如果您有一个高分辨率转录组数据

1、如果您有一份高分辨率转录组数据2016/2/1RNA工坊众所周知，基因调控是高度动态的和严格调控的。为了能够定量地解析基因调控，我们必须直接测定转录动力学。何为转录动力学(Transcriptkinetics),就是时间尺度上的转录本拷贝数的变化速率。从而我们可以解析不同的转录调控形式。转录动力学测定需要满足两个条件一是转录本数量的绝对定量；二是采样时间分辨率足够高。RNA-seq技术绝对胜任这项工作。然而，当前常规的RNA-seq却存在着两个问题:一是采样时间跨度大;二是采用相对定量法。这次来自FrancisCrickInstitute的科学家呈上了一份高分辨率的转录组数据。他们减小了采样时

2、间跨度，还有利用spike-inRNA来绝对定量转录本的数量，并借助了Gaussuanprocess方法来减小绝对定量过程中的技术噪音(technicalnoise)。x30min24x1lhourRelativeAbsoluteFr卜66hoursRNA-seqAeeflalospiketranscriptspermilliontranscriptsperembryo他们利用这份高分辨率转录组数据，给出了三个有意思的研究结果:(1)作者发现，针对某个基因，该基因的表达过程是平滑的轨迹。(+Aod)OAquJa)一s.9-osueJ_1224324042Stagex10smyodimix1o阳

3、/bp7AGo4LhlfooImyodiIIhlfoomyl2oClutchAClutchBXetro.101719OralbplOXetro.101719IImix1o口meplaooOmeplb0102030405060Time(hpf)2)转录动力学的跨度可以达到8个数量级。1000pDlyA+0-23.ShpfrdRNA0-23.5hpfPalyA-h0-23.5hpf舸IXMq_3gcncpuajio壮-PolyA+24-66hpf乂1GOTrdRNA0-23.5hpF4x1OkbhPolyA-t-.24J-iS6hpfW210410HMax.阳teincrease(kb/hour)

4、ClutchATime(hpf)SynexpressionwithGOEnrichmentClutchATime(hpf)SynexpressionwithGOEnrichment100genes0cellcycleRNAprocessing1000genes0204060204060omitexpressionSvnexoreunionGenestransientlyoninearlydevelopmentproteinlocalizationtranslationcellcycleproteolysisRNAprocessingcellcycleproteinlocalizationIpr

5、oteolysiscellcycleRNAprocessingchromatinorganization|reaulationortranscription,DNA-dependentITranscriptionFactors*|anterior/posteriodpatternspecificationIcardiovascularsystemdevelopmentImusclecontractionsynaptictransmission!signaltransductiontranslationsynaptictransmissionIcellsurfacereceptor,signal

6、ingpathwayIsignaltransductionnervoussystemdevelopmentvisualperceptionxmusclecontrac竹onregulationofWntreceptorsignalingpathwayTranscriptionFactors*nucleosomeassemblydorsal/ventralpatternformationsomitogenesisgastrulationendodermdevelopmentanterior/posteriorpatternspecificationneuraltubedevelopmentdet

7、erminationofleft/rightsymmetrymesodermdevelopmentBMPsignalingpathwaygrowthfactoractivityskeletalsystemdevlopmentcytoskeletalproteinbindingcontractilefiberTranscriptionFactors*anterior/posteriorpatternspecificationdeterminationofleft/rightsymmetryskeletalsystemdevlopmentepitheliumdevelopmenteardevelo

8、pmentlimbdevelopmentcardiovascularsystemdevelopmentcentralnervoussystemdevelopmentpancreasdevelopmentproximal/distalpatternformationkidneydevelopmentmuscletissuedevelopmentMax.rateofIncrease(trmnscriptsIhour)(3)作者通过表达动态相似性进行基因的聚类分析，发现了Temperalsynexpression这个现象。这些具有相似表达动态的基因应该受到相似的调控网络的控制。作者通过GO分析，并结

9、合Temperalsynexpression现象，能够预测基因的功能。(4)通过分析时间尺度，不仅能得到全部基因表达的时间尺度，还可以区分出基因调控阶段或发育过程。本文中还有其他一些有意思的现象。比如平常使用的参考基因(gapdh,odcl,eeflal等)基因表达变化幅度较大，不过RNAhelicaseddx3x表达水平比较一致。总之，就如作者所言，高分辨率的转录组数据能够更好的探究基因的表达过程。如果能再结合单细胞转录组测序技术，我们也许能创造出一个4-D的转录组图谱。本文系RNA工坊原创编译整理，欢迎转载！转载请注明来源并附原文链接。谢谢MeasuringAbsoluteRNACopyN

10、umbersatHighTemporalResolutionRevealsTranscriptomeKineticsinDevelopmentOwensND,BlitzIL,LaneMA,PatrushevI,OvertonJD,GilchristMJ,ChoKW,KhokhaMK.ABSTRACTTranscriptregulationisessentialforcellfunction,andmisregulationcanleadtodisease.Despitetechnologiestosurveythetranscriptome,welackacomprehensiveunders

11、tandingoftranscriptkinetics,whichlimitsquantitativebiology.Thisisanacutechallengeinembryonicdevelopment,whererapidchangesingeneexpressiondictatecellfatedecisions.Byultra-high-frequencysamplingofXenopusembryosandabsolutenormalizationofsequencereads,wepresentsmoothgeneexpressiontrajectoriesinabsolutet

12、ranscriptnumbers.Duringadevelopmentalperiodapproximatingthefirst8weeksofhumangestation,transcriptkineticsvarybyeightordersofmagnitude.Orderinggenesbyexpressiondynamics,wefindthat“temporalsynexpression”predictscommongenefunction.Remarkably,asingleparameter,thecharacteristictimescale,canclassifytranscriptkineticsgloballyanddistinguishgenesregulatingdevelopme