Mir-96 microRNA: Difference between revisions

microRNA mir-96
microRNA mir-96
	Predicted secondary structure and sequence conservation of mir-96
Identifiers
Symbol	mir-96
Alt. Symbols	MIR96
Rfam	RF00669
miRBase	MI0000098
miRBase family	MIPF0000072
Other data
RNA type	Gene; miRNA
Domain(s)	Eukaryota
GO	GO:0035068 GO:0035195
SO	SO:0001244
PDB structures	PDBe

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miR-96 microRNA precursor is a small non-coding RNA that regulates gene expression. microRNAs are transcribed as ~80 nucleotide precursors and subsequently processed by the Dicer enzyme to give a ~23 nucleotide products. In this case the mature sequence comes from the 5′ arm of the precursor. ^[1] The mature products are thought to have regulatory roles through complementarity to mRNA.

miR-96 is thought to be conserved within Nephrozoa, i.e. the Deuterostomes and Protostomes. ^[2]

Variation within the seed region of mature miR-96 has been associated with autosomal dominant, progressive hearing loss in humans and mice. The homozygous mutant mice were profoundly deaf, showing no cochlear responses. Heterozygous mice and humans progressively lose the ability to hear. ^[3] ^[4] ^[5] Five genes, of 132 predicted targets, have been experimentally validated as targets of miR-96: Aqp5, Celsr2, Myrip, Odf2 and Ryk.^[4]

Microarray analysis of 4-day old wildtype and mutant mice showed that in the 3′ UTR of upregulated genes, there was a significant enrichment in heptamers complementary to miR-96, implying that miR-96 normally affects a wide range of target genes, and that the mutation results in a loss of normal targets. Among the downregulated genes, there is a significant enrichment in heptamers complementary to the mutant miR-96, so the mutant miR-96 has gained novel targets.^[4] Among the downregulated genes were five of particular interest; Ocm, Pitpnm1, Prestin, Ptprq and Gfi1, all of which are strongly and specifically expressed in hair cells. Mice mutant for the latter three exhibit deafness and hair cell degeneration. ^[6] ^[7] ^[8]

References

^ Mourelatos Z, Dostie J, Paushkin S, Sharma A, Charroux B, Abel L, Rappsilber J, Mann M, Dreyfuss G (2002). "miRNPs: a novel class of ribonucleoproteins containing numerous microRNAs". Genes Dev. 16 (6): 720–728. doi:10.1101/gad.974702. PMC 155365. PMID 11914277.
^ Wheeler BM, Heimberg AM, Moy VN, Sperling EA, Holstein TW, Heber S, Peterson KJ (2009). "The deep evolution of metazoan microRNAs". Evol Dev. 11 (1): 50–68. doi:10.1111/j.1525-142X.2008.00302.x. PMID 19196333.
^ Mencía A, Modamio-Høybjør S, Redshaw N, Morín M, Mayo-Merino F, Olavarrieta L, Aguirre LA, del Castillo I, Steel KP, Dalmay T, Moreno F, Moreno-Pelayo MA (2009). "Mutations in the seed region of human miR-96 are responsible for nonsyndromic progressive hearing loss". Nat Genet. 41 (5): 609–613. doi:10.1038/ng.355. PMID 19363479.
^ ^a ^b ^c Lewis MA, Quint E, Glazier AM, Fuchs H, De Angelis MH, Langford C, van Dongen S, Abreu-Goodger C, Piipari M, Redshaw N, Dalmay T, Moreno-Pelayo MA, Enright AJ, Steel KP (2009). "An ENU-induced mutation of miR-96 associated with progressive hearing loss in mice". Nat Genet. 41 (5): 614–618. doi:10.1038/ng.369. PMC 2705913. PMID 19363478.
^ Soukup GA (2009). "Little but loud: Small RNAs have a resounding affect [sic] on ear development". Brain Res. 1277: 104–114. doi:10.1016/j.brainres.2009.02.027. PMC 2700218. PMID 19245798.
^ Liberman MC, Gao J, He DZ, Wu X, Jia S, Zuo J (2002). "Prestin is required for electromotility of the outer hair cell and for the cochlear amplifier". Nature. 419 (6904): 300–304. Bibcode:2002Natur.419..300L. doi:10.1038/nature01059. PMID 12239568.
^ Goodyear RJ, Legan PK, Wright MB, Marcotti W, Oganesian A, Coats SA, Booth CJ, Kros CJ, Seifert RA, Bowen-Pope DF, Richardson GP (2003). "A receptor-like inositol lipid phosphatase is required for the maturation of developing cochlear hair bundles". J Neurosci. 23 (27): 9208–9219. doi:10.1523/jneurosci.23-27-09208.2003. PMC 6740823. PMID 14534255.
^ Wallis D, Hamblen M, Zhou Y, Venken KJ, Schumacher A, Grimes HL, Zoghbi HY, Orkin SH, Bellen HJ (2003). "The zinc finger transcription factor Gfi1, implicated in lymphomagenesis, is required for inner ear hair cell differentiation and survival". Development. 130 (1): 221–232. doi:10.1242/dev.00190. PMID 12441305.

