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Cited by 1,578MicroRNA in disease regulationDevelopmental Biology and Gene RegulationNeurogenesis and neuroplasticity mechanisms

Expression profiling of mammalian microRNAs uncovers a subset of brain-expressed microRNAs with possible roles in murine and human neuronal differentiation

Open access
Sempere, Lorenzo F, Freemantle, Sarah, Pitha-Rowe, Ian, Moss, Eric, Dmitrovsky, Ethan, Ambros, Victor·2004·Genome Biology
DOI 10.1186/gb-2004-5-3-r13PMC PMC395763
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Abstract

BACKGROUND: The microRNAs (miRNAs) are an extensive class of small noncoding RNAs (18 to 25 nucleotides) with probable roles in the regulation of gene expression. In Caenorhabditis elegans, lin-4 and let-7 miRNAs control the timing of fate specification of neuronal and hypodermal cells during larval development. lin-4, let-7 and other miRNA genes are conserved in mammals, and their potential functions in mammalian development are under active study. RESULTS: In order to identify mammalian miRNAs that might function in development, we characterized the expression of 119 previously reported miRNAs in adult organs from mouse and human using northern blot analysis. Of these, 30 miRNAs were specifically expressed or greatly enriched in a particular organ (brain, lung, liver or skeletal muscle). This suggests organ- or tissue-specific functions for miRNAs. To test if any of the 66 brain-expressed miRNAs were present in neurons, embryonal carcinoma cells were treated with all-trans-retinoic acid to promote neuronal differentiation. A total of 19 brain-expressed miRNAs (including lin-4 and let-7 orthologs) were coordinately upregulated in both human and mouse embryonal carcinoma cells during neuronal differentiation. The mammalian ortholog of C. elegans lin-28, which is downregulated by lin-4 in worms via 3' untranslated region binding, was also repressed during neuronal differentiation of mammalian embryonal carcinoma cells. Mammalian lin-28 messenger RNAs contain conserved predicted binding sites in their 3' untranslated regions for neuron-expressed miR-125b (a lin-4 ortholog), let-7a, and miR-218. CONCLUSIONS: The identification of a subset of brain-expressed miRNAs whose expression behavior is conserved in both mouse and human differentiating neurons implicates these miRNAs in mammalian neuronal development or function.

AI snapshot

Written from the paper’s full text.

TL;DR

Northern blot profiling of 119 mammalian microRNAs in adult mouse and human organs identified conserved organ-specific and organ-enriched expression, including a prominent brain-expressed subset. Several brain-expressed miRNAs were induced during retinoic-acid-driven neuronal differentiation of mouse P19 and human NT2/D1 embryonal carcinoma cells, and LIN-28 was downregulated with conserved predicted miRNA binding sites.

Key findings

  • Of 119 miRNAs analyzed, 92 were previously cloned and 27 were computationally predicted; 21 of 27 predicted miRNAs were detected by northern blot. Seventeen miRNAs were detected exclusively in one mouse organ, including seven brain-specific miRNAs (miR-9, -124a, -124b, -135, -153, -183, -219), six lung-specific, two spleen-specific, one liver-specific, and one heart-specific miRNA. Among 75 miRNAs detected in two or more mouse organs, 14 were enriched at least two-fold in one organ, including seven brain-enriched miRNAs (miR-9*, -125a, -125b, -128, -132, -137, -139), three skeletal muscle-enriched, two kidney-enriched, and one spleen-enriched miRNA.
  • Hierarchical clustering identified at least six major groups of miRNAs with similar expression profiles, including a group of 17 miRNAs expressed in mouse and human brain; about 50% of expressed miRNAs were assigned to a specific or restricted set of organs.
  • Retinoic acid treatment induced 19 miRNAs in both P19 and NT2/D1 cells, including four brain-specific, four brain-enriched, and 11 brain-nonenriched miRNAs; induction in P19 cells typically occurred by day four after RA treatment.
  • LIN-28 protein levels began to decrease around day five and almost disappeared by day eight in P19 cells; in NT2/D1 cells, LIN-28 decreased slightly by day 14 and was still detectable at day 21. This kinetics paralleled upregulation of miR-125b, let-7a, and miR-218, and mouse and human Lin-28 mRNAs contain conserved predicted binding sites for these miRNAs.

