Difference between revisions of "ENST00000509909.1"

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Please input one-sentence summary here.
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CARMEN, a human super enhancer-associated long noncoding RNA, is a crucial regulator of cardiac specification, differentiation and homeostasis.
  
 
==Annotated Information==
 
==Annotated Information==
 
===Transcriptomic Nomeclature===
 
===Transcriptomic Nomeclature===
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Please input transcriptomic nomeclature information here.
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''CARMEN'': cardiac mesoderm enhancer-associated non-coding RNA <ref name="ref1" />
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===Characteristics===
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''CARMEN'', derived from a human super enhancer (SE) and proximal to an important developmental miRNA locus, encoding the MIR-143 and -145, represents a novel SE-associated lncRNA critical for cell fate determination and differentiation <ref name="ref1" />.
  
 
===Function===
 
===Function===
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Please input function information here.
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[[File: Knockdown of " CARMEN " impacts upon cardiac specification and differentiation.jpg|right|thumb|400px|'''Knockdown of ''CARMEN'' impacts upon cardiac specification and differentiation''' <ref name="ref1" />.]]
  
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===Regulation===
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''CARMEN'' knockdown inhibits cardiac specification and differentiation in cardiac precursor cells independently of MIR-143 and -145 expression, two microRNAs located proximal to the enhancer sequences<ref name="ref1" />
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Please input regulation information here.
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''CARMEN'' exhibits cis-acting function and associates with EZH2 and SUZ12, suggesting that CARMEN may have trans-repressive roles during cardiac differentiation <ref name="ref1" />.
  
 
===Expression===
 
===Expression===
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Please input expression information here.
 
  
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===Allelic Information and Variation===
 
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Please input allelic information and variation information here.
 
  
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===Evolution===
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''CARMEN'' expression increasing in the stressed heart reflects upregulation in a subset of cardiac cells other than cardiomyocytes, in particular CPCs <ref name="ref1" />.
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Please input evolution information here.
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''CARMEN'' expression was activated during pathological remodeling in the mouse and human hearts, and was necessary for maintaining cardiac identity in differentiated cardiomyocytes <ref name="ref1" />.
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{| class='wikitable' style="text-align:center"
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|-
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! | RT-qPCR
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! | Forward primer
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! | Reverse primer
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|-
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| rowspan="1"|CARMEN1
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| | 5'-GATGGAAAAGATGGCAGAGG-3'
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| | 5'-TAGGTGTTGGCTGAGTGCAG-3'<ref name="ref1" />
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|-
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| rowspan="1"|CARMEN2
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| | 5'-CCAACCACTCCCCAAACA-3'
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| | 5'-TTACAGCCGTTGCTCTCCTT-3'<ref name="ref1" />
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|-
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| rowspan="1"|CARMEN3
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| | 5'-GAGTAGGAGGGAGCCTTTGG-3'
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| | 5'-TTTGCCTCCATCTCCTCTGT-3'<ref name="ref1" />
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|-
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| rowspan="1"|Carmen
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| | 5'-AATAGACTGGGCCTCCACCT-3'
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| | 5'-GTTCCTCTCTGGGGCTCTTC-3'<ref name="ref1" />
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|-
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| rowspan="1"|CARMEN LncRNA cloning
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| | 5'-TACCGAGCTCGGATCCtcagtgccagctgcttaaaa-3'
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| | 5'-CTGGACTAGTGGATCCaggcacagtgttagagtttgct-3'<ref name="ref1" />
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|-
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|}
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===Disease===
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''CARMEN'' controls cardiac specification, differentiation and homeostasis <ref name="ref1" />
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===Conservation===
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''CARMEN'' is highly conserved in mouse <ref name="ref1" />.
  
 
You can also add sub-section(s) at will.
 
You can also add sub-section(s) at will.
  
 
==Labs working on this lncRNA==
 
==Labs working on this lncRNA==
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Please input related labs here.
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* Experimental Cardiology Unit, Department of Medicine, University of Lausanne Medical School, Lausanne, Switzerland <ref name="ref1" />.
  
