Dynamics of the epigenetic landscape during erythroid differentiation after GATA1 restoration
Open accessAbstract
Interplays among lineage-specific nuclear proteins, chromatin modifying enzymes, and the basal transcription machinery govern cellular differentiation, but their dynamics of action and coordination with transcriptional control are not fully understood. Alterations in chromatin structure appear to establish a permissive state for gene activation at some loci, but they play an integral role in activation at other loci. To determine the predominant roles of chromatin states and factor occupancy in directing gene regulation during differentiation, we mapped chromatin accessibility, histone modifications, and nuclear factor occupancy genome-wide during mouse erythroid differentiation dependent on the master regulatory transcription factor GATA1. Notably, despite extensive changes in gene expression, the chromatin state profiles (proportions of a gene in a chromatin state dominated by activating or repressive histone modifications) and accessibility remain largely unchanged during GATA1-induced erythroid differentiation. In contrast, gene induction and repression are strongly associated with changes in patterns of transcription factor occupancy. Our results indicate that during erythroid differentiation, the broad features of chromatin states are established at the stage of lineage commitment, largely independently of GATA1. These determine permissiveness for expression, with subsequent induction or repression mediated by distinctive combinations of transcription factors.
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
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?
A difference in GATA1 and SPI1 co-binding between the two types of SPI1-bound enhancers was also seen using GATA1 peaks from G1E-ER4 restored for GATA1 activity or Ter119+ foetal liver proerythroblasts.
“Such a difference in GATA1 and SPI1 co-binding between the two types of SPI1-bound enhancers was also seen using GATA1 peaks from G1E-ER4 restored for GATA1 activity (64,65) or Ter119+ foetal liver proerythroblasts (66) (Supplementary Figure S9A), revealing a specific enrichment for GATA1 binding sites at SPI1-deacetylated enhancers.”
From HDAC1 and PRC2 mediate combinatorial control in SPI1/PU.1-dependent gene repression in murine erythroleukaemia (2022) · cites this paper as [66]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing
Benjamini, Y., & Hochberg, Y. (1995) · Journal of the Royal Statistical Society Series B: Statistical Methodology · doi:10.1111/j.2517-6161.1995.tb02031.x · Cited by 109,482 · see citing works
Model-based Analysis of ChIP-Seq (MACS)
Zhang, Y., Liu, T., Meyer, C. A., Eeckhoute, J., Johnson, D. S., Bernstein, B. E., Nusbaum, C., Myers, R. M., Brown, M., Li, W., et al. (2008) · Genome Biology · doi:10.1186/gb-2008-9-9-r137 · Cited by 18,386 · see citing works
Self-citationHeinz, S., Benner, C., Spann, N., Bertolino, E., Lin, Y. C., Laslo, P., Cheng, J. X., Murre, C., Singh, H., & Glass, C. K. (2010) · Molecular Cell · doi:10.1016/j.molcel.2010.05.004 · Cited by 13,382 · see citing works
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 · see citing works
The ENCODE Project Consortium (2007) · Nature · doi:10.1038/nature05874 · Cited by 5,223 · see citing works
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× · see citing works
“tone H3 lysine 4 (H3K4me3) for promoters and monomethylation of the same amino acid (H3K4me1) for enhancers (The ENCODE Project Consortium 2007; Heintzman et al. 2007).”
