DOI: 10.1073/pnas.0511045103. Cell-type-specific signatures of microRNAs on target mRNA expression

Cell-type-specific signatures of microRNAs on target mRNA expression

10.1073/pnas.0511045103

Crossref journal-article

Proceedings of the National Academy of Sciences

Proceedings of the National Academy of Sciences (341)

Abstract

Although it is known that the human genome contains hundreds of microRNA (miRNA) genes and that each miRNA can regulate a large number of mRNA targets, the overall effect of miRNAs on mRNA tissue profiles has not been systematically elucidated. Here, we show that predicted human mRNA targets of several highly tissue-specific miRNAs are typically expressed in the same tissue as the miRNA but at significantly lower levels than in tissues where the miRNA is not present. Conversely, highly expressed genes are often enriched in mRNAs that do not have the recognition motifs for the miRNAs expressed in these tissues. Together, our data support the hypothesis that miRNA expression broadly contributes to tissue specificity of mRNA expression in many human tissues. Based on these insights, we apply a computational tool to directly correlate 3′ UTR motifs with changes in mRNA levels upon miRNA overexpression or knockdown. We show that this tool can identify functionally important 3′ UTR motifs without cross-species comparison.

Bibliography

Sood, P., Krek, A., Zavolan, M., Macino, G., & Rajewsky, N. (2006). Cell-type-specific signatures of microRNAs on target mRNA expression. Proceedings of the National Academy of Sciences, 103(8), 2746â2751.

Authors 5

Pranidhi Sood (first)
Azra Krek (additional)
Mihaela Zavolan (additional)
Giuseppe Macino (additional)
Nikolaus Rajewsky (additional)

References 25 Referenced 525

Dates

Type	When
Created	19 years, 6 months ago (Feb. 13, 2006, 8:44 p.m.)
Deposited	3 years, 4 months ago (April 12, 2022, 1:53 p.m.)
Indexed	2 days, 19 hours ago (Sept. 3, 2025, 5:51 a.m.)
Issued	19 years, 6 months ago (Feb. 13, 2006)
Published	19 years, 6 months ago (Feb. 13, 2006)
Published Online	19 years, 6 months ago (Feb. 13, 2006)
Published Print	19 years, 6 months ago (Feb. 21, 2006)

Funders 0

None

BibTeX

@article{Sood_2006, title={Cell-type-specific signatures of microRNAs on target mRNA expression}, volume={103}, ISSN={1091-6490}, url={http://dx.doi.org/10.1073/pnas.0511045103}, DOI={10.1073/pnas.0511045103}, number={8}, journal={Proceedings of the National Academy of Sciences}, publisher={Proceedings of the National Academy of Sciences}, author={Sood, Pranidhi and Krek, Azra and Zavolan, Mihaela and Macino, Giuseppe and Rajewsky, Nikolaus}, year={2006}, month=feb, pages={2746–2751} }

