The DOI matches its Crossref record; 43 of the 43 references it cites were found in a registry or an index.
Genome-wide MyoD Binding in Skeletal Muscle Cells: A Potential for Broad Cellular Reprogramming
Open accessAbstract
SUMMARY Recent studies have demonstrated that MyoD initiates a feed-forward regulation of skeletal muscle gene expression, predicting that MyoD binds directly to many genes expressed during differentiation. We have used chromatin immunoprecipitation and high throughput sequencing to identify genome-wide binding of MyoD in several skeletal muscle cell types. As anticipated, MyoD preferentially binds to a VCASCTG sequence that resembles the in vitro selected site for a MyoD:E-protein heterodimer, and MyoD binding increases during differentiation at many of the regulatory regions of genes expressed in skeletal muscle. Unanticipated findings were that MyoD was constitutively bound to thousands of additional sites in both myoblasts and myotubes, and that the genome-wide binding of MyoD was associated with regional histone acetylation. Therefore, in addition to regulating muscle gene expression, MyoD binds genome-wide and has the ability to broadly alter the epigenome in myoblasts and myotubes.
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
Bioconductor: open software development for computational biology and bioinformatics
Gentleman, R. C., Carey, V. J., Bates, D. M., Bolstad, B., Dettling, M., Dudoit, S., Ellis, B., Gautier, L., Ge, Y., Gentry, J., et al. (2004) · Genome Biology · doi:10.1186/gb-2004-5-10-r80 · Cited by 12,172
Self-citationSmyth, G. K. (2004) · Statistical Applications in Genetics and Molecular Biology · doi:10.2202/1544-6115.1027 · Cited by 11,829
Heintzman, N. D., Stuart, R. K., Hon, G., Fu, Y., Ching, C. W., Hawkins, R. D., Barrera, L. O., Van Calcar, S., Qu, C., Ching, K. A., et al. (2007) · Nature Genetics · doi:10.1038/ng1966 · Cited by 3,398 · cited 2×
“To determine whether the genome-wide binding of MyoD might alter regional chromatin structure, we assessed histone H3 lysine 4 tri-methylation (H3K4me3) and histone H4 acetylation (H4Ac), a marker of active promoters and a modification broadly associated with active chromatin at both enhancers and promoters (Heintzman…”
BackgroundHistone modifications at human enhancers reflect global cell-type-specific gene expression
Heintzman, N. D., Hon, G. C., Hawkins, R. D., Kheradpour, P., Stark, A., Harp, L. F., Ye, Z., Lee, L. K., Stuart, R. K., Ching, C. W., et al. (2009) · Nature · doi:10.1038/nature07829 · Cited by 2,533
Huber, W., von Heydebreck, A., Sültmann, H., Poustka, A., & Vingron, M. (2002) · Bioinformatics · doi:10.1093/bioinformatics/18.suppl_1.s96 · Cited by 2,440
The protein Id: A negative regulator of helix-loop-helix DNA binding proteins
Benezra, R., Davis, R. L., Lockshon, D., Turner, D. L., & Weintraub, H. (1990) · Cell · doi:10.1016/0092-8674(90)90214-y · Cited by 2,238
lumi: a pipeline for processing Illumina microarray
Du, P., Kibbe, W. A., & Lin, S. M. (2008) · Bioinformatics · doi:10.1093/bioinformatics/btn224 · Cited by 2,019
Using GOstats to test gene lists for GO term association
Falcon, S., & Gentleman, R. (2007) · Bioinformatics · doi:10.1093/bioinformatics/btl567 · Cited by 2,015
Self-citationRetention of differentiation potentialities during prolonged cultivation of myogenic cells.