Methods

  • Northern analysis of 119 miRNAs using StarFire probes on total RNA from adult mouse organs (six-week-old C57BL/6 mice, pooled organs from two to four mice) and human organs, plus P19 and NT2/D1 embryonal carcinoma cells treated with 1 μM and 10 μM retinoic acid, respectively.
  • Northern blot signals were quantified with ImageQuant and clustered with GeneTraffic 6.2 using Pearson hierarchical clustering; western analysis was used to measure LIN-28 protein.
  • miRNA::target mRNA predictions were made by testing 20-nucleotide 3′ UTR segments for RNA secondary structure with the RNAfold program of the Vienna RNA package, applying binding, free-energy, and mouse-human conservation filters and a numerical scoring formula.

Limitations

  • Stated: some cloned and predicted miRNAs were not detected, possibly because of low expression, expression limited to a small number of cells or a narrow developmental window, or lack of expression in the organs examined; the organ panel did not include all organs and tissues from which miRNAs were cloned, and human kidney, lung, and spleen were not examined.
  • Stated: glial expression was not directly examined, so the possibility that RA-induced miRNAs were also expressed in glial cells could not be eliminated; a luciferase reporter fused to the mouse Lin-28 3′ UTR was not downregulated in differentiating P19 cells, and endogenous Lin-28 mRNA decreased, suggesting that repression of native Lin-28 may be largely transcriptional and that miRNA regulation may be auxiliary.
  • Evident: the miRNA target predictions are computational and were not experimentally validated by loss-of-function experiments; the paper notes that miRNA loss-of-function experiments in these EC cells could prove useful for understanding their regulatory contribution.

Model-written summary. Check it against the paper before relying on it.

Integrity signals

Registry

Crossref · 10.1186/gb-2004-5-3-r13

Cites

50 of 50 references verified0 citation errors · 0 not checkable

Statistics

Nothing to recompute.

Claims the paper makes

0 of 42 cited sources checked · 0 supported · 0 flagged

  • Findingown data

    We observed a strong induction of miR-9/miR-9* expression in P19 cells.

    “We observed a strong induction of miR-9/miR-9* expression in P19 cells.”
    Quote in the paperSubstantial claim
  • Findingown data

    We did not detect downregulation, in differentiating P19 cells, of a luciferase reporter gene fused to the mouse Lin-28 3' UTR and driven by a CMV or TK promoter.

    “Yet, we did not detect downregulation, in differentiating P19 cells, of a luciferase reporter gene fused to the mouse Lin-28 3' UTR and driven by a cytomegalovirus (CMV) or thymidine kinase (TK) promoter (data not shown).”
    Quote in the paperSubstantial claim
  • Findingown data

    All of the indicated mouse brain-, liver- and heart-specific miRNAs were also detected in the human counterpart organs, with the exception of miR-183 in the human brain.

    “All of the indicated mouse brain-, liver- and heart-specific miRNAs were also detected in the human counterpart organs (miRNA expression was not examined in human kidney, lung or spleen), with the exception of miR-183 in the human brain.”
    Quote in the paperSubstantial claim
  • Findingown data

    A group of seven miRNAs was expressed in mouse lung and kidney (miR-18, -20, -24, -32, -141, -193, -200b).

    “A group of seven miRNAs was expressed in mouse lung and kidney (miR-18, -20, -24, -32, -141, -193, -200b).”
    Quote in the paperNot a substantial claim
  • Findingown data

    Among the 75 miRNAs detected in two or more mouse organs, 14 were detected in a particular mouse organ at levels at least two-fold higher than in any other organ.

    “Among the 75 miRNAs that were detected in two or more mouse organs, the levels of 14 of these were detected in a particular mouse organ at levels at least two-fold higher than in any other organ”
    Quote in the paperSubstantial claim
  • May combine two claims. 28
  • Classified as probably not a substantial claim. 13
  • The quote only partly states this claim. 1

  • May combine two claims.

    Findingown data

    The 19 induced miRNAs included four brain-specific (miR-9, -124a, -124b, -135), four brain-enriched (miR-9*, -125a, -125b, -128), and 11 brain-nonenriched (let-7a, let-7b, miR-30a, -30b, -30c, -30e, -98, -100, 103-1, -156, -218).

    “They included four of the brain-specific (miR-9, -124a, -124b, -135), four of the brain-enriched (miR-9*, -125a, -125b, -128), and 11 of the brain-nonenriched (let-7a, let-7b, miR-30a, -30b, -30c, -30e, -98, -100, 103-1, -156, -218).”
    Quote in the paperSubstantial claim
    • Rests on an assumption: miRNAs with evolutionarily conserved roles in neurons should be induced during neuronal differentiation of both mouse and human EC cells.
    • Rests on an assumption: The induction of miRNAs in RA-treated EC cells reflects their expression during neuronal differentiation in vivo.

