PWWP2A/B: Prominent players in the proteomic landscape.

The PWWP domain is a conserved motif unique to eukaryotes, playing a critical role in various cellular processes. Proteins containing the PWWP domain are typically found in chromatin, where they bind to DNA and histones in nucleosomes, facilitating chromatin-associated functions. Among these proteins, PWWP-domain containing proteins 2A and 2B (PWWP2A and PWWP2B), identified during the H2A interactome analysis, are DNA methyltransferase-related proteins, that are structurally disordered, except for their PWWP domain.

microRNA-150 targets major epigenetic repressors and inhibits cell proliferation.

The Polycomb Repressive Complex (PRC) proteins, EZH2 and EZH1 regulate many biological processes by generating the repressive H3K27me3 modifications in the chromatin. However, the factors that regulate the EZH1/EZH2 functions are poorly studied. We identify that the 3'UTRs of EZH2 and EZH1 mRNAs contain the binding sites for the miRNA, miR-150.

CREB acts as a common transcription factor for major epigenetic repressors; DNMT3B, EZH2, CUL4B and E2F6.

CREB signaling is known for several decades, but how it regulates both positive and negative regulators of cell proliferation is not well understood. On the other hand functions of major epigenetic repressors such as DNMT3B, EZH2 and CUL4B for their repressive epigenetic modifications on chromatin have also been well studied. However, there is very limited information available on how these repressors are regulated at their transcriptional level.

De novo methyltransferases: Potential players in diseases and new directions for targeted therapy.

Epigenetic modifications govern gene expression by guiding the human genome on 'what to express and what not to'. DNA methyltransferases (DNMTs) establish methylation patterns on DNA, particularly in CpG islands, and such patterns play a major role in gene silencing. DNMTs are a family of proteins/enzymes (DNMT1, 2, 3A, 3B, and 3L), among which, DNMT1 (maintenance methyltransferase) and DNMT3 (de novo methyltransferases) that direct mammalian development and genome imprinting are highly investigated.

A feedback regulation of CREB activation through the CUL4A and ERK signaling.

CUL4A; an E3 ubiquitin ligase is involved in the degradation of negative regulators of cell cycle such as p21, p27, p53, etc., through polyubiquitination-mediated protein degradation. The functional role(s) of CUL4A proteins on their targets are well characterized; however, the transcriptional regulation of CUL4A, particularly at its promoter level is not yet studied.

N-terminal truncations of human bHLH transcription factor Twist1 leads to the formation of aggresomes.

In the cell, misfolded proteins are processed by molecular chaperone-mediated refolding or through ubiquitin-mediated proteosome system. Dysregulation of these mechanisms facilitates the aggregation of misfolded proteins and forms aggresomes in the juxta nuclear position of the cell which are removed by lysosome-mediated autophagy pathway in the subsequent cell division. Accumulation of misfolded proteins in the cell is hallmark of several neurological disorders and other diseases including cancer.

miR-181a-2 downregulates the E3 ubiquitin ligase CUL4A transcript and promotes cell proliferation.

MiR-181a-2 plays a major role in cell proliferation both positively and negatively depending on tissue type by targeting several regulators 3'UTR regions. We have predicted several targets for miR-181a-2 through computational approaches and characterized one its interesting target, CUL4A, an E3 ubiquitin ligase. CUL4A regulates diverse functions in the cells including DNA repair, DNA replication, cell cycle, genomic stability through polyubiquitination of target proteins.

Identification of a novel leukemic-specific splice variant of DNMT3B and its stability.

DNA methyltransferases make use of alternative splicing mechanism to generate various splice variants, but their role(s) in modulating DNA methylation patterns in the cells is unclear. Notably, DNMT3B alone contains nearly 40 different splice variants. In this study, we have identified a novel splice variant of DNMT3B, which lacks exon 7 and 10 from leukemic cell lines which we termed as DNMT3B9.

Cullin 4A and 4B ubiquitin ligases interact with γ-tubulin and induce its polyubiquitination.

Regulated polyubiquitination is a key step for controlling protein degradation and maintaining proper balance between the proliferation of normal and uncontrolled cells. Addition of ubiquitin to the proteins by E3 ubiquitin ligases targets them for degradation by the 26S proteosome machinery. Discrepancies in ubiquitination and/or proteosome degradation might lead to multiple genetic disorders in humans.

E3 ubiquitin ligase Cullin4B mediated polyubiquitination of p53 for its degradation.

Controlled protein ubiquitination through E3 ubiquitin ligases and degradation via 26S proteasome machinery is required for orderly progression through cell cycle, chromatin remodeling, DNA repair, and development. Each cullin-dependent ubiquitin ligase (E3) complex can recruit various substrates for their degradation. Cullin 4A (CUL4A) and Cullin 4B (CUL4B) are members of cullin family proteins that mediate ubiquitin dependent proteolysis.

Differential effects of epigenetic modifiers on the expansion and maintenance of human cord blood stem/progenitor cells.

Epigenetic therapies, including DNA methyltransferase and histone deacetylase (HDAC) inhibitors, are increasingly being considered to treat hematological malignancies, but their effects on normal hematopoietic stem cells (HSCs) remain largely unexplored. We compared the effects of several HDAC inhibitors, including valproic acid (VPA) and trichostatin A (TSA), alone or in combination with 5-aza-2'-deoxycytidine (5azaD) on the expansion of HSCs. VPA induced the highest expansion of CD34+CD90+ cells and progenitor cells compared with other HDAC inhibitors or the sequential addition of 5azaD/TSA in culture.

