Team:Hong Kong HKUST/riboregulator/regulatory RNAs catalog
From 2014.igem.org
Catalog for regulatory RNAs
(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 <parttable> 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 far from complete and is expected to take shape by Spring 2015. We welcome and encourage constant update and adoption of this page in the future.)
Riboregulator
Riboregulators regulate translation by two elements: a cis-repressive sequence upstream of RBS in mRNA, and a ncRNA 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. Trans-activating RNA can form complementary bases to cis-repressive sequence and expose the RBS for ribosomal binding, allowing translation to occur.
Designer | Part Number | Description |
---|---|---|
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 |
RNA Aptamer
A RNA aptamer is any RNA molecule that can fold into a tertiary confirmation that binds with strong affinity and high specificity to small molecules through non-Watson-Crick base pairing.
Designer | Part Number | Description |
---|
Single-guide RNA (sgRNA)
sgRNAs work in the CRISPR/Cas system. They are constructed by fusing functional domains of CRISPR RNA (crRNA) and trans-acting crRNA (tracrRNA) together through RNA linkers. They associate with Cas proteins or their derivatives and guide them to DNA with complementarity with the targeting sequence of crRNA.
Designer | Part Number | Description |
---|
RNA-IN / RNA-OUT
RNA-OUT is a small ncRNA that works at the RNA level. RNA-OUT will bind to 5'UTR, which include the RBS of mRNA and prevents the ribosome from binding to mRNA to inhibit translation of downstream gene. RNA-IN is also a ncRNA 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 initiating translation.
Designer | Part Number | Description |
---|
RNA interference (RNAi)
Small interfering RNAs (siRNAs) and micro RNAs (miRNAs) work in the RNA interference (RNAi) pathway. siRNAs are usually produced by "dicing" exogenous, long double stranded RNA into 21-nucleotides small fragments. Whereas miRNAs usually have an endogenous origin and started as hairpin transcripts. They are then processed by Drosha in non-random manner and then by Dicer. siRNAs or miRNAs will then bind to Argonaute in the RNA-induced silencing complex (RISC). The complex then search for RNA targets using the siRNA/miRNA, and in most cases degrades the latter, resulting in inhibition of gene expression.
Reference:
Thomason MK, Storz G.,Bacterial antisense RNAs: how many are there, and what are they doing?, Annual Review of Genetics Vol 44:167±188(2010)
Designer | Part Number | Description |
---|
Riboswitch
A riboswitch is a segment on the mRNA that has the ability to detect small molecules or temperatures, and regulates gene expression in an on or off manner. Riboswitches usually contain sensor domains for binding of small molecules and regulatory domains for gene regulation. Riboswitches are therefore also aptamers in nature. Upon binding of a suitable ligand in the sensor domain, riboswitches undergo conformational changes that can lead to different outcomes like translation inhibition or mRNA degradation.
Designer | Part Number | Description |
---|
Ribozyme
A ribozyme is a RNA molecule with intrinsic catalytic activity, usually cleavage and ligation activity
Designer | Part Number | Description |
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Aptazyme
A RNA aptazyme are RNAs that carry properties from both aptamer and ribozyme. It is capable of sensing small molecules. Upon activation by a ligand, it can trigger ribozyme-mediated cleavage.
The aptamer and ribozyme domain MUST be Functionally related to be categorize as aptazyme, linkage of aptamer and ribozyme alone which results in no functional relation MUST be regarded as a composite device with aptamer and ribozyme only.
Designer | Part Number | Description |
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pT181
pT181 is a special class of ncRNAs derived from elements in Staphylococcus aureus pathogenicity plasmid pT181. A specific 5’ UTR region would normally form an anti-termination loop. Upon interacting with a pT181-RNAi, a premature terminator loop 5’ to the CDS will form and result in early termination before the mRNA can be completely transcribed.
Designer | Part Number | Description |
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Complex
This category contains ncRNA with dual or more functions resulting from combining 2 or multiple natures / functions of existing ncRNAs.
Designer | Part Number | Description |
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Target sequence
This category deals with segments of ncRNAs that are purposefully designed to serve as recognizable targets by other ncRNAs.
Designer | Part Number | Description |
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Other
Not belongs to any type of device listed above.
Designer | Part Number | Description |
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