BackgroundSelf-citationEpigenetics: A landscape takes shape
Goldberg, A. D., Allis, C. D., & Bernstein, E. (2007) · Cell · doi:10.1016/j.cell.2007.02.006 · Cited by 2,466 · see citing works
Weintraub, H., & Groudine, M. (1976) · Science · doi:10.1126/science.948749 · Cited by 1,809 · see citing works
Histone Methyltransferase Activity of a Drosophila Polycomb Group Repressor Complex
Müller, J., Hart, C. M., Francis, N. J., Vargas, M. L., Sengupta, A. K., Wild, B., Miller, E., O’Connor, M. B., Kingston, R. E., & Simon, J. A. (2002) · Cell · doi:10.1016/s0092-8674(02)00976-5 · Cited by 1,553 · see citing works
Cooperation between Complexes that Regulate Chromatin Structure and Transcription
Narlikar, G. J., Fan, H.-Y., & Kingston, R. E. (2002) · Cell · doi:10.1016/s0092-8674(02)00654-2 · Cited by 1,486 · see citing works
An early haematopoietic defect in mice lacking the transcription factor GATA-2
Tsai, F., Keller, G. M., Kuo, F. C., Weiss, M. J., Chen, J., Rosenblatt, M., Alt, F. W., & Orkin, S. H. (1994) · Nature · doi:10.1038/371221a0 · Cited by 1,419 · see citing works
Self-citationHigh-Resolution Mapping and Characterization of Open Chromatin across the Genome
Boyle, A. P., Davis, S., Shulha, H. P., Meltzer, P., Margulies, E. H., Weng, Z., Furey, T. S., & Crawford, G. E. (2008) · Cell · doi:10.1016/j.cell.2007.12.014 · Cited by 1,415 · see citing works
Self-citationNUCLEASE HYPERSENSITIVE SITES IN CHROMATIN
Gross, D. S., & Garrard, W. T. (1988) · Annual Review of Biochemistry · doi:10.1146/annurev.bi.57.070188.001111 · Cited by 1,233 · see citing works
Gene Regulatory Networks and the Evolution of Animal Body Plans
Davidson, E. H., & Erwin, D. H. (2006) · Science · doi:10.1126/science.1113832 · Cited by 1,207 · cited 1× · see citing works
“Regulation is exerted by the actions of transcription factors that bind to specific DNA sequences in cis -regulatory modules (CRMs), such as promoters and enhancers.”
BackgroundFelsenfeld, G., & Groudine, M. T. (2003) · Nature · doi:10.1038/nature01411 · Cited by 1,153 · see citing works
Discovery and characterization of chromatin states for systematic annotation of the human genome
Ernst, J., & Kellis, M. (2010) · Nature Biotechnology · doi:10.1038/nbt.1662 · Cited by 1,033 · see citing works
Self-citationSystematic Protein Location Mapping Reveals Five Principal Chromatin Types in Drosophila Cells
Filion, G. J. P., 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 963 · see citing works
Chromatin accessibility pre-determines glucocorticoid receptor binding patterns
John, S., Sabo, P. J., Thurman, R. E., Sung, M.-H., Biddie, S. C., Johnson, T. A., Hager, G. L., & Stamatoyannopoulos, J. A. (2011) · Nature Genetics · doi:10.1038/ng.759 · Cited by 954 · see citing works
Wadman, I., Osada, H., Grütz, G. G., Agulnick, A. D., Westphal, H., Forster, A., & Rabbitts, T. H. (1997) · The EMBO Journal · doi:10.1093/emboj/16.11.3145 · Cited by 836 · see citing works
Wilson, N. K., Foster, S. D., Wang, X., Knezevic, K., Schütte, J., Kaimakis, P., Chilarska, P. M., Kinston, S., Ouwehand, W. H., Dzierzak, E., et al. (2010) · Cell stem cell · doi:10.1016/j.stem.2010.07.016 · Cited by 728 · see citing works
Schotta, G., Ebert, A., Krauss, V., Fischer, A., Hoffmann, J., Rea, S., Jenuwein, T., Dorn, R., & Reuter, G. (2002) · The EMBO Journal · doi:10.1093/emboj/21.5.1121 · Cited by 714 · see citing works
Activity and tissue-specific expression of the transcription factor NF-E1 multigene family.Preprint
Yamamoto, M. P., Ko, L. J., Leonard, M. W., Beug, H., Orkin, S. H., & Engel, J. D. (1990) · Genes & Development · doi:10.1101/gad.4.10.1650 · Cited by 598 · see citing works
DNA-Binding Specificities of the GATA Transcription Factor Family
Ko, L. J., & Engel, J. D. (1993) · Molecular and Cellular Biology · doi:10.1128/mcb.13.7.4011-4022.1993 · Cited by 575 · see citing works
