RNA Polymerase II Dependent Crosstalk between H4K16 Deacetylation and H3K56 Acetylation Promotes Transcription of Constitutively Expressed Genes

Nucleosome dynamics in the coding region of a transcriptionally active locus is critical for understanding how RNA polymerase II progresses through the gene body. Histone acetylation and deacetylation critically influence nucleosome accessibility during DNA metabolic processes like transcription. Effect of such histone modifications is context and residue dependent. Rather than effect of individual histone residues, the network of modifications of several histone residues in combination generates a chromatin landscape that is conducive for transcription. Here we show that in Saccharomyces cerevisiae, crosstalk between deacetylation of the H4 N-terminal tail residue H4K16 and acetylation of the H3 core domain residue H3K56, promotes RNA polymerase II progression through the gene body. Results indicate that deacetylation of H4K16 precedes and in turn induces H3K56 acetylation. Effectively, recruitment of Rtt109, the HAT responsible for H3K56 acetylation is essentially dependent on H4K16 deacetylation. In Hos2 deletion strains, where H4K16 deacetylation is abolished, both H3K56 acetylation and RNA polymerase II recruitment gets significantly impaired. Notably, H4K16 deacetylation and H3K56 acetylation are found to be essentially dependent on active transcription. In summary, H4K16 deacetylation promotes H3K56 acetylation and the two modifications together work towards successful functioning of RNA polymerase II during active transcription.

RAV1 mediates cytokinin signaling for regulating primary root growth in Arabidopsis

Root growth dynamics is an outcome of complex hormonal crosstalk. The primary root meristem size, for example, is determined by antagonizing actions of cytokinin and auxin. Here we show that RAV1, a member of the AP2/ERF family of transcription factors, mediates cytokinin signaling in roots to regulate meristem size. The rav1 mutants have prominently longer primary roots, with a meristem that is significantly enlarged and contains higher cell numbers, compared with wild-type. The mutant phenotype could be restored on exogenous cytokinin application or by inhibiting auxin transport. At the transcript level, primary cytokinin-responsive genes like ARR1, ARR12 were significantly downregulated in the mutant root, indicating impaired cytokinin signaling. In concurrence, cytokinin induced regulation of SHY2, an Aux/IAA gene, and auxin efflux carrier PIN1 was hindered in rav1, leading to altered auxin transport and distribution. This effectively altered root meristem size in the mutant. Notably, CRF1, another member of the AP2/ERF family implicated in cytokinin signaling, is transcriptionally repressed by RAV1 to promote cytokinin response in roots. Further associating RAV1 with cytokinin signaling, our results demonstrate that cytokinin upregulates RAV1 expression through ARR1, during post-embryonic root development. Regulation of RAV1 expression is a part of secondary cytokinin response that eventually represses CRF1 to augment cytokinin signaling. To conclude, RAV1 functions in a branch pathway downstream to ARR1 that regulates CRF1 expression to enhance cytokinin action during primary root development in Arabidopsis.

Acetylation of H3K56 orchestrates UV-responsive chromatin events that generate DNA accessibility during Nucleotide Excision Repair

Histone modifications have long been related to DNA damage response. Nucleotide excision repair pathway that removes helix-distorting lesions necessitates DNA accessibility through chromatin modifications. Previous studies have linked H3 tail residue acetylation to UV-induced NER. Here we present evidences that acetylation of H3K56 is crucial for early phases of NER. Using H3K56 mutants K56Q and K56R, which mimic acetylated and unacetylated lysines respectively, we show that recruitment of the repair factor Rad16, a Swi/Snf family member is dependent on H3K56 acetylation. With constitutive H3K56 acetylation, Rad16 recruitment became UV-independent. Furthermore, H3K56 acetylation promoted UV-induced hyperacetylation of H3K9 and H3K14. Importantly, constitutive H3K56 acetylation prominently increased chromatin accessibility. During NER, lack of H3K56 acetylation that effectively aborted H3 tail residue acetylation and Rad16 recruitment, thus failed to impart essential chromatin modulations. The NER-responsive oscillation of chromatin structure observed in wild type, was distinctly eliminated in absence of H3K56 acetylation. In vitro assay with wild type and H3K56 mutant cell extracts further indicated that absence of H3K56 acetylation negatively affected DNA relaxation during NER. Overall, H3K56 acetylation regulates Rad16 redistribution and UV-induced H3 tail residue hyperacetylation, and the resultant modification code promotes chromatin accessibility and recruitment of subsequent repair factors during NER.

