Long Non-coding RNA ANRIL in Gene Regulation and Its Duality in Atherosclerosis

The antisense transcript long non-coding RNA（lnc RNA）（antisense non-coding RNA in the INK4 locus, ANRIL） is an antisense of the cyclin-dependent kinase inhibitor 2 B（CDKN2B） gene on chromosome 9 p21 that contains an overlapping 299-bp region and shares a bidirectional promoter with alternate open reading frame（ARF）. In the context of gene regulation, ANRIL is responsible for directly recruiting polycomb group（Pc G） proteins, including polycomb repressive complex-1（PRC-1） and polycomb repressive complex-2（PRC-2）, to modify the epigenetic chromatin state and subsequently inhibit gene expression in cis-regulation. On the other hand, previous reports have indicated that ANRIL is capable of binding to a specific site or sequence, including the Alu element, E2 F transcription factor 1（E2F1）, and CCCTC-binding factor（CTCF）, to achieve trans-regulation functions. In addition to its function in cell proliferation, adhesion and apoptosis, ANRIL is very closely associated with atherosclerosis-related diseases. The different transcripts and the SNPs that are related to atherosclerotic vascular diseases（ASVD-SNPs） are inextricably linked to the development and progression of atherosclerosis. Linear transcripts have been shown to be a risk factor for atherosclerosis, whereas circular transcripts are protective against atherosclerosis. Furthermore, ANRIL also acts as a component of the inflammatory pathway involved in the regulation of inflammation, which is considered to be one of the causes of atherosclerosis. Collectively, ANRIL plays an important role in the formation of atherosclerosis, and the artificial modification of ANRIL transcripts should be considered following the development of this disease.

Use of Rich BHI Medium Instead of Synthetic TMH Medium for Gene Regulation Study in Yersinia pestis

Objective This study is to verify the use of rich BHI medium to substitute synthetic media for gene regulation studies in Yersinia pestis. Methods The transcriptional regulation of rovA by PhoP or via temperature upshift, and that of pla by CRP were investigated when Y. pestis was cultured in BHI. After cultivation under 26 ~C, and with temperature shifting from 26 to 37 ~C, the wild-type （WT） strain or its phoP or crp null mutant （AphoP or Acrp, respectively） was subject to RNA isolation, and then the promoter activity of rovA or plo in the above strains was detected by the primer extension assay. The rovA promoter-proximal region was cloned into the pRW50 containing a promoterless lacZ gene. The recombinant LacZ reporter plasmid was transformed into WT and AphoP to measure the promoter activity of rovA in these two strains with the ^-Galactosidase enzyme assay system. Results When Y. pestis was cultured in BHI, the transcription of rovA was inhibited by PhoP and upon temperature upshift while that ofpla was stimulated by CRP. Conclusion The rich BHI medium without the need for modification to be introduced into the relevant stimulating conditions （which are essential to triggering relevant gene regulatory cascades）, can be used in lieu of synthetic TMH media to cultivate Y. pestis for gene regulation studies.

Direct somatic embryogenesis and related gene expression networks in leaf explants of Hippeastrum ‘Bangkok Rose’

Hippeastrum, a highly diverse genus in the Amaryllidaceae family, is a valuable ornamental bulbous flowering plant. Somatic embryogenesis(SE) is an efficient method for mass production of Hippeastrum plantlets. Previous studies have been devoted to the in vitro propagation of Hippeastrum, but the SE and its regulatory networks are rarely reported. In this study, we established a direct SE method of Hippeastrum Bangkok Rose' using leaf bases as explants. MS supplemented with 1.00 mg·L^(-1)NAA +1.00 mg·L^(-1)KT + 0.25 mg·L^(-1)TDZ was the optimal medium for SE. Histological observations showed that the bipolar somatic embryo originated from the epidermal cell layer and underwent initiation,globular, scutellar and coleoptile stages. During SE, endogenous hormones of IAA, CTK, ABA, and SA were highly accumulated. Transcriptomic analysis revealed the genes encoding auxin biosynthesis/metabolic enzymes and efflux carriers were induced, while the auxin receptor of TIR1 and ARF transcriptional repressor of Aux/IAA were down-regulated and up-regulated, respectively, leading to suppression of auxin signaling. In contrast, cytokine signaling was promoted at the early stage of SE, as biosynthesis, transport, and signaling components were up-regulated.Various stress-related genes were up-regulated at the early or late stages of SE. Chromatin remodeling could also be dynamically regulated via distinct expression enzymes that control histone methylation and acetylation during SE. Moreover, key SE regulators, including WOXs and SERKs were highly expressed along with SE. Overall, the present study provides insights into the SE regulatory mechanisms of the Hippeastrum.

