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第647行： − − ==完善的模体及其功能== − 许多实验工作致力于理解[[基因调控网络]]中的网络模体。在响应生物信号的过程中，这些网络控制细胞中的哪些基因来表达。这样的网络以基因作为节点，有向边代表对某个基因的调控，基因调控通过其他基因编码的转录因[[结合在DNA上的调控蛋白]]子来实现。因此，网络模体是基因之间相互调控转录速率的模式。在分析转录调控网络的时候，人们发现相同的网络模体在不同的物种中不断地出现，从细菌到人类。例如，''[[大肠杆菌]]''和酵母的转录网络由三种主要的网络模体家族组成，它们可以构建几乎整个网络。主要的假设是在进化的过程中，网络模体是被以收敛的方式独立选择出来的。<ref name="bab1">{{cite journal |vauthors=Babu MM, Luscombe NM, Aravind L, Gerstein M, Teichmann SA |title=Structure and evolution of transcriptional regulatory networks |journal=Current Opinion in Structural Biology |volume=14 |issue=3 |pages=283–91 |date=June 2004 |pmid=15193307 |doi=10.1016/j.sbi.2004.05.004 |citeseerx=10.1.1.471.9692 }}</ref><ref name="con1">{{cite journal |vauthors=Conant GC, Wagner A |title=Convergent evolution of gene circuits |journal=Nat. Genet. |volume=34 |issue=3 |pages=264–6 |date=July 2003 |pmid=12819781 |doi=10.1038/ng1181}}</ref> 因为相对于基因改变的速率，转录相互作用产生和消失的时间尺度在进化上是很快的。<ref name="bab1"/><ref name="con1"/><ref name="dek1">{{cite journal |vauthors=Dekel E, Alon U |title=Optimality and evolutionary tuning of the expression level of a protein |journal=Nature |volume=436 |issue=7050 |pages=588–92 |date=July 2005 |pmid=16049495 |doi=10.1038/nature03842 |bibcode=2005Natur.436..588D }}</ref> 此外，对活细胞中网络模体所产生的动力学行为的实验表明，它们具有典型的动力学功能。这表明，网络模体是基因调控网络中对生物体有益的基本单元。 − − 一些研究从理论和实验两方面探讨和论证了转录网络中与共同网络模体相关的功能。下面是一些最常见的网络模体及其相关功能。 第657行：
第652行： − ===负自反馈调节(NAR)===+ − [[Image:Autoregulation motif.png|thumb|Schematic representation of an auto-regulation motif]] − One of simplest and most abundant network motifs in ''[[Escherichia coli|E. coli]]'' is negative auto-regulation in which a transcription factor (TF) represses its own transcription. This motif was shown to perform two important functions. The first function is response acceleration. NAR was shown to speed-up the response to signals both theoretically <ref name="zab1">{{cite journal |doi=10.1016/j.jtbi.2011.06.021 |author=Zabet NR |title=Negative feedback and physical limits of genes |journal=Journal of Theoretical Biology |volume= 284|issue=1 |pages=82–91 |date=September 2011 |pmid=21723295 |arxiv=1408.1869 |citeseerx=10.1.1.759.5418 }}</ref> and experimentally. This was first shown in a synthetic transcription network<ref name="ros1">{{cite journal |doi=10.1016/S0022-2836(02)00994-4 |vauthors=Rosenfeld N, Elowitz MB, Alon U |title=Negative autoregulation speeds the response times of transcription networks |journal=J. Mol. Biol. |volume=323 |issue=5 |pages=785–93 |date=November 2002 |pmid=12417193 |citeseerx=10.1.1.126.2604 }}</ref> and later on in the natural context in the SOS DNA repair system of E .coli.<ref name="cam1">{{cite journal |vauthors=Camas FM, Blázquez J, Poyatos JF |title=Autogenous and nonautogenous control of response in a genetic network |journal=Proc. Natl. Acad. Sci. U.S.A. |volume=103 |issue=34 |pages=12718–23 |date=August 2006 |pmid=16908855 |pmc=1568915 |doi=10.1073/pnas.0602119103 |bibcode=2006PNAS..10312718C }}</ref> The second function is increased stability of the auto-regulated gene product concentration against stochastic noise, thus reducing variations in protein levels between different cells.<ref name="bec1">{{cite journal |vauthors=Becskei A, Serrano L |title=Engineering stability in gene networks by autoregulation |journal=Nature |volume=405 |issue=6786 |pages=590–3 |date=June 2000 |pmid=10850721 |doi=10.1038/35014651}}</ref><ref name="dub1">{{cite journal |vauthors=Dublanche Y, Michalodimitrakis K, Kümmerer N, Foglierini M, Serrano L |title=Noise in transcription negative feedback loops: simulation and experimental analysis |journal=Mol. Syst. Biol. |volume=2 |pages=41 |year=2006 |pmid=16883354 |pmc=1681513 |doi=10.1038/msb4100081 |issue=1}}</ref><ref name="shi1">{{cite journal |vauthors=Shimoga V, White J, Li Y, Sontag E, Bleris L |title= Synthetic mammalian transgene negative autoregulation |journal=Mol. Syst. Biol. |volume=9 |pages=670 |year=2013|doi=10.1038/msb.2013.27|pmid= 23736683 |pmc= 3964311 }}</ref> 第684行：
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→完善的模体及其功能
The functions associated with common network motifs in transcription networks were explored and demonstrated by several research projects both theoretically and experimentally. Below are some of the most common network motifs and their associated function.
