简介：

简介：探索真核细胞的抄写因素(TF)的性质有约束力的地点并且决定他们怎么不同于包围DNA序列，我们检验了与DNA有约束力的地点联系的四个特征：G+C内容，模式复杂性，palindromic结构，和Markov定序订。我们规章的主题的分析从TRANSFAC数据库获得了，用酵母内部是的遗传因子的序列背景，表明这四个特征在主题序列显示出可变丰富。例如，主题序列比是背景序列是更可能的有palindromic结构。另外，这些特征对规章的主题紧局部性，显示他们自己是主题序列的一个性质并且没被一般倡导者分享规章的主题在住的“环境”。由根据他们绑在的TF班毁坏主题序列，更特定的协会被识别。最后，当其它例如复杂性丰富，越过检验的种类是通用的时，我们发现一些关联例如G+C内容丰富，是种类特定的。这里提供的定量分析应该增加我们protein-DNA相互作用的理解并且也帮助通过生物信息学便于规章的主题的发现。

简介：Despitethefactthatironisoneofthemostabundantelementsoftheearth'scrust,irondeficienciesareseriousproblemsbothinhumannutrition[1]andinagriculture[2].Sixtoeightpercentoftheworld'spopulationispotentiallyaffectedbyirondeficiencyinducedanemia,aleadingcauseofmaternaldeathinAfricanandAsiancountrieswherepeoplerelymostlyonplantsfortheirdailyintakeofiron.Ironcanalsobealimitingfactorinthegrowthofeconomicallyimportantcropplantsbecauseofinadequatesoilchemistry,andsuchdeficienciescannoteasilybecorrectedbyamendingthesoil.Improvingtheplant'sabilitytoabsorbironinadverseconditionsandtoincreasetheiroverallcontentcouldoffersolutionstothesedramaticproblems.Thereforeunderstandingthemolecularmechanismsregulatingironuptakeandhomeostasisinplantshaspotentiallyimportantpracticalapplicationsbothinagricultureandhumanhealth[3].

简介：Mammaliancelltotipotencyisasubjectthathasfascinatedscientistsforgenerations.AlonglastingquestionwhethersomeofthesomaticcellsretainstotipotencywasansweredbythecloningofDollyattheendofthe20thcentury.Thedawnofthe218thasbroughtforwardgreatexpectationsinharnessingthepoweroftotipotentcyinmedicine.Throughstemcellbiology,itispossibletogenerateanypartsofthehumanbodybystemcellengineering.Considerableresourceswillbedevotedtoharnesstheuntappedpotentialsofstemcellsintheforeseeablefuturewhichmaytransformmedicineasweknowtoday.Atthemolecularlevel,totipotencyhasbeenlinkedtoasingulartranscriptionfactoranditsexpressionappearstodefinewhetheracellshouldbetotipotent.NamedOct4,itcanactivateorrepresstheexpressionofvariousgenes.Curiously,verylittleisknownaboutOct4beyonditsabilitytoregulategeneexpression.ThemechanismbywhichOct4specifiestotipotencyremainsentirelyunresolved.Inthisreview,wesummarizerethestructureandfunctionofOct4andaddresstoOct4functioninmaintainingtotipotencyorpluripotencyofembryonicstemcels.

简介：Mammaliantoothdevelopmentislargelydependentonsequentialandreciprocalepithelial-mesenchymalinteractions.Theseprocessesinvolveaseriesofinductiveandpermissiveinteractionsthatresultinthedetermination,differentiation,andorganizationofodontogenictissues.Multiplesignalingmolecules,includingBMPs,FGFs,Shh,andWntproteins,havebeenimplicatedinmediatingthesetissueinteractions.Transcriptionfactorsparticipateinepithelial-mesenchymalinteractionsvialinkingthesignalingloopsbetweentissuelayersbyrespondingtoinductivesignalsandregulatingtheexpressionofothersignalingmolecules.Adultstemcellsarehighlyplasticandmultipotent.Thesecellsincludingdentalpulpstemcellsandbonemarrowstromalcellscouldbereprogrammedintoodontogenicfateandparticipatedintoothformation.Recentprogressinthestudiesofmolecularbasisoftoothdevelopment,adultstemcellbiology,andregenerationwillprovidefundamentalknowledgefortherealizationofhumantoothregenerationinthenearfuture.