Weiss, M. J., Keller, G., & Orkin, S. H. (1994) · Genes & Development · doi:10.1101/gad.8.10.1184 · Cited by 541 · see citing works
Self-citationRippon, H. J., & Bishop, A. E. (2004) · Cell Proliferation · doi:10.1111/j.1365-2184.2004.00298.x · Cited by 536 · see citing works
Familial dyserythropoietic anaemia and thrombocytopenia due to an inherited mutation in GATA1
Nichols, K. E., Crispino, J. D., Poncz, M., White, J. G., Orkin, S. H., Maris, J. M., & Weiss, M. J. (2000) · Nature Genetics · doi:10.1038/73480 · Cited by 511 · see citing works
Self-citationFunctional selectivity of recombinant mammalian SWI/SNF subunitsPreprint
Kadam, S., McAlpine, G. S., Phelan, M. L., Kingston, R. E., Jones, K. A., & Emerson, B. M. (2000) · Genes & Development · doi:10.1101/gad.828000 · Cited by 497 · see citing works
Proximity among Distant Regulatory Elements at the β-Globin Locus Requires GATA-1 and FOG-1
Vakoc, C. R., Letting, D. L., Gheldof, N., Sawado, T., Bender, M. A., Groudine, M., Weiss, M. J., Dekker, J., & Blobel, G. A. (2005) · Molecular Cell · doi:10.1016/j.molcel.2004.12.028 · Cited by 490 · see citing works
Self-citationNucleosome dynamics define transcriptional enhancers
He, H. H., Meyer, C. A., Shin, H., Bailey, S. T., Wei, G., Wang, Q., Zhang, Y., Xu, K., Ni, M., Lupien, M., et al. (2010) · Nature Genetics · doi:10.1038/ng.545 · Cited by 476 · see citing works
Self-citationGlobal regulation of erythroid gene expression by transcription factor GATA-1
Welch, J. J. (2004) · Blood · doi:10.1182/blood-2004-04-1603 · Cited by 408 · see citing works
Zhang, J., Socolovsky, M., Gross, A. W., & Lodish, H. F. (2003) · Blood · doi:10.1182/blood-2003-05-1479 · Cited by 386 · see citing works
Gregory, T. C., Yu, C., Ma, A. I., Orkin, S. H., Blobel, G. A., & Weiss, M. J. (1999) · Blood · doi:10.1182/blood.v94.1.87.413k41_87_96 · Cited by 366 · see citing works
Self-citationF-Seq: a feature density estimator for high-throughput sequence tags
Boyle, A. P., Guinney, J., Crawford, G. E., & Furey, T. S. (2008) · Bioinformatics · doi:10.1093/bioinformatics/btn480 · Cited by 363 · see citing works
Self-citationGrass, J. A., Boyer, M. E., Pal, S. K., Wu, J., Weiss, M. J., & Bresnick, E. H. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1432147100 · Cited by 357 · see citing works
Self-citationWeiss, M. J., Yu, C., & Orkin, S. H. (1997) · Molecular and Cellular Biology · doi:10.1128/mcb.17.3.1642 · Cited by 349 · see citing works
Self-citationDiscovering Hematopoietic Mechanisms through Genome-wide Analysis of GATA Factor Chromatin Occupancy
Fujiwara, T., O’Geen, H., Keleş, S., Blahnik, K. R., Linnemann, A. K., Kang, Y.-A., Choi, K., Farnham, P., & Bresnick, E. H. (2009) · Molecular Cell · doi:10.1016/j.molcel.2009.11.001 · Cited by 347 · see citing works
Interaction of the Glucocorticoid Receptor with the Chromatin Landscape
John, S., Sabo, P. J., Johnson, T. A., Sung, M., Biddie, S. C., Lightman, S. L., Voss, T. C., Davis, S. R., Meltzer, P. S., Stamatoyannopoulos, J. A., et al. (2008) · Molecular Cell · doi:10.1016/j.molcel.2008.02.010 · Cited by 311 · see citing works
Yu, M., Riva, L., Xie, H., Schindler, Y. L., Moran, T. B., Cheng, Y., Yu, D., Hardison, R. C., Weiss, M. J., Orkin, S. H., et al. (2009) · Molecular Cell · doi:10.1016/j.molcel.2009.11.002 · Cited by 308 · see citing works
Self-citationWalsh, J. C., DeKoter, R. P., Lee, H.-J., Smith, E. D., Lancki, D. W., Gurish, M. F., Friend, D. S., Stevens, R. L., Anastasi, J., & Singh, H. (2002) · Immunity · doi:10.1016/s1074-7613(02)00452-1 · Cited by 262 · cited 3× · see citing works
“However, these patterns distinguished levels of expression, not response category or direction of response—the patterns were the same for induced or repressed genes.”
