Difference between revisions of "PINCR"

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''PINCR'' is a long noncoding RNA that regulates a subset of p53 target genes in human colorectal cancer cells through Matrin 3.
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==Annotated Information==
 
==Annotated Information==
 
===Name===
 
===Name===
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PINCR:p53-induced noncoding RNA
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''PINCR'': p53-induced noncoding RNA (HGNC nomenclature)
−
 
 
−
 
 
  
 
===Characteristics===
 
===Characteristics===
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PINCR is a noncoding RNA ; highly enriched in the nucleus , similar to the nuclear-retained lncRNA MALAT1 (Hutchinson et al., 2007); the 5’and 3’ends of PINCR match the annotated transcript based on analysis of our RNA-seq data from HCT116 cells (Li et al., unpublished); analysis of the length of the PINCR transcript by RT-PCR reveals two closely migrating bands that match the expected size of the amplicon (~1.8 kb); PINCR promoter including the p53RE, mature PINCR transcript and the transcription start site are quite conserved among primates but poorly conserved between human and mouse.<ref name="ref1" />
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''PINCR'' is six exons transcript of 2228 bp (GenBank) long noncoding RNA that is located on human cheomosome Xp11.3 <ref name="ref1" />. 
  
 
===Cellular Localization===
 
===Cellular Localization===
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Xp11.3
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PINCR is highly enriched in the nucleus <ref name="ref1" />.
  
 
===Function===
 
===Function===
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PINCR plays a role in p53-dependent G1 arrest and it has a prosurvival function in response to DNA damage. PINCR loss results in hypersensitivity to 5-FU and decreases tumor growth. PINCR regulates the induction of a subset of p53 targets after DNA damage.
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[[File:PINCR.jpg|right|thumb|400px|'''''PINCR'' regulates the induction of select p53 target genes important for G1 arrest after DNA damage'''<ref name="ref1" />]]
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RNA pulldowns and mass spectrometry identifies Matrin 3 as a PINCR interacting protein that mediates the effect of PINCR.
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PINCR is induced ~100-fold after DNA damage and exerts a prosurvival function in human colorectal cancer cells (CRC) in vitro and tumor growth in vivo <ref name="ref1" />. PINCR regulates a subset of p53 targets involved in G1 arrest and apoptosis (BTG2, RRM2B and GPX1) in human colorectal cancer cells by binding to Matrin 3, and plays an important role in p53-dependent G1 arrest <ref name="ref1" />.
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Matrin 3 associates with enhancers within insulated neighborhoods of PINCR targets.
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PINCR associates with the enhancer regions of select PINCR targets via Matrin 3<ref name="ref1" />
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===Expression===
 +
PINCR is induced ~100-fold after DNA damage <ref name="ref1" />.
  
 
===Regulation===
 
===Regulation===
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PINCR is a direct target of p53.<ref name="ref1" />
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PINCR promoter contains p53RE, and PINCR is a direct target of p53 <ref name="ref1" />.
 +
 
 +
===Conservation===
 +
Mature PINCR transcript and the transcription start site are quite conserved among primates but poorly conserved between human and mouse <ref name="ref1" />.
 +
 
 
===Diseases===
 
===Diseases===
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colorectal cancer <ref name="ref1" />
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* Colorectal cancer <ref name="ref1" />
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===Expression===
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PINCR is expressed at ~13–26 molecules per HCT116 cell after DNA damage and less than one molecule per cell without DNA damage based on comparison of the FPKM of PINCR with the lncRNA NORAD, known to be expressed at 500–1000 molecules per HCT116 cell (Lee et al., 2016). As an alternative approach, qRT-PCR using in vitro transcribed PINCR RNA showed that PINCR is expressed at ~27 molecules per HCT116 cell after DNA damage. <ref name="ref1" />
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==Labs working on this lncRNA==
 +
* Regulatory RNAs and Cancer Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, United States.<ref name="ref1" />
 +
* Oncogenomics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, United States; 3Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, United States.<ref name="ref1" />
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* Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, United States.<ref name="ref1" />
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* National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, United States.<ref name="ref1" />
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* Laboratory of Gene Regulation and Development, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, United States.<ref name="ref1" />
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* Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, United States.<ref name="ref1" />
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 +
==References==
 +
<references>
 +
<ref name="ref1">
 +
Chaudhary R, Gryder B, Woods WS, Subramanian M, Jones MF, Li XL et al. Prosurvival long noncoding RNA PINCR regulates a subset of p53 targets in human colorectal cancer cells by binding to Matrin 3[J]. Elife. 2017, 6:e23244.
 +
</ref>
 +
</references>
  
