromeres of most animals and plants consist of cenH3-containing particles that are precisely positioned over homogeneous tandem repeats, but in humans, different α-satellite subfamilies are occupied by CENP-A nucleosomes with very different conformations. We suggest that this extraordinary evolutionary diversity of centromeric chromatin architectures can be understood in terms of the simplicity of the task of equal chromosome segregation that is continually subverted by selfish DNA sequences.

Prevalence of electrolyte disturbances in perinatal asphyxia: a prospective study

BACKGROUND

Birth asphyxia is defined as the presence of hypoxia, hypercapnia, and acidosis leading the newborn to systemic disturbances probably electrolyte disturbance also. Knowledge of these electrolyte disturbances is very valuable as it can be an important parameter affecting perinatal morbidity, mortality and ongoing management.

METHODS

Serum sodium, potassium and ionized calcium of asphyxiated term newborn were sent within one hour of birth as per the inclusion criteria. Statistical comparison of mean values of different electrolytes between different groups of perinatal asphyxia was performed by ANOVA test for parametric data and significant data were further analyzed using post hoc test. Bivariate analysis was done to determine the correlations between Apgar score at 5 min and serum electrolytes. Pearson test was used to calculate the correlation coefficient. Box plot was used to show the median and quartile between serum electrolytes and Apgar score at 5 min.

RESULT

The mean values of sodium for mild, moderate and severe asphyxia were 135.52, 130.7 and 127.15 meq/l respectively. The values of potassium for mild, moderate and severe asphyxia were 4.96, 5.93 and 6.78 meq/l respectively. Similarly, the mean values of ionized calcium for mild, moderate and severe asphyxia were 1.07, 1.12 and 0.99 mmol/l respectively. The values of sodium and potassium among different severity of asphyxia were significantly different (p-value< 0.001). Significant positive correlation was found between serum sodium and Apgar score at 5 min. Significant negative correlation was present between serum potassium and Apgar score at 5 min.

CONCLUSION

The degree of hyponatremia and hyperkalemia was directly proportional to the severity of birth asphyxia. So these electrolyte disturbances should always be kept in mind while managing cases of perinatal asphyxia and should be managed accordingly.

Active enhancers strengthen insulation by RNA-mediated CTCF binding at chromatin domain boundaries

Vertebrate genomes are partitioned into chromatin domains or topologically associating domains (TADs), which are typically bound by head-to-head pairs of CTCF binding sites. Transcription at domain boundaries correlates with better insulation; however, it is not known whether the boundary transcripts themselves contribute to boundary function. Here we characterize boundary-associated RNAs genome-wide, focusing on the disease-relevant INK4a/ARF and MYC TAD. Using CTCF site deletions and boundary-associated RNA knockdowns, we observe that boundary-associated RNAs facilitate recruitment and clustering of CTCF at TAD borders. The resulting CTCF enrichment enhances TAD insulation, enhancer-promoter interactions, and TAD gene expression. Importantly, knockdown of boundary-associated RNAs results in loss of boundary insulation function. Using enhancer deletions and CRISPRi of promoters, we show that active TAD enhancers, but not promoters, induce boundary-associated RNA transcription, thus defining a novel class of regulatory enhancer RNAs.

CTCF-mediated insulation and chromatin environment modulate Car5b escape from X inactivation

Background

The number and escape levels of genes that escape X chromosome inactivation (XCI) in female somatic cells vary among tissues and cell types, potentially contributing to specific sex differences. Here we investigate the role of CTCF, a master chromatin conformation regulator, in regulating escape from XCI. CTCF binding profiles and epigenetic features were systematically examined at constitutive and facultative escape genes using mouse allelic systems to distinguish the inactive X (Xi) and active X (Xa) chromosomes.