Calcium carbonate nanoparticles: synthesis, characterization and biocompatibility.

The synthesis of nanoparticles and their functionalization to effectively utilize them in biological applications including drug delivery is currently a challenge. Calcium carbonate among many other inorganic nanosized particles offers promising results for such applications. We have synthesized calcium carbonate nanoparticles using polymer mediated growth technique, where one of the ions bound within polymer matrix and the other diffuses and reacts to form desired compound.

Reactive oxygen species mediated tissue damage in high energy proton irradiated mouse brain.

Although radiation related research has been conducted extensively, the molecular toxicology and cellular mechanisms affected by proton radiation remain poorly understood. We recently reported that the high energy protons induce cell death through activation of apoptotic signaling genes; caspase 3 and 8 (Baluchamy et al. J Biol Chem 285:24769-24774, 2010).

Epitaxial growth of the zinc oxide nanorods, their characterization and in vitro biocompatibility studies.

Here, we have synthesized Zinc Oxide (ZnO) nanorods at room temperature using zinc acetate and hexamethylenetetramine as precursors followed by characterization using X-ray diffraction (XRD), fourier transform infra red spectroscopy, scanning electron microscopy (SEM) and transmission electron microscopy. The growth of the synthesized ZnO was found to be very close to its hexagonal nature, which is confirmed by XRD. The nanorods were grown perpendicular to the long-axis and grew along the [001] direction, which is the nature of ZnO growth.

Pulmonary biocompatibility assessment of inhaled single-wall and multiwall carbon nanotubes in BALB/c mice.

With the widespread application of carbon nanotubes (CNTs) in diverse commercial processes, scientists are now concerned about the potential health risk of occupational exposures. In this study, CNT-induced pulmonary toxicity was investigated by exposing BALB/c mice to aerosolized single-wall (SW) CNT and multiwall (MW) CNT (5 μg/g of mice) for 7 consecutive days in a nose-only exposure system. Microscopic studies showed that inhaled CNTs were homogeneously distributed in the mouse lung.

Multiwalled carbon nanotubes activate NF-κB and AP-1 signaling pathways to induce apoptosis in rat lung epithelial cells.

Our previous report on multiwall carbon nanotubes (MWCNT) has demonstrated the generation of reactive radicals and depletion of intracellular antioxidants which in turn cause cell death through activation of caspases. The molecular mechanism of cellular death due to MWCNT is not clear yet. In this study, we investigated the signaling pathways implicated in MWCNT-induced apoptosis in rat lung epithelial cells.

Differential oxidative stress gene expression profile in mouse brain after proton exposure.

Radiation is known to potentially interfere with cellular functions at all levels of cell organization. The radiation-induced stress response is very complex and involves altered expression of many genes. Identification of specific genes may allow the determination of pathways important in radiation responses.

Induction of cell death through alteration of oxidants and antioxidants in lung epithelial cells exposed to high energy protons.

Radiation affects several cellular and molecular processes, including double strand breakage and modifications of sugar moieties and bases. In outer space, protons are the primary radiation source that poses a range of potential health risks to astronauts. On the other hand, the use of proton irradiation for tumor radiation therapy is increasing, as it largely spares healthy tissues while killing tumor tissues.

Cord blood stem cell expansion is permissive to epigenetic regulation and environmental cues.

Objective: Augmentation of the number of cord blood (CB) hematopoietic stem cells (HSC) present in a unit is required before it can be considered as an alternative graft for hematopoietic reconstitution for adult patients. In order to further optimize strategies to augment HSC numbers, we examined whether expansion of HSC mediated by epigenetic mechanisms remains permissive to external environmental cues.

Materials And Methods: The chromatin-modifying agents 5-aza-2'-deoxycytidine (5azaD) and trichostatin A (TSA) were used to ameliorate epigenetic alteration of CB cells during ex vivo culture by adding various cytokines.

p300 provides a corepressor function by cooperating with YY1 and HDAC3 to repress c-Myc.

We showed earlier that p300/CBP plays an important role in G1 progression by negatively regulating c-Myc and thereby preventing premature G1 exit. Here, we have studied the mechanism by which p300 represses c-Myc and show that in quiescent cells p300 cooperates with histone deacetylase 3 (HDAC3) to repress transcription. p300 and HDAC3 are recruited to the upstream YY1-binding site of the c-Myc promoter resulting in chromatin deacetylation and repression of c-Myc transcription.

Effects of depletion of CREB-binding protein on c-Myc regulation and cell cycle G1-S transition.

We recently reported that the transcriptional coactivator and histone acetyltransferase p300 plays an important role in the G(1) phase of the cell cycle by negatively regulating c-myc and thereby preventing premature G(1) exit (Kolli, et al. (2001) Proc. Natl.

Repression of c-Myc and inhibition of G1 exit in cells conditionally overexpressing p300 that is not dependent on its histone acetyltransferase activity.

p300 and cAMP response element binding protein (CREB)-binding protein (CBP) are two highly homologous, conserved transcriptional coactivators, and histone acetyltransferases (HATs) that link chromatin remodeling with transcription. Cell transformation by viral oncogene products such as adenovirus E1A and SV40 large T antigen depends on their ability to inactivate p300 and CBP. To investigate the role of p300 in cell-cycle progression, we constructed stable rat cell lines, which conditionally overexpress p300 from a tetracycline-responsive promoter.