DNA methylation and regulation of gene expression: Guardian of our health

One of the most critical epigenetic signatures present in the genome of higher eukaryotes is the methylation of DNA at the C-5 position of the cytosine ring. Based on the sites of DNA methylation in a locus, it can serve as a repressive or activation mark for gene expression. In a crosstalk with histone modifiers, DNA methylation can consequently either inhibit binding of the transcription machinery or generate a landscape conducive for transcription. During developmental phases, the DNA methylation pattern in the genome undergoes alterations as a result of regulated balance between de novo DNA methylation and demethylation. Resultantly, differentiated cells inherit a unique DNA methylation pattern that fine tunes tissue-specific gene expression. Although apparently a stable epigenetic mark, DNA methylation is actually labile and is a complex reflection of interaction between epigenome, genome and environmental factors prior to birth and during progression of life. Recent findings indicate that levels of DNA methylation in an individual is a dynamic outcome, strongly influenced by the dietary environment during germ cell formation, embryogenesis and post birth exposures. Loss of balances in DNA methylation during developmental stages may result in imprinting disorders, while at any later stage may lead to increased predisposition to various diseases and abnormalities. This review aims to provide an outline of how our epigenome is uniquely guided by our lifetime of experiences beginning in the womb and how understanding it better holds future possibilities of improvised clinical applications.

ABI3 plays a role in de-novo root regeneration from Arabidopsis thaliana callus cells

Developmental plasticity and the ability to regenerate organs during the life cycle are a signature feature of plant system. De novo organogenesis is a common mode of plant regeneration and may occur directly from the explant or indirectly via callus formation. It is now evident that callus formation occurs through the root development pathway. In fact, callus cells behave like a group of root primordium cells that are under the control of exogenous auxin. Presence or absence of auxin decides the subsequent fate of these cells. While in presence of external supplementation of auxin they are maintained as root primordia cells, absence of exogenous auxin induces the callus cells into patterning, differentiation and finally root emergence. Here we show that in absence of functional ABI3, a prominent member of the B3 superfamily of transcription factors, root regeneration is compromised in Arabidopsis callus cells. In culture medium free of any exogenous hormone supplementation, while adventitious root emergence and growth was prominently observed in wild type cells, no such features were observed in abi3-6 cells. Expression of auxin-responsive AUX1 and GH3 genes was significantly reduced in abi3-6 cells, indicating that auxin levels or distribution may be altered in absence of ABI3.

Deacetylation of H4 lysine16 affects acetylation of lysine residues in histone H3 and H4 and promotes transcription of constitutive genes

Histone modification map of H4 N-terminal tail residues in Saccharomyces cerevisiae reveals the prominence of lysine acetylation. Previous reports have indicated the importance of lysine acetylation in maintaining chromatin structure and function. H4K16, a residue with highly regulated acetylation dynamics has unique functions not overlapping with the other H4 N- terminal acetylable residues. The present work unravels the role of H4K16 acetylation in regulating expression of constitutive genes. H4K16 gets distinctly deacetylated over the coding region of constitutively expressed genes. Deacetylation of H4K16 reduces H3K9 acetylation at the cellular and gene level. Reduced H3K9 acetylation however did not negatively correlate with active gene transcription. Significantly, H4K16 deacetylation was found to be associated with hypoacetylated H4K12 throughout the locus of constitutive genes. H4K16 and K12 deacetylation is known to favour active transcription. Sas2, the HAT mutant showed similar patterns of hypoacetylated H3K9 and H4K12 at the active loci, clearly implying that the modifications were associated with deacetylation state of H4K16. Deacetylation of H4K16 was also concurrent with increased H3K56 acetylation in the promoter region and ORF of the constitutive genes. Combination of all these histone modifications significantly reduced H3 occupancy, increased promoter accessibility and enhanced RNAPII recruitment at the constitutively active loci. Consequently, we found that expression of active genes was higher in H4K16R mutant which mimic deacetylated state, but not in H4K16Q mimicking constitutive acetylation. To summarize, H4K16 deacetylation linked with H4K12 and H3K9 hypoacetylation along with H3K56 hyperacetylation generate a chromatin landscape that is conducive for transcription of constitutive genes.

