Epigenetic Histone Modifications Research Articles

Cellular Effects of Butyrate on Vascular Smooth Muscle Cells are Mediated through Disparate Actions on Dual Targets, Histone Deacetylase (HDAC) Activity and PI3K/Akt Signaling Network.

Vascular remodeling is a characteristic feature of cardiovascular diseases. Altered cellular processes of vascular smooth muscle cells (VSMCs) is a crucial component in vascular remodeling. Histone deacetylase inhibitor (HDACI), butyrate, arrests VSMC proliferation and promotes cell growth. The objective of the study is to determine the mechanism of butyrate-induced VSMC growth. Using proliferating VSMCs exposed to 5 mM butyrate, immunoblotting studies are performed to determine whether PI3K/Akt pathway that regulates different cellular effects is a target of butyrate-induced VSMC growth. Butyrate inhibits phosphorylation-dependent activation of PI3K, PDK1, and Akt, eliciting differential effects on downstream targets of Akt. Along with previously reported Ser9 phosphorylation-mediated GSK3 inactivation leading to stability, increased expression and accumulation of cyclin D1, and epigenetic histone modifications, inactivation of Akt by butyrate results in: transcriptional activation of FOXO1 and FOXO3 promoting G1 arrest through p21Cip1/Waf1 and p15INK4B upregulation; inactivation of mTOR inhibiting activation of its targets p70S6K and 4E-BP1 impeding protein synthesis; inhibition of caspase 3 cleavage and downregulation of PARP preventing apoptosis. Our findings imply butyrate abrogates Akt activation, causing differential effects on Akt targets promoting convergence of cross-talk between their complimentary actions leading to VSMC growth by arresting proliferation and inhibiting apoptosis through its effect on dual targets, HDAC activity and PI3K/Akt pathway network.

Immunogold FIB-SEM: Combining Volumetric Ultrastructure Visualization with 3D Biomolecular Analysis to Dissect Cell-Environment Interactions.

Volumetric imaging techniques capable of correlating structural and functional information with nanoscale resolution are necessary to broaden the insight into cellular processes within complex biological systems. The recent emergence of focused ion beam scanning electron microscopy (FIB-SEM) has provided unparalleled insight through the volumetric investigation of ultrastructure; however, it does not provide biomolecular information at equivalent resolution. Here, immunogold FIB-SEM, which combines antigen labeling with in situ FIB-SEM imaging, is developed in order to spatially map ultrastructural and biomolecular information simultaneously. This method is applied to investigate two different cell–material systems: the localization of histone epigenetic modifications in neural stem cells cultured on microstructured substrates and the distribution of nuclear pore complexes in myoblasts differentiated on a soft hydrogel surface. Immunogold FIB-SEM offers the potential for broad applicability to correlate structure and function with nanoscale resolution when addressing questions across cell biology, biomaterials, and regenerative medicine.

Genetic Contexts Characterize Dynamic Histone Modification Patterns Among Cell Types.

Histone modifications play critical roles in mammalian development, regulating chromatin structure and gene expression. Dynamic histone modifications among cell types have been shown to associate with changes in mammalian development. However, how to quantitatively measure the histone modification alterations and how histone modifications vary across cell types under different genetic contexts remain largely unexplored and whether these changes are related to the primary DNA sequence remains limited. Here, we employed an entropy-based method to measure histone modification alterations in six definite genomic regions across five cell types and identified lineage-specific histone modification genes. We observed that histone modification alterations prefer to enrich in 5'-UTR exons, and also in 3'-UTR exons and its downstream. Then we built a model to predict the histone modification patterns from the primary DNA sequence. We found that the frequencies of k-mer sequence compositions are predictive of histone modification patterns, suggesting that the primary DNA sequence correlated with the histone modification alterations among cell types. Additionally, the lineage-specific histone modification genes display a higher conservation and lower GC-content. Together, we performed a systematic analysis for histone modification alterations and demonstrated how to identify genomic region-specific elements of epigenetic and genetic regulation and histone modification patterns across different cell types.

