The DOI matches its Crossref record; 77 of the 77 references it cites were found in a registry or an index.
Cell-Type-Specific Profiling of Gene Expression and Chromatin Binding without Cell Isolation: Assaying RNA Pol II Occupancy in Neural Stem Cells
Open accessAbstract
Cell-type-specific transcriptional profiling often requires the isolation of specific cell types from complex tissues. We have developed "TaDa," a technique that enables cell-specific profiling without cell isolation. TaDa permits genome-wide profiling of DNA- or chromatin-binding proteins without cell sorting, fixation, or affinity purification. The method is simple, sensitive, highly reproducible, and transferable to any model system. We show that TaDa can be used to identify transcribed genes in a cell-type-specific manner with considerable temporal precision, enabling the identification of differential gene expression between neuroblasts and the neuroepithelial cells from which they derive. We profile the genome-wide binding of RNA polymerase II in these adjacent, clonally related stem cells within intact Drosophila brains. Our data reveal expression of specific metabolic genes in neuroepithelial cells, but not in neuroblasts, and highlight gene regulatory networks that may pattern neural stem cell fates.
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
Targeted gene expression as a means of altering cell fates and generating dominant phenotypes
Brand, A. H., & Perrimon, N. (1993) · Development · doi:10.1242/dev.118.2.401 · Cited by 9,612
Self-citationShaner, N. C., Campbell, R. E., Steinbach, P. A., Giepmans, B. N. G., Palmer, A. E., & Tsien, R. Y. (2004) · Nature Biotechnology · doi:10.1038/nbt1037 · Cited by 4,619
Hayes, J. D., Flanagan, J. U., & Jowsey, I. R. (2005) · Annual Review of Pharmacology and Toxicology · doi:10.1146/annurev.pharmtox.45.120403.095857 · Cited by 3,544
Szklarczyk, D., Franceschini, A., Kuhn, M., Simonovic, M., Roth, A., Minguez, P., Doerks, T., Stark, M., Muller, J., Bork, P., et al. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkq973 · Cited by 3,460
Lee, T., & Luo, L. (1999) · Neuron · doi:10.1016/s0896-6273(00)80701-1 · Cited by 2,571
Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions
Guelen, L., Pagie, L., Brasset, E., Meuleman, W., Faza, M. B., Talhout, W., Eussen, B. H., de Klein, A., Wessels, L., de Laat, W., et al. (2008) · Nature · doi:10.1038/nature06947 · Cited by 1,953
An optimized transgenesis system for Drosophila using germ-line-specific φC31 integrases
Bischof, J., Maeda, R. K., Hediger, M., Karch, F., & Basler, K. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0611511104 · Cited by 1,866
Induction of Ectopic Eyes by Targeted Expression of the eyeless Gene in Drosophila
Halder, G., Callaerts, P., & Gehring, W. J. (1995) · Science · doi:10.1126/science.7892602 · Cited by 1,573
A GAL4-Driver Line Resource for Drosophila Neurobiology
Jenett, A., Rubin, G. M., Ngo, T.-T. B., Shepherd, D., Murphy, C., Dionne, H., Pfeiffer, B. D., Cavallaro, A., Hall, D., Jeter, J., et al. (2012) · Cell Reports · doi:10.1016/j.celrep.2012.09.011 · Cited by 1,449
Spatiotemporal Rescue of Memory Dysfunction in Drosophila
McGuire, S. E., Le, P. T., Osborn, A. J., Matsumoto, K., & Davis, R. L. (2003) · Science · doi:10.1126/science.1089035 · Cited by 1,316
Luo, L., Liao, Y. J., Jan, L. Y., & Jan, Y. N. (1994) · Genes & Development · doi:10.1101/gad.8.15.1787 · Cited by 983