 
===Sequence===
 
===Sequence===
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>NR_110387.1 Homo sapiens p53-induced noncoding RNA (PINCR), long non-coding RNA
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>gi|101927501|ref|NR_110387.1| Homo sapiens p53-induced noncoding RNA (PINCR), long non-coding RNA
 
<dnaseq>ATTCAATCTGTGAGGTGGATGCGTGTTGGAAGGACCCCTTTTGGTTTCTTTTTGCTCAGAGCTTTCTTTT
 
<dnaseq>ATTCAATCTGTGAGGTGGATGCGTGTTGGAAGGACCCCTTTTGGTTTCTTTTTGCTCAGAGCTTTCTTTT
 
AATAAATTCCGCTCTCCTCACCTTTCAATGTGTCCGTATGCCTAATTTTTCCTGGTCCTGTGACAAGAAC
 
AATAAATTCCGCTCTCCTCACCTTTCAATGTGTCCGTATGCCTAATTTTTCCTGGTCCTGTGACAAGAAC
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GCTCCAGCTGCACCTTTTGCCACAATTGTAAGCTTTGTGAGTCCCTCAACAGAAGCTGAGCAAATGCTGG
 
GCTCCAGCTGCACCTTTTGCCACAATTGTAAGCTTTGTGAGTCCCTCAACAGAAGCTGAGCAAATGCTGG
 
CACCATGCTTCTTGTACAGCCTACAGAACTGTGAACCAAATAAAACTTTTATTTTTAT</dnaseq>
 
CACCATGCTTCTTGTACAGCCTACAGAACTGTGAACCAAATAAAACTTTTATTTTTAT</dnaseq>
−
==Labs working on this lncRNA==
 
−
*Regulatory RNAs and Cancer Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, United States.
 
−
==References==
 
−
<references>
 
−
<ref name="ref1">
 
−
Chaudhary R, Gryder B, Woods WS, Subramanian M, Jones MF, Li XL, Jenkins LM,
 
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Shabalina SA, Mo M, Dasso M, Yang Y, Wakefield LM, Zhu Y, Frier SM, Moriarity BS,
 
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Prasanth KV, Perez-Pinera P, Lal A. Prosurvival long noncoding RNA PINCR
 
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regulates a subset of p53 targets in human colorectal cancer cells by binding to
 
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Matrin 3. Elife. 2017 Jun 5;6.
 
−
 
−
</ref>
 
−
</references>
 

Latest revision as of 05:31, 26 November 2018

PINCR is a long noncoding RNA that regulates a subset of p53 target genes in human colorectal cancer cells through Matrin 3.

Annotated Information

Name

PINCR: p53-induced noncoding RNA (HGNC nomenclature)

Characteristics

PINCR is six exons transcript of 2228 bp (GenBank) long noncoding RNA that is located on human cheomosome Xp11.3 [1].

Cellular Localization

PINCR is highly enriched in the nucleus [1].

Function

PINCR regulates the induction of select p53 target genes important for G1 arrest after DNA damage[1]

PINCR is induced ~100-fold after DNA damage and exerts a prosurvival function in human colorectal cancer cells (CRC) in vitro and tumor growth in vivo [1]. PINCR regulates a subset of p53 targets involved in G1 arrest and apoptosis (BTG2, RRM2B and GPX1) in human colorectal cancer cells by binding to Matrin 3, and plays an important role in p53-dependent G1 arrest [1].

Expression

PINCR is induced ~100-fold after DNA damage [1].

Regulation

PINCR promoter contains p53RE, and PINCR is a direct target of p53 [1].

Conservation

Mature PINCR transcript and the transcription start site are quite conserved among primates but poorly conserved between human and mouse [1].