Media reports

External links

[pmid11914277-1] Mourelatos Z, Dostie J, Paushkin S, Sharma A, Charroux B, Abel L, Rappsilber J, Mann M, Dreyfuss G (2002). "miRNPs: a novel class of ribonucleoproteins containing numerous microRNAs". Genes Dev. 16 (6): 720–728. doi:10.1101/gad.974702. PMC 155365. PMID 11914277.

[pmid19196333-2] Wheeler BM, Heimberg AM, Moy VN, Sperling EA, Holstein TW, Heber S, Peterson KJ (2009). "The deep evolution of metazoan microRNAs". Evol Dev. 11 (1): 50–68. doi:10.1111/j.1525-142X.2008.00302.x. PMID 19196333.

[pmid19363479-3] Mencía A, Modamio-Høybjør S, Redshaw N, Morín M, Mayo-Merino F, Olavarrieta L, Aguirre LA, del Castillo I, Steel KP, Dalmay T, Moreno F, Moreno-Pelayo MA (2009). "Mutations in the seed region of human miR-96 are responsible for nonsyndromic progressive hearing loss". Nat Genet. 41 (5): 609–613. doi:10.1038/ng.355. PMID 19363479.

[pmid19363478-4] Lewis MA, Quint E, Glazier AM, Fuchs H, De Angelis MH, Langford C, van Dongen S, Abreu-Goodger C, Piipari M, Redshaw N, Dalmay T, Moreno-Pelayo MA, Enright AJ, Steel KP (2009). "An ENU-induced mutation of miR-96 associated with progressive hearing loss in mice". Nat Genet. 41 (5): 614–618. doi:10.1038/ng.369. PMC 2705913. PMID 19363478.

[pmid19245798-5] Soukup GA (2009). "Little but loud: Small RNAs have a resounding affect [sic] on ear development". Brain Res. 1277: 104–114. doi:10.1016/j.brainres.2009.02.027. PMC 2700218. PMID 19245798.

[pmid12239568-6] Liberman MC, Gao J, He DZ, Wu X, Jia S, Zuo J (2002). "Prestin is required for electromotility of the outer hair cell and for the cochlear amplifier". Nature. 419 (6904): 300–304. Bibcode:2002Natur.419..300L. doi:10.1038/nature01059. PMID 12239568.

[pmid14534255-7] Goodyear RJ, Legan PK, Wright MB, Marcotti W, Oganesian A, Coats SA, Booth CJ, Kros CJ, Seifert RA, Bowen-Pope DF, Richardson GP (2003). "A receptor-like inositol lipid phosphatase is required for the maturation of developing cochlear hair bundles". J Neurosci. 23 (27): 9208–9219. doi:10.1523/jneurosci.23-27-09208.2003. PMC 6740823. PMID 14534255.

[pmid12441305-8] Wallis D, Hamblen M, Zhou Y, Venken KJ, Schumacher A, Grimes HL, Zoghbi HY, Orkin SH, Bellen HJ (2003). "The zinc finger transcription factor Gfi1, implicated in lymphomagenesis, is required for inner ear hair cell differentiation and survival". Development. 130 (1): 221–232. doi:10.1242/dev.00190. PMID 12441305.