Systematic Protein Location Mapping Reveals Five Principal Chromatin Types in Drosophila Cells
Filion, G. J., van Bemmel, J. G., Braunschweig, U., Talhout, W., Kind, J., Ward, L. D., Brugman, W., de Castro, I. J., Kerkhoven, R. M., Bussemaker, H. J., et al. (2010) · Cell · doi:10.1016/j.cell.2010.09.009 · Cited by 964
Identification of in vivo DNA targets of chromatin proteins using tethered Dam methyltransferase
Steensel, B. V., & Henikoff, S. (2000) · Nature Biotechnology · doi:10.1038/74487 · Cited by 626
Markstein, M., Pitsouli, C., Villalta, C., Celniker, S. E., & Perrimon, N. (2008) · Nature Genetics · doi:10.1038/ng.101 · Cited by 515
Bonn, S., Zinzen, R. P., Girardot, C., Gustafson, E. H., Perez-Gonzalez, A., Delhomme, N., Ghavi-Helm, Y., Wilczyński, B., Riddell, A., & Furlong, E. E. M. (2012) · Nature Genetics · doi:10.1038/ng.1064 · Cited by 502
Nechaev, S., Fargo, D. C., dos Santos, G., Liu, L., Gao, Y., & Adelman, K. (2010) · Science · doi:10.1126/science.1181421 · Cited by 424
Gilchrist, D. A., Dos Santos, G., Fargo, D. C., Xie, B., Gao, Y., Li, L., & Adelman, K. (2010) · Cell · doi:10.1016/j.cell.2010.10.004 · Cited by 414
Chromosomal clustering of muscle-expressed genes in Caenorhabditis elegans
Roy, P. J., Stuart, J. M., Lund, J., & Kim, S. K. (2002) · Nature · doi:10.1038/nature01012 · Cited by 412
Choksi, S. P., Southall, T. D., Bossing, T., Edoff, K., de Wit, E., Fischer, B. E., van Steensel, B., Micklem, G., & Brand, A. H. (2006) · Developmental Cell · doi:10.1016/j.devcel.2006.09.015 · Cited by 410
Self-citationLaborde, E. (2010) · Cell Death & Differentiation · doi:10.1038/cdd.2010.80 · Cited by 409
A Simple Method for Gene Expression and Chromatin Profiling of Individual Cell Types within a Tissue
Deal, R. B., & Henikoff, S. (2010) · Developmental Cell · doi:10.1016/j.devcel.2010.05.013 · Cited by 390
Genome-wide profiling of PRC1 and PRC2 Polycomb chromatin binding in Drosophila melanogaster
Tolhuis, B., Muijrers, I., de Wit, E., Teunissen, H., Talhout, W., van Steensel, B., & van Lohuizen, M. (2006) · Nature Genetics · doi:10.1038/ng1792 · Cited by 381
Control of sexual differentiation and behavior by the doublesex gene in Drosophila melanogaster
Rideout, E. J., Dornan, A. J., Neville, M. C., Eadie, S., & Goodwin, S. F. (2010) · Nature Neuroscience · doi:10.1038/nn.2515 · Cited by 372
Chapter 33 Ectopic Expression in Drosophila
Brand, A. H., Manoukian, A. S., & Perrimon, N. (1994) · Methods in Cell Biology · doi:10.1016/s0091-679x(08)60936-x · Cited by 351
Self-citationDetection of in vivo protein–DNA interactions using DamID in mammalian cells
Vogel, M. J., Peric-Hupkes, D., & van Steensel, B. (2007) · Nature Protocols · doi:10.1038/nprot.2007.148 · Cited by 336
Chromatin profiling using targeted DNA adenine methyltransferase
van Steensel, B., Delrow, J., & Henikoff, S. (2001) · Nature Genetics · doi:10.1038/85871 · Cited by 326
Constraints on reinitiation of translation in mammals
Kozak, M. (2001) · Nucleic Acids Research · doi:10.1093/nar/29.24.5226 · Cited by 303
Truman, J. W., Talbot, W. S., Fahrbach, S. E., & Hogness, D. S. (1994) · Development · doi:10.1242/dev.120.1.219 · Cited by 283
Farkas, L. M., & Huttner, W. B. (2008) · Current Opinion in Cell Biology · doi:10.1016/j.ceb.2008.09.008 · Cited by 248
Gradients of the Drosophila Chinmo BTB-Zinc Finger Protein Govern Neuronal Temporal Identity
Zhu, S., Lin, S., Kao, C.-F., Awasaki, T., Chiang, A.-S., & Lee, T. (2006) · Cell · doi:10.1016/j.cell.2006.08.045 · Cited by 248
