Team:Hong Kong HKUST/riboregulator/regulatory RNAs catalog

From 2014.igem.org

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<h2>RNA devices catalog</h2>
<h2>RNA devices catalog</h2>
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<p>(The page was created as part of iGEM 2014 HKUST team's effort in Project Riboregulator to catalog existing regulatory RNAs. Over the years, the number of regulatory RNAs in Part Registry has steadily increased over time and many has been made available to end users. Based on different mode actions and natures of regulatory RNAs, they can be grouped into different categories. However, the Part Registry currently does not have a catalog page, categorizing methods or guidelines to organize and curate existing regulatory RNAs. Some of them are grouped under type &quot;RNA&quot;, while others are not. This was not useful who looking up and utilizing those regulatory RNAs.
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<p>(The page was created as part of iGEM 2014 HKUST team's effort in <a href="http://2014.igem.org/Team:Hong_Kong_HKUST/riboregulator/characterization">"Project Riboregulator"</a> to catalog existing regulatory RNAs. Over the years, the number of regulatory RNAs in Part Registry has steadily increased over time and many has been made available to end users. Based on different mode actions and natures of regulatory RNAs, they can be grouped into different categories. However, the Part Registry currently does not have a catalog page, categorizing methods or guidelines to organize and curate existing regulatory RNAs. Some of them are grouped under type &quot;RNA&quot;, while others are not. This is not useful for looking up and utilizing them.
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<br><br>We would like to solve this problem by grouping RNA devices according
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to the natures and functions. We are designing a list of category tags as well as a guideline for automated display of regulatory RNAs on this page. By doing so, we hope that we can assist other users to find and use those parts efficiently.
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<br><br>
<br><br>
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This page was written in compliance with Part Registry's format for general Catalog Pages. Currently, the information is uploaded manually because we have yet to submit our suggestions to iGEM HQ. Upon approval of suggestions, we will continue to tag existing regulatory RNAs and complete the page. We welcome and encourage constant update and adoption of this page in the future.)
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We would like to solve this problem by designing a list of category tags as well as a guideline, so that automated display of regulatory RNAs by the <parttable> function can be facilitated. By doing so, we hope that we can assist other users to find and use those parts efficiently.
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<br><br>
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</p>
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This page was written in compliance with Part Registry's format for general Catalog Pages. Currently, the information is uploaded manually because we have yet to submit our suggestions to iGEM HQ. Upon approval, we will tag existing regulatory RNAs and complete the page. Being part of the cross-cohort "Project Riboregulator", the page is expected to be completed by Spring 2015. We welcome and encourage constant update and adoption of this page in the future.)</p>
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Revision as of 08:04, 17 October 2014



RNA devices catalog

(The page was created as part of iGEM 2014 HKUST team's effort in "Project Riboregulator" to catalog existing regulatory RNAs. Over the years, the number of regulatory RNAs in Part Registry has steadily increased over time and many has been made available to end users. Based on different mode actions and natures of regulatory RNAs, they can be grouped into different categories. However, the Part Registry currently does not have a catalog page, categorizing methods or guidelines to organize and curate existing regulatory RNAs. Some of them are grouped under type "RNA", while others are not. This is not useful for looking up and utilizing them.

We would like to solve this problem by designing a list of category tags as well as a guideline, so that automated display of regulatory RNAs by the function can be facilitated. By doing so, we hope that we can assist other users to find and use those parts efficiently.

This page was written in compliance with Part Registry's format for general Catalog Pages. Currently, the information is uploaded manually because we have yet to submit our suggestions to iGEM HQ. Upon approval, we will tag existing regulatory RNAs and complete the page. Being part of the cross-cohort "Project Riboregulator", the page is expected to be completed by Spring 2015. We welcome and encourage constant update and adoption of this page in the future.)