The functions associated with common network motifs in transcription networks were explored and demonstrated by several research projects both theoretically and experimentally. Below are some of the most common network motifs and their associated function.
===Negative auto-regulation (NAR)===
===Negative auto-regulation (NAR)===
One of simplest and most abundant network motifs in ''[[Escherichia coli|E. coli]]'' is negative auto-regulation in which a transcription factor (TF) represses its own transcription. This motif was shown to perform two important functions. The first function is response acceleration. NAR was shown to speed-up the response to signals both theoretically <ref name="zab1">{{cite journal |doi=10.1016/j.jtbi.2011.06.021 |author=Zabet NR |title=Negative feedback and physical limits of genes |journal=Journal of Theoretical Biology |volume= 284|issue=1 |pages=82–91 |date=September 2011 |pmid=21723295 |arxiv=1408.1869 |citeseerx=10.1.1.759.5418 }}</ref> and experimentally. This was first shown in a synthetic transcription network<ref name="ros1">{{cite journal |doi=10.1016/S0022-2836(02)00994-4 |vauthors=Rosenfeld N, Elowitz MB, Alon U |title=Negative autoregulation speeds the response times of transcription networks |journal=J. Mol. Biol. |volume=323 |issue=5 |pages=785–93 |date=November 2002 |pmid=12417193 |citeseerx=10.1.1.126.2604 }}</ref> and later on in the natural context in the SOS DNA repair system of E .coli.<ref name="cam1">{{cite journal |vauthors=Camas FM, Blázquez J, Poyatos JF |title=Autogenous and nonautogenous control of response in a genetic network |journal=Proc. Natl. Acad. Sci. U.S.A. |volume=103 |issue=34 |pages=12718–23 |date=August 2006 |pmid=16908855 |pmc=1568915 |doi=10.1073/pnas.0602119103 |bibcode=2006PNAS..10312718C }}</ref> The second function is increased stability of the auto-regulated gene product concentration against stochastic noise, thus reducing variations in protein levels between different cells.<ref name="bec1">{{cite journal |vauthors=Becskei A, Serrano L |title=Engineering stability in gene networks by autoregulation |journal=Nature |volume=405 |issue=6786 |pages=590–3 |date=June 2000 |pmid=10850721 |doi=10.1038/35014651}}</ref><ref name="dub1">{{cite journal |vauthors=Dublanche Y, Michalodimitrakis K, Kümmerer N, Foglierini M, Serrano L |title=Noise in transcription negative feedback loops: simulation and experimental analysis |journal=Mol. Syst. Biol. |volume=2 |pages=41 |year=2006 |pmid=16883354 |pmc=1681513 |doi=10.1038/msb4100081 |issue=1}}</ref><ref name="shi1">{{cite journal |vauthors=Shimoga V, White J, Li Y, Sontag E, Bleris L |title= Synthetic mammalian transgene negative autoregulation |journal=Mol. Syst. Biol. |volume=9 |pages=670 |year=2013|doi=10.1038/msb.2013.27|pmid= 23736683 |pmc= 3964311 }}</ref>
One of simplest and most abundant network motifs in ''[[Escherichia coli|E. coli]]'' is negative auto-regulation in which a transcription factor (TF) represses its own transcription. This motif was shown to perform two important functions. The first function is response acceleration. NAR was shown to speed-up the response to signals both theoretically <ref name="zab1">{{cite journal |doi=10.1016/j.jtbi.2011.06.021 |author=Zabet NR |title=Negative feedback and physical limits of genes |journal=Journal of Theoretical Biology |volume= 284|issue=1 |pages=82–91 |date=September 2011 |pmid=21723295 |arxiv=1408.1869 |citeseerx=10.1.1.759.5418 }}</ref> and experimentally. This was first shown in a synthetic transcription network<ref name="ros1">{{cite journal |doi=10.1016/S0022-2836(02)00994-4 |vauthors=Rosenfeld N, Elowitz MB, Alon U |title=Negative autoregulation speeds the response times of transcription networks |journal=J. Mol. Biol. |volume=323 |issue=5 |pages=785–93 |date=November 2002 |pmid=12417193 |citeseerx=10.1.1.126.2604 }}</ref> and later on in the natural context in the SOS DNA repair system of E .coli.