GAL4 enhancer traps expressed in the embryo, larval brain, imaginal discs, and ovary of drosophila
Manseau, L. J., Baradaran, A., Brower, D. L., Budhu, A., Elefant, F., Phan, H., Philp, A. V., Yang, M., Glover, D. M., Kaiser, K., et al. (1997) · Developmental Dynamics · Cited by 244
Miranda mediates asymmetric protein and RNA localization in the developing nervous system
Schuldt, A. J., Adams, J. H. J., Davidson, C. M., Micklem, D. R., Haseloff, J., Johnston, D. S., & Brand, A. H. (1998) · Genes & Development · doi:10.1101/gad.12.12.1847 · Cited by 243
Self-citationRegulation of spindle orientation and neural stem cell fate in the Drosophila optic lobe
Egger, B., Boone, J. Q., Stevens, N. R., Brand, A. H., & Doe, C. Q. (2007) · Neural Development · doi:10.1186/1749-8104-2-1 · Cited by 226
Self-citationProliferation pattern and early differentiation of the optic lobes in Drosophila melanogaster
Hofbauer, A., & Campos-Ortega, J. A. (1990) · Roux's Archives of Developmental Biology · doi:10.1007/bf00377393 · Cited by 218
Regulation of post-embryonic neuroblasts by Drosophila Grainyhead
Almeida, M. S., & Bray, S. J. (2005) · Mechanisms of Development · doi:10.1016/j.mod.2005.08.004 · Cited by 195
Jitrapakdee, S. (2012) · The International Journal of Biochemistry & Cell Biology · doi:10.1016/j.biocel.2011.10.001 · Cited by 195
Richardson, H., O’Keefe, L. V., & Marty, T. (1995) · Development · doi:10.1242/dev.121.10.3371 · Cited by 189
Luukkonen, B. G., Tan, W., & Schwartz, S. (1995) · Journal of Virology · doi:10.1128/jvi.69.7.4086-4094.1995 · Cited by 181
TU-tagging: cell type–specific RNA isolation from intact complex tissues
Miller, M. R., Robinson, K. J., Cleary, M. D., & Doe, C. Q. (2009) · Nature Methods · doi:10.1038/nmeth.1329 · Cited by 176
Egger, B., Gold, K. S., & Brand, A. H. (2010) · Development · doi:10.1242/dev.051250 · Cited by 159
Self-citationYasugi, T., Umetsu, D., Murakami, S., Sato, M., & Tabata, T. (2008) · Development · doi:10.1242/dev.019117 · Cited by 156
Vactor, D. V., Cagan, R. L., Krämer, H., & Zipursky, S. L. (1991) · Cell · doi:10.1016/0092-8674(91)90291-6 · Cited by 154
Human heterochromatin proteins form large domains containing KRAB-ZNF genesPreprint
Vogel, M. J., Guelen, L., de Wit, E., Peric‐Hupkes, D., Lodén, M., Talhout, W., Feenstra, M., Abbas, B., Classen, A.-K., & van Steensel, B. (2006) · Genome Research · doi:10.1101/gr.5391806 · Cited by 154
Reddy, B. V. V. G., Rauskolb, C., & Irvine, K. D. (2010) · Development · doi:10.1242/dev.050013 · Cited by 144
Cell type–specific genomics of Drosophila neurons
Henry, G. L., Davis, F. P., Picard, S., & Eddy, S. R. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks671 · Cited by 143
Neural stem cell transcriptional networks highlight genes essential for nervous system development
Southall, T. D., & Brand, A. H. (2009) · The EMBO Journal · doi:10.1038/emboj.2009.309 · Cited by 134
Self-citationA Versatile Method for Cell-Specific Profiling of Translated mRNAs in Drosophila
Thomas‐Wilson, A., Lee, P.-J., Dalton, J. E., Nomie, K. J., Stoica, L., Costa‐Mattioli, M., Chang, P. L., Nuzhdin, S. V., Arbeitman, M. N., & Dierick, H. A. (2012) · PLoS ONE · doi:10.1371/journal.pone.0040276 · Cited by 129
Perlecan participates in proliferation activation of quiescent Drosophila neuroblasts
Voigt, A., Pflanz, R., Schäfer, U., & Jäckle, H. (2002) · Developmental Dynamics · doi:10.1002/dvdy.10120 · Cited by 126