JSON

{
  "indexed": {
    "date-parts": [
      [
        2025,
        9,
        3
      ]
    ],
    "date-time": "2025-09-03T09:51:10Z",
    "timestamp": 1756893070004
  },
  "reference-count": 25,
  "publisher": "Proceedings of the National Academy of Sciences",
  "issue": "8",
  "content-domain": {
    "domain": [
      "www.pnas.org"
    ],
    "crossmark-restriction": true
  },
  "published-print": {
    "date-parts": [
      [
        2006,
        2,
        21
      ]
    ]
  },
  "abstract": "<jats:p>Although it is known that the human genome contains hundreds of microRNA (miRNA) genes and that each miRNA can regulate a large number of mRNA targets, the overall effect of miRNAs on mRNA tissue profiles has not been systematically elucidated. Here, we show that predicted human mRNA targets of several highly tissue-specific miRNAs are typically expressed in the same tissue as the miRNA but at significantly lower levels than in tissues where the miRNA is not present. Conversely, highly expressed genes are often enriched in mRNAs that do not have the recognition motifs for the miRNAs expressed in these tissues. Together, our data support the hypothesis that miRNA expression broadly contributes to tissue specificity of mRNA expression in many human tissues. Based on these insights, we apply a computational tool to directly correlate 3\u2032 UTR motifs with changes in mRNA levels upon miRNA overexpression or knockdown. We show that this tool can identify functionally important 3\u2032 UTR motifs without cross-species comparison.</jats:p>",
  "DOI": "10.1073/pnas.0511045103",
  "type": "journal-article",
  "created": {
    "date-parts": [
      [
        2006,
        2,
        14
      ]
    ],
    "date-time": "2006-02-14T01:44:07Z",
    "timestamp": 1139881447000
  },
  "page": "2746-2751",
  "update-policy": "http://dx.doi.org/10.1073/pnas.cm10313",
  "source": "Crossref",
  "is-referenced-by-count": 525,
  "title": "Cell-type-specific signatures of microRNAs on target mRNA expression",
  "prefix": "10.1073",
  "volume": "103",
  "author": [
    {
      "given": "Pranidhi",
      "family": "Sood",
      "sequence": "first",
      "affiliation": [
        {
          "name": "*Center for Comparative Functional Genomics, Department of Biology, New York University, 100 Washington Square East, New York, NY 10003;"
        }
      ]
    },
    {
      "given": "Azra",
      "family": "Krek",
      "sequence": "additional",
      "affiliation": [
        {
          "name": "*Center for Comparative Functional Genomics, Department of Biology, New York University, 100 Washington Square East, New York, NY 10003;"
        },
        {
          "name": "Department of Physics, New York University, 4 Washington Place, New York, NY 10003;"
        }
      ]
    },
    {
      "given": "Mihaela",
      "family": "Zavolan",
      "sequence": "additional",
      "affiliation": [
        {
          "name": "Biozentrum, University of Basel, Klingelbergstrasse 50/70, CH-4056 Basel, Switzerland; and"
        }
      ]
    },
    {
      "given": "Giuseppe",
      "family": "Macino",
      "sequence": "additional",
      "affiliation": [
        {
          "name": "Dipartimento di Biotecnologie Cellulari ed Ematologia, Universita di Roma La Sapienza, Viale Regina Elena 324, 00161 Rome, Italy"
        }
      ]
    },
    {
      "given": "Nikolaus",
      "family": "Rajewsky",
      "sequence": "additional",
      "affiliation": [
        {
          "name": "*Center for Comparative Functional Genomics, Department of Biology, New York University, 100 Washington Square East, New York, NY 10003;"
        }
      ]
    }
  ],
  "member": "341",
  "published-online": {
    "date-parts": [
      [
        2006,
        2,
        13
      ]
    ]
  },
  "reference": [
    {
      "key": "e_1_3_3_1_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/S0092-8674(04)00045-5"
    },
    {
      "key": "e_1_3_3_2_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1038/nature02871"
    },
    {
      "key": "e_1_3_3_3_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1242/dev.02070"
    },
    {
      "key": "e_1_3_3_4_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1056/NEJMp058190"
    },
    {
      "key": "e_1_3_3_5_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1038/nature04303"
    },
    {
      "key": "e_1_3_3_6_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1038/nbt831"
    },
    {
      "key": "e_1_3_3_7_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1038/nature03315"
    },
    {
      "key": "e_1_3_3_8_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/j.cell.2005.07.031"
    },
    {
      "key": "e_1_3_3_9_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1073/pnas.0400782101"
    },
    {
      "key": "e_1_3_3_10_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1126/science.1090100"
    },
    {
      "key": "e_1_3_3_11_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1038/ng1536"
    },
    {
      "key": "e_1_3_3_12_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1261/rna.7240905"
    },
    {
      "key": "e_1_3_3_13_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1038/nature03552"
    },
    {
      "key": "e_1_3_3_14_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/j.cell.2004.12.035"
    },
    {
      "key": "e_1_3_3_15_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1038/nature03441"
    },
    {
      "key": "e_1_3_3_16_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1038/nmeth746"
    },
    {
      "key": "e_1_3_3_17_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1038/ng1590"
    },
    {
      "key": "e_1_3_3_18_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/j.cell.2004.12.031"
    },
    {
      "key": "e_1_3_3_19_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1038/ng865"
    },
    {
      "key": "e_1_3_3_20_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1371/journal.pbio.0030085"
    },
    {
      "key": "e_1_3_3_21_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1371/journal.pbio.0020363"
    },
    {
      "key": "e_1_3_3_22_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/j.devcel.2005.01.018"
    },
    {
      "key": "e_1_3_3_23_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1038/84792"
    },
    {
      "key": "e_1_3_3_24_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1128/MCB.15.4.2219"
    },
    {
      "key": "e_1_3_3_25_2",
      "doi-asserted-by": "publisher",
      "DOI": "10.1016/j.cell.2004.12.038"
    }
  ],
  "container-title": "Proceedings of the National Academy of Sciences",
  "original-title": [],
  "language": "en",
  "link": [
    {
      "URL": "https://pnas.org/doi/pdf/10.1073/pnas.0511045103",
      "content-type": "unspecified",
      "content-version": "vor",
      "intended-application": "similarity-checking"
    }
  ],
  "deposited": {
    "date-parts": [
      [
        2022,
        4,
        12
      ]
    ],
    "date-time": "2022-04-12T17:53:21Z",
    "timestamp": 1649786001000
  },
  "score": 1,
  "resource": {
    "primary": {
      "URL": "https://pnas.org/doi/full/10.1073/pnas.0511045103"
    }
  },
  "subtitle": [],
  "short-title": [],
  "issued": {
    "date-parts": [
      [
        2006,
        2,
        13
      ]
    ]
  },
  "references-count": 25,
  "journal-issue": {
    "issue": "8",
    "published-print": {
      "date-parts": [
        [
          2006,
          2,
          21
        ]
      ]
    }
  },
  "alternative-id": [
    "10.1073/pnas.0511045103"
  ],
  "URL": "http://dx.doi.org/10.1073/pnas.0511045103",
  "relation": {},
  "ISSN": [
    "0027-8424",
    "1091-6490"
  ],
  "subject": [],
  "container-title-short": "Proc. Natl. Acad. Sci. U.S.A.",
  "published": {
    "date-parts": [
      [
        2006,
        2,
        13
      ]
    ]
  },
  "assertion": [
    {
      "value": "2005-11-16",
      "order": 0,
      "name": "received",
      "label": "Received",
      "group": {
        "name": "publication_history",
        "label": "Publication History"
      }
    },
    {
      "value": "2006-02-13",
      "order": 2,
      "name": "published",
      "label": "Published",
      "group": {
        "name": "publication_history",
        "label": "Publication History"
      }
    }
  ]
}