BackgroundSequence census methods for functional genomics
Wold, B. J., & Myers, R. (2007) · Nature Methods · doi:10.1038/nmeth1157 · Cited by 257 · see citing works
The genome-wide dynamics of the binding of Ldb1 complexes during erythroid differentiation
Soler, E., Andrieu-Soler, C., de Boer, E., Bryne, J. C., Thongjuea, S., Stadhouders, R., Palstra, R.-J., Stevens, M., Kockx, C., van IJcken, W., et al. (2010) · Genes & Development · doi:10.1101/gad.551810 · Cited by 245 · see citing works
Dynamics of GATA transcription factor expression during erythroid differentiation
Leonard, M. O., Brice, M. C., Engel, J., & Papayannopoulou, T. (1993) · Blood · doi:10.1182/blood.v82.4.1071.1071 · Cited by 238 · see citing works
Cheng, Y., Wu, W., Ashok Kumar, S., Yu, D., Deng, W., Tripic, T., King, D. C., Chen, K.-B., Zhang, Y., Drautz, D., et al. (2009) · Genome Research · doi:10.1101/gr.098921.109 · Cited by 223 · see citing works
Self-citationA global role for KLF1 in erythropoiesis revealed by ChIP-seq in primary erythroid cellsPreprint
Tallack, M. R., Whitington, T., Yuen, W. S., Wainwright, E. N., Keys, J. R., Gardiner, B., Nourbakhsh, E., Cloonan, N., Grimmond, S. M., Bailey, T. L., et al. (2010) · Genome Research · doi:10.1101/gr.106575.110 · Cited by 220 · see citing works
Jing, H., Vakoc, C. R., Ying, L., Mandat, S. A., Wang, H., Zheng, X., & Blobel, G. A. (2008) · Molecular Cell · doi:10.1016/j.molcel.2007.11.020 · Cited by 213 · see citing works
Self-citationAnguita, E., Hughes, J., Heyworth, C., Blobel, G. A., Wood, W. G., & Higgs, D. R. (2004) · The EMBO Journal · doi:10.1038/sj.emboj.7600274 · Cited by 207 · see citing works
Self-citationGATA-1-Mediated Proliferation Arrest during Erythroid Maturation
Rylski, M., Welch, J. J., Chen, Y., Letting, D. L., Diehl, J. A., Chodosh, L. A., Blobel, G. A., & Weiss, M. J. (2003) · Molecular and Cellular Biology · doi:10.1128/mcb.23.14.5031-5042.2003 · Cited by 195 · see citing works
Self-citationPop, R., Shearstone, J. R., Shen, Q., Liu, Y., Hallstrom, K., Koulnis, M., Gribnau, J., & Socolovsky, M. (2010) · PLoS Biology · doi:10.1371/journal.pbio.1000484 · Cited by 179 · see citing works
SCL and associated proteins distinguish active from repressive GATA transcription factor complexes
Tripic, T., Deng, W., Cheng, Y., Zhang, Y., Vakoc, C. R., Gregory, G. D., Hardison, R. C., & Blobel, G. A. (2008) · Blood · doi:10.1182/blood-2008-07-169417 · Cited by 176 · see citing works
Self-citationKassouf, M. T., Hughes, J. R., Taylor, S., McGowan, S. J., Soneji, S., Green, A. L., Vyas, P., & Porcher, C. (2010) · Genome Research · doi:10.1101/gr.104935.110 · Cited by 176 · see citing works
Activation of globin genes during chicken development
Groudine, M. T., & Weintraub, H. M. (1981) · Cell · doi:10.1016/0092-8674(81)90329-9 · Cited by 164 · see citing works
Porcher, C., Liao, E. C.-W., Fujiwara, Y., Zon, L. I., & Orkin, S. H. (1999) · Development · doi:10.1242/dev.126.20.4603 · Cited by 161 · see citing works
Letting, D. L., Rakowski, C., Weiss, M. J., & Blobel, G. A. (2003) · Molecular and Cellular Biology · doi:10.1128/mcb.23.4.1334-1340.2003 · Cited by 137 · see citing works