Riboregulator

Riboregulators regulate translation by having two elements, a cis-repressive sequence upstream of RBS in mRNA, and a non-coding RNA device, called trans-activating RNA. The cis-repressive sequence will binds to the 5'UTR, including the RBS by Watson-Crick base pairing, the sequestration of RBS represses translation. While trans-activating RNA will form complementary bases to cis-repressive sequence and exposing RBS for ribosomal binding and allow translation.

Proposed Categories: /RNA/non_coding/post_transcriptional/Riboregulator

Part number Description Designer
Delft 2009 BBa_K175029 Weak lock
Delft 2009 BBa_K175030 Key for lcok of weak RBS
Delft 2009 BBa_K175030 Medium lock
Delft 2009 BBa_K175030 Key for Medium lock
Delft 2009 BBa_K175034 (Constitutive expression of GFP with weak RBS lock and inducible production of key for the lock Composite of K175029 + K175030
Delft 2009 BBa_K175034 Constitutive expression of GFP with medium RBS lock and inducible production of key for the lock Composite of K175031 + K175032
Caltech 2007 BBa_I759015 cis3-repressed, tet-regulated YFP
Caltech 2007 BBa_I759016 cis4-repressed, tet-regulated YFP
Caltech 2007 BBa_I759020 cis8-repressed, tet-regulated YFP
Caltech 2007 BBa_I759027 cis3-repressed, tet-regulated Q
Caltech 2007 BBa_I759028 cis4-repressed, tet-regulated Q
Caltech 2007 BBa_I759014 (cis2-repressed, tet-regulated YFP
Caltech 2007 BBa_I759017 cis5-repressed, tet-regulated YFP
Caltech 2007 BBa_I759018 cis6-repressed, tet-regulated YFP
Caltech 2007 BBa_I759019 cis7-repressed, tet-regulated YFP
Caltech 2007 BBa_I759013 cis1-repressed, tet-regulated YFP
Caltech 2007 BBa_I759032 Ptet_cis1_YFP
Caltech 2007 BBa_I759034 Ptet_cis2_YFP
Caltech 2007 BBa_I759036 Ptet_cis3_YFP
Caltech 2007 BBa_I759038 Ptet_cis4_YFP
Caltech 2007 BBa_I759040 Ptet_cis5_YFP
Caltech 2007 BBa_I759042 Ptet_cis6_YFP
Caltech 2007 BBa_I759044 Ptet_cis7_YFP
Caltech 2007 BBa_I759046 Ptet_cis8_YFP
Caltech 2007 BBa_I759023 pBAD-trans2
Caltech 2007 BBa_I759022 pBAD-trans1
Caltech 2007 BBa_I759024 pBAD-trans3
Caltech 2007 BBa_I759025 pBAD-trans4
Caltech 2007 BBa_I759026 pBAD-trans5
Peking 2007 BBa_I714070 R0040-J23078-pTet-Lock3
Peking 2007 BBa_I714080 [R0040][J23078][E0040][B0015]
Peking 2007 BBa_I714081 R0040-J01010-E0040-B0015
Peking 2007 BBa_I714037 R751+ C600 E.coli cells with traI-R751 knockout
Peking 2007 BBa_I714074 R0010-J23066-pLac-Key3-DblTerm Uses Lock and Key 3 from berkeley
K.U. Leuven 2008 BBa_K145215 FILTER Key (TetR promoter + key)
K.U. Leuven 2008 BBa_K145216 FILTER T7 RNA pol Lock from berkeley
K.U. Leuven 2008 BBa_K145217 FILTER Complete The two previous together
K.U. Leuven 2008 BBa_K145220 INVERTED TIMER
K.U. Leuven 2008 BBa_K145225 RESET lactonase
K.U. Leuven 2008 BBa_K145300 Lactonase controlled by key/lock
K.U. Leuven 2008 BBa_K145301 lacI controlled by key/lock
K.U. Leuven 2008 BBa_K145302 luxI generator controlled by key/lock
K.U. Leuven 2008 BBa_K145303 GFP generator controlled by key/lock
K.U. Leuven 2008 BBa_K145003 T7 PoPS -> RiboKey 3d
K.U. Leuven 2008 BBa_K145004 T7 PoPS + RiboLock |> LuxI
K.U. Leuven 2008 BBa_K145005 T7 PoPS + PR -> cI
K.U. Leuven 2008 BBa_K145216 FILTER T7 RNA pol
