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}}Antisense small RNA are short RNA sequences (about 50-500 nucleotides long) that are complementary to other [[small RNA]] (sRNA) in the cell. <ref>{{Cite journal|last=Bhatt|first=Shantanu|last2=Egan|first2=Marisa|last3=Jenkins|first3=Valerie|last4=Muche|first4=Sarah|last5=El-Fenej|first5=Jihad|date=2016|title=The Tip of the Iceberg: On the Roles of Regulatory Small RNAs in the Virulence of Enterohemorrhagic and Enteropathogenic Escherichia coli|url=https://www.frontiersin.org/articles/10.3389/fcimb.2016.00105/full#B38|journal=Frontiers in Cellular and Infection Microbiology|language=English|volume=6|doi=10.3389/fcimb.2016.00105|issn=2235-2988}}</ref>
}}Antisense small RNA are short RNA sequences (about 50-500 nucleotides long) that are complementary to other [[small RNA]] (sRNA) in the cell. <ref>{{cite journal | vauthors = Bhatt S, Egan M, Jenkins V, Muche S, El-Fenej J | title = Escherichia coli | language = English | journal = Frontiers in Cellular and Infection Microbiology | volume = 6 | pages = 105 | date = 2016 | pmid = 27709103 | pmc = 5030294 | doi = 10.3389/fcimb.2016.00105 }}</ref>


sRNAs can repress [[Translation (biology)|translation]] via complementary base-pairing with their target [[Messenger RNA|mRNA]] sequence.<ref>{{Cite journal|last=Großhans|first=Helge|last2=Filipowicz|first2=Witold|date=January 2008|title=The expanding world of small RNAs|url=https://www.nature.com/articles/451414a|journal=Nature|language=en|volume=451|issue=7177|pages=414–416|doi=10.1038/451414a|issn=1476-4687}}</ref> Anti-sRNAs function by complementary pairing with sRNAs before the mRNA can be bound, thus freeing the mRNA and relieving translation inhibition.<ref name=":0">{{Cite journal|last=Tree|first=Jai J.|last2=Granneman|first2=Sander|last3=McAteer|first3=Sean P.|last4=Tollervey|first4=David|last5=Gally|first5=David L.|date=2014-07-17|title=Identification of Bacteriophage-Encoded Anti-sRNAs in Pathogenic Escherichia coli|url=https://www.cell.com/molecular-cell/abstract/S1097-2765(14)00400-6|journal=Molecular Cell|language=English|volume=55|issue=2|pages=199–213|doi=10.1016/j.molcel.2014.05.006|issn=1097-2765|pmid=24910100}}</ref>
sRNAs can repress [[Translation (biology)|translation]] via complementary base-pairing with their target [[Messenger RNA|mRNA]] sequence.<ref>{{cite journal | vauthors = Grosshans H, Filipowicz W | title = Molecular biology: the expanding world of small RNAs | journal = Nature | volume = 451 | issue = 7177 | pages = 414–6 | date = January 2008 | pmid = 18216846 | doi = 10.1038/451414a | bibcode = 2008Natur.451..414G }}</ref> Anti-sRNAs function by complementary pairing with sRNAs before the mRNA can be bound, thus freeing the mRNA and relieving translation inhibition.<ref name=":0">{{cite journal | vauthors = Tree JJ, Granneman S, McAteer SP, Tollervey D, Gally DL | title = Identification of bacteriophage-encoded anti-sRNAs in pathogenic Escherichia coli | language = English | journal = Molecular Cell | volume = 55 | issue = 2 | pages = 199–213 | date = July 2014 | pmid = 24910100 | pmc = 4104026 | doi = 10.1016/j.molcel.2014.05.006 | url = https://www.cell.com/molecular-cell/abstract/S1097-2765(14)00400-6 }}</ref>