Self-citationWilson, N. K., Miranda‐Saavedra, D., Kinston, S., Bonadies, N., Foster, S. D., Calero‐Nieto, F. J., Dawson, M. A., Donaldson, I. J., Dumon, S., Frampton, J., et al. (2009) · Blood · doi:10.1182/blood-2009-01-200048 · Cited by 120 · see citing works
Munugalavadla, V., Doré, L. C., Tan, B. L., Hong, L., Vishnu, M. R., Weiss, M. J., & Kapur, R. (2005) · Molecular and Cellular Biology · doi:10.1128/mcb.25.15.6747-6759.2005 · Cited by 110 · see citing works
Self-citationPilon, A. M., Ajay, S. S., Kumar, S. A., Steiner, L. A., Cherukuri, P. F., Wincovitch, S., Anderson, S. M., Mullikin, J. C., Gallagher, P. G., Hardison, R. C., et al. (2011) · Blood · doi:10.1182/blood-2011-05-355107 · Cited by 104 · see citing works
Self-citationPioneer factors in embryonic stem cells and differentiation
Smale, S. T. (2010) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2010.06.010 · Cited by 82 · see citing works
Dynamic GATA Factor Interplay at a Multicomponent Regulatory Region of the GATA-2 Locus
Martowicz, M. L., Grass, J. A., Boyer, M. E., Guend, H., & Bresnick, E. H. (2004) · Journal of Biological Chemistry · doi:10.1074/jbc.m406038200 · Cited by 79 · see citing works
Molecular Hallmarks of Endogenous Chromatin Complexes Containing Master Regulators of Hematopoiesis
Wozniak, R. J., Keleş, S., Lugus, J. J., Young, K. H., Boyer, M. E., Tran, T. M., Choi, K., & Bresnick, E. H. (2008) · Molecular and Cellular Biology · doi:10.1128/mcb.01061-08 · Cited by 63 · see citing works
Experimental validation of predicted mammalian erythroid cis-regulatory modulesPreprint
Wang, H., Zhang, Y., Cheng, Y., Zhou, Y., King, D. C., Taylor, J., Chiaromonte, F., Kasturi, J., Petrykowska, H. M., Gibb, B., et al. (2006) · Genome Research · doi:10.1101/gr.5353806 · Cited by 60 · see citing works
Self-citationDifferential use of SCL/TAL-1 DNA-binding domain in developmental hematopoiesis
Kassouf, M. T., Chagraoui, H., Vyas, P., & Porcher, C. (2008) · Blood · doi:10.1182/blood-2007-12-128900 · Cited by 46 · see citing works
Steiner, L. A., Maksimova, Y. D., Schulz, V., Wong, C., Raha, D., Mahajan, M. C., Weissman, S. M., & Gallagher, P. G. (2009) · Molecular and Cellular Biology · doi:10.1128/mcb.00777-09 · Cited by 35 · see citing works
Primary sequence and epigenetic determinants of in vivo occupancy of genomic DNA by GATA1
Zhang, Y., Wu, W.-S., Cheng, Y., King, D. C., Harris, R. S., Taylor, J., Chiaromonte, F., & Hardison, R. C. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkp747 · Cited by 32 · see citing works
Self-citationLayon, M. E., Ackley, C. J., West, R. J., & Lowrey, C. H. (2006) · Journal of Molecular Biology · doi:10.1016/j.jmb.2006.11.094 · Cited by 30 · see citing works
Cheng, Y., King, D. C., Doré, L. C., Zhang, X., Zhou, Y., Zhang, Y., Dorman, C. M., Abebe, D. F., Kumar, S. A., Chiaromonte, F., et al. (2008) · Genome Research · doi:10.1101/gr.083089.108 · Cited by 29 · see citing works
Self-citationChromatin alteration, transcription and replication: What's the opening line to the story?