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@@ Line 1: / Line 1: @@
+{{Infobox rfam
-{{Rfam_box|acc=RNA_secondary_structure_and_sequence_conservation_for_miR-96|description=mir-96 microRNA precursor family|abbreviation=mir-96|type=Gene; miRNA;|avg_length=78.3|avg_identity=74|ss=Predicted; WAR|se=miRBase; Wilkinson A|type=Gene; miRNA;}}
+| Name = microRNA mir-96
+| image = RNA_secondary_structure_and_sequence_conservation_for_miR-96.jpg
+| width =
+| caption = Predicted [[secondary structure]] and [[sequence conservation]] of mir-96
+| Symbol = mir-96
+| AltSymbols = MIR96
+| Rfam = RF00669
+| miRBase = MI0000098
+| miRBase_family = MIPF0000072
+| RNA_type = [[Gene]]; [[MicroRNA|miRNA]]
+| Tax_domain = [[Eukaryota]]
+| GO = {{GO|0035068}} {{GO|0035195}}
+| SO = {{SO|0001244}}
+| CAS_number =
+| EntrezGene =
+| HGNCid =
+| OMIM =
+| PDB =
+| RefSeq =
+| Chromosome =
+| Arm =
+| Band =
+| LocusSupplementaryData =
+}}__NOTOC__
+'''miR-96 microRNA precursor''' is a small [[non-coding RNA]] that regulates [[gene expression]]. [[microRNAs]] are transcribed as ~80 [[nucleotide]] precursors and subsequently processed by the [[Dicer]] enzyme to give a ~23 nucleotide products. In this case the mature sequence comes from the 5′ arm of the precursor.
-[[Image:MiR-96_sequence_alignment.png|thumb|left|400px|A multiple sequence alignment of precursor miR-96 molecules. Highly conserved nucleotides are coloured in red, less well conserved nucleotides are coloured orange and non-conserved nucleotides are coloured blue or white. The columns corresponding to the mature and seed sequence are indicated above the alignment. The canonical human sequence and the two human variant sequences that are implicated in hearing loss (13G>A and 14C>A) are in the first, second and third rows respectively.]]
+<ref name="pmid11914277">{{cite journal |vauthors=Mourelatos Z, Dostie J, Paushkin S, Sharma A, Charroux B, Abel L, [[Juri Rappsilber|Rappsilber J]], Mann M, Dreyfuss G |title=miRNPs: a novel class of ribonucleoproteins containing numerous microRNAs. |journal=Genes Dev |volume=16 |issue=6 |pages=720–728 |year=2002 |pmid=11914277 |doi=10.1101/gad.974702 |pmc=155365}}</ref>
+The mature products are thought to have regulatory roles through complementarity to mRNA.
+miR-96 is thought to be conserved within [[:species:Nephrozoa|Nephrozoa]], i.e. the [[Deuterostome]]s and [[Protostome]]s.
-'''miR-96 microRNA precursor''' is a small [[non-coding RNA]] that regulates [[gene expression]]. [[microRNAs]] are transcribed as ~80 [[nucleotide]] precursors and subsequently processed by the [[Dicer]] enzyme to give a ~23 nucleotide products. In this case the mature sequence comes from the 5' arm of the precursor.
-<ref name="pmid11914277">{{cite journal |author=Mourelatos Z, Dostie J, Paushkin S, Sharma A, Charroux B, Abel L, Rappsilber J, Mann M, Dreyfuss G |title=miRNPs: a novel class of ribonucleoproteins containing numerous microRNAs. |journal=Genes Dev |volume=16 |issue=6 |pages=720-8 |year=2002 |pmid=11914277}}</ref>
+<ref name="pmid19196333">{{cite journal |vauthors=Wheeler BM, Heimberg AM, Moy VN, Sperling EA, Holstein TW, Heber S, Peterson KJ |title=The deep evolution of metazoan microRNAs. |journal=Evol Dev |volume=11 |issue=1 |pages=50–68 |year= 2009|pmid=19196333 |doi=10.1111/j.1525-142X.2008.00302.x}}</ref>
-The mature products are thought to have regulatory roles through complementarity to mRNA. These microRNAs are expressed specifically in the inner ear and the adult eye.<ref name="pmid16904081">{{cite journal |author=Weston MD, Pierce ML, Rocha-Sanchez S, Beisel KW, Soukup GA |title=MicroRNA gene expression in the mouse inner ear. |journal=Brain Res |volume=1111 |issue=1 |pages=95-104 |year=2006 |pmid=16904081}}</ref><ref name="pmid17597072">{{cite journal |author=Xu S, Witmer PD, Lumayag S, Kovacs B, Valle D |title=MicroRNA (miRNA) transcriptome of mouse retina and identification of a sensory organ-specific miRNA cluster. |journal=J Biol Chem |volume=282 |issue=34 |pages=25053-66 |year=2007 |pmid=17597072}}</ref>