Yaffe, D. (1968) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.61.2.477 · Cited by 976
Blackwell, T. K., & Weintraub, H. (1990) · Science · doi:10.1126/science.2174572 · Cited by 930
MyoD and the transcriptional control of myogenesis
Berkes, C. A., & Tapscott, S. J. (2005) · Seminars in Cell & Developmental Biology · doi:10.1016/j.semcdb.2005.07.006 · Cited by 849
Self-citationMyoD1: A Nuclear Phosphoprotein Requiring a Myc Homology Region to Convert Fibroblasts to Myoblasts
Tapscott, S. J., Davis, R. L., Thayer, M. J., Cheng, P.-F., Weintraub, H., & Lassar, A. B. (1988) · Science · doi:10.1126/science.3175662 · Cited by 845
Self-citationCytoplasmic activation of human nuclear genes in stable heterocaryons
Blau, H. M., Chiu, C.-P., & Webster, C. (1983) · Cell · doi:10.1016/0092-8674(83)90300-8 · Cited by 825
The MyoD DNA binding domain contains a recognition code for muscle-specific gene activation
Davis, R. L., Cheng, P.-F., Lassar, A. B., & Weintraub, H. (1990) · Cell · doi:10.1016/0092-8674(90)90088-v · Cited by 765
The circuitry of a master switch: Myod and the regulation of skeletal muscle gene transcription
Tapscott, S. J. (2005) · Development · doi:10.1242/dev.01874 · Cited by 763
Self-citationSchoenfelder, S., Sexton, T., Chakalova, L., Cope, N. F., Horton, A., Andrews, S., Kurukuti, S., Mitchell, J. A., Umlauf, D., Dimitrova, D. S., et al. (2010) · Nature Genetics · doi:10.1038/ng.496 · Cited by 714
Transcription Factors Bind Thousands of Active and Inactive Regions in the Drosophila Blastoderm
Li, X.-Y., MacArthur, S., Bourgon, R., Nix, D., Pollard, D. A., Iyer, V. N., Hechmer, A., Simirenko, L., Stapleton, M., Hendriks, C. L. L., et al. (2008) · PLoS Biology · doi:10.1371/journal.pbio.0060027 · Cited by 474
Jen, Y., Weintraub, H., & Benezra, R. (1992) · Genes & Development · doi:10.1101/gad.6.8.1466 · Cited by 471
An initial blueprint for myogenic differentiation
Blais, A., Tsikitis, M., Acosta-Alvear, D., Sharan, R., Kluger, Y., & Dynlacht, B. D. (2005) · Genes & Development · doi:10.1101/gad.1281105 · Cited by 464
The Incoherent Feedforward Loop Can Provide Fold-Change Detection in Gene Regulation
Goentoro, L., Shoval, O., Kirschner, M. W., & Alon, U. (2009) · Molecular Cell · doi:10.1016/j.molcel.2009.11.018 · Cited by 424
Differential Roles of p300 and PCAF Acetyltransferases in Muscle Differentiation
Puri, P. L., Sartorelli, V., Yang, X.-J., Hamamori, Y., Ogryzko, V. V., Howard, B. H., Kedes, L., Wang, J. Y. J., Graessmann, A., Nakatani, Y., et al. (1997) · Molecular Cell · doi:10.1016/s1097-2765(00)80005-2 · Cited by 421
The in vitro cultivation and differentiation capacities of myogenic cell lines
Richler, C., & Yaffe, D. (1970) · Developmental Biology · doi:10.1016/s0012-1606(70)80004-5 · Cited by 384
Muscle-specific transcriptional activation by MyoD.
Weintraub, H., Dwarki, V. J., Verma, I., Davis, R., Hollenberg, S., Snider, L., Lassar, A., & Tapscott, S. J. (1991) · Genes & Development · doi:10.1101/gad.5.8.1377 · Cited by 334
Self-citationBerkes, C. A., Bergstrom, D. A., Penn, B. H., Seaver, K. J., Knoepfler, P. S., & Tapscott, S. J. (2004) · Molecular Cell · doi:10.1016/s1097-2765(04)00260-6 · Cited by 332
Self-citationBergstrom, D. A., Penn, B. H., Strand, A., Perry, R. L. S., Rudnicki, M. A., & Tapscott, S. J. (2002) · Molecular Cell · doi:10.1016/s1097-2765(02)00481-1 · Cited by 332
Self-citationMacArthur, S., Li, X.-Y., Li, J., Brown, J. B., Chu, H. C., Zeng, L., Grondona, B. P., Hechmer, A., Simirenko, L., Keränen, S. V., et al. (2009) · Genome Biology · doi:10.1186/gb-2009-10-7-r80 · Cited by 332
Form follows function: the genomic organization of cellular differentiation
Kosak, S. T., & Groudine, M. (2004) · Genes & Development · doi:10.1101/gad.1209304 · Cited by 293
Global and gene‐specific analyses show distinct roles for Myod and Myog at a common set of promoters
Cao, Y., Kumar, R. M., Penn, B. H., Berkes, C. A., Kooperberg, C., Boyer, L. A., Young, R. A., & Tapscott, S. J. (2006) · The EMBO Journal · doi:10.1038/sj.emboj.7600958 · Cited by 282
Self-citationHu, Q., Kwon, Y.-S., Nunez, E., Cardamone, M. D., Hutt, K. R., Ohgi, K. A., Garcia-Bassets, I., Rose, D. W., Glass, C. K., Rosenfeld, M. G., et al. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0810634105 · Cited by 264
Finding distal regulatory elements in the human genome
Heintzman, N. D., & Ren, B. (2009) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2009.09.006 · Cited by 235