Gene Expression and Regulation of Blastocyst Formation

Blastocyst formation is a crucial stage of early embryo development.Cell junction proteins and cell adhesion associated proteins are involved in the establishment of cell junction,and subsequently induce cell compaction,blastocyst formation,differentiation of trophectoderm and maintenance of blastocyst expansion.Genes regulating development and differentiation participate in embryo development and differentiation of inner cell mass and trophectoderm,which controls the transition from the undifferentiation to differentiation state.Furthermore,cytokine and growth factor have influence on the proliferation of cells of inner cell mass.In a word,many proteins and factors are involved in the gene expression and regulation of blastocyst formation.

Role of long non-coding RNAs in gene regulation and oncogenesis

Objective This article aims to review recent studies on the biological characteristics of long non-coding RNAs （IncRNAs）, transcription regulation by IncRNAs, and the results of recent studies on the mechanism of action of IncRNAs in tumor development. Data sources The data cited in this review were mainly obtained from the articles listed in PubMed and HighWire that were published from January 2002 to June 2010. The search terms were ＂long non-coding RNA＂, ＂gene regulation＂, and ＂tumor＂. Study selection The mechanism of IncRNAs in gene expression regulation, and tumors concerned with IncRNAs and the role of IncRNAs in oncogenesis. Results IncRNAs play an important role in transcription control, and post-transcriptional controlling. IncRNAs are suppressing and promoting factors. regulation by controlling chromatin remodeling, transcriptional involved in many kinds of tumors and play key roles as both Conclusion IncRNAs could perfectly regulate the balance of gene expression system and play important roles in oncogenic cellular transformation.

SWR1 Chromatin-Remodeling Complex Subunits and H2A.Z Have Non-overlapping Functions in Immunity and Gene Regulation in Arabidopsis

Incorporation of the histone variant H2A.Z into nucleosomes by the SWR1 chromatin remodeling complex is a critical step in eukaryotic gene regulation. In Arabidopsis, SWRlc and H2A.Z have been shown to con- trol gene expression underlying development and environmental responses. Although they have been implicated in defense, the specific roles of the complex subunits and H2A.Z in immunity are not well under- stood. In this study, we analyzed the roles of the SWRlc subunits, PHOTOPERIOD-INDEPENDENT EARLY FLOWERING1 （PIE1）, ACTIN-RELATED PROTEIN6 （ARP6）, and SWR1 COMPLEX 6 （SWC6）, as well as H2A.Z, in defense and gene regulation. We found that SWRlc components play different roles in resistance to different pathogens. Loss of PIE1 and SWC6 function as well as depletion of H2A.Z led to reduced basal resistance, while loss of ARP6 fucntion resulted in enhanced resistance. We found that mutations in PIE1 and SWC6 resulted in impaired effector-triggered immunity. Mutation in SWRlc components and H2A.Z also resulted in compromised jasmonic acid/ethylene-mediated immunity. Genome-wide expres- sion analyses similarly reveal distinct roles for H2A.Z and SWRlc components in gene regulation, and sug- gest a potential role for PIE1 in the regulation of the cross talk between defense signaling pathways. Our data show that although they are part of the same complex, Arabidopsis SWRlc components could have non-redundant functions in plant immunity and gene regulation.

PRMT5 in gene regulation and hematologic malignancies

Arginine methylation is a common posttranslational modification that governs important cellular processes and impacts development,cell growth,proliferation,and differentiation.Arginine methylation is catalyzed by protein arginine methyltransferases(PRMTs),which are classified as type I and type II enzymes responsible for the formation of asymmetric and symmetric dimethylarginine,respectively.PRMT5 is the main type II enzyme that catalyzes symmetric dimethylarginine of histone proteins to induce gene silencing by generating repressive histone marks,including H2AR3me2s,H3R8me2s,and H4R3me2s.PRMT5 can also methylate nonhistone proteins such as the transcription factors p53,E2F1 and p65.Modifications of these proteins by PRMT5 are involved in diverse cellular processes,including transcription,translation,DNA repair,RNA processing,and metabolism.A growing literature demonstrates that PRMT5 expression is upregulated in hematologic malignancies,including leukemia and lymphoma,where PRMT5 regulates gene expression to promote cancer cell proliferation.Targeting PRMT5 by specific inhibitors has emerged as a potential therapeutic strategy to treat these diseases.