Host factors involved in HBV cccDNA formation and transcription

The genome of hepatitis B virus (HBV) is an incomplete double-stranded circular DNA, also known as relaxed circular (RC) DNA. RC-DNA needs to be converted to covalently closed circular (ccc) DNA during the replication process. cccDNA acts as the transcription template for viral RNAs. One of those viral RNAs, pgRNA, acts as the template in the reverse-transcription process, producing minus-DNA and plus-DNA. Subsequently, the two finally form RC-DNA and finish the viral genome replication process. The existence of cccDNA is the key obstacle for curing hepatitis type B and eliminating HBV antigen using medicines such as interferons or nucleos(t)ide analogues (NAs). Many host factors are involved in HBV cccDNA formation and transcription. We summarized some of these host factors and explained their related functions in HBV infection and replication, detailing the mechanisms of cccDNA formation and subsequent transcription. When HBV enters host cells, its surface protein L interacts with the receptor NTCP on the cell surface, allowing HBV to enter through endocytosis and leaving its envelope behind. Subsequently, the HBV genome, the RC-DNA, enters the cell nucleus, and leaves the empty nucleocapsid behind. The genome RC-DNA must convert into cccDNA to start the replication process. Many host factors participate in this process in various ways, including helping to remove special constructions, fixing the gaps and the single stand areas. These host factors include TDP1, TDP2, FEN1 and factors involved in the DNA damage response (DDR) system. This process also requires host DNA polymerase to extend DNA sequences, including POLK, POLH and POLL. cccDNA does not exist independently, but rather it exists in combination with many histones and nonhistones. The epigenetic modification of histone influences cccDNA transcription in various ways. For example, acetylization of H3 and H4 induces transcription and some acetylases such as CBP, p300, PCAF, HAT1, and KAT8 are involved. Interestingly, most of the host acetylases are recruited by two viral proteins, HBX and HBC, suggesting that these two virus proteins may help the virus to kidnap host factors for the benefit of the virus. In addition to epigenetic modification, cccDNA transcription also requires many cis-elements and host transcription factors. Many ubiquitous and liver-enriched host factors such as NF-1, sp-1, TBP, CREB, HNF3, HNF1, HNF4, C/EBP, PPARα, FXR, FTF, PGC-1αcombine with cis-elements in HBV genome, including promoter regions and enhancer regions. This combination induces or inhibits the cccDNA transcription process. In truth, HBV cccDNA formation and transcription processes require more host involvement than this article mentions. Many new factors and interactions as well as key regulators still waiting to be discovered. This article may supply suggestions for research into the detailed mechanism of the two processes of HBV cccDNA.

Genome-wide analysis of H3K4me3 and H3K27me3 modifications throughout the mouse urogenital ridge at E11.5

In mammals, the adrenal gland, testis and ovary arise from a common progenitor tissue known as the urogenital ridge (UGR). This small population of cells will adopt a number of different cell fates following sex determination, including forming the precursors of somatic cells (such as Sertoli and granulosa cells) and steroidogenic cells. In addition, these tissues also contain the Wolffian and Müllerian ducts that later form components of the reproductive tracts. A potential mechanism to maintain developmental plasticity of the UGR until gonad formation is complete, is through the epigenetic modification of histone proteins.In order to provide a resource for future studies, we used chromatin immunoprecipitation followed by high throughput sequencing (ChIP-seq) for two histone modifications, H3K4me3 and H3K27me3, in the E11.5 mouse UGR. These marks are both known to reflect the active, repressive or a poised chromatin state. We found that enrichment for each histone mark reflected transcriptional activity in precursor cells of the developing gonad. From the analysis of potential enhancer/regulator peak regions for DNA binding motifs, we identified several candidate transcription factors that may contribute to gonadal cell lineage specification. We additionally identified signaling pathway genes that are targeted by both chromatin modifications. Together, these datasets provide a useful resource for investigating gene regulatory networks functioning during UGR development at E11.5.