  • May combine two claims.

    Findingown data

    We observed a high percentage of brain-specific and brain-enriched miRNAs compared to miRNAs enriched or specific to other organs (14 out of 30 miRNAs in mouse), and an overall prevalence of miRNAs expressed in the brain (66 out of 90 miRNAs in mouse).

    “We observed a high percentage of brain-specific and brain-enriched miRNAs compared to miRNAs enriched or specific to other organs (14 out of 30 miRNAs in mouse), and an overall prevalence of miRNAs expressed in the brain (66 out of 90 miRNAs in mouse).”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Findingcitation

    mir-208 is expressed in the mouse and human heart and resides in an intron of human cardiac α-myosin heavy chain.

    “mir-208, which is expressed in the mouse and human heart, resides in an intron of human cardiac α-myosin heavy chain.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingcitation

    miR-9/miR-9* and miR-145 were cloned in cDNA libraries from human hypothalamus (gi|28436750) and trachea (gi|21752921), respectively.

    “miR-9/miR-9* and miR-145 were cloned in cDNA libraries from human hypothalamus (gi|28436750) and trachea (gi|21752921), respectively.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    The 14 organ-enriched mouse miRNAs included seven brain-enriched miRNAs (miR-9*, -125a, -125b, -128, -132, -137, -139), three skeletal muscle-enriched miRNAs (miR-1d, -133, -206), two kidney-enriched miRNAs (miR-30b, -30c), and one spleen-enriched miRNA (miR-99a).

    “these included: seven brain-enriched miRNAs (miR-9*, -125a, -125b, -128, -132, -137, -139), three skeletal muscle-enriched miRNAs (miR-1d, -133, -206), two kidney-enriched miRNAs (miR-30b, -30c), and one spleen-enriched miRNA (miR-99a)”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    In NT2/D1 cells, LIN-28 levels decreased slightly, typically by day 14, and were still detectable at day 21.

    “A similar result was observed in NT2/D1 cells; LIN-28 levels decreased slightly, typically by day 14, and were still detectable at day 21.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    A group of six miRNAs was expressed in mouse and human skeletal muscle and heart: miR-1b, -1d, -133 and -206 had elevated expression in heart and skeletal muscle with low expression in other organs and miR-143 and -208 were almost exclusively detected in heart and skeletal muscle.

    “A group of six miRNAs was expressed in mouse and human skeletal muscle and heart: miR-1b, -1d, -133 and -206 had elevated expression in heart and skeletal muscle with low expression in other organs and miR-143 and -208 were almost exclusively detected in heart and skeletal muscle.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    We observed similar expression profiles for the pair of linked miRNAs, mir-194 and mir-215, and also for both members of the mir-1d~mir-133 cluster.

    “We observed similar expression profiles for the pair of linked miRNAs, mir-194 and mir-215, and also for both members of the mir-1d~mir-133 cluster (Figure 3).”
    Quote in the paperNot a substantial claim
    • Rests on an assumption: Closely linked miRNAs arranged in tandem often exhibit similar expression profiles, consistent with shared cis-regulatory elements and possibly a polycistronic precursor transcript.

  • May combine two claims.

    Findingcitation

    Both miR-191 and miR-214 were contained in long transcripts cloned in cDNA libraries from mouse neonate head (gi|26096865) and eyeball (gi|26094816), respectively.

    “Both miR-191 and miR-214 were contained in long transcripts cloned in cDNA libraries from mouse neonate head (gi|26096865) and eyeball (gi|26094816), respectively.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    LIN-28 levels began to decrease on about day five after RA-treatment, and almost disappeared by day eight, when P19 cells reached their final state of neuronal differentiation.

    “LIN-28 levels began to decrease on about day five after RA-treatment, and almost disappeared by day eight, when cells reached their final state of neuronal differentiation.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    The 17 organ-specific mouse miRNAs included seven brain-specific miRNAs (miR-9, -124a, -124b, -135, -153, -183, -219), six lung-specific miRNAs (miR-18, -19a, -24, -32, -130, -213), two spleen-specific miRNAs (miR-189, -212), one liver-specific miRNA (miR-122a), and one heart-specific miRNA (miR-208).

    “these included: seven brain-specific miRNAs (miR-9, -124a, -124b, -135, -153, -183, -219), six lung-specific miRNAs (miR-18, -19a, -24, -32, -130, -213), two spleen-specific miRNAs (miR-189, -212), one liver-specific miRNA (miR-122a), and one heart-specific miRNA (miR-208)”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Not only the protein levels but also the RNA levels of Lin-28 decreased upon RA treatment, suggesting that other factors must also mediate this process.