 
==References==
 
==References==
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<references>
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<ref name="ref1"> Ounzain S, Micheletti R, Arnan C, Plaisance I, Cecchi D, Schroen B, et al. CARMEN, a human super enhancer-associated long noncoding RNA controlling cardiac specification, differentiation and homeostasis[J]. Journal of molecular and cellular cardiology. 2015,89(Pt A):98-112.</ref>(1)
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</references>
  
 
{{basic|
 
{{basic|
 
tID = ENST00000509909.1|
 
tID = ENST00000509909.1|
 
source = Gencode19|
 
source = Gencode19|
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same = lnc-PCYOX1L-2:11,NONHSAT104500|
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same = lnc-PCYOX1L-2:11,NONHSAT104500|CARMEN
 
classification = intergenic|
 
classification = intergenic|
 
length = 550 nt|
 
length = 550 nt|
Line 42: Line 80:
 
sequence = <dnaseq>CCAGAGGCTGGGTCTAATTAGTTGAGAAGCAGTGACACCCCCAACCACTCCCCAAACAGGCTGGCTCCCGTCTCCAGGCCCCAAGGAGCCACACCTGGACCAGACCCCAGGAAAGACATGTGGTGGAAACCCTACGGCCCTGGAGCCCAAGGAGAGCAACGGCTGTAACAAGTGCACAGGCAAGGGCGCTAGCTGGTGGGAGCCACCCCGCCATGCTGATGTCAGAGAAGCAAGAACTCTGGAGAAGCAGCCTCCTGGGACCAGAGGAGGGCCAGCAGCAGGCAGCCCGGAGACAGAACTCTCACCCACGCCTCTCCAAGCCTCCCAACAGAAGACAGAGGTCCCCCACAGCCAGAGACATTTCCTGAAGACATGGGGAACACAGAGGCAGAAACAGCCCATCCACCCAGGAGCTGTCCCCCACACTGCCGGGAGCCGGCACCCAGAGCCGCCAGGTAAAACTGAGGCCACCTGGTTCAACATCACCTTTCACAGAAGGGGAAGCAGCCACAGAAAGAAGGGCCTCGTTAAGAAGTGGAACCTGGGACCC</dnaseq>|
 
sequence = <dnaseq>CCAGAGGCTGGGTCTAATTAGTTGAGAAGCAGTGACACCCCCAACCACTCCCCAAACAGGCTGGCTCCCGTCTCCAGGCCCCAAGGAGCCACACCTGGACCAGACCCCAGGAAAGACATGTGGTGGAAACCCTACGGCCCTGGAGCCCAAGGAGAGCAACGGCTGTAACAAGTGCACAGGCAAGGGCGCTAGCTGGTGGGAGCCACCCCGCCATGCTGATGTCAGAGAAGCAAGAACTCTGGAGAAGCAGCCTCCTGGGACCAGAGGAGGGCCAGCAGCAGGCAGCCCGGAGACAGAACTCTCACCCACGCCTCTCCAAGCCTCCCAACAGAAGACAGAGGTCCCCCACAGCCAGAGACATTTCCTGAAGACATGGGGAACACAGAGGCAGAAACAGCCCATCCACCCAGGAGCTGTCCCCCACACTGCCGGGAGCCGGCACCCAGAGCCGCCAGGTAAAACTGAGGCCACCTGGTTCAACATCACCTTTCACAGAAGGGGAAGCAGCCACAGAAAGAAGGGCCTCGTTAAGAAGTGGAACCTGGGACCC</dnaseq>|
 
}}
 
}}
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[[Category:Intergenic]][[Category:lnc-PCYOX1L-2]][[Category:NONHSAG041903]][[Category:ENSG00000249669.3]][[Category:Transcripts]]
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[[Category:Intergenic]][[Category:lnc-PCYOX1L-2]][[Category:NONHSAG041903]][[Category:ENSG00000249669.3]][[Category:Transcripts]][[Category:Transcripts]]

Latest revision as of 15:48, 22 June 2016

CARMEN, a human super enhancer-associated long noncoding RNA, is a crucial regulator of cardiac specification, differentiation and homeostasis.

Annotated Information

Transcriptomic Nomeclature

CARMEN: cardiac mesoderm enhancer-associated non-coding RNA [1]

Characteristics

CARMEN, derived from a human super enhancer (SE) and proximal to an important developmental miRNA locus, encoding the MIR-143 and -145, represents a novel SE-associated lncRNA critical for cell fate determination and differentiation [1].