Transcriptome and histone epigenome of Plasmodium vivax salivary-gland sporozoites point to tight regulatory control and mechanisms for liver-stage differentiation in relapsing malaria

Plasmodium vivax is the key obstacle to malaria elimination in Asia and Latin America, largely attributed to its ability to form resilient hypnozoites (sleeper cells) in the host liver that escape treatment and cause relapsing infections. The decision to form hypnozoites is made early in the liver infection and may already be set in sporozoites prior to invasion. To better understand these early stages of infection, we undertook a comprehensive transcriptomic and histone epigenetic characterization of P. vivax sporozoites. Through comparisons with recently published proteomic data for the P. vivax sporozoite, our study found that although highly transcribed, transcripts associated with functions needed for early infection of the vertebrate host are not detectable as proteins and may be regulated through translational repression. We identified differential transcription between the sporozoite and published transcriptomes of asexual blood stages and mixed versus hypnozoite-enriched liver stages. These comparisons point to multiple layers of transcriptional, post-transcriptional and post-translational control that appear active in sporozoites and to a lesser extent hypnozoites, but are largely absent in replicating liver schizonts or mixed blood stages. We also characterised histone epigenetic modifications in the P. vivax sporozoite and explored their role in regulating transcription. Collectively, these data support the hypothesis that the sporozoite is a tightly programmed stage to infect the human host and identify mechanisms for hypnozoite formation that may be further explored in liver stage models.

Genome-wide DNA methylation analysis revealed stable DNA methylation status during decidualization in human endometrial stromal cells

BackgroundDuring decidualization in endometrial stromal cells (ESCs), expressions of a number of genes and epigenetic modifications of histones are altered. However, there is little information about whether DNA methylation, which is another epigenetic mechanism, also changes during decidualization. Here, we examined the genome-wide DNA methylation profiles in ESCs during decidualization and their associations with the changes of gene expressions and histone modifications.ResultsESCs were incubated with estradiol and medroxyprogesterone acetate for 14 days to induce decidualization. The genome-wide DNA methylation profiles were compared between the non-decidualized ESCs and the decidualized ESCs. Of 482,005 CpGs, only 23 CpGs (0.0048%) showed different DNA methylation statuses. The DNA methylation statuses of the differentially expressed genes and the regions with different histone modifications (H3K4 tri-methylation and H3K27 acetylation) were also compared between the ESCs. In the upregulated and downregulated genes in decidualized ESCs, DNA methylation statuses around the promoter region of the genes did not significantly differ between the ESCs. In the regions with different histone modification, DNA methylation statuses did not differ between the ESCs. The differentially expressed genes and the differential histone modification regions were hypomethylated.ConclusionsCulturing ESCs with estrogen/progesterone did not distort the physiological pattern of DNA methylation, although mRNA expression and histone modifications were dynamically altered. A genome-wide DNA methylation analysis revealed stable DNA methylation statuses during decidualization in human endometrial stromal cells. DNA hypomethylation is maintained for the variable changes of histone modifications and gene expression during decidualization.

Epigenética: mecanismos, herança e implicações no melhoramento animal

A epigenética é definida como mudanças na expressão gênica que podem ser herdadas e que não alteram a sequência do DNA. Existem dois mecanismos epigenéticos principais, a metilação do DNA e a modificação de histonas. Também se destaca o imprinting genômico, o qual está relacionado com a regulação gênica quando apenas um alelo (herdado do pai ou da mãe) se expressa. A herança epigenética transgeracional consiste da herança de marcas epigenéticas através de células germinativas, que controla os padrões de expressão gênica e são passados de uma geração para a outra. Dentro do programa de melhoramento animal é importante avaliar a extensão com que a herança epigenética transgeracional também afeta a eficiência da seleção. Uma melhor compreensão dos mecanismos epigenéticos e seus efeitos transgeracionais no desempenho dos animais poderá permitir maiores ganhos sobre as características de importância econômica.

Acute Skeletal Muscle Contractions Orchestrate Signaling Mechanisms to Trigger Nuclear NFATc1 Shuttling and Epigenetic Histone Modifications.

