The DOI matches its Crossref record; 24 of the 24 references it cites were found in a registry or an index.
Gene expression map of the Arabidopsis shoot apical meristem stem cell niche
Open accessAbstract
Despite the central importance of stem cells in plant growth and development, the molecular signatures associated with them have not been revealed. Shoot apical meristems (SAMs) harbor a small set of stem cells located at the tip of each plant and they are surrounded by several million differentiating cells. This imposes a major limitation in isolating pure populations of stem cells for genomic analyses. We have developed a system to isolate pure populations of distinct cell types of the SAMs, including stem cells. We have used this system to profile gene expression from 4 different cell samples of SAMs. The cell sample-specific gene expression profiling has resulted in a high-resolution gene expression map to reveal gene expression networks specific to individual spatial domains of SAMs. We demonstrate that the cell sample-specific expression profiling is sensitive in identifying rare transcripts expressed in a few specific subsets of cells of SAMs. Our extensive RNA in situ analysis reveals that the expression map can be used as a predictive tool in analyzing the spatial expression patterns of genes and it has led to the identification of unique gene expression patterns within the SAMs. Furthermore, our work reveals an enrichment of DNA repair and chromatin modification pathways in stem cells suggesting that maintenance of genome stability and flexible chromatin may be crucial for stem cell function. The gene expression map should guide future reverse genetics experiments, high-resolution analyses of cell–cell communication networks and epigenetic modifications.
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.
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 forAgrobacterium‐mediated transformation ofArabidopsis thaliana
Clough, S. J., & Bent, A. F. (1998) · The Plant Journal · doi:10.1046/j.1365-313x.1998.00343.x · Cited by 21,934
A bivalent chromatin structure marks key developmental genes in embryonic stem cells
Bernstein, B. E., Mikkelsen, T. S., Xie, X., Kamal, M., Huebert, D. J., Cuff, J., Fry, B., Meissner, A., Wernig, M., Plath, K., et al. (2006) · Cell · doi:10.1016/j.cell.2006.02.041 · Cited by 5,361
Genome-wide maps of chromatin state in pluripotent and lineage-committed cells
Mikkelsen, T. S., Ku, M., Jaffe, D. B., Issac, B., Lieberman, E., Giannoukos, G., Alvarez, P., Brockman, W., Kim, T.-K., Koche, R. P., et al. (2007) · Nature · doi:10.1038/nature06008 · Cited by 4,129
A gene expression map of Arabidopsis thaliana development
Schmid, M., Davison, T. S., Henz, S. R., Pape, U. J., Demar, M., Vingron, M., Schölkopf, B., Weigel, D., & Lohmann, J. U. (2005) · Nature Genetics · doi:10.1038/ng1543 · Cited by 2,523
Stem Cells and Niches: Mechanisms That Promote Stem Cell Maintenance throughout Life
Morrison, S. J., & Spradling, A. C. (2008) · Cell · doi:10.1016/j.cell.2008.01.038 · Cited by 1,955
Role of WUSCHEL in Regulating Stem Cell Fate in the Arabidopsis Shoot Meristem
Mayer, K. F. X., Schoof, H., Haecker, A., Lenhard, M., Jürgens, G., & Laux, T. (1998) · Cell · doi:10.1016/s0092-8674(00)81703-1 · Cited by 1,702
Signaling of Cell Fate Decisions by CLAVATA3 in Arabidopsis Shoot Meristems
Fletcher, J. C., Brand, U., Running, M. P., Simon, R., & Meyerowitz, E. M. (1999) · Science · doi:10.1126/science.283.5409.1911 · Cited by 1,357
A Gene Expression Map of the Arabidopsis Root
Birnbaum, K., Shasha, D. E., Wang, J. Y., Jung, J. W., Lambert, G. M., Galbraith, D. W., & Benfey, P. N. (2003) · Science · doi:10.1126/science.1090022 · Cited by 1,258
Heisler, M. G., Ohno, C., Das, P., Sieber, P., Reddy, G. V., Long, J. A., & Meyerowitz, E. M. (2005) · Current Biology · doi:10.1016/j.cub.2005.09.052 · Cited by 1,189
Self-citationA High-Resolution Root Spatiotemporal Map Reveals Dominant Expression Patterns
Brady, S. M., Orlando, D. A., Lee, J.-Y., Wang, J. Y., Koch, J., Dinneny, J. R., Mace, D., Ohler, U., & Benfey, P. N. (2007) · Science · doi:10.1126/science.1146265 · Cited by 1,182
Cited by
Twenty years on: The inner workings of the shoot apical meristem, a developmental dynamo
Barton, M. K. (2010) · Developmental Biology · doi:10.1016/j.ydbio.2009.11.029 · Cited by 372
DNA methylation dynamics during early plant life
Bouyer, D., Kramdi, A., Kassam, M., Heese, M., Schnittger, A., Roudier, F., & Colot, V. (2017) · Genome Biology · doi:10.1186/s13059-017-1313-0 · Cited by 239
Tian, C., Zhang, X., He, J., Yu, H., Wang, Y., Shi, B., Han, Y., Wang, G., Feng, X., Zhang, C., et al. (2014) · Molecular Systems Biology · doi:10.15252/msb.20145470 · Cited by 133
Nitric oxide controls shoot meristem activity via regulation of DNA methylation
Zeng, J., Zhao, X., Liang, Z., Hidalgo, I., Gebert, M., Fan, P., Wenzl, C., Gornik, S. G., & Lohmann, J. U. (2023) · Nature Communications · doi:10.1038/s41467-023-43705-1 · Cited by 36
Metadata
- Authors
- Yadav, R. K., Girke, T., Pasala, S., Xie, M., & Reddy, G. V.
- Venue
- Proceedings of the National Academy of Sciences
- Published
- 2009-03-24
- Volume
- 106
- Issue
- 12
- Pages
- 4941-4946
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- OpenAlex
- W2023230492
- Cited by
- 337
- References
- 24
- FWCI
- 40.43
- Type
- journal article
- Language
- en
- Open access
- green
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
How to cite
Cite CoChat for the checks on this page, and the paper for its own findings.
- This page
- CoChat. (2026). Citation check: Gene expression map of the Arabidopsis shoot apical meristem stem cell niche. https://app.cochat.ai/papers/10.1073/pnas.0900843106
- The paper
- Yadav, R. K., Girke, T., Pasala, S., Xie, M., & Reddy, G. V. (2009). Gene expression map of the Arabidopsis shoot apical meristem stem cell niche. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.0900843106
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