K.U. Leuven 2008 BBa_K145251 OLD RESET lactonase
K.U. Leuven 2008 BBa_K145253 OLD INVERTIMER Part 1
K.U. Leuven 2008 BBa_K145255 NEW INVERTIMER part 1
K.U. Leuven 2008 BBa_K145264 test FILTER (new)
K.U. Leuven 2008 BBa_K145265 test FILTER (old)
K.U. Leuven 2008 BBa_K145271 GFP regulated by AND-gate
K.U. Leuven 2008 BBa_K145272 GFP regulated by AND-gate
K.U. Leuven 2008 BBa_K145275 T7 polymerase generator under TetR repressible promoter (filter)
K.U. Leuven 2008 BBa_K145276 T7 polymerase generator under TetR repressible promoter
K.U. Leuven 2008 BBa_K145277 T7 DNA polymerase regulated by lock
K.U. Leuven 2008 BBa_K145278 T7 DNA polymerase regulated by [lock3d]
K.U. Leuven 2009 BBa_K238004 Vanillin synthesis
K.U. Leuven 2009 BBa_K238006 Short version of vanillin synthesis
K.U. Leuven 2009 BBa_K238012 short version II of vanillin synthesis
Groningen 2011 BBa_K607005 short version II of vanillin synthesis
Groningen 2011 BBa_K607000 PhybB_taRNA
VictoriaBC 2009 BBa_K235010 [K145303] (ribokey-controlled GFP generator)
VictoriaBC 2009 BBa_K235000 [R0010][J23066] (pLac+ribokey+stop)
VictoriaBC 2009 BBa_K235001 [J23102][J23066] (constitutive promoter+ribokey+stop)
VictoriaBC 2009 BBa_K235009 [J23102][J23032] (constitutive promoter+ribolocked RBS)
VictoriaBC 2009 BBa_K235011 [K235009][K235005] (ribokey-controlled mCherry generator)
VictoriaBC 2009 BBa_K235013 [K145303][K235000] (ribokey-mediated pLac-controlled GFP reporter)
VictoriaBC 2009 BBa_K235014 [K145303][K235001] (ribokey-mediated GFP generator)
VictoriaBC 2009 BBa_K235016 [I0500][J23032] (pAra+ribolocked RBS)
VictoriaBC 2009 BBa_K235019 [K235016][K235003] (ribokey-mediated pAra-controlled lambda repressor generator)
VictoriaBC 2009 BBa_K235021 [K235009][K235003] (ribokey-mediated lambda repressor generator)
VictoriaBC 2009 BBa_K235022 [K235018][K235019] (mCherry generator, pAra-controlled ribokey-mediated signal inversion)
VictoriaBC 2009 BBa_K235024 [K235018][K235021] (mCherry generator, ribokey-mediated signal inversion)
VictoriaBC 2009 BBa_K235025 [K235022][K235000] (NAND gate, pAra and pLac input signal control, mCherry output signal)
VictoriaBC 2009 BBa_K235026 [K235022][K235001] (NAND gate control test, pLac positive control)
VictoriaBC 2009 BBa_K235027 [K235024][K235000] (NAND gate control test, arabinose positive control)
VictoriaBC 2009 BBa_K235028 [K235024][K235001] (NAND gate control test, positive control)
Melborne2008 BBa_K085000 (lacI)promoter->key3c
Melborne2008 BBa_K085002 pTet->lock3d->GFP
Calgary 2007 BBa_I737003 OmpF controlled RNA Key
Calgary 2007 BBa_I737006 Temperature induced repression/activation of an RNA key
Calgary 2007 BBa_I737005 AHL and RNA lock controlled AraC

Riboswitch

A riboswitch is a segment on mRNA that have the ability to detect small molecules or temperature, and regulate gene expression in on or off manner. Riboswitches usually contain a region for binding of small molecules, as known as sensor domain, and a region for gene regulation, as known as regulatory domain.In the presence of suitable ligand in the sensor domain, the structure of riboswitch will change. This change in conformation of riboswitch may give various action including translation inhibition or mRNA degradation.