Function

Knockdown of CARMEN impacts upon cardiac specification and differentiation [1].

CARMEN knockdown inhibits cardiac specification and differentiation in cardiac precursor cells independently of MIR-143 and -145 expression, two microRNAs located proximal to the enhancer sequences[1]

CARMEN exhibits cis-acting function and associates with EZH2 and SUZ12, suggesting that CARMEN may have trans-repressive roles during cardiac differentiation [1].

Expression

CARMEN expression increasing in the stressed heart reflects upregulation in a subset of cardiac cells other than cardiomyocytes, in particular CPCs [1].

CARMEN expression was activated during pathological remodeling in the mouse and human hearts, and was necessary for maintaining cardiac identity in differentiated cardiomyocytes [1].

RT-qPCR Forward primer Reverse primer
CARMEN1 5'-GATGGAAAAGATGGCAGAGG-3' 5'-TAGGTGTTGGCTGAGTGCAG-3'[1]
CARMEN2 5'-CCAACCACTCCCCAAACA-3' 5'-TTACAGCCGTTGCTCTCCTT-3'[1]
CARMEN3 5'-GAGTAGGAGGGAGCCTTTGG-3' 5'-TTTGCCTCCATCTCCTCTGT-3'[1]
Carmen 5'-AATAGACTGGGCCTCCACCT-3' 5'-GTTCCTCTCTGGGGCTCTTC-3'[1]
CARMEN LncRNA cloning 5'-TACCGAGCTCGGATCCtcagtgccagctgcttaaaa-3' 5'-CTGGACTAGTGGATCCaggcacagtgttagagtttgct-3'[1]

Disease

CARMEN controls cardiac specification, differentiation and homeostasis [1]

Conservation

CARMEN is highly conserved in mouse [1].

You can also add sub-section(s) at will.

Labs working on this lncRNA

  • Experimental Cardiology Unit, Department of Medicine, University of Lausanne Medical School, Lausanne, Switzerland [1].

References

  1. ↑ 1.00 1.01 1.02 1.03 1.04 1.05 1.06 1.07 1.08 1.09 1.10 1.11 1.12 1.13 1.14 Ounzain S, Micheletti R, Arnan C, Plaisance I, Cecchi D, Schroen B, et al. CARMEN, a human super enhancer-associated long noncoding RNA controlling cardiac specification, differentiation and homeostasis[J]. Journal of molecular and cellular cardiology. 2015,89(Pt A):98-112.

Basic Information

Transcript ID

ENST00000509909.1

Source

Gencode19

Same with

lnc-PCYOX1L-2:11,NONHSAT104500

Classification

{{{classification}}}

Length

550 nt

Genomic location

chr5+:148786527..148803902

Exon number

4

Exons

148786527..148786641,148800044..148800107,148801044..148801164,148803653..148803902

Genome context

Sequence
000001 CCAGAGGCTG GGTCTAATTA GTTGAGAAGC AGTGACACCC CCAACCACTC CCCAAACAGG CTGGCTCCCG TCTCCAGGCC 000080
000081 CCAAGGAGCC ACACCTGGAC CAGACCCCAG GAAAGACATG TGGTGGAAAC CCTACGGCCC TGGAGCCCAA GGAGAGCAAC 000160
000161 GGCTGTAACA AGTGCACAGG CAAGGGCGCT AGCTGGTGGG AGCCACCCCG CCATGCTGAT GTCAGAGAAG CAAGAACTCT 000240
000241 GGAGAAGCAG CCTCCTGGGA CCAGAGGAGG GCCAGCAGCA GGCAGCCCGG AGACAGAACT CTCACCCACG CCTCTCCAAG 000320
000321 CCTCCCAACA GAAGACAGAG GTCCCCCACA GCCAGAGACA TTTCCTGAAG ACATGGGGAA CACAGAGGCA GAAACAGCCC 000400
000401 ATCCACCCAG GAGCTGTCCC CCACACTGCC GGGAGCCGGC ACCCAGAGCC GCCAGGTAAA ACTGAGGCCA CCTGGTTCAA 000480
000481 CATCACCTTT CACAGAAGGG GAAGCAGCCA CAGAAAGAAG GGCCTCGTTA AGAAGTGGAA CCTGGGACCC
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