Calcium (Ca²⁺) coordinates skeletal muscle functions by controlling contractions as well as signaling pathways and transcriptional properties. The ryanodine receptor 1 (RyR1), its phosphorylation site (pRyR1Ser²⁸⁴⁰) and its stabilizers navigate Ca²⁺ oscillations to command muscle signaling cascades and transcriptional activities. While chronic exercise increases pRyR1Ser²⁸⁴⁰, investigations on acute exercise's effects on RyR1 and Ca²⁺-dependent modifications of skeletal muscle are rare. The aim of this study was to examine molecular events leading to RyR1 phosphorylation in a physiological model of acute exercise. We hypothesized that exercise-induced RyR1 phosphorylation is associated with altered Ca²⁺-dependent physiological phenotypes. We analyzed pRyR1Ser²⁸⁴⁰, its stabilizers, involved signaling pathways, and Ca²⁺-sensitive muscle-determining factors (i.e. NFATc1 and epigenetic histone H3 modifications) in rat muscles upon one single running bout of either concentric or eccentric contractions. Both acute exercises significantly increased pRyRSer²⁸⁴⁰ levels in muscles, which was accompanied by dissociations of stabilizers from RyR1. Additionally, RyR1 phosphorylation-inducing signaling cascades PTEN/CaMKII/ PKA were significantly activated upon exercise. Further, RyR1 phosphorylations were associated with increased Ca²⁺-dependent NFATc1 nuclear abundances as well as increased Ca²⁺-dependent epigenetic H3 acetylations pointing to a pRyR1Ser²⁸⁴⁰-dependent rapid and novel Ca²⁺ equilibrium upon exercise. Our data report synergistic actions of several distinct pathways to modify RyR1 function to govern physiological phenotypes, here expressed as increased nuclear NFATc1 abundances and epigenetic H3 modifications.

Leishmania-Host Interactions-An Epigenetic Paradigm.

Leishmaniasis is one of the major neglected tropical diseases, for which no vaccines exist. Chemotherapy is hampered by limited efficacy coupled with development of resistance and other side effects. Leishmania parasites elude the host defensive mechanisms by modulating their surface proteins as well as dampening the host's immune responses. The parasites use the conventional RNA polymerases peculiarly under different environmental cues or pressures such as the host's milieu or the drugs. The mechanisms that restructure post-translational modifications are poorly understood but altered epigenetic histone modifications are believed to be instrumental in influencing the chromatin remodeling in the parasite. Interestingly, the parasite also modulates gene expression of the hosts, thereby hijacking or dampening the host immune response. Epigenetic factor such as DNA methylation of cytosine residues has been incriminated in silencing of macrophage-specific genes responsible for defense against these parasites. Although there is dearth of information regarding the epigenetic alterations-mediated pathogenesis in these parasites and the host, the unique epigenetic marks may represent targets for potential anti-leishmanial drug candidates. This review circumscribes the epigenetic changes during Leishmania infection, and the epigenetic modifications they enforce upon the host cells to ensure a safe haven. The non-coding micro RNAs as post-transcriptional regulators and correlates of wound healing and toll-like receptor signaling, as well as prognostic biomarkers of therapeutic failure and healing time are also explored. Finally, we highlight the recent advances on how the epigenetic perturbations may impact leishmaniasis vaccine development as biomarkers of safety and immunogenicity.

Transcriptional activity of epigenetic remodeling genes declines in keratinocytes after in vitro expansion

PurposeIn vitro expansion is an invaluable method to obtain keratinocytes in amounts necessary for effective transplantation therapies. In vitro cell culturing provokes questions concerning potential epigenetic alterations occurring in expanded cells in the context of usefulness for transplantation and safety. The purpose of this study was to investigate as to whether keratinocyte expansion is associated with changes in the activity of genes responsible for the maintenance of epigenetic stability. Materials and methodsWe focussed on the transcriptional activity of genes involved in different epigenetic mechanisms including DNA methylation and histone modifications. We used quantitative real-time PCR to determine transcript levels of 16 epigenetic remodelling markers in 14 patients in the epidermal cells directly after collection and after in vitro expansion. ResultsWe observed a remarkable decline in the transcriptional activity of the epigenetic remodelling genes following in vitro expansion, while no further fall of expression with passaging. In whole skin, we found even higher expression levels of the epigenetic markers. ConclusionsTransmission to in vitro environment challenges cellular signalling and metabolism. The regulation of epigenetic remodelling maintains the balance between cellular plasticity and phenotype deviation. This preliminary research demonstrated reduced activity of genes responsible for epigenetic modifications of DNA and histones in in vitro expanded epidermal cells. This observation indicates that epigenome re-patterning in cultured epidermal cells is significantly less intensive than in the skin. Also, this observation may imply that after adaptation to in vitro conditions, the epigenome does not undergo extensive transformation during further cultivation.

Epigenetic control in skin development, homeostasis and injury repair.