Photoresponsive nucleic acids for gene regulation

For the main purpose of manipulating the functions of molecules, researchers have made great achievements on photoresponsive molecules using light as a trigger. Light has become a promising scientific tool due to it being a clean and noninvasive external stimulant. By attachment of photoresponsive moieties to molecules, the biological activities of molecules can be attenuated by light activation. With wide applications of laser in life sciences, it will be possible to achieve high spatiotemporal resolution. In this review, we focus on photoresponsive nucleic acids for photomodulating gene expression with light activation. With incorporation of photoswitchable or photocleavable moieties, biological behaviors of nucleic acids are photoregulated reversibly or irreversibly. Recent development and applications of photoresponsive nucleic acid in vitro and in vivo have shown a very promising future for manipulation of specific functional genes or disease genes. We expect that photoresponsive nucleic acids will be powerful scientific tools for studying biological events as well as gene therapy agents for genetic diseases.

Toward an understanding of the relation between gene regulation and 3D genome organization

Background:High-order chromatin structure has been shown to play a vital role in gene regulation.Previously we identified two types of sequence domains,CGI(CpG island)forest and CGI prairie,which tend to spatially segregate,but to different extent in different tissues.Here we aim to further quantify the association of domain segregation with gene regulation and therefore differentiation.Methods:By means of the published RNA-seq and Hi-C data,we identified tissue-specific genes and quantitatively investigated how their regulation is relevant to chromatin structure.Besides,two types of gene networks were constructed and the association between gene pair co-regulation and genome organization is discussed.Results:We show that compared to forests,tissue-specific genes tend to be enriched in prairies.Highly specific genes also tend to cluster according to their functions in a relatively small number of prairies.Furthermore,tissue-specific forest-prairie contact formation was associated with the regulation of tissue-specific genes,in particular those in the prairie domains,pointing to the important role of gene positioning,in the linear DNA sequence as well as in 3D chromatin structure,in gene regulatory network formation.Conclusion:We investigated how gene regulation is related to genome organization from the perspective of forest-prairie spatial interactions.Since unlike compartments A and B,forest and prairie are identified solely based on sequence properties.Therefore,the simple and uniform framework(forest-prairie domain segregation)provided here can be utilized to further understand the chromatin structure changes as well as the underlying biological significances in different stages,such as tumorgenesis.

The Change-Over of Yin-yang and Gene Regulation in Kidney Deficiency Syndromes

The present paper studies gene regulation in kidney deficiency syndromes from the simple Nephrotic Syndrome and with the principle of positive-negative regulation to control the change-over ofyin-yang, the modem molecular biological techniques can be used, such as gene chip, representational difference analysis （RDA） and gene sequence analysis, so as to investigate the inner relationship between the genes and kidney deficiency syndromes and prove the effect given by these genes on the pathophysiological status of change-over ofyin-yang in kidney deficiency syndromes. This philosophical approach and method can also be adopted for studies of the related genes in other TCM syndromes.

A modified Gillespie algorithm for E.coli gene regulation systems

The dynamics of complex gene regulation systems can be simulated by the Gillespie algorithm. The classic Gillespie algorithm is appropriate to simulate a stochastic

Reprogramming the endogenous type I CRISPR-Cas system for simultaneous gene regulation and editing in Haloarcula hispanica

The type I system is the most widely distributed CRISPR-Cas system identified so far.Recently,we have revealed the natural reprogramming of the type I CRISPR effector for gene regulation with a crRNA-resembling RNA in halophilic archaea.Here,we conducted a comprehensive study of the impact of redesigned crRNAs with different spacer lengths on gene regulation with the native type I-B CRISPR system in Haloarcula hispanica.When the spacer targeting the chromosomal gene was shortened from 36 to 28 bp,transformation efficiencies of the spacer-encoding plasmids were improved by over three orders of magnitude,indicating a significant loss of interference.However,by conducting whole-genome sequencing and measuring the growth curves of the hosts,we still detected DNA cleavage and its influence on cell growth.Intriguingly,when the spacer was shortened to 24 bp,the transcription of the target gene was downregulated to 10.80%,while both interference and primed adaptation disappeared.By modifying the lengths of the spacers,the expression of the target gene could be suppressed to varying degrees.Significantly,by designing crRNAs with different spacer lengths and targeting different genes,we achieved simultaneous gene editing(cdc6E)and gene regulation(crtB)for the first time with the endogenous type I CRISPR-Cas system.