Regulated acetylation and deacetylation of H4 K16 is essential for efficient NER in Saccharomyces cerevisiae

Acetylation status of H4 K16, a residue in the histone H4 N-terminal tail plays a unique role in regulating chromatin structure and function. Here we show that, during UV-induced nucleotide excision repair H4 K16 gets hyperacetylated following an initial phase of hypoacetylation. Disrupting H4 K16 acetylation-deacetylation by mutating H4 K16 to R (deacetylated state) or Q (acetylated state) leads to compromised chromatin functions. In the silenced mating locus and telomere region H4 K16 mutants show higher recruitment of Sir proteins and spreading beyond the designated boundaries. More significantly, chromatin of both the H4 K16 mutants has reduced accessibility in the silenced regions and genome wide. On UV irradiation, the mutants showed higher UV sensitivity, reduced NER rate and altered H3 N-terminal tail acetylation, compared to wild type. NER efficiency is affected by reduced or delayed recruitment of early NER proteins and chromatin remodeller Swi/Snf along with lack of nucleosome rearrangement during repair. Additionally UV-induced expression of RAD and SNF5 genes was reduced in the mutants. Hindered chromatin accessibility in the H4 K16 mutants is thus non-conducive for gene expression as well as recruitment of NER and chromatin remodeller proteins. Subsequently, inadequate nucleosomal rearrangement during early phases of repair impeded accessibility of the NER complex to DNA lesions, in the H4 K16 mutants. Effectively, NER efficiency was found to be compromised in the mutants. Interestingly, in the transcriptionally active chromatin region, both the H4 K16 mutants showed reduced NER rate during early repair time points. However, with progression of repair H4 K16R repaired faster than K16Q mutants and rate of CPD removal became differential between the two mutants during later NER phases. To summarize, our results establish the essentiality of regulated acetylation and deacetylation of H4 K16 residue in maintaining chromatin accessibility and efficiency of functions like NER and gene expression.

ABI3 mediates dehydration stress recovery response in Arabidopsis thaliana by regulating expression of downstream genes

ABI3, originally discovered as a seed-specific transcription factor is now implicated to act beyond seed physiology, especially during abiotic stress. In non-seed plants, ABI3 is known to act in desiccation stress signaling. Here we show that ABI3 plays a role in dehydration stress response in Arabidopsis. ABI3 gene was upregulated during dehydration stress and its expression was maintained during subsequent stress recovery phases. Comparative gene expression studies in response to dehydration stress and stress recovery were done with genes which had potential ABI3 binding sites in their upstream regulatory regions. Such studies showed that several genes including known seed-specific factors like CRUCIFERIN1, CRUCIFERIN3 and LEA-group of genes like LEA76, LEA6, DEHYDRIN LEA and LEA-LIKE got upregulated in an ABI3-dependent manner, especially during the stress recovery phase. ABI3 got recruited to regions upstream to the transcription start site of these genes during dehydration stress response through direct or indirect DNA binding. Interestingly, ABI3 also binds to its own promoter region during such stress signaling. Nucleosomes covering potential ABI3 binding sites in the upstream sequences of the above-mentioned genes alter positions, and show increased H3 K9 acetylation during stress-induced transcription. ABI3 thus mediates dehydration stress signaling in Arabidopsis through regulation of a group of genes that play a role primarily during stress recovery phase.