Diseases

  • Colorectal cancer [1]

Labs working on this lncRNA

  • Regulatory RNAs and Cancer Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, United States.[1]
  • Oncogenomics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, United States; 3Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, United States.[1]
  • Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, United States.[1]
  • National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, United States.[1]
  • Laboratory of Gene Regulation and Development, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, United States.[1]
  • Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, United States.[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 Chaudhary R, Gryder B, Woods WS, Subramanian M, Jones MF, Li XL et al. Prosurvival long noncoding RNA PINCR regulates a subset of p53 targets in human colorectal cancer cells by binding to Matrin 3[J]. Elife. 2017, 6:e23244.

Sequence

>gi|101927501|ref|NR_110387.1| Homo sapiens p53-induced noncoding RNA (PINCR), long non-coding RNA

000001 ATTCAATCTG TGAGGTGGAT GCGTGTTGGA AGGACCCCTT TTGGTTTCTT TTTGCTCAGA GCTTTCTTTT AATAAATTCC 000080
000081 GCTCTCCTCA CCTTTCAATG TGTCCGTATG CCTAATTTTT CCTGGTCCTG TGACAAGAAC CTGATTTTAG CTGAACTAAG 000160
000161 GAGCGAAAGA TCCTGGATCA TTTTGGTGAC CCATACTGGT ACATGAGGAA AGCTCCTATT CCAGATTCTC AGAGTATAGA 000240
000241 TTCTGACTGG ATTACCCTGG TCCTTGAAGT ATACCTAGGA GATGGAATAA CATTGTATAA GCATCCACGT TGTCATTAAG 000320
000321 AGGAAAGAGT TTCCATTAAA ACAGCAGGTC ACAAAACCCT CCTGTGAGAG GAACCCTCTG TGGAAGAACA GAATATGTCA 000400
000401 CCCCAAAATA TGAAGAATTG TTGAGCTGAA GATGATTAAG AAGAAGCGGA TGCAGGAAAG CTCTCTGCTC TCCCTCTATT 000480
000481 TGCTTAAAAG CAGGATAAAC ACTTACAAAG ACTAAAGACG CCACAATCAA GAACTCAGAA GGGTAGAAGA AAAAGATAGT 000560
000561 TTCCCTTCCC TACACAGGTG TTGATCCCTT CATAAATATT ATGCATGCTA AGCCCTATCT CAAGGTCTAC ATCCAGGAGA 000640
000641 ACCCAACCTG CAACATTAAG TTACTGACTG TGCAAGAACC CTTTGATCAC GTACCTTACA GACCAAGATA AGTGAGGATG 000720
000721 CCCATGTATA ACCTGCTGTC TTTCTGGTCT CTTATGTTTT TGTACCAGAA AGGGACAACT TTTTGGGTAA CCATAGGTCT 000800
000801 CTAGTATATC TGTGATTACA ATAAAGATTT TTGATATACC AAAACTGATG AACCAAAATT CCACTGAAAT AGCGAGTAAA 000880
000881 TGGAGTTCTT TTATCCTTTG CAGTATACCA GGGTGAACTT TTTACATGAT TTCTTGCTCC AAAGGGAGAA GTGTTATGAC 000960
000961 AAAGTACATT TAAGGACCCT AACTGATCAC AGAAAAAATA TTAATGGCAT TGGGAAAAAA ATGCAGACTA ATGAATCCAC 001040
001041 TACTAAATTT TATCTATCTT GTAGCTCTAA AATTGCACTG TTTAGAATAC ACTATGGTAG CCACTAGACA TATGGCTACT 001120
001121 TGAACTTGAA TTGGTTAAAA TCAAAATTAA GAATTTAATT TCTCACTCAC ATTAGCCACA TTTCAAGTGC TCAACAGACA 001200
001201 CATGTGGCTA GTGTCTACCA TATTGGACAG CATAGATTTA AAGCACATTT CCATCATTGC AACACTGCAA TATGGAGGAT 001280
001281 GTATCCTCAA TACATTGATA TTGCCCCCTC AAAATTCATA ACCCCTAGAT ATCTTATCTC TGTATGTGAG GATAGTGTAT 001360
001361 TAACTTGCAC CTGG