<ref name="cam1">{{cite journal |vauthors=Camas FM, Blázquez J, Poyatos JF |title=Autogenous and nonautogenous control of response in a genetic network |journal=Proc. Natl. Acad. Sci. U.S.A. |volume=103 |issue=34 |pages=12718–23 |date=August 2006 |pmid=16908855 |pmc=1568915 |doi=10.1073/pnas.0602119103 |bibcode=2006PNAS..10312718C }}</ref> The second function is increased stability of the auto-regulated gene product concentration against stochastic noise, thus reducing variations in protein levels between different cells.<ref name="bec1">{{cite journal |vauthors=Becskei A, Serrano L |title=Engineering stability in gene networks by autoregulation |journal=Nature |volume=405 |issue=6786 |pages=590–3 |date=June 2000 |pmid=10850721 |doi=10.1038/35014651}}</ref><ref name="dub1">{{cite journal |vauthors=Dublanche Y, Michalodimitrakis K, Kümmerer N, Foglierini M, Serrano L |title=Noise in transcription negative feedback loops: simulation and experimental analysis |journal=Mol. Syst. Biol. |volume=2 |pages=41 |year=2006 |pmid=16883354 |pmc=1681513 |doi=10.1038/msb4100081 |issue=1}}</ref><ref name="shi1">{{cite journal |vauthors=Shimoga V, White J, Li Y, Sontag E, Bleris L |title= Synthetic mammalian transgene negative autoregulation |journal=Mol. Syst. Biol. |volume=9 |pages=670 |year=2013|doi=10.1038/msb.2013.27|pmid= 23736683 |pmc= 3964311 }}</ref>
===Positive auto-regulation (PAR)===
===Positive auto-regulation (PAR)===
===Dense overlapping regulons (DOR)===
===Dense overlapping regulons (DOR)===
This motif occurs in the case that several regulators combinatorially control a set of genes with diverse regulatory combinations. This motif was found in ''[[Escherichia coli|E. coli]]'' in various systems such as carbon utilization, anaerobic growth, stress response and others.<ref name="she1"/><ref name="boy1"/> In order to better understand the function of this motif one has to obtain more information about the way the multiple inputs are integrated by the genes. Kaplan ''et al.''<ref name="kap2">{{cite journal |vauthors=Kaplan S, Bren A, Zaslaver A, Dekel E, Alon U |title=Diverse two-dimensional input functions control bacterial sugar genes |journal=Mol. Cell |volume=29 |issue=6 |pages=786–92 |date=March 2008 |pmid=18374652 |pmc=2366073 |doi=10.1016/j.molcel.2008.01.021 }}</ref> has mapped the input functions of the sugar utilization genes in ''[[Escherichia coli|E. coli]]'', showing diverse shapes.
This motif occurs in the case that several regulators combinatorially control a set of genes with diverse regulatory combinations. This motif was found in ''[[Escherichia coli|E. coli]]'' in various systems such as carbon utilization, anaerobic growth, stress response and others.<ref name="she1"/><ref name="boy1"/> In order to better understand the function of this motif one has to obtain more information about the way the multiple inputs are integrated by the genes. Kaplan ''et al.''<ref name="kap2">{{cite journal |vauthors=Kaplan S, Bren A, Zaslaver A, Dekel E, Alon U |title=Diverse two-dimensional input functions control bacterial sugar genes |journal=Mol. Cell |volume=29 |issue=6 |pages=786–92 |date=March 2008 |pmid=18374652 |pmc=2366073 |doi=10.1016/j.molcel.2008.01.021 }}</ref> has mapped the input functions of the sugar utilization genes in ''[[Escherichia coli|E. coli]]'', showing diverse shapes.
==完善的模体及其功能==
==完善的模体及其功能==