== Function ==
== Function ==
Antisense small RNA are found in all of life including [[Eukaryote|Eukaryotes]], [[Bacteria]] and [[Archaea]].<ref name=":1">{{Cite journal|last=Bernick|first=David L.|last2=Dennis|first2=Patrick P.|last3=Lui|first3=Lauren M.|last4=Lowe|first4=Todd M.|date=2012|title=Diversity of Antisense and Other Non-Coding RNAs in Archaea Revealed by Comparative Small RNA Sequencing in Four Pyrobaculum Species|url=https://www.frontiersin.org/articles/10.3389/fmicb.2012.00231/full|journal=Frontiers in Microbiology|language=English|volume=3|doi=10.3389/fmicb.2012.00231|issn=1664-302X}}</ref><ref>{{Cite journal|last=Figueroa-Bossi|first=Nara|last2=Valentini|first2=Martina|last3=Malleret|first3=Laurette|last4=Bossi|first4=Lionello|date=2009-09-01|title=Caught at its own game: regulatory small RNA inactivated by an inducible transcript mimicking its target|url=http://genesdev.cshlp.org/content/23/17/2004|journal=Genes & Development|language=en|volume=23|issue=17|pages=2004–2015|doi=10.1101/gad.541609|issn=0890-9369|pmid=19638370}}</ref> They are non-coding RNA sequences involved in regulatory processes, metabolism, and aiding [[Transcription (biology)|transcription]].<ref name=":1" />
Antisense small RNA are found in all of life including [[Eukaryote|Eukaryotes]], [[Bacteria]] and [[Archaea]].<ref name=":1">{{cite journal | vauthors = Bernick DL, Dennis PP, Lui LM, Lowe TM | title = Diversity of Antisense and Other Non-Coding RNAs in Archaea Revealed by Comparative Small RNA Sequencing in Four Pyrobaculum Species | language = English | journal = Frontiers in Microbiology | volume = 3 | pages = 231 | date = 2012 | pmid = 22783241 | pmc = 3388794 | doi = 10.3389/fmicb.2012.00231 }}</ref><ref>{{cite journal | vauthors = Figueroa-Bossi N, Valentini M, Malleret L, Fiorini F, Bossi L | title = Caught at its own game: regulatory small RNA inactivated by an inducible transcript mimicking its target | journal = Genes & Development | volume = 23 | issue = 17 | pages = 2004–15 | date = September 2009 | pmid = 19638370 | pmc = 2751969 | doi = 10.1101/gad.541609 }}</ref> They are non-coding RNA sequences involved in regulatory processes, metabolism, and aiding [[Transcription (biology)|transcription]].<ref name=":1" />


Antisense RNA can also be engineered and utilized by scientists to perform experimental functions.<ref>{{Cite journal|last=Rodrigo|first=Guillermo|last2=Prakash|first2=Satya|last3=Cordero|first3=Teresa|last4=Kushwaha|first4=Manish|last5=Jaramillo|first5=Alfonso|date=2016-02-27|title=Functionalization of an Antisense Small RNA|url=http://www.sciencedirect.com/science/article/pii/S0022283615007135|journal=Journal of Molecular Biology|series=Engineering Tools and Prospects in Synthetic Biology|volume=428|issue=5, Part B|pages=889–892|doi=10.1016/j.jmb.2015.12.022|issn=0022-2836}}</ref>
Antisense RNA can also be engineered and utilized by scientists to perform experimental functions.<ref>{{cite journal | vauthors = Rodrigo G, Prakash S, Cordero T, Kushwaha M, Jaramillo A | title = Functionalization of an Antisense Small RNA | journal = Journal of Molecular Biology | volume = 428 | issue = 5 Pt B | pages = 889–92 | date = February 2016 | pmid = 26756967 | pmc = 4819895 | doi = 10.1016/j.jmb.2015.12.022 | series = Engineering Tools and Prospects in Synthetic Biology }}</ref>


