Showing papers in "Frontiers of Biology in China in 2011"

An overview of inflammation: mechanism and consequences

Abstract: Inflammation is an essential response provided by the immune systems that ensures the survival during infection and tissue injury. Inflammatory responses are essential for the maintenance of normal tissue homeostasis. The molecular mechanism of inflammation is quite a complicated process which is initiated by the recognition of specific molecular patterns associated with either infection or tissue injury. The entire process of the inflammatory response is mediated by several key regulators involved in the selective expression of proinflammatory molecules. Prolonged inflammations are often associated with severe detrimental side effects on health. Alterations in inflammatory responses due to persistent inducers or genetic variations are on the rise over the last couple of decades, causing a variety of inflammatory diseases and pathophysiological conditions.

Enterococcus : review of its physiology, pathogenesis, diseases and the challenges it poses for clinical microbiology

Abstract: The genus Enterococcus is composed of 38 species, the most important of which are Enterococcus faecalis and Enterococcus faecium—both human intestinal colonizers. Hospitals within the United States and around the world commonly isolate these bacteria because they are a cause of bacteremia, urinary tract infections (UTIs), endocarditis, wound infections, meningitis, intraabdominal and pelvic infections, and nosocomial and iatrogenic infections. Given the ubiquity of enterococci within the human population, it is important for laboratories to be able to distinguish these agents within hospitalized patients from other bacterial genera and also differentiate different species within the Enterococcus genus as well as different strains within each species. Unfortunately, the enterococci are emerging as serious pathogens in both the developed world, where surveillance needs to be improved and speciation procedures are inadequate or cumbersome, and in developing nations, which lack the trained hospital personnel or funding to sufficiently identify enterococci to the genus or species level. This review explores the Enterococcus genus and highlights some of the concerns for national and international clinical microbiology laboratories.

Membrane-bound O-acyltransferases (MBOATs)

Abstract: The MBOATenzyme family, identified in 2000, comprises 11 genes in the human genome that participate in a variety of biological processes. MBOAT enzymes contain multiple transmembrane domains and share two active site residues, histidine and asparagine. Several MBOAT members are drug targets for major human diseases, including atherosclerosis, obesity, Alzheimer disease, and viral infections. Here we review the historical aspects of MBOAT enzymes, classify them biochemically into 3 subgroups, and describe the essential features of each member.

NMDA receptor signaling: death or survival?

Abstract: Glutamate-induced neuronal damage is mainly caused by overactivation of N-methyl-D-aspartate (NMDA) receptors. Conversely, normal physiological brain function and neuronal survival require adequate activation of NMDA receptors. Studies have revealed that NMDA receptor-induced neuronal death or survival is mediated through distinct subset of NMDA receptors triggering different intracellular signaling pathways. Here we discuss recent advances in the characterization of NMDA receptors in neuronal protection, emphasizing subunit-specific role, which contributes to temporal-spatial distribution, subcellular localization and diverse channel properties of NMDA receptors.

Heat shock proteins: Molecules with assorted functions

Abstract: Heat shock proteins (Hsps) or molecular chaperones, are highly conserved protein families present in all studied organisms. Following cellular stress, the intracellular concentration of Hsps generally increases several folds. Hsps undergo ATP-driven conformational changes to stabilize unfolded proteins or unfold them for translocation across membranes or mark them for degradation. They are broadly classified in several families according to their molecular weights and functional properties. Extensive studies during the past few decades suggest that Hsps play a vital role in both normal cellular homeostasis and stress response. Hsps have been reported to interact with numerous substrates and are involved in many biological functions such as cellular communication, immune response, protein transport, apoptosis, cell cycle regulation, gametogenesis and aging. The present review attempts to provide a brief overview of various Hsps and summarizes their involvement in diverse biological activities.

