The DOI matches its Crossref record; 42 of the 42 references it cites were found in a registry or an index.
Cell signalling by microRNA165/6 directs gene dose-dependent root cell fate
Open accessAbstract
A key question in developmental biology is how cells exchange positional information for proper patterning during organ development. In plant roots the radial tissue organization is highly conserved with a central vascular cylinder in which two water conducting cell types, protoxylem and metaxylem, are patterned centripetally. We show that this patterning occurs through crosstalk between the vascular cylinder and the surrounding endodermis mediated by cell-to-cell movement of a transcription factor in one direction and microRNAs in the other. SHORT ROOT, produced in the vascular cylinder, moves into the endodermis to activate SCARECROW. Together these transcription factors activate MIR165a and MIR166b. Endodermally produced microRNA165/6 then acts to degrade its target mRNAs encoding class III homeodomain-leucine zipper transcription factors in the endodermis and stele periphery. The resulting differential distribution of target mRNA in the vascular cylinder determines xylem cell types in a dosage-dependent manner.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
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?
The source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“Another key epigenetic mechanism involves small RNA pathways, especially microRNAs (miRNAs) and small interfering RNAs (siRNAs), which play a vital role in regulating gene expression at both transcriptional and post-transcriptional levels, influencing essential processes such as cell fate in eukaryotes [59,60].”
From Somaclonal Variation and Clonal Fidelity in Commercial Micropropagation: Challenges and Perspectives (2025) · cites this paper as [59]
Experimental — accuracy not yet measured
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Floral dip: a simplified method for Agrobacterium ‐mediated transformation of Arabidopsis thaliana
Clough, S. J., & Bent, A. F. (1998) · The Plant Journal · doi:10.1046/j.1365-313x.1998.00343.x · Cited by 22,014
Esau, K. (1960) · Soil Science · doi:10.1097/00010694-196008000-00031 · Cited by 2,092
Radial Patterning of Arabidopsis Shoots by Class III HD-ZIP and KANADI Genes
Emery, J. F., Floyd, S. K., Alvarez, J., Eshed, Y., Hawker, N. P., Izhaki, A., Baum, S. F., & Bowman, J. L. (2003) · Current Biology · doi:10.1016/j.cub.2003.09.035 · Cited by 1,143
Self-citationDi Laurenzio, L., Wysocka-Diller, J., Malamy, J. E., Pysh, L., Helariutta, Y., Freshour, G., Hahn, M. G., Feldmann, K. A., & Benfey, P. N. (1996) · Cell · doi:10.1016/s0092-8674(00)80115-4 · Cited by 1,124
Self-citationThe SHORT-ROOT Gene Controls Radial Patterning of the Arabidopsis Root through Radial Signaling
Helariutta, Y., Fukaki, H., Wysocka‐Diller, J. W., Nakajima, K., Jung, J. W., Sena, G., Hauser, M., & Benfey, P. N. (2000) · Cell · doi:10.1016/s0092-8674(00)80865-x · Cited by 1,123
Self-citationRole of PHABULOSA and PHAVOLUTA in determining radial patterning in shoots
McConnell, J. R., Emery, J. F., Eshed, Y., Bao, N., Bowman, J. L., & Barton, M. K. (2001) · Nature · doi:10.1038/35079635 · Cited by 1,104
Self-citationStark, A., Brennecke, J., Bushati, N., Russell, R. B., & Cohen, S. M. (2005) · Cell · doi:10.1016/j.cell.2005.11.023 · Cited by 1,080
Intercellular movement of the putative transcription factor SHR in root patterning
Nakajima, K., Sena, G., Nawy, T., & Benfey, P. N. (2001) · Nature · doi:10.1038/35095061 · Cited by 870
Self-citationPrigge, M. J., Otsuga, D., Alonso, J. M., Ecker, J. R., Drews, G. N., & Clark, S. E. (2004) · The Plant Cell · doi:10.1105/tpc.104.026161 · Cited by 777