简介：抄写开始地点(TSS)区域与另外的倡导者元素相比显示出更大的可变性。我们被感兴趣由把信息内容用作一项措施寻找它的可变性。我们在这研究注意可变性在与15nt的块相比包围TSS区域的5核苷酸(nt)的块是重要的。这建议可以被包含的实际区域在在尺寸的5-10nt的范围。为Escherichia关口i，我们注意从dinucleotide替换矩阵的信息内容清楚地显示出更好的辨别，建议一些关联的存在。然而，为人，这效果是少得多，并且为老鼠，它实际上是不在的。我们能断定存在短期在TSS区域以内的关联是种类依赖者并且不是通用的。我们进一步观察到在除了TSS的mitochondrial控制元素有另外的可变区域。有效比较能仅仅在块上被做，这也被注意，当单个核苷酸比较不给我们任何可检测的信号时。

简介：

简介：HELcells,ahumanerythroleukemiacellline,mainlyexpressthefetal(γ)globingeneandtraceamountoftheembryonic(ε)globingene,butnotadult(β)globingene.Hereweshowthathydroxyurea(HU)caninduceHELcellstoexpressadult(β)globingeneandleadthesecellstoterminaldifferentiation.ResultsshowedinGelmobilityshiftassaysthatGATAfactorscouldspecificallybindtotheregulatoryelementsofhumanβ-globingene,includingtheproximalregulatoryelement(theβ-promoter)andthedistalregulatoryelements(theDNaseIhypersensitivesitesintheLCR,HS2-HS4coresequences).However,theDNAbindingpatternsofGATAfactorswerequitedifferentbetweenHU-inducedanduninducedHELcells.Western-blotanalysisofnuclearextractsfromboththeuninducedandHU-inducedHELcellsrevealedthatthelevelofGATA-2transcriptionfactordecreased,whereasthelevelofGATA-1transcriptionfactorincreasedfollowingthetimeofhydroxyureainduction.Furthermore,usingRT-PCRanalysistheexpressionofhumanβ-globingeneinHU-inducedHELcellscouldbeblockedagainwhenHELcellswereincubatedinthepresenceofantisenseoligonucleotidesforhGATA-1,suggestingthattheupregulationofhGATA-1transcriptionfactormightbecriticalfortheexpressionofhumanβ-globingeneinHU-inducedHELcells.

简介：Inordertostudythefunctionalstructureofthetranscriptionterminatorsandthemechanismoftemination,asurveyofthechromatinstructure,includingthelocationofDNaseIhypersensitivesitesandthenucleosomearrangement,ofyeastADH1andFLPterminatorswasmade.TheresultsshowthatthereisnorelationshipbetweenthefunctionoftheterminatorsandtheexistenceofDNaseIhypersensitivesites.However,itisfoundthatthereisalwaysanucleosmoeattheimmediateupstreamofthetranscriptionalterminationsites.Asacontrol,thechromatinstructuresofthepBR322DNAfragmentsontheyeastshuttervectorsarealsoinvestigatedatthesametime.TherandomnucleosomearrangementonthebacterialDNAinyesastagreeswiththepublishedreports.Anewhypothesis,aboutthemechanismoftranscriptionalterminationisputforwardandthereasonofdifferentnucleosomearrengementontheDNAswhichareoriginallyfromdifferentspeciesinyeastisdiscussed.

简介：组蛋白deacetylases(HDAC)并且嘘一乙酰转移ases(帽子)是其酶的活动控制蛋白质离氨酸残余的乙酰化状态的二抵抗酶家庭，尤其是在核心histones.Acetylation的N终端扩展包含的那些嘘通过它对染色质符合构造的影响影响基因表示。Inaddition，几non-histone蛋白质由特定的离氨酸残余的乙酰化状态在他们的稳定性或生物功能被调整。HDAC在大量的生物学过程干涉并且是部分一多每个成员在有它的专业化功能的蛋白质家庭。另外，HDAC活动紧通过指向的招募，protein-proteininteractions和translational以后修正被控制。房间周期前进，房间幸存和区别的控制在这些酶的最重要的角色之中。因为这些过程被恶意的转变影响，HDAC禁止者作为反被开发在癌症病人的肿瘤的药和areshowing鼓励功效。