The spindle assembly checkpoint: perspectives in tumorigenesis and cancer therapy

Abstract: Loss or gain of chromosomes, a condition known as aneuploidy, is a common feature of tumor cells and has therefore been proposed as the driving force for tumorigenesis. Such chromosomal instability can arise during mitosis as a result of mis-segregation of the duplicated sister chromatids to the two daughter cells. In normal cells, missegregation is usually prevented by the spindle assembly checkpoint (SAC), a sophisticated surveillance mechanism that inhibits mitotic exit until all chromosomes have successfully achieved bipolar attachment to spindle microtubules. Complete abrogation of SAC activity is lethal to normal as well as to tumor cells, as a consequence of massive chromosome mis-segregation. Importantly, many human aneuploid tumor cells exhibit a weakened SAC activity that allows them to tolerate gains or losses of a small number of chromosomes; and interfering with this SAC residual activity may constitute a suitable strategy to kill cancer cells. This review focuses on the potential link between SAC and tumorigenesis, and the therapeutic strategy to target the SAC for cancer treatment.

MicroRNA-mediated DNA methylation in plants

Abstract: DNA methylation, a major event in epigenetics, plays an essential role in the control of gene expression. Increasing evidence suggests that long and short non-coding RNAs are involved extensively in plants to direct the establishment, spread, and removal of DNA cytosine methylation throughout their genomes. Yet, little has been known about the role of microRNAs (miRNAs) in DNA methylation although the role of small interfering RNAs (siRNAs) in DNA methylation has been well established. Several recent studies, however, provided the evidence for miRNA-directed DNA methylation in plants, and the working mechanisms still need to be fully explored. In this review, we highlight the key features of miRNA-directed DNA methylation in plants and provide insight into the complexities of such an event in plants. The interaction between miRNAs and the epigenetic machinery and the future potential research questions are briefly discussed.

Amygdala, an important regulator for food intake

Abstract: Amygdala plays a critical role in the regulation of emotional behavior and food intake. Neuropeptides are short chains of amino acids secreted by neurons as intercellular messengers, which regulate different functions such as emotion, food intake, learning and memory. In this review, we summarize the recent progress on the regulation of food intake by amygadala, which is mediated by those neuropeptides known to be critical in the regulation of this process.

The mechanism of protein kinase C regulation

Abstract: Protein kinase C (PKC) is a family of serine/threonine protein kinases that plays a central role in transducing extracellular signals into a variety of intracellular responses ranging from cell proliferation to apoptosis. Nine PKC genes have been identified in the human genome, which encode 10 proteins. Each member of this protein kinase family displays distinct biochemical characteristics and is enriched in different cellular and subcellular locations. Activation of PKC has been implicated in the regulation of cell growth and differentiation. This review summarizes works of the past years in the field of PKC biochemistry that covers regulation and activation mechanism of different PKC isoforms.

Metabolic regulation by salt inducible kinases

Abstract: In fasting mammals, the liver is the primary source of glucose production for maintenance of normoglycemia. In this setting, circulating peptide hormones and catecholamines cause hepatic glucose output by stimulating glycogen breakdown as well as de novo glucose production through gluconeogenesis. Fasting gluconeogenesis is regulated by a complex transcriptional cascade culminating in elevated expression of hepatic enzymes that promote gluconeogenesis and glucose export to the blood. The cAMP response element binding protein CREB and its co-activator CRTC2 play crucial roles in signal-dependent transcriptional regulation of gluconeogenesis. Recent work has identified a family of serine/threonine kinases, the salt inducible kinases (SIKs), which are subject to hormonal control and constrain gluconeogenic and lipogenic gene expression in liver. As normal regulation of gluconeogenesis and lipogenesis is disrupted in diabetic states, SIK kinases are poised to serve as therapeutic targets to modulate metabolic disturbances in diabetic patients. The purpose of this review is to 1) describe the identification of CRTCs CREB co-activators and their regulation by SIKs, 2) discuss recent progress toward understanding regulation and function of SIKs in metabolism and 3) examine the potential clinical impact of therapeutics that target SIK kinase function.

The plant Mediator and its role in noncoding RNA production.