+Variation within the seed region of mature miR-96 has been associated with [[autosomal dominant]], progressive hearing loss in humans and mice. The [[homozygous]] mutant mice were profoundly deaf, showing no [[cochlea]]r responses. [[Zygosity|Heterozygous]] mice and humans progressively lose the ability to hear.
-miR-96 is thought to be conserved within [http://species.wikimedia.org/wiki/Nephrozoa Nephrozoa], i.e. the [[Deuterostome|Deuterostomes]] and [[Protostome|Protostomes]].
-<ref name="pmid19196333">{{cite journal |author=Wheeler BM, Heimberg AM, Moy VN, Sperling EA, Holstein TW, Heber S, Peterson KJ |title=The deep evolution of metazoan microRNAs. |journal=Evol Dev |volume=11 |issue=1 |pages=50-68 |year= |pmid=19196333}}</ref>
+<ref name="pmid19363479">{{cite journal |vauthors=Mencía A, Modamio-Høybjør S, Redshaw N, Morín M, Mayo-Merino F, Olavarrieta L, Aguirre LA, del Castillo I, Steel KP, Dalmay T, Moreno F, Moreno-Pelayo MA |title=Mutations in the seed region of human miR-96 are responsible for nonsyndromic progressive hearing loss. |journal=Nat Genet |volume=41 |issue=5 |pages=609–613 |year=2009 |pmid=19363479 |doi=10.1038/ng.355}}</ref>
+<ref name="pmid19363478">{{cite journal |vauthors=Lewis MA, Quint E, Glazier AM, Fuchs H, De Angelis MH, Langford C, van Dongen S, Abreu-Goodger C, Piipari M, Redshaw N, Dalmay T, Moreno-Pelayo MA, Enright AJ, Steel KP |title=An ENU-induced mutation of miR-96 associated with progressive hearing loss in mice. |journal=Nat Genet |volume=41 |issue=5 |pages=614–618 |year=2009 |pmid=19363478 |doi=10.1038/ng.369 |pmc=2705913}}</ref>
+<ref name="pmid19245798">{{cite journal |author=Soukup GA |title=Little but loud: Small RNAs have a resounding affect [sic] on ear development. |journal=Brain Res |volume= 1277|pages= 104–114|year=2009 |pmid=19245798 |doi=10.1016/j.brainres.2009.02.027 |pmc=2700218}}</ref>
+Five genes, of 132 predicted targets, have been experimentally validated as targets of miR-96: [[AQP5|Aqp5]], [[CELSR2|Celsr2]], [[Myrip]], [[ODF2|Odf2]] and [[Related to receptor tyrosine kinase|Ryk]].<ref name="pmid19363478"/>
+[[DNA microarray|Microarray]] analysis of 4-day old wildtype and mutant mice showed that in the [[Three prime untranslated region|3′ UTR]] of upregulated genes, there was a significant enrichment in heptamers complementary to miR-96, implying that miR-96 normally affects a wide range of target genes, and that the mutation results in a loss of normal targets. Among the downregulated genes, there is a significant enrichment in heptamers complementary to the mutant miR-96, so the mutant miR-96 has gained novel targets.<ref name="pmid19363478"/> Among the downregulated genes were five of particular interest; [[LOC4951|Ocm]], [[PITPNM1|Pitpnm1]], [[Prestin]], [[PTPRR|Ptprq]] and [[GFI1|Gfi1]], all of which are strongly and specifically expressed in hair cells. Mice mutant for the latter three exhibit deafness and hair cell degeneration.
-Variation within the seed region of mature miR-96 has been associated with [[autosomal dominant]], progressive hearing loss in humans and mice. The [[homozygous]] mutant mice were profoundly deaf, showing no [[Cochlea|cochlear]] responses. [[Zygosity|Heterozygous]] mice and humans progressively lose the ability to hear.
-<ref name="pmid19363479">{{cite journal |author=Mencía A, Modamio-Høybjør S, Redshaw N, Morín M, Mayo-Merino F, Olavarrieta L, Aguirre LA, del Castillo I, Steel KP, Dalmay T, Moreno F, Moreno-Pelayo MA |title=Mutations in the seed region of human miR-96 are responsible for nonsyndromic progressive hearing loss. |journal=Nat Genet |volume=41 |issue=5 |pages=609-13 |year=2009 |pmid=19363479}}</ref>
+<ref name="pmid12239568">{{cite journal |vauthors=Liberman MC, Gao J, He DZ, Wu X, Jia S, Zuo J |title=Prestin is required for electromotility of the outer hair cell and for the cochlear amplifier. |journal=Nature |volume=419 |issue=6904 |pages=300–304 |year=2002 |pmid=12239568 |doi=10.1038/nature01059|bibcode=2002Natur.419..300L }}</ref>
-<ref name="pmid19363478">{{cite journal |author=Lewis MA, Quint E, Glazier AM, Fuchs H, De Angelis MH, Langford C, van Dongen S, Abreu-Goodger C, Piipari M, Redshaw N, Dalmay T, Moreno-Pelayo MA, Enright AJ, Steel KP |title=An ENU-induced mutation of miR-96 associated with progressive hearing loss in mice. |journal=Nat Genet |volume=41 |issue=5 |pages=614-8 |year=2009 |pmid=19363478}}</ref>