简介：Inthepost-genomicera,identificationofspecificregulatorymotifsortranscrip-tionfactorbindingsites(TFBSs)innon-codingDNAsequences,whichisessentialtoelucidatetranscriptionalregulatorynetworks,hasemergedasanobstaclethatfrustratesmanyresearchers.Consequently,numerousmotifdiscoverytoolsandcorrelateddatabaseshavebeenappliedtosolvingthisproblem.However,theseexistingmethods,basedondifferentcomputationalalgorithms,showdiversemotifpredictionefficiencyinnon-codingDNAsequences.Therefore,understandingthesimilaritiesanddifferencesofcomputationalalgorithmsandenrichingthemotifdiscoveryliteraturesareimportantforuserstochoosethemostappropriateoneamongtheonlineavailabletools.Moreover,therestilllackscrediblecriteriontoassessmotifdiscoverytoolsandinstructionsforresearcherstochoosethebestaccordingtotheirownprojects.Thusintegrationoftherelatedresourcesmightbeagoodapproachtoimproveaccuracyoftheapplication.Recentstudiesintegrateregulatorymotifdiscoverytoolswithexperimentalmethodstoofferacomplemen-taryapproachforresearchers,andalsoprovideamuch-neededmodelforcurrentresearchesontranscriptionalregulatorynetworks.HerewepresentacomparativeanalysisofregulatorymotifdiscoverytoolsforTFBSs.

简介：Inordertostudythefunctionalstructureofthetranscriptionterminatorsandthemechanismoftermination,asurveyofthechromatinstructure,includingthelocationofDNaseIhypersensitivesitesandthenucleosomearrangement,ofyeastADH1andFLPterminatorswasmade.TheresultsshowthatthereisnorelationshipbetweenthefunctionoftheterminatorsandtheexistenceofDNaseIhypersensitivesites.However,itisfoundthatthereisalwaysanucleosomeattheimmediateupstreamofthetranscrip-tionalterminationsites.Asacontrol,thechromatinstructuresofthepBR322DNAfragmentsontheyeastshuttervectorsarealsoinvestigatedatthesametime.TherandomnucleosomearrangementonthebacterialDNAinyeastagreeswiththepublishedreports.Anewhypothesis,aboutthemechanismoftranscriptionalterminationisputforwardandthereasonofdifferentnucleosomearrangementontheDNAswhichareori-ginallyfromdifferentspeciesinyeastisdiscussed.

简介：Transcriptionfactor(TF)bindingtoitsDNAtargetsiteplaysanessentialroleingeneregulation.Thelocation,orientationandspacingoftranscriptionfactorbindingsites(TFBSs)alsoaffectregulatoryfunctionoftheTF.However,hownucleosomalcontextofTFBSsinfluencesTFbindingandsubsequentgeneregulationremainstobeelucidated.Usinggenome-widenucleosomepositioningandTFbindingdatainbuddingyeast,wefoundthatbindingaffinitiesofTFstoDNAtendtodecreasewithincreasingnucleosomeoccupancyoftheassociatedbindingsites.WefurtherdemonstratedthatnucleosomalcontextofbindingsitesiscorrelatedwithgeneregulationofthecorrespondingTF.Nucleosome-depletedTFBSsarelinkedtohighgeneactivityandlowexpressionnoise,whereasnucleosome-coveredTFBSsareassociatedwithlowgeneactivityandhighexpressionnoise.Moreover,nucleosome-coveredTFBSstendtodisruptcoexpressionofthecorrespondingTFtargetgenes.WeconcludethatnucleosomalcontextofbindingsitesinfluencesTFbindingaffinity,subsequentlyaffectingtheregulationofTFsontheirtargetgenes.ThisemphasizestheneedtoincludenucleosomalcontextofTFBSsinmodelinggeneregulation.