Abstract: Mediator, a conserved multiprotein complex in animals, plants, and fungi, is a cofactor of RNA polymerase II (Pol II). It is known to promote basal Pol II-mediated transcription as well as bridge sequence-specific transcriptional regulators and Pol II to integrate regulatory information. Pol II transcribes not only protein-coding genes but also intergenic regions to generate noncoding RNAs such as small RNAs (microRNAs and small interfering RNAs) and long noncoding RNAs. Intriguingly, two plant-specific polymerases, Pol IV and Pol V, have evolved from Pol II and play a role in the production of small interfering RNAs and long noncoding RNAs at heterochromatic regions to maintain genome stability through transcriptional gene silencing (TGS). Recent studies have defined the composition of the plant Mediator and evaluated its role in noncoding RNA production in relationship to Pol II, Pol IV and Pol V. Here, we review the functions of Mediator and that of noncoding RNAs generated by Pol II, Pol IV and Pol V in plants, and discuss a role of Mediator in epigenetic regulation via noncoding RNA production.

Triacylglycerol lipases of the yeast

Abstract: All eukaryotes including the yeast contain a lipid storage compartment which is named lipid particle, lipid droplet or oil body. Lipids accumulating in this subcellular fraction serve as a depot of energy and building blocks for membrane lipid synthesis. In the yeast, the major storage lipids are triacylglycerols (TGs) and steryl esters (SEs). An important step in the life cycle of these non-polar lipids is their mobilization from their site of storage and channeling of their degradation components to the appropriate metabolic pathways. A key step in this mobilization process is hydrolysis of TG and SE which is accomplished by lipases and hydrolases. In this review, we describe our recent knowledge of TG lipases from the yeast based on biochemical, molecular biological and cell biological information. We report about recent findings addressing the versatile role of TG lipases in lipid metabolism, and discuss non-polar lipid homeostasis and its newly discovered links to various cell biological processes in the yeast.

Epigenetics, a mode for plants to respond to abiotic stresses

Abstract: Epigenetics has been becoming a hot topic in recent years. It can be mechanisms that regulate gene expression without changing DNA base sequence. In plants epigenetic regulation has been implicated to be a very important phenomenon and mechanism for the regulation of responses to environmental stresses. Environmental signals induce various epigenetic modifications in the genome, and these epigenetic modifications might likely be inherited to the next generation that behaves with enhanced ability to tolerate stresses. This review highlights recent advances in the study of epigenetics in plant stress responses.

Molecular evolution of methanogens based on their metabolic facets

Abstract: The information provided by completely sequenced genomes of methanogens can yield insights into a deeper molecular understanding of evolutionary mechanisms. This review describes the advantages of using metabolic pathways to clarify evolutionary correlation of methanogens with archaea and prokaryotes. Metabolic trees can be used to highlight similarities in metabolic networks related to the biology of methanogens. Metabolic genes are among the most modular in the cell and their genes are expected to travel laterally, even in recent evolution. Phylogenetic analysis of protein superfamilies provides a perspective on the evolutionary history of some key metabolic modules of methanogens. Phage-related genes from distantly related organisms typically invade methanogens by horizontal gene transfer. Metabolic modules in methanogenesis are phylogenetically aligned in closely related methanogens. Reverse order reactions of methanogenesis are achieved in methylotrophic methanogens using metabolic and structural modules of key enzymes. A significant evolutionary process is thought to couple the utilization of heavy metal ions with energetic metabolism in methanogens. Over 30 of methanogens genomes have been sequenced to date, and a variety of databases are being developed that will provide for genome annotation and phylogenomic analysis of methanogens. Into the context of the evolutionary hypothesis, the integration of metabolomic and proteomic data into large-scale mathematical models holds promise for fostering rational strategies for strain improvement.

The discovery of the fat-regulating phosphatidic acid phosphatase gene

Abstract: Phosphatidic acid phosphatase is a fat-regulating enzyme that plays a major role in controlling the balance of phosphatidic acid (substrate) and diacylglycerol (product), which are lipid precursors used for the synthesis of membrane phospholipids and triacylglycerol. Phosphatidic acid is also a signaling molecule that triggers phospholipid synthesis gene expression, membrane expansion, secretion, and endocytosis. While this important enzyme has been known for several decades, its gene was only identified recently from yeast. This discovery showed the importance of phosphatidic acid phosphatase in lipid metabolism in yeast as well as in higher eukaryotes including humans.