Post-transcriptional gene regulation by RNA-binding proteins in vascular endothelial dysfunction

Endothelial cell dysfunction is a term which implies the dysregulation of normal endothelial cell functions,including impairment of the barrier functions,control of vascular tone,disturbance of proliferative and migratory capacity of endothelial cells,as well as control of leukocyte trafficking.Endothelial dysfunction is an early step in vascular inflammatory diseases such as atherosclerosis,diabetic vascular complications,sepsis-induced or severe virus infection-induced organ injuries.The expressions of inflammatory cytokines and vascular adhesion molecules induced by various stimuli,such as modified lipids,smoking,advanced glycation end products and bacteria toxin,significantly contribute to the development of endothelial dysfunction.The transcriptional regulation of inflammatory cytokines and vascular adhesion molecules has been well-studied.However,the regulation of those gene expressions at post-transcriptional level is emerging.RNA-binding proteins have emerged as critical regulators of gene expression acting predominantly at the post-transcriptional level in microRNA-dependent or independent manners.This review summarizes the latest insights into the roles of RNA-binding proteins in controlling vascular endothelial cell functions and their contribution to the pathogenesis of vascular inflammatory diseases.

Nucleosomal Context of Binding Sites Influences Transcription Factor Binding Affinity and Gene Regulation

Transcription factor （TF） binding to its DNA target site plays an essential role in gene regulation. The location, orientation and spacing of transcription factor binding sites （TFBSs） also affect regulatory function of the TF. However, how nucleosomal context of TFBSs influences TF binding and subsequent gene regulation remains to be elucidated. Using genome-wide nucleosome positioning and TF binding data in budding yeast, we found that binding affinities of TFs to DNA tend to decrease with increasing nucleosome occupancy of the associated binding sites. We further demonstrated that nucleosomal context of binding sites is correlated with gene regulation of the corresponding TF. Nucleosome-depleted TFBSs are linked to high gene activity and low expression noise, whereas nucleosome-covered TFBSs are associated with low gene activity and high expression noise. Moreover, nucleosome-covered TFBSs tend to disrupt coexpression of the corresponding TF target genes. We conclude that nucleosomal context of binding sites influences TF binding affinity, subsequently affecting the regulation of TFs on their target genes. This emphasizes the need to include nucleosomal context of TFBSs in modeling gene regulation.

MeCP2:multifaceted roles in gene regulation and neural development

Methyl-CpG-binding protein 2 （MeCP2） is a classic methylated-DNA-binding protein, dysfunctions of which lead to various neurodevelopmental disorders such as Rett syndrome and autism spectrum disorder. Initially recognized as a transcriptional repressor, MeCP2 has been studied extensively and its functions have been expanded dramatically in the past two decades. Recently, it was found to be involved in gene regulation at the post-transcriptional level. MeCP2 represses nuclear microRNA processing by interacting directly with the Drosha/DGCR8 complex. In addition to its multifaceted functions, MeCP2 is remarkably modulated by post- translational modifications such as phosphorylation, SUMOylation, and acetylation, providing more regulatory dimensions to its functions. The role of MeCP2 in the central nervous system has been studied extensively, from neurons to glia. Future investigations combining molecular, cellular, and physiological methods are necessary for defining the roles of MeCP2 in the brain and developing efficient treatments for MeCP2-related brain disorders.

Genetic engineering and lignin biosynthetic regulation in forest tree species

Genetic engineering of forest tree species is regarded as a strategy to reduce worldwide pressure on natural forests, to conserve genetic resources and ameliorate stress on global climate, and to meet growing demand for forest wood and timber products. Genetic engineering approaches toward the control or management of fungal pathogens, arthropod herbivores, bacterial and viral diseases, the use of pest resistance genes, and weed competitors are being studied. Although the production of transgenic trees is relatively recent and only a few species have been successfully genetically engineered in forest tree species, very useful and valuable information is available on the application of transgenic trees. Genes involved in important agricultural traits such as herbicide resistance, insect resistance, and wood quality have been isolated and have been used to genetically engineer trees. New technologies of plant molecular biology and genomics now make it possible high-efficient genetic improvement of forest trees. Genetic engineering promises to expand greatly the potential for genetic manipulation as new genes of commercial interest are discovered and utilized. Lignification is a process essential to the nature and evolution of vascular plants that is still poorly understood, even though it has been studied for more than a century. Recent studies on mutant and transgenic plants indicate that lignification may be far more flexible than previously realized. Rines with a mutation affecting the biosynthesis of the major lignin precursor, coniferyl alcohol, show a high level of an unusual subunit, dihydroconiferyl alcohol. It is also unusual as a plant polymer in that there are no plant enzymes for its degradation. These results have significant implications regarding the tradiational definition of lignin, and highlight the need for a better understanding of the lignin precursor biosynthetic pathway. In this review, we describe the progress made recently in genetic engineering of forest tree species.