Matsumoto, K., Toh‐e, A., & Oshima, Y. (1978) · Journal of Bacteriology · doi:10.1128/jb.134.2.446-457.1978 · Cited by 124
Chotard, C., Leung, W., & Salecker, I. (2005) · Neuron · doi:10.1016/j.neuron.2005.09.019 · Cited by 124
DamID in C. elegans reveals longevity‐associated targets of DAF‐16/FoxO
Schuster, E. F., McElwee, J. J., Tullet, J. M. A., Doonan, R., Matthijssens, F., Reece-Hoyes, J. S., Hope, I. A., Vanfleteren, J. R., Thornton, J. M., & Gems, D. (2010) · Molecular Systems Biology · doi:10.1038/msb.2010.54 · Cited by 124
Steiner, F. A., Talbert, P. B., Kasinathan, S., Deal, R. B., & Henikoff, S. (2012) · Genome Research · doi:10.1101/gr.131748.111 · Cited by 123
The molecular circuitry governing retinal determination
Kumar, J. P. (2008) · Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms · doi:10.1016/j.bbagrm.2008.10.001 · Cited by 118
Bardin, A. J., & Schweisguth, F. (2006) · Developmental Cell · doi:10.1016/j.devcel.2005.12.017 · Cited by 115
Kaphingst, K. A., & Kunes, S. M. (1994) · Cell · doi:10.1016/0092-8674(94)90422-7 · Cited by 113
Nassif, C., Noveen, A., & Hartenstein, V. (2002) · The Journal of Comparative Neurology · doi:10.1002/cne.10482 · Cited by 110
Bryant, Z. D., Subrahmanyan, L., Tworoger, M., LaTray, L., Liu, C.-R., Li, M.-J., van den Engh, G., & Ruohola‐Baker, H. (1999) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.96.10.5559 · Cited by 110
Costantino, B. F. B., Bricker, D. K., Alexandre, K. M., Shen, K., Merriam, J. R., Antoniewski, C., Callender, J., Henrich, V. C., Presente, A., & Andres, A. J. (2008) · PLoS Genetics · doi:10.1371/journal.pgen.1000102 · Cited by 109
Yasugi, T., Sugie, A., Umetsu, D., & Tabata, T. (2010) · Development · doi:10.1242/dev.048058 · Cited by 107
The NSL Complex Regulates Housekeeping Genes in Drosophila
Lam, K. C., Dündar, F., Vaquerizas, J. M., Raja, S. J., Holz, H., Luscombe, N. M., Manke, T., & Akhtar, A. (2012) · PLoS Genetics · doi:10.1371/journal.pgen.1002736 · Cited by 105
Translational Control by an Upstream Open Reading Frame in the HER-2/neu Transcript
Child, S. J., Miller, M. K., & Geballe, A. P. (1999) · Journal of Biological Chemistry · doi:10.1074/jbc.274.34.24335 · Cited by 105
Hairy Transcriptional Repression Targets and Cofactor Recruitment in Drosophila
Bianchi-Frias, D., Orian, A., Delrow, J. J., Vazquez, J., Rosales‐Nieves, A. E., & Parkhurst, S. M. (2004) · PLoS Biology · doi:10.1371/journal.pbio.0020178 · Cited by 100
Cell type–specific chromatin immunoprecipitation from multicellular complex samples using BiTS-ChIP
Bonn, S., Zinzen, R. P., Perez‐Gonzalez, A., Riddell, A., Gavin, A., & Furlong, E. E. M. (2012) · Nature Protocols · doi:10.1038/nprot.2012.049 · Cited by 91
Dorsal-Ventral Pattern of Delta Trafficking Is Established by a Snail-Tom-Neuralized Pathway
Renzis, S. D., Yu, J., Zinzen, R. P., & Wieschaus, E. F. (2006) · Developmental Cell · doi:10.1016/j.devcel.2006.01.011 · Cited by 84
Wu, J., & Cohen, S. M. (2000) · Mechanisms of Development · doi:10.1016/s0925-4773(00)00311-7 · Cited by 83
DrosophilaDosage Compensation Involves Enhanced Pol II Recruitment to Male X-Linked Promoters
Conrad, T., Cavalli, F. M. G., Vaquerizas, J. M., Luscombe, N. M., & Akhtar, A. (2012) · Science · doi:10.1126/science.1221428 · Cited by 77
Protein–DNA interaction mapping using genomic tiling path microarrays in Drosophila
Sun, L. V., Chen, L., Greil, F., Nègre, N., Li, T.-R., Cavalli, G., Zhao, H., van Steensel, B., & White, K. P. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1533393100 · Cited by 73