SCARECROW is involved in positioning the stem cell niche in the Arabidopsis root meristemPreprint
Sabatini, S., Heidstra, R., Wildwater, M., & Scheres, B. (2003) · Genes & Development · doi:10.1101/gad.252503 · Cited by 727
Facile Means for Quantifying Microrna Expression by Real-Time PCR
Shi, R., & Chiang, V. L. (2005) · BioTechniques · doi:10.2144/000112010 · Cited by 715
microRNA-mediated repression of rolled leaf1 specifies maize leaf polarity
Juarez, M. T., Kui, J. S., Thomas, J., Heller, B. A., & Timmermans, M. C. P. (2004) · Nature · doi:10.1038/nature02363 · Cited by 704
MicroRNA control of PHABULOSA in leaf development: importance of pairing to the microRNA 5′ region
Mallory, A. C., Reinhart, B. J., Jones-Rhoades, M. W., Tang, G., Zamore, P. D., Barton, M. K., & Bartel, D. P. (2004) · The EMBO Journal · doi:10.1038/sj.emboj.7600340 · Cited by 681
Cytokinin Signaling and Its Inhibitor AHP6 Regulate Cell Fate During Vascular Development
Mähönen, A. P., Bishopp, A., Higuchi, M., Nieminen, K. M., Kinoshita, K., Törmäkangas, K., Ikeda, Y., Oka, A., Kakimoto, T., & Helariutta, Y. (2006) · Science · doi:10.1126/science.1118875 · Cited by 617
Self-citationCui, H., Levesque, M. P., Vernoux, T., Jung, J. W., Paquette, A. J., Gallagher, K. L., Wang, J. Y., Blilou, I., Scheres, B., & Benfey, P. N. (2007) · Science · doi:10.1126/science.1139531 · Cited by 602
Self-citationA novel two-component hybrid molecule regulates vascular morphogenesis of the Arabidopsis rootPreprint
Mähönen, A. P., Bonke, M., Kauppinen, L., Riikonen, M., Benfey, P. N., & Helariutta, Y. (2000) · Genes & Development · doi:10.1101/gad.189200 · Cited by 552
Self-citationVazquez, F., Gasciolli, V., Crété, P., & Vaucheret, H. (2004) · Current Biology · doi:10.1016/j.cub.2004.01.035 · Cited by 544
Han, M.-H., Goud, S., Song, L., & Fedoroff, N. V. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0307969100 · Cited by 522
Regulatory Network of MicroRNA399 and PHO2 by Systemic Signaling
Lin, S.-I., Chiang, S., Lin, W., Chen, J.-W., Tseng, C.-Y., Wu, P., & Chiou, T. (2008) · PLANT PHYSIOLOGY · doi:10.1104/pp.108.116269 · Cited by 480
Baima, S., Possenti, M., Matteucci, A., Wisman, E., Altamura, M. M., Ruberti, I., & Morelli, G. (2001) · PLANT PHYSIOLOGY · doi:10.1104/pp.126.2.643 · Cited by 461
(2005) · Choice Reviews Online · doi:10.5860/choice.42-4627 · Cited by 420
Ancient microRNA target sequences in plants
Floyd, S. K., & Bowman, J. L. (2004) · Nature · doi:10.1038/428485a · Cited by 403
Self-citationPattern formation via small RNA mobilityPreprint
Chitwood, D. H., Nogueira, F. T. S., Howell, M. D., Montgomery, T. A., Carrington, J. C., & Timmermans, M. C. P. (2009) · Genes & Development · doi:10.1101/gad.1770009 · Cited by 399
Parizotto, E. A., Dunoyer, P., Rahm, N., Himber, C., & Voinnet, O. (2004) · Genes & Development · doi:10.1101/gad.307804 · Cited by 367
Whole-Genome Analysis of the SHORT-ROOT Developmental Pathway in Arabidopsis
Levesque, M. P., Vernoux, T., Busch, W., Cui, H., Wang, J. Y., Blilou, I., Hassan, H., Nakajima, K., Matsumoto, N., Lohmann, J. U., et al. (2006) · PLoS Biology · doi:10.1371/journal.pbio.0040143 · Cited by 345
Self-citationLee, J., Colinas, J., Wang, J. Y., Mace, D., Ohler, U., & Benfey, P. N. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0510607103 · Cited by 292
Self-citationThe Ancestral Developmental Tool Kit of Land Plants
Floyd, S. K., & Bowman, J. L. (2006) · International Journal of Plant Sciences · doi:10.1086/509079 · Cited by 292
Self-citationDunoyer, P., Himber, C., Ruíz‐Ferrer, V., Alioua, A., & Voinnet, O. (2007) · Nature Genetics · doi:10.1038/ng2081 · Cited by 250
Mechanisms regulating SHORT-ROOT intercellular movement.