Regulation of lipid metabolism

Abstract: Lipids including cholesterol, phospholipids, fatty acids and triacylglycerols are important cellular constituents involved in membrane structure, energy homeostasis and many biological processes such as signal transduction, organelle development and cell differentiation. Recently, the area of lipid metabolism has drawn a great deal of attention due to its emerging role in the development of metabolic disorders such as obesity, diabetes, atherosclerosis and liver steatosis. We decided to organize a special issue of Frontiers in Biology focusing on our current understanding of lipid metabolism. Regulation of lipid metabolism in eukaryotic cells takes place at multiple steps, including lipid synthesis, trafficking, and storage. In this issue, Carman and Chang et al. give an overview of the identification, biochemical activity and physiological roles of two important classes of proteins: phosphatidic acid phosphatases and membrane-bound O-acyltransferases (MBOATs) in controlling lipid synthesis. Shui covers basic strategies to systematically identify lipid metabolites or important signaling lipid(s), emphasizing on the MS-based lipidomics approaches in combination with computational tools/softwares (chemometrics). Du and Yang summarize the role of sterol-binding proteins in endosomal cholesterol transport. Furthermore, Grillitsch and Daum describe the biochemical, molecular and cell biological information of yeast triacylglycerol lipases in the dynamic formation of lipid droplets and lipid storage therein, and lipid mobilization. Abnormal lipid metabolism often results in the development of metabolic disorders such as obesity and diabetes. He et al. present the interrelationship between obesity and breast cancer development in postmenopausal women and discuss the cross-talk of leptin and estrogen signaling pathways. Xu and Zhao summarize an emerging area of metabolic regulation by a posttranslational modification: lysine acetylation of a variety of metabolic enzymes and their potential physiological significance. Due to the diversity and complexity of the cellular lipids, identification and characterization of individual lipids under various physiological and pathological conditions necessitate new techniques. Finally, Gelissen and Brown give us a brief history and recent development of anti-cholesterol therapies with a particular focus on pharmacological interventions on cholesterol biosynthetic pathway and novel targets. Overall, these eight articles present the most exciting and emerging areas of regulation of lipid metabolism, spanning from basic research to technological innovation and therapeutical intervention of metabolic diseases. We are convinced that research in lipid metabolism will attract many more young talents, which will be invaluable for tackling the prevalent metabolic diseases inflicting on a large population. We greatly appreciate the contribution of all the authors for this special issue.

Advances in medical decision support systems for diagnosis of acute graft-versus-host disease: molecular and computational intelligence joint approaches

Abstract: Acute graft-versus-host disease (aGVHD) is a serious systemic complication of allogeneic hematopoietic stem cell transplantation (HSCT) causing considerable morbidity and mortality. Acute GVHD occurs when alloreactive donor-derived T cells recognize host-recipient antigens as foreign. These trigger a complex multiphase process that ultimately results in apoptotic injury in target organs. The early events leading to GVHD seem to occur very soon, presumably within hours from the graft infusion. Therefore, when the first signs of aGVHD clinically manifest, the disease has been ongoing for several days at the cellular level, and the inflammatory cytokine cascade is fully activated. So, it comes as no surprise that progress in treatment based on clinical diagnosis of aGVHD has been limited in the past 30 years. It is likely that a pre-emptive strategy using systemic high-dose corticosteroids as early as possible could improve the outcome of aGVHD. Due to the deleterious effects of such treatment particularly in terms of infection risk posed by systemic steroid administration in a population that is already immune-suppressed, it is critical to identify biomarker signatures for approaching this very complex task. Some research groups have begun addressing this issue through molecular and proteomic analyses, combining these approaches with computational intelligence techniques, with the specific aim of facilitating the identification of diagnostic biomarkers in aGVHD. In this review, we focus on the aGVHD scenario and on the more recent state-of-the-art. We also attempt to give an overview of the classical and novel techniques proposed as medical decision support system for the diagnosis of GVHD.