Regulation of HIF-1 α to Expression of N-myc Downstream Regulated Gene 1 in Colorectal Carcinoma

Plasmid expressing small interfering RNA （siRNA） against HIF-1α （pSilence-2.1-U6-siRNA） was constructed and transfected into LS174T cells in hypoxia condition.After expression of siRNA against HIF-1 α in LS174T cells, expressions of HIF-1 α and N-myc downstream regulated gene 1 （NDRG1） gene were inhibited significantly. HIF-1 cta transcripts were positive in 67.7% （42/62） and 44.4% （8/18） of colorectal adenocarcinoma and adenoma, re- spectively. The mean percentage of cells with positive hybridization of HIF-1 α mRNA increases with the development from Duke stage A to stage C＋D （p〈 0.05）. The positive staining rate of NDRG1 protein was significant higher in than that in colorectal adenoma colorectal adenocarcinoma group group （p〈 0.05）. The level of HIF-1 a transcripts was positively correlated with the level of NDRG1 protein （p 〈 0.05） during colorectal tumor progression. HIF-1α and its down stream gene NDRG1 may play roles in tumor progression of human colorectal carcinoma.

Regulatory role of NFAT1 signaling in articular chondrocyteactivities and osteoarthritis pathogenesis

Osteoarthritis (OA), the most common form of joint disease, is characterized clinically by joint pain, stiffness,and deformity. OA is now considered a whole joint disease;however, the breakdown of the articular cartilage remains themajor hallmark of the disease. Current treatments targeting OA symptoms have a limited impact on impeding orreversing the OA progression. Understanding the molecular and cellular mechanisms underlying OA development isa critical barrier to progress in OA therapy. Recent studies by the current authors’ group and others have revealedthat the nuclear factor of activated T cell 1 (NFAT1), a member of the NFAT family of transcription factors, regulatesthe expression of many anabolic and catabolic genes in articular chondrocytes of adult mice. Mice lacking NFAT1exhibit normal skeletal development but display OA in both appendicular and spinal facet joints as adults. Thisreview mainly focuses on the recent advances in the regulatory role of NFAT1 transcription factor in the activities ofarticular chondrocytes and its implication in the pathogenesis of OA.

The virulence regulator AbsR in avian pathogenic Escherichia coli has pleiotropic effects on bacterial physiology

Avian pathogenic Escherichia coli(APEC)belonging to extraintestinal pathogenic E.coli(ExPEC)can cause severe infections in extraintestinal tissues in birds and humans,such as the lungs and blood.MprA(microcin production regulation,locus A,herein renamed AbsR,a blood survival regulator),a member of the MarR(multiple antibiotic resistance regulator)transcriptional regulator family,governs the expression of capsule biosynthetic genes in human ExPEC and represents a promising druggable target for antimicrobials.However,a deep understanding of the AbsR regulatory mechanism as well as its regulon is lacking.In this study,we present a systems-level analysis of the APEC AbsR regulon using ChIP-Seq(chromatin immunoprecipitation sequencing)and RNA-Seq(RNA sequencing)methods.We found that AbsR directly regulates 99 genes and indirectly regulates 667 genes.Furthermore,we showed that:1)AbsR contributes to antiphagocytotic effects by macrophages and virulence in a mouse model for systemic infection by directly activating the capsular gene cluster;2)AbsR positively impacts biofilm formation via direct regulation of the T2SS(type II secretion system)but plays a marginal role in virulence;and 3)AbsR directly upregulates the acid tolerance signaling system EvgAS to withstand acid stress but is dispensable in ExPEC virulence.Finally,our data indicate that the role of AbsR in virulence gene regulation is relatively conserved in ExPEC strains.Altogether,this study provides a comprehensive analysis of the AbsR regulon and regulatory mechanism,and our data suggest that AbsR likely influences virulence primarily through the control of capsule production.Interestingly,we found that AbsR severely represses the expression of the type I-F CRISPR(clustered regularly interspaced short palindromic repeats)-Cas(CRISPR associated)systems,which could have implications in CRISPR biology and application.

Regulatory genes controlling neural stem cells differentiation into neurons

The recent progress in neural stem cells （NSCs） research has shed lights on possibility of repair and restoration of neuronal function in neurodegenerative diseases using stem cells. Induction of stem cells differentiate into mature neurons is critical to achieve the clinical applications of NSCs. At present, molecular mechanisms modulating NSC differentiation are not fully understood. Differentiation of stem cells into neuronal and glial cells involves an array of changes in expression of transcription factors. Transcription factors then trigger the expression of a variety of central nervous system （CNS） genes that lead NSCs to differentiate towards different cell types. In this paper, we summarized the recent findings on the gene regulation of NSCs differentiation into neuronal cells.