    “However, not only the protein levels but also the RNA levels of Lin-28 decreased upon RA treatment suggesting that other factors must also mediate this process.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    In both mouse and human examined organs, seven miRNAs were expressed specifically in a particular organ and ten miRNAs were greatly enriched in a particular organ over all others.

    “In both mouse and human examined organs, seven miRNAs were expressed specifically in a particular organ and ten miRNAs were greatly enriched in a particular organ over all others (Figure 2).”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Premisecitation

    mir-15 and mir-16 reside on chromosome 13q14, a region associated with chronic lymphocytic leukemia (CLL).

    “mir-15 and mir-16 reside on chromosome 13q14, a region associated with chronic lymphocytic leukemia (CLL) (Figure 3b).”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [36] Calin GA, Dumitru CD, Shimizu M, Bichi R, Zupo S, Noch E, Aldler H, Rattan S, Keating M, Rai K, et al.: Frequent deletions and down-regulation of micro-RNA genes miR15 and miR16 at 13q14 in chronic lymphocytic leukemia.Proc Natl Acad Sci USA 2002, 99:15524–15529. source

  • May combine two claims.

    Interpretationcitation

    The panel of organs tested did not include all the organs and tissues that miRNAs were cloned from, and thus some organ-specific or organ-enriched miRNAs may be expressed in additional organs or tissues.

    “The panel of organs that we tested in our study did not include all the organs and tissues that miRNAs were cloned from [1-3,9,10], and thus some organ-specific or organ-enriched miRNAs may be expressed in additional organs or tissues.”
    Quote in the paperNot a substantial claim0 of 5 sources checked
    • cites [1] Lagos-Quintana M, Rauhut R, Lendeckel W, Tuschl T: Identification of novel genes coding for small expressed RNAs.Science 2001, 294:853–858. source
    • cites [2] Lagos-Quintana M, Rauhut R, Yalcin A, Meyer J, Lendeckel W, Tuschl T: Identification of tissue-specific microRNAs from mouse.Curr Biol 2002, 12:735–739. source

      Checked before — its earlier verdict is held back until a new check runs.

    • cites [3] Lagos-Quintana M, Rauhut R, Meyer J, Borkhardt A, Tuschl T: New microRNAs from mouse and human.RNA 2003, 9:175–179. source

      Checked before — its earlier verdict is held back until a new check runs.

    • cites [9] Mourelatos Z, Dostie J, Paushkin S, Sharma A, Charroux B, Abel L, Rappsilber J, Mann M, Dreyfuss G: miRNPs: a novel class of ribonucleoproteins containing numerous microRNAs.Genes Dev 2002, 16:720–728. source

      Checked before — its earlier verdict is held back until a new check runs.

    • cites [10] Dostie J, Mourelatos Z, Yang M, Sharma A, Dreyfuss G: Numerous microRNPs in neuronal cells containing novel microRNAs.RNA 2003, 9:180–186. source

      Checked before — its earlier verdict is held back until a new check runs.

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Premisecitation

    mir-142s/mir-142as are located in the junction of the t(8;17) chromosomal rearrangement, which fuses Bcl3 and Myc genes and results in an aggressive B-cell leukemia.

    “Notably, mir-142s/mir-142as are located in the junction of the t(8;17) chromosomal rearrangement. This translocation fuses Bcl3 and Myc genes, thus resulting in an aggressive B-cell leukemia [2,37].”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites [2] Lagos-Quintana M, Rauhut R, Yalcin A, Meyer J, Lendeckel W, Tuschl T: Identification of tissue-specific microRNAs from mouse.Curr Biol 2002, 12:735–739. source

      Checked before — its earlier verdict is held back until a new check runs.

    • cites [37] Gauwerky CE, Huebner K, Isobe M, Nowell PC, Croce CM: Activation of MYC in a masked t(8;17) translocation results in an aggressive B-cell leukemia.Proc Natl Acad Sci USA 1989, 86:8867–8871. source

      Checked before — its earlier verdict is held back until a new check runs.

  • May combine two claims.

    Premisecitation

    P19 and NT2/D1 have similar programs of neuronal differentiation, though the differentiation of P19 cells progresses more rapidly than that of NT2/D1 cells.