Split decision: why it matters?

Abstract: The establishment and faithful maintenance of epigenetic information in the context of chromatin are crucial for a great number of biologic phenomena, including position effect variegation, Polycomb silencing, X-chromosome inactivation and genomic imprinting. However, mechanisms by which that the correct histone modification patterns propagate into daughter cells during mitotic divisions remain to be elucidated. The partitioning pattern of parental histone H3–H4 tetramers is a critical question toward our understanding of the epigenetic inheritance. In this review, we discuss why the histone H3–H4 tetramer split decision matters.

Population level virulence in polymicrobial communities associated with chronic disease

Abstract: Renewed studies of chronic infection have shifted the focus from single pathogens to multi-microbial communities as culture-independent techniques reveal complex consortia of microbes associated with chronic disease. Despite a general acceptance that some chronic diseases are caused by mixed microbial communities, areas of research exploring community interactions as they relate to the alteration of virulence are still in the early stages. Members of the NIH Human Microbiome Project have been actively characterizing the microbial communities of the skin, nasal, oral, gastrointestinal, and urogenital cavities of healthy adults. Concomitantly, several independent studies have begun to characterize the oral, nasal, sinus, upper and lower respiratory microbiomes in healthy and diseased human tissue. The interactions among the members of these polymicrobial communities have not been thoroughly explored and it is clear there is a need to identify the functional interactions that drive population-level virulence if new therapeutic approaches to chronic disease are to be developed. For example, multiple studies have examined the role of quorum sensing (QS) in microbial virulence, and QS antagonists are being developed and tested as novel therapeutics. Other potential targets include the Gram-negative type III signaling system (T3SS), type IV pili, and two component regulatory systems (TCRS). Initial results from these studies indicate limited efficacy in vivo, further suggesting that the interactions in a heterogeneous community are complex and poorly understood. If progress is to be made in the development of more effective treatments for chronic diseases, a better understanding of the composition and functional interactions that occur within multi-microbial communities must be developed.

Kinases and glutathione transferases: selective and sensitive targeting

Abstract: Kinases, representing almost 500 proteins in the human genome, are responsible for catalyzing the phosphorylation reaction of amino acid residues at their targets. As the largest family of kinases, the protein tyrosine kinases (PTKs) have roles in controlling the essential cellular activities, and their deregulation is generally related to pathologic conditions. The recent efforts on identifying their signal transducer or mediator role in cellular signaling revealed the interaction of PTKs with numerous enzymes of different classes, such as Ser/Thr kinases (STKs), glutathione transferases (GSTs), and receptor tyrosine kinases (RTKs). In either regulation or enhancing the signaling, PTKs are determined in close interaction with these enzymes, under specific cellular conditions, such as oxidative stress and inflammation. In this concept, intensive research on thiol metabolizing enzymes recently showed their involvement in the physiologic functions in cellular signaling besides their well known traditional role in antioxidant defense. The shared signaling components between PTK and GST family enzymes will be discussed in depth in this research review to evaluate the results of recent studies important in drug targeting for therapeutic intervention, such as cell viability, migration, differentiation and proliferation.

Tumor suppressor p53: new functions of an old protein

Abstract: p53 was discovered 30 years ago. Extensive studies have been done on p53 since then, which makes p53 one of the most extensively studied genes. p53 has long been recognized as a key tumor suppressor. Cell cycle arrest, apoptosis and senescence have been traditionally recognized as the main functions of p53 in tumor suppression. Recently, some novel functions of p53 have been identified, including the regulation of energy metabolism, antioxidant defense, and microRNA expression and maturation, which all contribute to the role of p53 in tumor suppression. Furthermore, the contribution of p53 to normal biologic processes (e.g. reproduction and aging) and some other aspects of diseases (e.g. neurodegenerative diseases) is only now being appreciated. Here we will review recent advances in the study of some new functions of p53.