Gallagher, K. L., Paquette, A. J., Nakajima, K., & Benfey, P. N. (2004) · Current Biology · doi:10.1016/j.cub.2004.09.081 · Cited by 248
Self-citationHolbrook, N. M., & Zwieniecki, M. A. (2005) · Cited by 237
Zhou, G., Kubo, M., Zhong, R., Demura, T., & Ye, Z. (2007) · Plant and Cell Physiology · doi:10.1093/pcp/pcm008 · Cited by 232
Jung, J., & Park, C. (2006) · Planta · doi:10.1007/s00425-006-0439-1 · Cited by 207
Roles for Class III HD-Zip and KANADI Genes in Arabidopsis Root Development
Hawker, N. P., & Bowman, J. L. (2004) · PLANT PHYSIOLOGY · doi:10.1104/pp.104.040196 · Cited by 177
Self-citationACAULIS5 controls Arabidopsis xylem specification through the prevention of premature cell death
Muñiz, L. M., Minguet, E. G., Singh, S. K., Pesquet, E., Vera‐Sirera, F., Courtois-Moreau, C., Carbonell, J., Blázquez, M. A., & Tuominen, H. (2008) · Development · doi:10.1242/dev.019349 · Cited by 167
Both the conserved GRAS domain and nuclear localization are required for SHORT‐ROOT movement
Gallagher, K. L., & Benfey, P. N. (2008) · The Plant Journal · doi:10.1111/j.1365-313x.2008.03735.x · Cited by 152
Self-citationRegulation of Small RNA Accumulation in the Maize Shoot Apex
Nogueira, F. T. S., Chitwood, D. H., Madi, S., Ohtsu, K., Schnable, P. S., Scanlon, M. J., & Timmermans, M. C. P. (2009) · PLoS Genetics · doi:10.1371/journal.pgen.1000320 · Cited by 144
Small Regulatory RNAs May Sharpen Spatial Expression Patterns
Levine, E., McHale, P. T., & Levine, H. (2007) · PLoS Computational Biology · doi:10.1371/journal.pcbi.0030233 · Cited by 101
Why cells move messages: The biological functions of mRNA localization
Du, T., Schmid, M., & Jansen, R. (2007) · Seminars in Cell and Developmental Biology · doi:10.1016/j.semcdb.2007.01.010 · Cited by 98
Class III Homeodomain Leucine-Zipper Proteins Regulate Xylem Cell Differentiation
Ohashi‐Ito, K., Kubo, M., Demura, T., & Fukuda, H. (2005) · Plant and Cell Physiology · doi:10.1093/pcp/pci180 · Cited by 93
The Evolutionary History of Roots and Leaves
Boyce, C. K. (2005) · Elsevier eBooks · doi:10.1016/b978-012088457-5/50025-3 · Cited by 60
Activity Range of Arabidopsis Small RNAs Derived from Different Biogenesis Pathways
Tretter, E. M., Alvarez, J. P., Eshed, Y., & Bowman, J. L. (2008) · PLANT PHYSIOLOGY · doi:10.1104/pp.108.117119 · Cited by 54
Self-citationThe Radiation of Vascular Plants
Pryer, K. M., Schneider, H., & Magallón, S. (2004) · doi:10.1093/oso/9780195172348.003.0011 · Cited by 22
Flagged first, then by citations
Cited by
Sorted by citations
The widespread regulation of microRNA biogenesis, function and decay
Krol, J., Loedige, I., & Filipowicz, W. (2010) · Nature Reviews Genetics · doi:10.1038/nrg2843 · Cited by 4,672
The expanding world of small RNAs in plants
Borges, F., & Martienssen, R. A. (2015) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm4085 · Cited by 1,049