Results

We found that escape genes are located inside domains flanked by convergent arrays of CTCF binding sites, consistent with the formation of loops. In addition, strong and divergent CTCF binding sites often located at the boundaries between escape genes and adjacent neighbors subject to XCI would help insulate domains. Facultative escapees show clear differences in CTCF binding dependent on their XCI status in specific cell types/tissues. Concordantly, deletion but not inversion of a CTCF binding site at the boundary between the facultative escape gene Car5b and its silent neighbor Siah1b resulted in loss of Car5b escape. Reduced CTCF binding and enrichment of a repressive mark over Car5b in cells with a boundary deletion indicated loss of looping and insulation. In mutant lines in which either the Xi-specific compact structure or its H3K27me3 enrichment was disrupted, escape genes showed an increase in gene expression and associated active marks, supporting the roles of the 3D Xi structure and heterochromatic marks in constraining levels of escape.

Conclusion

Our findings indicate that escape from XCI is modulated both by looping and insulation of chromatin via convergent arrays of CTCF binding sites and by compaction and epigenetic features of the surrounding heterochromatin.

Prevalence of Tuberculosis in Severe Acute Malnutrition: A Prospective Observational Study

Introduction: Tuberculosis (TB) and malnutrition are important causes of morbidity and mortality in children in the developing world. This study was done to determine the prevalence of tuberculosis in severe acute malnutrition (SAM) cases and to observe different presentations of SAM. Method: This prospective observational study was carried out in the Department of Paediatrics and Adolescent Medicine at a tertiary care center in Nepal for a duration of one year from December 2018 to November 2019. All cases of SAM meeting the inclusion criteria were evaluated with Mantoux test, chest X-ray, gastric aspirate / sputum analysis and gene-Xpert for diagnosis of TB. Other relevant investigations for diagnosis of TB were also sent as per the clinical scenario. Data were entered and analyzed using Microsoft excel. Descriptive statistics was used for analysis of data. Results: Total 107 SAM cases were analyzed. The hospital prevalence of wasting and severe wasting was 11.98% and 0.73% respectively. The prevalence of TB in SAM was 4.67%, commonest being pulmonary TB (60%). Among TB cases, 40% were without any systemic complaints. Only 19.6% cases presented with nutritional complaint. Conclusions: This study found that a significant percentage of cases with SAM had TB and hence adds on the importance of screening for TB (Pulmonary TB) in every case of SAM, irrespective of symptoms.

Role of Renal Biopsy in Managing Paediatric Renal Disease in a Tertiary Care Setting

Introduction: The contribution of renal biopsy is of major importance in many paediatrics renal diseases. This prospective study analysed the clinic-pathological spectrum of the biopsied cases, complications related to renal biopsy and its effect on management. Methods: USG guided percutaneous renal biopsy was performed in indicated children. Laboratory findings, complications of the procedure, histological diagnosis and its effect on management were obtained from all patients who underwent renal biopsy from April 2019 to March 2020. The data were finally analysed using descriptive statistics. Results: Total 50 cases were enrolled during the study period. There were 24 males and 26 females with age range from two to 16 years. The common indications for biopsy were acute nephritic syndrome (25 cases), including both primary glomerulonephritis (11 cases) and secondary glomerulonephritis (14 cases), of which lupus nephritis contributed (11/25) cases, followed by atypical/ steroid resistant or dependent nephrotic syndrome (18 cases). Among primary glomerulonephritis, diffuse proliferative glomerulonephritis was most common pathological finding (11/25). One had crescentric glomerulonephritis. Lupus nephritis predominantly had Class IV/V pathology (6/11). Of 18 nephrotic syndrome cases, nine had minimal-change-disease and five had focal-segmental-glomerulosclerosis. The complications associated with procedure were self-resolving gross hematuria in eight cases, perirenal hematoma requiring plasma transfusion in one case. Adequate renal tissue sample was obtained in 47 of the renal biopsies. Three cases underwent repeat biopsy. Immunosuppressive therapy was altered as per the biopsy report among 18 cases. Conclusions: Our study showed that renal biopsy is a safe, reliable and effective technique in children. It resolutes many diagnostic dilemma and helps in effective management.