简介：杀虫药剂抵抗是因为化学杀虫药剂，快速的产生时间和大人口尺寸的高选择压力，在蚊子相当快速发展的进化改编。与杀虫药剂抵抗联系的基因的鉴定是基本的理解为抵抗负责的复杂过程。我们用抑制的联合比较了对硫磷抵抗、易受影响的一种蚊虫pipiensquinquefasciatus的基因transcriptional侧面减少性的杂交和互补DNA(cDNA)microarray技术。278colonies的一个总数从抵抗易受影响的蚊子被选择减少性的图书馆，其38个证明超过二用cDNAmicroarray比在易受影响的紧张在抵抗紧张合拢更强壮的immunoblotting信号选择。定序的结果证明38colonies能被匹配到C的12基因。p。quinquefasciatus。八基因被证实是由在抵抗紧张的超过二褶层的overexpressed。这些基因编码chymotrypsin-1，theta谷胱甘肽S-transferase，脂肪分解酵素3，幼虫的浆液蛋白质1β链，细胞色素b，mitochondrialribosomal有未知功能的大子单元，28SrRNA，和蛋白质。这研究用作一次初步的尝试识别在这蚊子种与organophosphate抵抗联系的新基因并且提供卓见进杀虫药剂抵抗的复杂生理的现象。

简介：理解控制全球基因表达模式的改变的规章的机制继续是在计算生物学的一项挑战性的任务。我们以前开发了一个蚂蚁算法，为微数组数据的一种生物学上启发的计算技术，和预言的通常认为的抄写因素绑定主题(TFBM)通过模仿国王自然蚂蚁的交互行为。这里，我们把算法扩大了到一套基于万维网的软件，蚂蚁Modeler，并且使用了它调查transcriptional机制内在的骨头形成。机械装载和骨头morphogenic蛋白质(BMP)的管理是二个已知的处理加强骨头。我们探讨了一个问题：有任何TFBM，刺激“机械装载的anabolism的回答”并且“调停BMP的osteogenic发信号”吗？尽管在在二回答的基因之中没有重要重叠，比较基于模型的分析建议二个独立osteogenic过程采用普通TFBM，例如一个压力为peroxisome的应答的元素和一个主题激活proliferator的受体(PPAR)。在用老鼠造骨细胞房间的vitro分析的modeling以后响应机械装载支持了象PPAR，Ikaros3，和LMO2那样的预言的TFBM的参与。总起来说，结果将是有用的导出一套可试验的假设并且在骨头形成的复杂transcriptional控制检验特定的管理者的角色。

简介：Heme(铁protoporphyrinIX)是为众多的生活有机体的一个必要分子。不仅它在酶担任一个修复术的组，它也充当控制从信号transduction到蛋白质建筑群汇编的多样的分子、细胞的进程的一个发信号的分子。缺乏他我合成或功能影响造血，肝并且在人的神经系统。最近的研究包括Hap1揭示了一系列调整heme的抄写因素和信号变换器，调停的一个激活heme的抄写因素在酵母Saccharomycescerevisiae的基因抄写上的氧的效果；Bach1，否定地被调整由的一个transcriptional抑压者他我在哺乳动物的房间；IRR，一个熨斗调停的规章的蛋白质铁家属规定他我在细菌Bradyrhizobium的合成日本嗯；并且调整heme的禁止者，协调蛋白质合成与的eucaryotic开始因素2alphakinase他我在网状细胞的可获得性。在这评论，我们总结的当前的知识他我控制这些transcriptional管理者的活动并且表明变换器，并且讨论与有缺陷者联系的疾病他我合成，降级和函数。房间研究(2006)16：681-692。做i：10.1038/sj.cr.7310086；出版联机2006年8月8日。

简介：POU抄写因素OCT4不仅在维持pluripotent和房间而且幕作为通过基因剂量的一个房间命运决定因素完成的胚胎的茎(ES)的自我更新的状态起一个必要作用。然而，控制细胞内部的OCT4蛋白质水平的分子的机制留下逃犯。这里，我们报导那人的WWP2，E3ubiquitin(Ub)蛋白质ligase，通过它的WW领域明确地与OCT4交往并且在vitro并且在vivo提高OCT4的Ub修正。我们首先证明在人的ES房间的内长的OCT4能被Ubpost-translationally修改。而且，我们发现WWP2以一种剂量依赖者方式，和WWP2的活跃地点半胱氨酸残余通过26Sproteasome支持了OCT4的降级在OCT4上为它的酶的活动和解朊的效果被要求。显著地，我们当WWP2表示是由特定的RNA干扰(RNAi)的downregulated时，内长的OCT4蛋白质水平显著地被提高的数据表演，建议那WWP2是为在人的ES房间维持合适的OCT4蛋白质水平的一个重要管理者。而且，北污点分析证明WWP2抄本在多样的人的织物/器官是广泛地在场的并且高度在无差别的人的ES房间表示了。然而，它的表示水平快速在区分的人的ES房间以后被减少，显示WWP2表示力量发展地被调整。我们的调查结果证明WWP2是在人的ES房间的OCT4蛋白质水平的一个重要管理者。