== Identification Methods ==
== Identification Methods ==
Numerous studies have been performed to identify potential antisense sRNA candidates. Recent experiments have used [[Northern blot]] analysis and 5'-end mapping to correctly identify potential antisense sRNA candidates.<ref>{{Cite journal|last=Thomason|first=Maureen Kiley|last2=Storz|first2=Gisela|date=2010|title=Bacterial Antisense RNAs: How Many Are There, and What Are They Doing?|url=http://www.annualreviews.org/doi/10.1146/annurev-genet-102209-163523|journal=Annual Review of Genetics|language=en|volume=44|issue=1|pages=167–188|doi=10.1146/annurev-genet-102209-163523|issn=0066-4197|via=}}</ref> In 2019, a new algorithm called APERO was established which allows the detection of small transcripts from paired-end bacterial RNA-seq data. <ref name=":2">{{Cite journal|last=Leonard|first=Simon|last2=Meyer|first2=Sam|last3=Lacour|first3=Stephan|last4=Nasser|first4=William|last5=Hommais|first5=Florence|last6=Reverchon|first6=Sylvie|date=2019-09-05|title=APERO: a genome-wide approach for identifying bacterial small RNAs from RNA-Seq data|url=https://academic.oup.com/nar/article/47/15/e88/5506866|journal=Nucleic Acids Research|language=en|volume=47|issue=15|pages=e88–e88|doi=10.1093/nar/gkz485|issn=0305-1048}}</ref>  [[RNA-Seq|RNA-seq]] is a popular method used for the identification of small RNA. <ref name=":2" /> However, while reliable for eukaryotic sRNA, it remains inaccurate for bacterial sRNA. <ref name=":2" />
Numerous studies have been performed to identify potential antisense sRNA candidates. Recent experiments have used [[Northern blot]] analysis and 5'-end mapping to correctly identify potential antisense sRNA candidates.<ref>{{cite journal | vauthors = Thomason MK, Storz G | title = Bacterial antisense RNAs: how many are there, and what are they doing? | journal = Annual Review of Genetics | volume = 44 | issue = 1 | pages = 167–88 | date = 2010 | pmid = 20707673 | pmc = 3030471 | doi = 10.1146/annurev-genet-102209-163523 }}</ref> In 2019, a new algorithm called APERO was established which allows the detection of small transcripts from paired-end bacterial RNA-seq data. <ref name=":2">{{cite journal | vauthors = Leonard S, Meyer S, Lacour S, Nasser W, Hommais F, Reverchon S | title = APERO: a genome-wide approach for identifying bacterial small RNAs from RNA-Seq data | journal = Nucleic Acids Research | volume = 47 | issue = 15 | pages = e88 | date = September 2019 | pmid = 31147705 | pmc = 6735904 | doi = 10.1093/nar/gkz485 }}</ref>  [[RNA-Seq|RNA-seq]] is a popular method used for the identification of small RNA. <ref name=":2" /> However, while reliable for eukaryotic sRNA, it remains inaccurate for bacterial sRNA. <ref name=":2" />


== Examples ==
== Examples ==

Revision as of 08:41, 19 December 2019

Proposed mechanism for anti-sRNA relief of sRNA mediated translation inhibition. [1]
Anti GcvB sRNA
Predicted secondary structure and sequence conservation Anti GcvB sRNA
Identifiers
RfamRF02702
Other data
Domain(s)Bacteria
GOGO:0045975
SOSO:0000370
PDB structuresPDBe
Anti stx2 sRNA
Predicted secondary structure and sequence conservation Anti stx2 sRNA
Identifiers
RfamRF02703
Other data
Domain(s)Bacteria
GOGO:0045975
SOSO:0000370
PDB structuresPDBe

Antisense small RNA are short RNA sequences (about 50-500 nucleotides long) that are complementary to other small RNA (sRNA) in the cell. [2]

sRNAs can repress translation via complementary base-pairing with their target mRNA sequence.[3] Anti-sRNAs function by complementary pairing with sRNAs before the mRNA can be bound, thus freeing the mRNA and relieving translation inhibition.[1]

Function

Antisense small RNA are found in all of life including Eukaryotes, Bacteria and Archaea.[4][5] They are non-coding RNA sequences involved in regulatory processes, metabolism, and aiding transcription.[4]