An unconventional role for miRNA: let-7 activates toll-like receptor 7 and causes neurodegeneration
Lehmann, S. M., Krüger, C., Park, B., Derkow, K., Rosenberger, K., Baumgart, J., Trimbuch, T., Eom, G., Hinz, M., Kaul, D., et al. (2012) · Nature Neuroscience · doi:10.1038/nn.3113 · Cited by 786
The Plant Vascular System: Evolution, Development and Functions F
Lucas, W. J., Groover, A. T., Lichtenberger, R., Furuta, K. M., Yadav, S. R., Helariutta, Y., He, X., Fukuda, H., Kang, J., Brady, S. M., et al. (2013) · Journal of Integrative Plant Biology · doi:10.1111/jipb.12041 · Cited by 790
Self-citationAn Arabidopsis gene regulatory network for secondary cell wall synthesis
Taylor‐Teeples, M., Lin, L., de Lucas, M., Turco, G. M., Toal, T., Gaudinier, A., Young, N. F., Trabucco, G. M., Veling, M. T., Lamothe, R. M., et al. (2014) · Nature · doi:10.1038/nature14099 · Cited by 765
Metadata
- Authors
- Carlsbecker, A., Lee, J.-Y., Roberts, C. J., Dettmer, J., Lehesranta, S., Zhou, J., Lindgren, O., Moreno-Risueno, M. A., Vatén, A., Thitamadee, S., Campilho, A., Sebastian, J., Bowman, J. L., Helariutta, Y., & Benfey, P. N.
- Affiliations
- University of Helsinki (FI)
- Cornell University (US)
- Uppsala University (SE)
- Monash University (AU)
- Duke University (US)
- Corresponding author
- Helariutta, Ykä
- Benfey, Philip N.
- ORCID
- Venue
- Nature
- Published
- 2010-04-21
- Volume
- 465
- Issue
- 7296
- Pages
- 316-321
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC2967782
- OpenAlex
- W2083540641
- Cited by
- 861
- References
- 42
- Citations by year
- 2026: 32 · 2025: 31 · 2024: 36 · 2023: 39 · 2022: 58 · 2021: 57 · 2020: 67 · 2019: 53 · 2018: 45 · 2017: 54 · 2016: 55 · 2015: 65 · 2014: 57 · 2013: 65 · 2012: 61
- FWCI
- 81.61
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- ORCA Online Research @Cardiff (Cardiff University) (submittedVersion)
- Funders
- National Institute of General Medical Sciences (R01GM043778)
- Topics
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Plant Molecular Biology Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Developmental Biology and Gene Regulation
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Plant nutrient uptake and metabolism
- Keywords
- SHORT-ROOT, scarecrow, protoxylem, metaxylem, endodermis, vascular cylinder, positional information, root development, Arabidopsis thaliana
- MeSH terms
- Cell Movement, Endoderm, Transcription Factors, Signal Transduction, Arabidopsis, Gene Expression Regulation, Plant, Plant Roots, Gene Dosage, RNA, Plant, Cell Lineage, Body Patterning, Arabidopsis Proteins, RNA Transport, MicroRNAs, Organogenesis, Xylem
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.
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.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