Cell-type- and cell-state-specific patterns of covalent modifications on DNA and histone tails form global epigenetic profiles that enable spatiotemporal regulation of gene expression. These epigenetic profiles arise from coordinated activities of transcription factors and epigenetic modifiers, which result in cell-type-specific outputs in response to dynamic environmental conditions and signalling pathways. Recent mouse genetic and functional studies have highlighted the physiological significance of global DNA and histone epigenetic modifications in skin. Importantly, specific epigenetic profiles are emerging for adult skin stem cells that are associated with their cell fate plasticity and proper activity in tissue regeneration. We can now begin to draw a more comprehensive picture of how epigenetic modifiers orchestrate their cell-intrinsic role with microenvironmental cues for proper skin development, homeostasis and wound repair. The field is ripe to begin to implement these findings from the laboratory into skin therapies.

Genes upregulated in the amnion at labour are bivalently marked by activating and repressive histone modifications.

Inflammatory genes are expressed increasingly in the foetal membranes at late gestation triggering birth. Here we have examined whether epigenetic histone modifications contribute to the upregulation of proinflammatory genes in the amnion in late pregnancy and at labour. Amnion samples were collected from early pregnancy, at term in the absence of labour and after spontaneous birth. The expression of the labour-associated proinflammatory genes PTGS2, BMP2 and NAMPT was determined by reverse transcription-coupled quantitative real-time PCR (qRT-PCR). Chromatin immunoprecipitation (ChIP) and sequential double ChIP were performed to determine the levels and co-occurrence of activating histone-3, lysine-4 trimethylation (H3K4me3) and repressive histone-3, lysine-27 trimethylation (H3K27me3) at the gene promoters. H3K4 methyltransferase, H3K27me3 demethylase and H3K27 methyltransferase expression was determined by qRT-PCR and immunofluorescence confocal microscopy. PTGS2, BMP2 and NAMPT expression was upregulated robustly between early pregnancy and term (P < 0.05). The promoters were marked bivalently by both the H3K4me3 and H3K27me3 modifications. Bivalence was reduced at term by the decrease of the H3K27me3-modified fraction of promoter copies marked by H3K4me3 indicating epigenetic activation. Messenger RNAs encoding the H3K4-specific methyl transferases MLL1,-2,-3,-4, SETD1A,-B and the H3K27me3-specific demethylases KDM6A,-B were expressed increasingly while the H3K27 methyl transferase EZH2 was expressed decreasingly at term. Histone modifying enzyme proteins were detected in amnion epithelial and mesenchymal cells. These results with prototypical proinflammatory genes suggest that nucleosomes at labour-promoting genes are marked bivalently in the amnion, which is shifted towards monovalent H3K4me3 modification at term when the genes are upregulated. Bivalent epigenetic regulation by histone modifying enzymes may control the timing of labour.

Multi-omic Analyses Reveal Minimal Impact of the CRISPR-Cas9 Nuclease on Cultured Human Cells.

The CRISPR-Cas9 system is a genomic editing tool widely used in basic research and under investigation for potential applications in gene therapies for human diseases. To accomplish genomic editing, the system requires the expression of a prokaryotic DNA endonuclease enzyme, Cas9, in host cells. Previous studies have mainly focused on the specificity of Cas9 on the host genome, and thus it is unclear whether this bacterium-derived enzyme affects the protein homeostasis of host cells. Here we applied multi-omic analyses, including transcriptome, proteome, phosphoproteome, Cas9-associated protein interactome, protein synthesis, and histone epigenetic modification, to investigate the cellular response of human cells upon the expression of Cas9. We demonstrate that Cas9 has minimal impact on host cells. Our assessment of intracellular effects of Cas9 paves a path for its broad applications in biological studies and potential clinical translations.

Effects of activin A on the transcriptome of mouse oogenesis in vitro.

From the previous research, it has been supported that activin A (ActA) is conducive to ovarian development in vitro. In the present paper, with the aim to identify the molecular pathways through which ActA can influence processes of the fetal and early postnatal oogenesis, we analyzed the transcriptome of embryonic ovaries (12.5 days postcoitum) in vitro cultured with or without ActA for 6 days, as well as the produced oocytes for 28 days, and further compared the gene expression profile with their in vivo counterparts. With the confirmation of designed test, we found that the addition of ActA to the ovary culture tended, generally, to align oocyte gene expression to the in vivo condition, in particular of a number of genes involved in meiosis and epigenetic modifications of histones. In particular, we identified DNA recombination during the oocyte meiotic prophase I and lysine trimethylation of the histone H3K27 during the oocyte growth phase as molecular pathways modulated by ActA.