Ngo, K., Wang, J. C., Junker, M., Kriz, S., Vo, G., Asem, B., Olson, J. M., Banerjee, U. K., & Hartenstein, V. (2010) · Developmental Biology · doi:10.1016/j.ydbio.2010.07.036 · Cited by 70
Regulating the balance between symmetric and asymmetric stem cell division in the developing brain
Egger, B., Gold, K. S., & Brand, A. H. (2011) · Fly · doi:10.4161/fly.5.3.15640 · Cited by 63
Self-citationAn MMP liberates the Ninjurin A ectodomain to signal a lossof cell adhesionPreprint
Zhang, S., Dailey, G. M., Kwan, E., Glasheen, B. M., Sroga, G. E., & Page, A. W. (2006) · Genes & Development · doi:10.1101/gad.1426906 · Cited by 54
Sugaya, K., Vigneron, M., & Cook, P. R. (2000) · Journal of Cell Science · doi:10.1242/jcs.113.15.2679 · Cited by 53
Wang, W., Li, Y., Zhou, L., Yue, H., & Luo, H. (2011) · Biochemical and Biophysical Research Communications · doi:10.1016/j.bbrc.2011.05.119 · Cited by 41
Pym, E. C. G., Southall, T. D., Mee, C., Brand, A. H., & Baines, R. (2006) · Neural Development · doi:10.1186/1749-8104-1-3 · Cited by 39
Self-citationMethods to create a stringent selection system for mammalian cell lines
Blokland, H. J. M. V., Hoeksema, F., Siep, M., Otte, A. P., & Verhees, J. (2011) · Cytotechnology · doi:10.1007/s10616-011-9354-9 · Cited by 16
Kim, J. Y., Shin, J., Kim, M., Hann, S., & Oh, S. H. (2011) · Journal of Dermatological Science · doi:10.1016/j.jdermsci.2011.12.007 · Cited by 14
Takaesu, N. T., Johnson, A., & Newfeld, S. J. (2002) · genesis · doi:10.1002/gene.10109 · Cited by 12
[24] Gene Discovery with laser Capture Microscopy
Neira, M., & Azen, E. A. (2002) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/s0076-6879(02)56941-x · Cited by 8
Cited by
Decoding gene regulation in the fly brain
Janssens, J., Aibar, S., Taskiran, I. I., Ismail, J. N., Spanier, K. I., Bravo González-Blas, C., Quan, X. J., Papasokrati, D., Hulselmans, G., Makhzami, S., et al. (2021) · doi:10.1101/2021.08.11.454937 · Cited by 170
Decoding gene regulation in the fly brain
Janssens, J., Aibar, S., Taskiran, I. I., Ismail, J. N., Gomez, A. E., Aughey, G., Spanier, K. I., De Rop, F. V., González-Blas, C. B., Dionne, M., et al. (2022) · Nature · doi:10.1038/s41586-021-04262-z · Cited by 170
Self-citationEarly stem cell aging in the mature brain
Ibrayeva, A., Bay, M., Pu, E., Jörg, D. J., Peng, L., Jun, H., Zhang, N., Aaron, D., Lin, C., Resler, G., et al. (2021) · Cell Stem Cell · doi:10.1016/j.stem.2021.03.018 · Cited by 137
Aughey, G. N., Estacio Gomez, A., Thomson, J., Yin, H., & Southall, T. D. (2018) · eLife · doi:10.7554/elife.32341 · Cited by 89
Self-citationSOX9 maintains human foetal lung tip progenitor state by enhancing WNT and RTK signalling
Sun, D., Llora Batlle, O., van den Ameele, J., Thomas, J. C., He, P., Lim, K., Tang, W., Xu, C., Meyer, K. B., Teichmann, S. A., et al. (2022) · The EMBO Journal · doi:10.15252/embj.2022111338 · Cited by 38
Self-citation
Metadata
- Authors
- Southall, T. D., Gold, K. S., Egger, B., Davidson, C. M., Caygill, E. E., Marshall, O. J., & Brand, A. H.
- Venue
- Developmental Cell
- Publisher
- Elsevier BV
- Published
- 2013-07
- Volume
- 26
- Issue
- 1
- Pages
- 101-112
- ISSN
- 1534-5807 (ISSN-L)
- OpenAlex
- W2114709909
- Cited by
- 256
- References
- 77
- FWCI
- 4.84
- Type
- journal article
- Language
- en
- Open access
- hybrid
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
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.