    “P19 and NT2/D1 have similar programs of neuronal differentiation, though the differentiation of P19 cells progresses more rapidly than that of NT2/D1 cells [42,43].”
    Quote in the paperSubstantial claim0 of 2 sources checked
    • cites [42] Bain G, Ray WJ, Yao M, Gottlieb DI: From embryonal carcinoma cells to neurons: the P19 pathway.Bioessays 1994, 16:343–348. source
    • cites [43] Andrews PW: Teratocarcinomas and human embryology: pluripotent human EC cell lines. Review article.APMIS 1998, 106:158–167. source

  • May combine two claims.

    Interpretationown data

    The decline of Lin-28 during neuronal differentiation of P19 cells involves primarily transcriptional repression, unlike C. elegans larval development where lin-28 downregulation is primarily caused by translational repression by lin-4 RNA.

    “These results therefore suggest that, unlike C. elegans larval development, where lin-28 downregulation is primarily caused by translational repression by lin-4 RNA, the decline of Lin-28 during neuronal differentiation of P19 cells involves primarily transcriptional repression.”
    Quote in the paperSubstantial claim

  • Classified as probably not a substantial claim. May combine two claims.

    Premisecitation

    lin-4 RNA binds to the 3' UTR of target mRNAs, including lin-28, and inhibits their translation.

    “lin-4 RNA binds to the 3' UTR of target mRNAs, including lin-28, and inhibits their translation [27,45].”
    Quote in the paperSubstantial claim0 of 2 sources checked
    • cites [27] Olsen PH, Ambros V: The lin-4 regulatory RNA controls developmental timing inCaenorhabditis elegansby blocking LIN-14 protein synthesis after the initiation of translation.Dev Biol 1999, 216:671–680. source
    • cites [45] Moss EG, Lee RC, Ambros V: The cold shock domain protein LIN-28 controls developmental timing inC. elegansand is regulated by the lin-4 RNA.Cell 1997, 88:637–646. source

      Checked before — its earlier verdict is held back until a new check runs.

  • Classified as probably not a substantial claim.

    Premisecitation

    In C. elegans, lin-4 (the ortholog of mir-125) and let-7 are engaged in a genetic pathway that controls temporal cell fates during larval development.

    “In C. elegans, lin-4 (the ortholog of mir-125) and let-7 are engaged in a genetic pathway that controls temporal cell fates during larval development [25,26].”
    Quote in the paperSubstantial claim0 of 2 sources checked
    • cites [25] Pasquinelli AE, Ruvkun G: Control of developmental timing by microRNAs and their targets.Annu Rev Cell Dev Biol 2002, 18:495–513. source
    • cites [26] Rougvie AE: Control of developmental timing in animals.Nat Rev Genet 2001, 2:690–701. source

  • May combine two claims.

    Premisecitation

    LIN-28 is present in undifferentiated P19 and NT2/D1 cells, but it is not detected in neuronal or liver tissues.

    “Interestingly, LIN-28 is present in undifferentiated P19 and NT2/D1 cells, but it is not detected in neuronal or liver tissues [46].”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [46] Moss EG, Tang L: Conservation of the heterochronic regulator Lin-28, its developmental expression and microRNA complementary sites.Dev Biol 2003, 258:432–442. source

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Upregulation of lin-4 RNA during the first larval stage (L1) triggers the progression from early (L1) to late (L2-L3) fate programs.

    “Upregulation of lin-4 RNA during the first larval stage (L1) triggers the progression from early (L1) to late (L2-L3) fate programs [24].”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [24] Feinbaum R, Ambros V: The timing of lin-4 RNA accumulation controls the timing of postembryonic developmental events inCaenorhabditis elegans.Dev Biol 1999, 210:87–95. source

      Checked before — its earlier verdict is held back until a new check runs.

  • May combine two claims.

    Interpretationreasoning

    These clustered miRNAs probably belong to the same transcriptional unit, but accumulate differentially in vivo as a result of differences in post-transcriptional processing or stability.

    “which suggests that these clustered miRNAs probably belong to the same transcriptional unit, but accumulate differentially in vivo as a result of differences in post-transcriptional processing or stability.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Interpretationreasoning

    Only a subset of the brain-expressed miRNAs were detected in neurons derived from RA-treated EC cells, suggesting that other brain-expressed miRNAs are present primarily in nonneuronal cell types such as glia, or in neuronal subtypes not represented in differentiated neurons derived from EC cells.