Calebin-A induced death of malignant peripheral nerve sheath tumor cells by activation of histone acetyltransferase

BackgroundNeurofibromatosis type 1 (NF1) is one of the most common hereditary neurocutaneous disorders. The malignant peripheral nerve sheath tumor (MPNST), transformed from NF1 related plexiform neurofibroma, is a rapidly growing and highly invasive tumor. No effective chemotherapeutic agent is currently available. Calebin-A is a derivative from turmeric Curcuma longa. Given the anti-inflammatory and anticancer potentials of curcumin, whether Calebin-A also had the tumoricidal effect upon MPNST cells is still elusive. PurposeTo determine whether Calebin-A has the potential for anti-MPNST effect. MethodsThe MTT and FACS analysis of normal Schwann (HSC) and MPNST cells have been employed to determine the tumoricidal effect of Calebin-A. The expression of the signal pathway molecules was assessed by Western blotting. The CHIP with quantitative PCR assay was performed to quantify the promoter DNA binding to acetylated histone 3 (acetyl H3). The enzyme activities of histone acetyltransferase (HAT) and deacetylase (HDAC) have been evaluated by commercial kits. The measurements of tumor size of the xenograft mouse model were also performed. ResultsCalebin-A inhibited the proliferation of MPNST and primary neurofibroma cells in a dose-dependent manner. The flow cytometry analysis of the MPNST cells after treatment of 25 μm of Calebin-A demonstrated an increase of population in the G0/G1 phase but decrease in G2/M phase. Before treatment, the expression of Axl, Tyro3, and acetyl H3 was significantly higher in MPNST cells when compared to HSC. The expression of phosphorylated-AKT, -ERK1/2, survivin, hTERT, and acetyl H3 proteins were reduced after treatment. The CHIP assay shows the promoter DNA copies of survivin (BRIC5) and hTERT genes are significantly reduced post-treatment. The enzyme activity of HAT was significantly reduced, but not that of HDAC. Two HAT inhibitors, epigallocatechin-3-gallate (EGCG) and anacardic acid (AA) have also demonstrated a significant inhibitory effect on MPNST cells. Finally, the measurements of tumor size showed a significant reduction of the xenograft tumors after treatment of Calebin-A. ConclusionBoth in vitro and in vivo studies showed Calebin-A could inhibit the proliferation of MPNST with suppression of survivin and hTERT. The reduced expression of these two factors might be through the epigenetic histone modification resulting from the decreased activity of HAT.

Can uterine secretion of modified histones alter blastocyst implantation, embryo nutrition, and transgenerational phenotype?

Extracellular histones support rodent and human embryo development in at least two ways. First, these molecules in uterine secretions protect embryos from inflammation caused by pathogens that gain access to the reproductive tract. Also, histones in uterine secretions likely support penetration of the uterine epithelium by blastocysts during embryo implantation. Extracellular histones seem to preserve amino acid transport system B0,+ in blastocysts by inhibiting its activity. Preservation of system B0,+ is needed because, at the time of invasion of the uterine epithelium by motile trophoblasts, system B0,+ is likely reactivated to help remove tryptophan from the implantation chamber. If tryptophan is not removed, T-cells proliferate and reject the implanting blastocyst. Epigenetic modification of histones could alter their promotion of normal implantation through, say, incomplete tryptophan removal and, thus, allow partial T-cell rejection of the conceptus. Such partial rejection could impair placental development, embryonal/fetal nutrition, and weight gain prior to birth. Small-for-gestational-age offspring are predisposed to developing metabolic syndrome, obesity, and associated complications as adults. Shifting expression of these phenotypes might contribute to transgenerational variation and evolution. The spectrum of possible extracellular histone targets in early development warrant new research, especially since the effects of epigenetic histone modifications might be transgenerational.

Role of HDAC3-miRNA-CAGE Network in Anti-Cancer Drug-Resistance.