Antisense RNA can also be engineered and utilized by scientists to perform experimental functions.[6]

Identification Methods

Numerous studies have been performed to identify potential antisense sRNA candidates. Recent experiments have used Northern blot analysis and 5'-end mapping to correctly identify potential antisense sRNA candidates.[7] In 2019, a new algorithm called APERO was established which allows the detection of small transcripts from paired-end bacterial RNA-seq data. [8]  RNA-seq is a popular method used for the identification of small RNA. [8] However, while reliable for eukaryotic sRNA, it remains inaccurate for bacterial sRNA. [8]

Examples

AsxR

AsxR, previously known as EcOnc02, is an anti-sRNA encoded within the 3' region of the stx2B gene of E.Coli bacteria.[1] It acts to increase expression of the ChuS heme oxygenase via destabilisation of FnrS sRNA[1]. This aids bacterial infection of the animal host gut. [1]

AgvB

AgvB, previously known as EcOnc01, inhibits GcvB sRNA repression.[1] Pathogenicity island associated AgvB aids enterohemorrhagic E. coli growth at the colonized site within the host animal.[1]

References

  1. ^ a b c d e f g Tree JJ, Granneman S, McAteer SP, Tollervey D, Gally DL (July 2014). "Identification of bacteriophage-encoded anti-sRNAs in pathogenic Escherichia coli". Molecular Cell. 55 (2): 199–213. doi:10.1016/j.molcel.2014.05.006. PMC 4104026. PMID 24910100.
  2. ^ Bhatt S, Egan M, Jenkins V, Muche S, El-Fenej J (2016). "Escherichia coli". Frontiers in Cellular and Infection Microbiology. 6: 105. doi:10.3389/fcimb.2016.00105. PMC 5030294. PMID 27709103.{{cite journal}}: CS1 maint: unflagged free DOI (link)
  3. ^ Grosshans H, Filipowicz W (January 2008). "Molecular biology: the expanding world of small RNAs". Nature. 451 (7177): 414–6. Bibcode:2008Natur.451..414G. doi:10.1038/451414a. PMID 18216846.
  4. ^ a b Bernick DL, Dennis PP, Lui LM, Lowe TM (2012). "Diversity of Antisense and Other Non-Coding RNAs in Archaea Revealed by Comparative Small RNA Sequencing in Four Pyrobaculum Species". Frontiers in Microbiology. 3: 231. doi:10.3389/fmicb.2012.00231. PMC 3388794. PMID 22783241.{{cite journal}}: CS1 maint: unflagged free DOI (link)
  5. ^ Figueroa-Bossi N, Valentini M, Malleret L, Fiorini F, Bossi L (September 2009). "Caught at its own game: regulatory small RNA inactivated by an inducible transcript mimicking its target". Genes & Development. 23 (17): 2004–15. doi:10.1101/gad.541609. PMC 2751969. PMID 19638370.
  6. ^ Rodrigo G, Prakash S, Cordero T, Kushwaha M, Jaramillo A (February 2016). "Functionalization of an Antisense Small RNA". Journal of Molecular Biology. Engineering Tools and Prospects in Synthetic Biology. 428 (5 Pt B): 889–92. doi:10.1016/j.jmb.2015.12.022. PMC 4819895. PMID 26756967.
  7. ^ Thomason MK, Storz G (2010). "Bacterial antisense RNAs: how many are there, and what are they doing?". Annual Review of Genetics. 44 (1): 167–88. doi:10.1146/annurev-genet-102209-163523. PMC 3030471. PMID 20707673.
  8. ^ a b c Leonard S, Meyer S, Lacour S, Nasser W, Hommais F, Reverchon S (September 2019). "APERO: a genome-wide approach for identifying bacterial small RNAs from RNA-Seq data". Nucleic Acids Research. 47 (15): e88. doi:10.1093/nar/gkz485. PMC 6735904. PMID 31147705.
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