Hospital-based perinatal outcomes and complications in teenage pregnancy in India

Teenage pregnancy is a worldwide problem bearing serious social and medical implications relating to maternal and child health. A cross-sectional observational study was undertaken to compare the different sociodemographic characteristics and perinatal outcomes of teenage primigravida mothers with those of adult primigravida mothers in a tertiary-care hospital in eastern India. A sample of 350 each in cases and comparison group comprised the study subjects. Data were collected through interviews and by observations using a pretested and predesigned schedule. Results revealed that the teenage mothers had a higher proportion (27.7%) of preterm deliveries compared to 13.1% in the adult mothers and had low-birthweight babies (38.9% vs 30.4% respectively). Stillbirth rate was also significantly higher in teenage deliveries (5.1% vs 0.9% respectively). The teenage mothers developed more adverse perinatal complications, such as preterm births, stillbirths, neonatal deaths, and delivered low-birthweight babies, when compared with those of the adult primigravida mothers. Teenage pregnancy is still a rampant and important public-health problem in India with unfavourable perinatal outcomes and needs to be tackled on a priority basis.

Gender inequality in nutritional status among under five children in a village in Hooghly district, West Bengal

A community based, cross-sectional study was conducted in the Mollasimla village of Hooghly district of West Bengal, to examine the differences in nutritional status of under-five males and females and to determine the different bio-social factors associated with such differences. It was found that 55.9%, 51.4% and 42.3% of the girls were underweight, stunted and wasted respectively compared to 46.6%, 40.5% and 35.3% of the boys and a significantly higher proportion of malnutrition was found to be present among female children of higher birth order and those belonging to families with lower per capita income compared to the males.

An epidemiological study of low birth weight newborns in the district of Puruliya, West Bengal

BACKGROUND

A community-based epidemiological study on birth weight of newborns was undertaken in the rural domain of a backward district of West Bengal.

OBJECTIVES

To find out the magnitude of low birth weight (< 2.5 kg.) newborns and to highlight association, if any, of the socio-demographic, maternal and obstetric factors with birth weight of newborns.

METHODS

The study was undertaken in 30 sub-centre areas (cluster), selected by '30 clusters sampling technique', in the rural area of Puruliya district. An adequate sample of 512 newborns (466 plus 10% extra allowance) delivered in those selected clusters (17 consecutive deliveries in each cluster) were to be studied. But, due to inability to record birth weight within 48 hours (in home deliveries) and other reasons, 487 newborns were included in assessing magnitude of the LBW problem. In-depth information on several variables was obtained from 439 mothers of the newborns. Health Workers (F), Anganwadi Workers, Trained dais and Health Supervisors -(F), specially trained for the survey, collected information by using pre-designed and pre-tested proforma.

RESULTS & CONCLUSION

The incidence of LBW was 31.3%. Among different variables studied, statistically significant association was found in case of educational level of mothers and also place of delivery of newborns. More such community-based studies should be conducted

A study on catch up growth among low birth weight infants in an urban slum of Kolkata

OBJECTIVES

To study the catch up growth among low birth weight infants in relation to the normal birth weight counterparts in first six months of age.

METHODS

A longitudinal community based study was done in 2004 -05 in an urban slum of Chetla, Kolkata among 126 singleton live born babies. Growth pattern of these babies was followed up at 15+/-5 days interval by house visit till six months of age.

RESULTS

The incidence of low birth weight babies was 28.6%. 86.1% LBW infants caught up in length at 3rd month, 63.9% in chest circumference at 4th month, 66.7% in head circumference at 5th month, while 72.2% in weight at 6th month. Regular growth monitoring is essential for LBW babies to detect signs of growth faltering at the earliest.

A study on the delivery practices in riverine & non-riverine blocks of the district of South 24-Parganas, West Bengal

A cross sectional study was undertaken in three riverine and two non-riverine blocks of South 24 Parganas district, West Bengal to study the delivery practices and compare between two locality. During the reference period of one year, of 3073 total deliveries, 89.36% were home deliveries. Home deliveries were higher in the riverine blocks (95.07%) compared to non-riverine blocks (81.64%). 'Dai' conducted 58.36% and 90.62% of home deliveries in riverine and non-riverine blocks respectively. Only 18.4% of the 'Dai' were trained.