Histone modification is associated with resistance to anti-cancer drugs. Epigenetic modifications of histones can regulate resistance to anti-cancer drugs. It has been reported that histone deacetylase 3 (HDAC3) regulates responses to anti-cancer drugs, angiogenic potential, and tumorigenic potential of cancer cells in association with cancer-associated genes (CAGE), and in particular, a cancer/testis antigen gene. In this paper, we report the roles of microRNAs that regulate the expression of HDAC3 and CAGE involved in resistance to anti-cancer drugs and associated mechanisms. In this review, roles of HDAC3-miRNAs-CAGE molecular networks in resistance to anti-cancer drugs, and the relevance of HDAC3 as a target for developing anti-cancer drugs are discussed.

Induction of a Long Noncoding RNA Transcript, NR_045064, Promotes Defense Gene Transcription and Facilitates Intestinal Epithelial Cell Responses against Cryptosporidium Infection.

Cryptosporidium is an important opportunistic intestinal pathogen for immunocompromised individuals and a common cause of diarrhea in young children in developing countries. Gastrointestinal epithelial cells play a central role in activating and orchestrating host immune responses against Cryptosporidium infection, but underlying molecular mechanisms are not fully understood. We report in this paper that C. parvum infection causes significant alterations in long noncoding RNA (lncRNA) expression profiles in murine intestinal epithelial cells. Transcription of a panel of lncRNA genes, including NR_045064, in infected cells is controlled by the NF-κB signaling. Functionally, inhibition of NR_045064 induction increases parasite burden in intestinal epithelial cells. Induction of NR_045064 enhances the transcription of selected defense genes in host cells following C. parvum infection. Epigenetic histone modifications are involved in NR_045064-mediated transcription of associated defense genes in infected host cells. Moreover, the p300/MLL-associated chromatin remodeling is involved in NR_045064-mediated transcription of associated defense genes in intestinal epithelial cells following C. parvum infection. Expression of NR_045064 and associated genes is also identified in intestinal epithelium in C57BL/6J mice following phosphorothioate oligodeoxynucleotide or LPS stimulation. Our data demonstrate that lncRNAs, such as NR_045064, play a role in regulating epithelial defense against microbial infection.

PGC-1α Promoter Histone Acetylation is Life Saving in Fibrotic Hepatectomy

Background and Aim: A fibrotic liver may have impaired regenerative capacity. Liver transplantation is a donor-limited, expensive therapeutic option for the restoration of the structural and function integrity of the liver following regeneration failure. Thus, gaining the clinical ability to restore the regenerative capacity of the fibrotic liver is important. This study aimed to investigate the mechanisms involved in regenerative failure of the fibrotic liver after resection. Methods: A two-thirds partial hepatectomy (PH) was performed in C57Bl/6 mice with or without carbon tetrachloride (CCl4) treatment. Cell proliferation in the fibrotic liver post-PH was assessed by the intrahepatic expression of P53, PGC-1α, P21 and PCNA with RT-PCR, Western-blot and immunohistochemical staining. Histone epigenetic modification of the PGC-1α promoter was investigated by ChIP and RT-PCR assay. The impact of PGC-1α on liver regeneration after hepatectomy was further evaluated in PGC-1α gene knockout mice. Results: An association was detected between a decreased expression of PGC-1α and p53 in the fibrotic liver and liver injury and cell proliferation 24 hours after PH. Moreover, the oxidative stress observed following PH in the fibrotic liver inhibited the PGC-1α expression through histone deacetylation of the PGC-1α promoter. This PGC-1α mediated liver regeneration was further demonstrated in PGC-1αf/f alb cre /0 mice. Conclusion: Altered p53 expression, which was preceded by abnormal histone epigenetic modification of the promoter of PGC-1α, led to inefficient regeneration in the fibrotic liver after PH. Targeting the histone modification of PGC-1α may represent a strategy which may improve PH treatment in patients with liver fibrosis. Funding Statement: This work was supported by National Natural Science Foundation of China Award number 81470864. Declaration of Interests: All the authors declare no competing interests. Ethics Approval Statement: All experimental procedures were conducted in accordance with the guidelines of Laboratory Animal Welfare Assurance issued by the National Institute of Health (NIH) and were approved by the Animal Care and Use Committee of Capital Medical University.