简介：Werecentlyreportedtheuseofagene-trappingapproachtoisolatecellclonesinwhichareportergenehadintegratedintogenesmodulatedbyT-cellactivation.WehavenowtestedapanelofclonesfromthatreportandidentifiedtheonethatrespondstoavarietyofG-proteincoupledreceptors(GPCR).TheβlactamasetaggedEGR-3JurkatcellwasusedtodissectspecificGPCRsignalinginvivo.ThreeGPCRswerestudied,includingthechemokinereceptorCXCR4(Gicoupled)thatwasendogenouslyexpressed,theplateletactivationfactor(PAF)receptor(Gq-coupled),andβ2adrenergicreceptor(Gs-coupled)thatwasbothstablytransfected.Agonistsforeachreceptoractivatedtranscriptionoftheβ-lactamasetaggedEGR-3gene.InductionofEGR-3throughCXCR4wasblockedbypertussistoxinandPD58059,aspecificinhibitorofMEK(MAPK/ERKkinase).NeitheroftheseinhibitorsblockedisoproterenolorPAF-mediatedactivationofEGR-3.Conversely,β2-andPAF-mediatedEGR-3activationwasblockedbythep38,specificinhibitorSB580.Inaddition,bothβ2-andPAF-mediatedEGR-3activationcouldbesynergisticallyactivatedbyCXCR4activation.ThiscombinedresultindicatesthatEGR-3canbeactivatedthroughdistinctsignaltransductionpathwaysbydifferentGPCRsandthatsignalscanbeintegratedandamplifiedtoefficientlytunethelevelofactivation.

简介：在monocot米饭种类OryzasativaL.，最惹人注目的词法过程之一在繁殖开发期间是有上面的internodes(合众国际社)的顺序的延伸的圆锥花序开发的同时发生。阐明内在的分子的机制，我们克隆米饭基因颈叶1(NL1)，什么时候变异，它在flowering时间，有簇叶丛生的苞的更小的圆锥花序和反常合众国际社延伸模式导致延期。NL1基因与一个单个锌手指领域，和它的抄本编码一个GATA类型抄写因素在苞primordia主要被检测，它通常在野类型的植物堕落。在转基因的植物的NL1的Overexpression经常产生严重生长延迟，不太植物的phytomers和更小的叶子，建议NL1起在器官区别的一个重要作用。PLASTOCHRON1(PLA1)的新奇变异的等位基因，知道在调整叶开始起一个关键作用的基因，在这研究被识别。基因分析表明了在nl1和pla1之间的一个相互作用，与PLA1在上游的代理的NL1。表示水平和PLA1的空间模式被发现在nl1被改变变异。而且，flowering，Hd3a和OsMADS1的二个管理者的表示，也在nl1异种被影响。根据这些调查结果，我们建议NL1是通过在米饭在繁殖开发期间调整PLA1和另外的规章的基因的表示调制并且协调organogenesis的一个内在的因素。

简介：Thecommonapproachtofindco-regulatedgenesistoclustergenesbasedongeneexpression.However,duetothelimitedinformationpresentinanydataset,genesinthesameclustermightbeco-expressedbutnotnecessarilyco-regulated.Inthispaper,weproposetointegrateknowntranscriptionfactorbindingsiteinformationandgeneexpressiondataintoasingleclusteringscheme.Thisschemewillfindclustersofco-regulatedgenesthatarenotonlyexpressedsimilarlyunderthemeasuredconditions,butalsosharearegulatorystructurethatmayexplaintheircommonregulation.Wedemonstratetheutilityofthisapproachonamicroarraydatasetofyeastgrownunderdifferentnutrientandoxygenlimitations.Ourintegratedclusteringmethodnotonlyunravelsmanyregulatorymodulesthatareconsistentwithcurrentbiologicalknowledge,butalsoprovidesamoreprofoundunderstandingoftheunderlyingprocess.Theaddedvalueofourapproach,comparedwiththeclusteringsolelybasedongeneexpression,isitsabilitytouncoverclustersofgenesthatareinvolvedinmorespecificbiologicalprocessesandareevidentlyregulatedbyasetoftranscriptionfactors.