Occupational health problems among agricultural and plantation workers

Agricultural and plantation works are associated with a variety of unique occupational health hazards in the form of physical factors like extreme weather conditions, sunrays, etc; chemicaVtoxicological hazards in the form of pesticides/fertilisers, etc, including different forms of biological and mechanical hazards. As most of our rural people are engaged in varied types of agricultural activities, they are highly susceptible for suffering from numerous work related health disorders. There are very few data regarding the epidemiology of occupational health disorders among agricultural and plantation workers. Clinically well recognised group of occupationally acquired health problems may be respiratory, dermatological, traumatic, poisoning and neoplastic in nature. Prevalence of some specific zoonotic diseases and behavioural health problems are also found to be more among them. There is lack of attention for prevention and control of these occupational health problems. An adequately developed comprehensive occupational health care programme having all the components of preventive, curative and rehabilitative aspects can only promote and maintain the highest degree of physical, mental and social well-being in all types of agricultural and plantation workers of rural India.

Risk assessment of cardiovascular diseases among bank employees--a biochemical approach

In different epidemiological studies, an association between sedentary life style and incidence of cardiovascular diseases has been demonstrated. This study was carried out among 50 sedentary bank employees working at different nationalized banks within Calcutta City, India and 50 individuals with non-sedentary jobs matched for age group and sex for the control group. Body mass index (BMI), blood pressure (BP), plasma level of glucose, total cholesterol, low density lipoprotein (LDL), very low density lipoprotein (VLDL) and triglycerides (Tgs) were found to be significantly higher whereas high density lipoprotein (HDL) and reduced glutathione were found to be significantly lower among the bank employees as compared with the control subjects. Further, significant alteration in the activity of different enzymes (e.g., glutathione reductase, glutathione S-transferase, glucose 6 phosphate dehydrogenase, catalase and superoxide dismutase) involved in glutathione-mediated antioxidant scavenging systems and increases in lipid peroxidation were also observed in the bank employees. From the study, it appears that the relative risk for cardiovascular disease is increased among bank employees due to the sedentary nature of their jobs.

Influence of cigarette smoking on Vitamin C, glutathione and lipid peroxidation status

There has been a growing interest during recent years in the role of free radicals and lipid-peroxidation at tissue-level for the causation of cancer and other age-related diseases like atherosclerosis, rheumatoid arthritis, cataract etc. Free radicals and increased lipid peroxidation play a significant role for causation of human diseases by oxidative damage and functional degeneration of the tissues. Vitamin C, a well-known dietary antioxidant, and other enzymatic antioxidants like glutathione can protect the lipids of lipoproteins and other biomembranes against peroxidative damage by intercepting oxidants before they can attack the tissues. But cigarette smoking was found to affect the antioxidant protective action of Vitamin C, glutathione etc. A group of adult male smokers in this study were found to have lowered Vitamin 'C' & glutathione levels, but increased lipid-peroxide levels in their blood. Thus the increased pathogenicity of the smoking may also be due to indirect biochemical effect of enhanced oxidative stress by increased lipid-peroxidation and lowered Vitamin C & other antioxidants at tissue-level.

Drug consumption pattern in low socio-economic group in an urban community

117 families, having a total population of 558 were studied regarding drug consumption pattern. It was found that the average no. of episodes per person was 0.99 of which drugs were consumed for 72% of episodes. Significant difference was observed in consumption of drugs between males and females. Allopathic medicines were consumed for 93.3% of the episodes and the major source (53.8%) of medical care was from private practitioners. It was seen that the number of drugs consumed per episode of sickness rose as the per capita income increased. Vitamins and Minerals (22.3%) were the main group of drugs consumed. Drugs acting on the alimentary system (17.5%), Respiratory System (14.7%), Antimicrobials (14.6%) and Analgesics (10.8%) contributed to 80% of drug intake.