Part number Description Designer
Delft 2009 BBa_K175029 Weak lock
Delft 2009 BBa_K175030 Key for lcok of weak RBS
Delft 2009 BBa_K175030 Medium lock
Delft 2009 BBa_K175030 Key for Medium lock
Delft 2009 BBa_K175034 (Constitutive expression of GFP with weak RBS lock and inducible production of key for the lock Composite of K175029 + K175030
Delft 2009 BBa_K175034 Constitutive expression of GFP with medium RBS lock and inducible production of key for the lock Composite of K175031 + K175032
Caltech 2007 BBa_I759015 cis3-repressed, tet-regulated YFP
Caltech 2007 BBa_I759016 cis4-repressed, tet-regulated YFP
Caltech 2007 BBa_I759020 cis8-repressed, tet-regulated YFP
Caltech 2007 BBa_I759027 cis3-repressed, tet-regulated Q

RNA-IN-RNA-OUT

RNA-OUT is a small non-coding RNA that works at RNA level . RNA-OUT will bind to 5'UTR, which include RBS, of mRNA and prevents ribosome from binding to mRNA to inhibit translation of downstream gene. RNA-IN is also a non-coding RNA that is antisense to RNA-OUT and the binding of RNA-IN and RNA-OUT will prevent RNA-OUT from binding to mRNA, thus allowing ribosome to bind to mRNA and initiate translation.

Part number Description Designer
Delft 2009 BBa_K175029 Weak lock
Delft 2009 BBa_K175030 Key for lcok of weak RBS
Delft 2009 BBa_K175030 Medium lock
Delft 2009 BBa_K175030 Key for Medium lock
Delft 2009 BBa_K175034 (Constitutive expression of GFP with weak RBS lock and inducible production of key for the lock Composite of K175029 + K175030
Delft 2009 BBa_K175034 Constitutive expression of GFP with medium RBS lock and inducible production of key for the lock Composite of K175031 + K175032
Caltech 2007 BBa_I759015 cis3-repressed, tet-regulated YFP
Caltech 2007 BBa_I759016 cis4-repressed, tet-regulated YFP
Caltech 2007 BBa_I759020 cis8-repressed, tet-regulated YFP
Caltech 2007 BBa_I759027 cis3-repressed, tet-regulated Q

Small interfering RNAs (siRNAs)

siRNAs usually involved in RNA interference pathway. siRNA s are produced by "dicing" long double stranded RNA into 21-nucleotides small fragments. The siRNAs will then bind to a protein and one strand of siRNA is removed. Then siRNA, which have complementary base pairs with its target mRNA, will binds to target mRNA. The binding of siRNA usually causes the degradation of target mRNA, result in inhibition of gene expression.

Part number Description Designer
Delft 2009 BBa_K175029 Weak lock
Delft 2009 BBa_K175030 Key for lcok of weak RBS
Delft 2009 BBa_K175030 Medium lock
Delft 2009 BBa_K175030 Key for Medium lock
Delft 2009 BBa_K175034 (Constitutive expression of GFP with weak RBS lock and inducible production of key for the lock Composite of K175029 + K175030
Delft 2009 BBa_K175034 Constitutive expression of GFP with medium RBS lock and inducible production of key for the lock Composite of K175031 + K175032
Caltech 2007 BBa_I759015 cis3-repressed, tet-regulated YFP
Caltech 2007 BBa_I759016 cis4-repressed, tet-regulated YFP
Caltech 2007 BBa_I759020 cis8-repressed, tet-regulated YFP
Caltech 2007 BBa_I759027 cis3-repressed, tet-regulated Q

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