    “Only a subset of the brain-expressed miRNAs were detected in neurons derived from RA-treated EC cells suggesting that other brain-expressed miRNAs are present primarily in nonneuronal cell types such as glia. Alternatively, these other brain-expressed miRNAs may be present in neuronal subtypes not represented in differentiated neurons derived from EC cells.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Premisecitation

    An early phase of commitment to neuronal fate occurs within two days after RA-treatment for P19 and NT2/D1 cells; a later phase of terminal differentiation takes place between days five to eight in P19 cells and is delayed for more than three weeks in NT2/D1 cells.

    “An early phase of commitment to neuronal fate occurs within two days after RA-treatment for P19 and NT2/D1 cells. A later phase of terminal differentiation takes place between days five to eight in P19 cells and is delayed for more than three weeks in NT2/D1 cells [42,43].”
    Quote in the paperSubstantial claim0 of 2 sources checked
    • cites [42] Bain G, Ray WJ, Yao M, Gottlieb DI: From embryonal carcinoma cells to neurons: the P19 pathway.Bioessays 1994, 16:343–348. source
    • cites [43] Andrews PW: Teratocarcinomas and human embryology: pluripotent human EC cell lines. Review article.APMIS 1998, 106:158–167. source

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductreasoning

    Since we did not directly examine expression of miRNAs in glial cells, we could not eliminate the possibility that RA-induced miRNAs were also expressed in glial cells.

    “Since we did not directly examine expression of miRNAs in glial cells, we could not eliminate the possibility that RA-induced miRNAs were also expressed in glial cells.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Premisecitation

    mir-29 resides on chromosome 7q31, a FRA7G region frequently altered in different tumor types including prostate, breast, and ovarian cancer.

    “mir-29 resides on chromosome 7q31. This FRA7G region is frequently altered in different tumor types including prostate, breast, and ovarian cancer [38].”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [38] Huang H, Qian J, Proffit J, Wilber K, Jenkins R, Smith DI: FRA7G extends over a broad region: coincidence of human endogenous retroviral sequences (HERV-H) and small polydispersed circular DNAs (spcDNA) and fragile sites.Oncogene 1998, 16:2311–2319. source

  • Probably not a substantial claim: may not pass S3 (load-bearing), S4 (based).

    Interpretationnone given

    Other cases of clustered miRNAs with different expression profiles, such as mir-132 and mir-212, could represent closely linked but independent transcription units.

    “Other cases of clustered miRNAs with different expression profiles, such as mir-132 and mir-212, could represent closely linked but independent transcription units.”
    Quote in the paperNot a substantial claim

  • Classified as probably not a substantial claim. May combine two claims. The quote only partly states this claim.

    Study design and conductcitation

    RNA folding output generated by ViennaRNA was analyzed using software filters requiring at least two out of the three first and last bases of the miRNA bound, at least 65% of the miRNA sequence bound, free energy greater than -7 Kcal/mole, and the interaction site within regions of at least 76% identity between mouse and human target 3' UTRs.

    “RNA folding output generated by ViennaRNA was analyzed using the following software filters to evaluate the strength of the predicted target::miRNA interaction: at least two out of the three first and last bases of the miRNA had to be bound to the target sequence; at least 65% of the miRNA sequence had to be bound to the target sequence; the free energy (ΔG) of the binding had to be greater than -”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [51] Vienna RNA package[http://www.tbi.univie.ac.at/~ivo/RNA/]

      Couldn’t be matched to a paper in Crossref, so it can’t be checked.

  • May combine two claims.

    Interpretationreasoning

    In the case of targets whose expression is primarily controlled on the translational level, miRNAs could play a primary regulatory role; in other cases, such as mammalian Lin-28, where the primary mode of regulation is transcriptional, translational repression by miRNAs could play an auxiliary, or supplementary regulatory role.

    “In the case of targets whose expression is primarily controlled on the translational level, miRNAs could play a primary regulatory role; in other cases, such as mammalian Lin-28, where the primary mode of regulation is transcriptional, translational repression by miRNAs could play an auxiliary, or supplementary regulatory role.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Interpretationown data

    These data associate miRNAs to particular organs and suggest their participation in conserved developmental or physiological pathways within these spatial domains in mouse and human.

    “These data associate miRNAs to particular organs and suggest their participation in conserved developmental or physiological pathways within these spatial domains in mouse and human.”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductnone given

    Hybridization/background ratios of ≤ 1.1 were not reported as positive signals, except when the band was readily detectable by eye.

    “Hybridization/background ratios of ≤ 1.1 were not reported as positive signals, except when the band was readily detectable by eye (Figures 2, 5).”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Study design and conductnone given

    Membranes were stripped by boiling in 0.1% SDS and re-hybridized up to five times without observing decreases in quality or intensity of radioactive signals.