Fate determination of fetal Leydig cells

Abstract: Leydig cell (LC) is one of the most important somatic cell types in testis, which localized in the interstitium between seminiferous tubules. The major function of Leydig cells is to produce steroid hormone, androgens. LC differentiation exhibits a biphasic pattern in rodent testes, which are divided into two different temporal mature populations, fetal Leydig cells (FLCs) and adult Leydig cells (ALCs). FLCs are transiently present in fetal testes and undergo involution or degeneration after birth. FLCs are completely devoid and replaced by ALCs in adult testes. Comparing to ALCs, FLCs display unique morphology, ultrastructure and functions. The origin of FLCs has been debated for many years, but it is still a mystery. Many factors have been reported regulating the specification, proliferation and differentiation of FLCs. FLCs degenerate in a few weeks postnatally, however, the underlying mechanism is still unknown. In this review, we will focus on the fate determination of FLCs, and summarize the resent progress on the morphology, ultrastructure, function, origin and involution of FLCs.

Drug targets beyond HMG-CoA reductase: Why venture beyond the statins?

Abstract: In this review, we aim to convey a brief, select history of the development of cholesterol-lowering therapies. We focus particularly on the highly successful statins as well as setbacks that should serve as cautionary tales. We go on to preview recent developments that may complement, if not one day replace, the statins. Our focus is on pharmacological interventions, particularly those targeting the cholesterol biosynthetic pathway. Also, we examine therapies under current investigation that target the assembly of atherogenic lipoproteins (via apolipoprotein B or microsomal triglyceride transfer protein), the stability of the low-density lipoprotein-receptor (via PCSK9, proprotein convertase subtilisin kexin 9), or are designed to increase high-density lipoprotein-cholesterol (via inhibition of cholesteryl ester transfer protein).

Mechanisms of testicular immune privilege

Abstract: The testis exhibits a distinctive form of immune privilege to protect the germ cells from the host immune attack. The property of testicular immune privilege was originally attributed to the blood-testis barrier in the seminiferous epithelium, which sequesters antigens. Recent studies have uncovered several levels of immune control besides the blood-testis barrier involved in the privilege of the testis, including the mechanisms of immune tolerance, reduced immune activation, localized active immunosuppression and antigen-specific immunoregulation. The somatic cells of the testis, especially Sertoli cells, play a key role in regulating the testicular immune privileged status. The constitutive expression of anti-inflammatory factors in the testis by somatic cells is essential for local immunosuppression. Growing evidence shows that androgens orchestrate the inhibition of proinflammatory factors and shift cytokine balance toward a tolerogenic environment. Disruption of these protective mechanisms, which may be caused by trauma, infection and genetic factors, can lead to orchitis and infertility. This review article highlights the unique immune environment of the testis, particularly focuses on the regulation of testicular immune privilege.

Techniques of cell type-specific transcriptome analysis and applications in researches of sexual plant reproduction

Abstract: In higher plants, specific cell differentiation and fate decision are controlled by differential gene expression. Cell type-specific transcriptome analysis has become an important tool for investigating cell regulatory mechanisms. In recent years, many different techniques have been developed for the isolation of specific cells and the subsequent transcriptome analysis, and considerable data are available regarding the transcriptional profiles of some specific cells. These cell type-specific transcriptome analyses hold significant promise for elucidating the gene expression linked to cellular identities and functions, and are extraordinarily important for research in functional genomics and systems biology aimed toward basic understanding of molecular networks and pathway interactions. Moreover, to reveal the critical mechanisms about sexual plant reproduction, the gamete and embryo cells have long been treated as good subjects for cell-specific transcriptome analysis, and there has been important progress in recent decades. In this review, we summarize current technologies in cell type-specific transcriptome analysis and review the applications of these technologies in research into the mechanisms of sexual reproduction in higher plants.