+<ref name="pmid14534255">{{cite journal |vauthors=Goodyear RJ, Legan PK, Wright MB, Marcotti W, Oganesian A, Coats SA, Booth CJ, Kros CJ, Seifert RA, Bowen-Pope DF, Richardson GP |title=A receptor-like inositol lipid phosphatase is required for the maturation of developing cochlear hair bundles. |journal=J Neurosci |volume=23 |issue=27 |pages=9208–9219 |year=2003 |pmid=14534255 |doi=10.1523/jneurosci.23-27-09208.2003|doi-access=free |pmc=6740823 }}</ref>
-<ref name="pmid19245798">{{cite journal |author=Soukup GA |title=Little but loud: Small RNAs have a resounding affect on ear development. |journal=Brain Res |volume= |issue= |pages= |year=2009 |pmid=19245798}}</ref>
+<ref name="pmid12441305">{{cite journal |doi=10.1242/dev.00190|author-link7=Huda Zoghbi |vauthors=Wallis D, Hamblen M, Zhou Y, Venken KJ, Schumacher A, Grimes HL, Zoghbi HY, Orkin SH, Bellen HJ |title=The zinc finger transcription factor Gfi1, implicated in lymphomagenesis, is required for inner ear hair cell differentiation and survival. |journal=Development |volume=130 |issue=1 |pages=221–232 |year=2003 |pmid=12441305|doi-access=free }}</ref>
+[[File:MiR-96 sequence alignment.png|thumb|450px|left|A multiple sequence alignment of precursor miR-96 molecules. Highly conserved nucleotides are coloured in red, less well conserved nucleotides are coloured orange and non-conserved nucleotides are coloured blue or white. The columns corresponding to the mature and seed sequence are indicated above the alignment. The canonical human sequence and the two human variant sequences that are implicated in hearing loss (13G>A and 14C>A) are in the first, second and third rows respectively.]]
+{{clear|left}}
 ==References==
+{{reflist|30em}}
-{{reflist|2}}
 ==Media reports==
 * [http://www.sanger.ac.uk/Info/Press/2009/090412.shtml Sanger press release]
 * [http://www.medicalnewstoday.com/articles/145551.php New Insights Into Progressive Hearing Loss]
+==Further reading==
+{{refbegin | 2}}
+*{{cite journal   |vauthors=Kondkar AA, Bray MS, Leal SM, etal |title=VAMP8/endobrevin is overexpressed in hyperreactive human platelets: suggested role for platelet microRNA. |journal=J. Thromb. Haemost. |volume=8 |issue= 2 |pages= 369–378 |year= 2010 |pmid= 19943878 |doi= 10.1111/j.1538-7836.2009.03700.x |pmc=3312605}}
+*{{cite journal   |vauthors=Modamio-Høybjør S, Moreno-Pelayo MA, Mencía A, etal |title=A novel locus for autosomal dominant nonsyndromic hearing loss, DFNA50, maps to chromosome 7q32 between the DFNB17 and DFNB13 deafness loci. |journal=J. Med. Genet. |volume=41 |issue= 2 |pages= 14e–14 |year= 2004 |pmid= 14757864  |pmc=1735673 |doi=10.1136/jmg.2003.012500  }}
+*{{cite journal  |vauthors=Guttilla IK, White BA |title=Coordinate regulation of FOXO1 by miR-27a, miR-96, and miR-182 in breast cancer cells. |journal=J. Biol. Chem. |volume=284 |issue= 35 |pages= 23204–23216 |year= 2009 |pmid= 19574223  |pmc=2749094 |doi= 10.1074/jbc.M109.031427 |doi-access=free }}
+{{refend}}
 ==External links==
 * {{Rfam|id=RF00669|name=the mir-96 microRNA precursor family}}
-* [http://microrna.sanger.ac.uk/cgi-bin/sequences/mirna_summary.pl?fam=MIPF0000072 miRBase page for the mir-96 microRNA precursor family]
+* [https://archive.today/20121223100628/http://microrna.sanger.ac.uk/cgi-bin/sequences/mirna_summary.pl?fam=MIPF0000072 miRBase page for the mir-96 microRNA precursor family]
-* [http://www.genenames.org/data/hgnc_data.php?hgnc_id=31648 HGNC page for the mir-96 microRNA precursor family]
+* [https://www.genenames.org/data/hgnc_data.php?hgnc_id=31648 HGNC page for the mir-96 microRNA precursor family]
-* [http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=611606 OMIM page for the mir-96 microRNA precursor family]
+* [https://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=611606 OMIM page for the mir-96 microRNA precursor family]
+* [https://www.ncbi.nlm.nih.gov/sites/entrez?Db=gene&Cmd=ShowDetailView&TermToSearch=407053 ENTREZ page for the mir-96 microRNA precursor family]
+{{miRNA precursor families}}
 [[Category:Non-coding RNA]]
-[[Category:microRNA]]
+[[Category:MicroRNA]]
-{{molecular-cell-biology-stub}}