    “Membranes were stripped by boiling in 0.1% SDS and re-hybridized up to five times without observing decreases in quality or intensity of radioactive signals.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductnone given

    The scoring scheme for miRNA::target mRNA predictions was modeled based on the experimentally confirmed interaction between lin-4 RNA::lin-28 3' UTR in C. elegans.

    “The scoring scheme was modeled based on the experimentally confirmed interaction between lin-4 RNA::lin-28 3' UTR in C. elegans.”
    Quote in the paperNot a substantial claim
34 of 34

  • The paper relies on this without support.

    Closely linked miRNAs arranged in tandem often exhibit similar expression profiles, consistent with shared cis-regulatory elements and possibly a polycistronic precursor transcript.

    “Closely linked miRNAs that are arranged in tandem often exhibit similar expression profiles, consistent with shared cis-regulatory elements, and possibly a polycistronic precursor transcript.”

  • The paper relies on this without support.

    miRNAs with evolutionarily conserved roles in neurons should be induced during neuronal differentiation of both mouse and human EC cells.

    “We reasoned that miRNAs with evolutionarily conserved roles in neurons should be induced during neuronal differentiation of both mouse and human EC cells.”

  • The paper relies on this without support.

    The induction of miRNAs in RA-treated EC cells reflects their expression during neuronal differentiation in vivo.

    “To determine which of brain-expressed miRNAs were associated with neuronal differentiation, we examined their expression during neuronal differentiation of EC cells.”
3 of 3

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

  • A subset of miR-15/107 miRNA genes has been detected in mammalian tissues including heart, skeletal muscle, brain, lung, liver, kidney, spleen and placenta.

    “A subset of these miRNA genes has been detected in mammalian tissues including heart, skeletal muscle, brain, lung, liver, kidney, spleen and placenta [25–31].”

    From Expression of miR-15/107 Family MicroRNAs in Human Tissues and Cultured Rat Brain Cells (2014) · cites this paper as [28]

    The Results and discussion section (“Diverse miRNA expression patterns in mammalian organs”; page unavailable) reports miRNA expression across the listed organs other than placenta. It does not establish that the detected miRNAs were a subset of the miR-15/107 family, and the searched passages do not report detection in placenta. (LLM, conf=0.82)

    Experimental — accuracy not yet measured

  • The neuronal cluster included miR-124, a miRNA especially abundant in neurons, affirming specificity of methodology.

    “The neuronal cluster included miR-124, a miRNA that is especially abundant in neurons affirming the specificity of the methodology [20]–[22].”

    From MicroRNA 146a (miR-146a) Is Over-Expressed during Prion Disease and Modulates the Innate Immune Response and the Microglial Activation State (2012) · cites this paper as [21]

    In “Diverse miRNA expression patterns in mammalian organs” (page not supplied), the paper places miR-124a and miR-124b in a brain-expressed cluster. In “A subset of brain-expressed miRNAs is induced in retinoic acid-treated EC cells” (page not supplied), it reports their induction during neuronal differentiation, but says it did not examine expression in glial cells. It therefore supports the cluster finding, not the stronger assertion that miR-124 is especially abundant in neurons specifically. (LLM, conf=0.86)

    Experimental — accuracy not yet measured

  • Recent studies on brain-enriched miR-9 have revealed its importance in development and lineage commitment.

    “Recent studies on the brain enriched miR-9 have revealed its importance in development and lineage commitment (Sempere et al., 2004; Krichevsky et al., 2006).”

    From The Bifunctional microRNA miR-9/miR-9* Regulates REST and CoREST and Is Downregulated in Huntington's Disease (2008) · cites this paper as Sempere et al., 2004

    In Results and discussion, the paper identifies miR-9 as brain-specific and reports its strong induction during retinoic-acid-induced neuronal differentiation. It concludes that miR-9/miR-9* may play an important role in rodent neurogenesis; it does not establish that miR-9 is important for development or lineage commitment as the citing sentence implies. (LLM, conf=0.85)

    Experimental — accuracy not yet measured

  • During development, many miRNAs are expressed in neurons or show distinct expression patterns within the developing CNS, implying their importance in brain development and function.

    “During development, many miRNAs are expressed in neurons or show distinct expression patterns within the developing central nervous system (CNS), implying their importance in brain development and function (Krichevsky et al. 2003;Miska et al. 2004;Sempere et al. 2004;Smirnova et al. 2005;Wienholds et al. 2005).”