The trafficking and behavior of cellulose synthase and a glimpse of potential cellulose synthesis regulators

Abstract: Cellulose biosynthesis is a topic of intensive research not only due to the significance of cellulose in the integrity of plant cell walls, but also due to the potential of using cellulose, a natural carbon source, in the production of biofuels. Characterization of the composition, regulation, and trafficking of cellulose synthase complexes (CSCs) is critical to an understanding of cellulose biosynthesis as well as the characterization of additional proteins that contribute to the production of cellulose either through direct interactions with CSCs or through indirect mechanisms. In this review, a highlight of a few proteins that appear to affect cellulose biosynthesis, which includes: KORRIGAN (KOR), Cellulose Synthase-Interactive Protein 1 (CSI1), and the poplar microtubule-associated protein, PttMAP20, will accompany a description of cellulose synthase (CESA) behavior and a discussion of CESA trafficking compartments that might act in the regulation of cellulose biosynthesis.

Metabolism is regulated by protein acetylation

Abstract: Lysine acetylation, first identified in histones, was initially thought to be a posttranslational modification occuring only in eukaryotic cells that controlled gene transcription either via remodeling chromatin or altering the transcriptional machinery. Recent studies, however, have shown that acetylation is a well-conserved metabolic regulatory mechanism that plays critical roles in regulating and coordinating cell metabolism. Acetylation regulates metabolism through controlling gene transcription, altering the metabolic enzymes activity and possibly other functional aspects, of metabolic enzymes. In this review, we provide an overview of the roles and significance of acetylation in metabolic regulation.

Gold glitters everywhere: nucleus microRNAs and their functions

Abstract: As a highly conserved class of endogenous small (∼22 nucleotides) non-coding RNAs, microRNAs (miRNAs) regulate a broad spectrum of biological processes Increasing evidences suggested that miRNAs generally regulated gene expression at the posttranscriptional stage via inhibiting the translational process or degrading mRNA Recent studies have also revealed that there is extensive amount of miRNA, as well as miRNA function-related proteins, in the cell nucleus Although the molecular basis underneath the biogenesis and function of nucleus miRNAs remains largely unknown, the presence of various miRNAs and miRNA function-related proteins in the nucleus strongly argue that miRNAs may execute their role throughout the whole gene expression pathway Here we review the recent advances in the researches about the nucleus miRNAs, including the biosynthesis pathways, biological functions and potential regulation machinery of nucleus miRNAs

Conservation and divergence of the histone H2B monoubiquitination pathway from yeast to humans and plants

Abstract: Histone ubiquitination plays a critical role in the regulation of transcription, and histone H2B monoubiquitination (H2Bub1) is mainly associated with transcriptional activation. Recent studies in yeast, humans, and Arabidopsis have revealed the conservation of chromatin modification via H2Bub1 during evolution. Rad6-Bre1 and their homologs are responsible for H2B monoubiquitination in diverse eukaryotic organisms, and the PAF complex is required for H2Bub1 to proceed. H2Bub1 is involved in many developmental processes in yeast, humans, and Arabidopsis, and it activates gene transcription by regulating the H3K4 methylation state. Notably, the level of H3K4 methylation is entirely dependent on H2Bub1 in yeast and humans, whereas the H3K4 methylation level of only a small number of genes in Arabidopsis is dependent on H2Bub1. In this review, we summarize the enzymes involved in H2B monoubiquitination and deubiquitination, and discuss the biologic functions of H2Bub1 in different organisms. In addition, we focus on recent advances in our understanding of the molecular mechanisms that enable H2Bub1 to perform its function.

3C-based methods to detect long-range chromatin interactions

Abstract: Transcriptional regulatory regions are often located several thousand bases from the gene that they control. To function, the chromatin strand forms loops to juxtapose distal regions with the promoter. These long-range chromatin interactions have profound influences on the regulation of gene expression and mapping these interactions is currently a subject of intensive investigation. Chromosome conformation capture (3C) technology and its derivatives have been widely used to detect chromatin interactions and greatly contributed to understanding of the relationship between genome organization and genome function. Here we review these 3C-based methods for the study of long-range chromatin interactions and recent exciting findings obtained by using these technologies.