v t e miRNA precursor families
1-100	1 2 3 5 6 7 8/141/200 9/79 10 11 14 15 16 17 19 21 22 23 24 25 26 28 29 30 31 32 33 34 42 46/47/281 48 52 58 61 62 67 71 84 92 96
101-200	101 103/107 122 124 126 127 129 130 132 133 134 135 137 138 141 143 144 145 146 148/152 150 153 154 155 156 160 166 172 181 184 185 186 187 188 190 191 192/215 193 194 196 198 199 200
201-300	202 203 203a 205 208 210 212 214 216 218 219 221 223 224 241 275 277 278 279 281 282 296 299
301-400	301 305 322 326 330 331 337 338 339 340 344 345 346 350 351 361 363 365 367 370 374 383 384 390 394 395 396 397 398 399
401-500	403 408 423 425 430 431 432 433 434 444 448 449 451 452 454 455 474 484 488 489 491 492 497 498 500
501-600	503 504 505 506 529 535 541 542 544 548 549 550 552 558 562 569 572 575 580 584 589 590 592 598
601+	601 605 612 615 612 612 624 625 632 633 636 638 650 652 657 661 663 671 672 675 708 711 720 744 764 765 767 786 802 824 828 854 872 873 874 885 938 939 3180
Other	BART1 BART2 BHRF1-1 BHRF1-2 BHRF1-3 Let-7 Lin-4 Lsy-6