    From MicroRNA expression in the adult mouse central nervous system (2008) · cites this paper as Sempere et al. 2004

  • The human brain has been examined for miR expression and miR-219-5p, miR-338-5p, miR-338-3p, and members of the miR-17-92 cluster have been reported to be expressed.

    “The human brain has also been examined for miR expression and miR-219-5p, miR-338-5p, miR-338-3p, and members of the miR-17-92 cluster have been reported to be expressed (Barad et al., 2004; Sempere et al., 2004).”

    From Regulation of miRNA 219 and miRNA Clusters 338 and 17-92 in Oligodendrocytes (2012) · cites this paper as Sempere et al., 2004

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

Each contradiction between two passages listed here was confirmed by an independent check.

  • Five broadly expressed miRNAs claimed, but only four listed

    Minor

    The parenthetical list names four miRNAs, not the stated five.

  • Organ-enriched miRNA categories total 13, not 14

    Minor

    The listed categories contain 7 brain-, 3 skeletal muscle-, 2 kidney-, and 1 spleen-enriched miRNA, totaling 13 rather than the stated 14.

    Reported 14 · recomputed 13

  • miR-183 described as both present and absent in human brain

    Minor

    miR-183 appears in a group described as expressed in both mouse and human brain, but the earlier passage explicitly says it was the exception not detected in human brain.

3 of 3

Cites

Flagged first, then by citations

1 of the 51 references couldn’t be matched to a known paper.

Research works printed but not linked: 2

  1. Chen X: A microRNA as a translational repressor of APETALA2 inArabidopsisflower development.Science 2003, 101126/science.1088060.
  2. National Center for Biotechnology Information[http://www.ncbi.nlm.nih.gov/]

Cited by

Sorted by citations

Related

Authors
Sempere, L. F., Freemantle, S., Pitha-Rowe, I., Moss, E., Dmitrovsky, E., & Ambros, V.
Affiliations
Dartmouth College (US)
Corresponding author
Ambros, Victor
ORCID
Venue
Genome Biology
Publisher
Springer Science and Business Media LLC
Published
2004-02-16
Volume
5
Issue
3
Pages
R13-R13
ISSN
  • 1465-6906 (ISSN-L)
  • 1474-760X
DOI
10.1186/gb-2004-5-3-r13
PMC
PMC395763
OpenAlex
W2138954682
Cited by
1,578
References
51
Citations by year
2026: 13 · 2025: 33 · 2024: 36 · 2023: 39 · 2022: 55 · 2021: 68 · 2020: 56 · 2019: 62 · 2018: 65 · 2017: 62 · 2016: 78 · 2015: 89 · 2014: 106 · 2013: 108 · 2012: 90
FWCI
29.01
Type
journal article
Language
en
Open access
Licence
Locations
  • Genome biology (publishedVersion)
  • PubMed Central (publishedVersion, other-oa)
  • PubMed (publishedVersion)
Funders
  • Lance Armstrong Foundation
  • Armstrong Foundation
  • National Institutes of Health
  • National Cancer Institute (R01CA062275, T32CA009658, R01CA087546)
  • National Institute of General Medical Sciences (R01GM034028)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › MicroRNA in disease regulation
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Developmental Biology and Gene Regulation
  • Life Sciences › Neuroscience › Developmental Neuroscience › Neurogenesis and neuroplasticity mechanisms
Keywords
microRNA, neuronal differentiation, lin-4, let-7 microRNA, Lin28, miR-125b, miR-218, embryonal carcinoma cells, all-trans retinoic acid, 3' untranslated region, tissue-specific gene expression, neuronal development, miRNA expression profiling
MeSH terms
Adult, Animals, Brain, Cell Differentiation, Cell Line, Embryo, Mammalian, Humans, Genetic Linkage, Mice, Inbred C57BL, Neurons, Repressor Proteins, RNA, Messenger, Sequence Homology, Nucleic Acid, Stem Cells, Translocation, Genetic, Tretinoin, Down-Regulation, Gene Expression Regulation, Neoplastic, Carcinoma, Embryonal, Gene Expression Regulation, Developmental, Gene Expression Profiling, Caenorhabditis elegans Proteins, MicroRNAs, Cell Line, Tumor, Mice, Genes, Neoplasm

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Claims read by deepseek-v4.1-flash under definition version 3 (extract-v3) on 2026-11-06.

Classified by jev-1.13-20260917 (gold-guideline-v0.2) on 2026-11-06.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

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