Yokoyama, S., Ito, Y., Ueno-Kudoh, H., Shimizu, H., Uchibe, K., Albini, S., Mitsuoka, K., Miyaki, S., Kiso, M., Nagai, A., et al. (2009) · Developmental Cell · doi:10.1016/j.devcel.2009.10.011 · Cited by 213
Rampalli, S., Li, L., Mak, E., Ge, K., Brand, M., Tapscott, S. J., & Dilworth, F. J. (2007) · Nature Structural & Molecular Biology · doi:10.1038/nsmb1316 · Cited by 213
Self-citationPenn, B. H., Bergstrom, D. A., Dilworth, F. J., Bengal, E., & Tapscott, S. J. (2004) · Genes & Development · doi:10.1101/gad.1234304 · Cited by 184
Self-citationPbx homeodomain proteins direct Myod activity to promote fast-muscle differentiation
Maves, L., Waskiewicz, A. J., Paul, B., Cao, Y., Tyler, A. E., Moens, C. B., & Tapscott, S. J. (2007) · Development · doi:10.1242/dev.003905 · Cited by 137
Self-citationRegulatory Elements that Control the Lineage-Specific Expression of myoD
Goldhamer, D. J., Faerman, A., Shani, M., & Emerson, C. P. (1992) · Science · doi:10.1126/science.1315077 · Cited by 134
A Novel Myoblast Enhancer Element Mediates MyoD Transcription
Tapscott, S. J., Lassar, A. B., & Weintraub, H. M. (1992) · Molecular and Cellular Biology · doi:10.1128/mcb.12.11.4994 · Cited by 133
Self-citationCoordinate Gene Regulation during Hematopoiesis Is Related to Genomic Organization
Kosak, S. T., Scalzo, D., Alworth, S., Li, F., Palmer, S., Enver, T., Lee, J. S. J., & Groudine, M. T. (2007) · PLoS Biology · doi:10.1371/journal.pbio.0050309 · Cited by 125
Asakura, A., Lyons, G. E., & Tapscott, S. J. (1995) · Developmental Biology · doi:10.1006/dbio.1995.1290 · Cited by 117
Self-citationThe emergence of lineage-specific chromosomal topologies from coordinate gene regulation
Rajapakse, I., Perlman, M. D., Scalzo, D., Kooperberg, C. L., Groudine, M. T., & Kosak, S. T. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0900986106 · Cited by 94
RP58 Associates with Condensed Chromatin and Mediates a Sequence-specific Transcriptional Repression
Aoki, K., Meng, G., Suzuki, K., Takashi, T., Kameoka, Y., Nakahara, K., Ishida, R., & Kasai, M. (1998) · Journal of Biological Chemistry · doi:10.1074/jbc.273.41.26698 · Cited by 92
Composition and Function of AP-1 Transcription Complexes during Muscle Cell Differentiation
Andreucci, J. J., Grant, D., Cox, D. M., Tomc, L. K., Prywes, R., Goldhamer, D. J., Rodrigues, N., Bédard, P., & McDermott, J. C. (2002) · Journal of Biological Chemistry · doi:10.1074/jbc.m110891200 · Cited by 81
Huang, J., Blackwell, T. K., Kedes, L., & Weintraub, H. M. (1996) · Molecular and Cellular Biology · doi:10.1128/mcb.16.7.3893 · Cited by 42
The human desmin locus: Gene organization and LCR-mediated transcriptional control
Tam, J. L. Y., Triantaphyllopoulos, K. A., Todd, H., Raguz, S., de Wit, T., Morgan, J. E., Partridge, T. A., Makrinou, E., Grosveld, F. G., & Antoniou, M. N. (2006) · Genomics · doi:10.1016/j.ygeno.2006.01.009 · Cited by 20
Cited by
Transcription factors: from enhancer binding to developmental control
Spitz, F., & Furlong, E. E. M. (2012) · Nature Reviews Genetics · doi:10.1038/nrg3207 · Cited by 2,227
Satellite Cells and the Muscle Stem Cell Niche
Yin, H., Price, F., & Rudnicki, M. A. (2013) · Physiological Reviews · doi:10.1152/physrev.00043.2011 · Cited by 2,166
Cicero predicts cis-regulatory DNA interactions from single-cell chromatin accessibility data
Pliner, H. A., Packer, J. S., McFaline-Figueroa, J. L., Cusanovich, D. A., Daza, R. M., Aghamirzaie, D., Srivatsan, S., Qiu, X., Jackson, D., Minkina, A., et al. (2018) · Molecular Cell · doi:10.1016/j.molcel.2018.06.044 · Cited by 789
Zammit, P. S. (2017) · Seminars in Cell & Developmental Biology · doi:10.1016/j.semcdb.2017.11.011 · Cited by 887
Gene Regulatory Networks and Transcriptional Mechanisms that Control Myogenesis
Buckingham, M., & Rigby, P. W. J. (2014) · Developmental Cell · doi:10.1016/j.devcel.2013.12.020 · Cited by 667
Metadata
- Authors
- Cao, Y., Yao, Z., Sarkar, D., Lawrence, M., Sanchez, G. J., Parker, M. H., MacQuarrie, K. L., Davison, J., Morgan, M. T., Ruzzo, W. L., Gentleman, R. C., & Tapscott, S. J.
- Venue
- Developmental Cell
- Publisher
- Elsevier BV
- Published
- 2010-04
- Volume
- 18
- Issue
- 4
- Pages
- 662-674
- ISSN
- 1534-5807 (ISSN-L)
- OpenAlex
- W1972822540
- Cited by
- 481
- References
- 43
- FWCI
- 18.43
- Type
- journal article
- Language
- en
- Open access
- bronze
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.