Barton, M. C., & Crowe, A. J. (2001) · Oncogene · doi:10.1038/sj.onc.1204334 · Cited by 16 · see citing works
A varying threshold method for ChIP peak-calling using multiple sources of information
Chen, K.-B., & Zhang, Y. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq379 · Cited by 11 · see citing works
Self-citation
Flagged first, then by citations
Cited by
Sorted by citations
A comparative encyclopedia of DNA elements in the mouse genome
Yue, F., Cheng, Y., Breschi, A., Vierstra, J., Wu, W., Ryba, T., Sandstrom, R., Ma, Z., Davis, C., Pope, B. D., et al. (2014) · Nature · doi:10.1038/nature13992 · Cited by 1,781 · see citing works
Self-citationFurey, T. S. (2012) · Nature Reviews Genetics · doi:10.1038/nrg3306 · Cited by 825 · see citing works
Self-citationDeng, W., Lee, J., Wang, H., Miller, J., Reik, A., Gregory, P. D., Dean, A., & Blobel, G. A. (2012) · Cell · doi:10.1016/j.cell.2012.03.051 · Cited by 734 · see citing works
Self-citationAbsence of a simple code: how transcription factors read the genome
Slattery, M., Zhou, T., Yang, L., Dantas Machado, A. C., Gordân, R., & Rohs, R. (2014) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2014.07.002 · Cited by 537 · see citing works
Dynamic regulation of transcriptional states by chromatin and transcription factors
Voss, T. C., & Hager, G. L. (2014) · Nature Reviews Genetics · doi:10.1038/nrg3623 · Cited by 504 · see citing works
Hattangadi, S. M., Wong, P., Zhang, L., Flygare, J., & Lodish, H. F. (2011) · Blood · doi:10.1182/blood-2011-07-356006 · Cited by 452 · see citing works
Distinct Properties of Cell-Type-Specific and Shared Transcription Factor Binding Sites
Gertz, J., Savic, D., Varley, K. E., Partridge, E. C., Safi, A., Jain, P., Cooper, G. M., Reddy, T. E., Crawford, G. E., & Myers, R. (2013) · Molecular Cell · doi:10.1016/j.molcel.2013.08.037 · Cited by 363 · see citing works
Self-citationKing, H. W., & Klose, R. J. (2017) · eLife · doi:10.7554/elife.22631 · Cited by 270 · see citing works
Unlinking an lncRNA from Its Associated cis Element
Paralkar, V. R., Taborda, C., Huang, P., Yao, Y., Kossenkov, A. V., Prasad, R., Luan, J. Y., Davies, J. O. J., Hughes, J. R., Hardison, R. C., et al. (2016) · Molecular Cell · doi:10.1016/j.molcel.2016.02.029 · Cited by 253 · see citing works
Self-citationGenomic approaches towards finding cis-regulatory modules in animals
Hardison, R. C., & Taylor, J. (2012) · Nature Reviews Genetics · doi:10.1038/nrg3242 · Cited by 234 · see citing works
Self-citationTissue-Specific Mitotic Bookmarking by Hematopoietic Transcription Factor GATA1
Kadauke, S., Udugama, M., Pawlicki, J. M., Achtman, J. C., Jain, D., Cheng, Y., Hardison, R. C., & Blobel, G. A. (2012) · Cell · doi:10.1016/j.cell.2012.06.038 · Cited by 232 · see citing works
Self-citationEvolution of Hemoglobin and Its Genes
Hardison, R. C. (2012) · Cold Spring Harbor Perspectives in Medicine · doi:10.1101/cshperspect.a011627 · Cited by 217 · see citing works
Self-citationGlobal discovery of erythroid long noncoding RNAs reveals novel regulators of red cell maturation
Alvarez‐Dominguez, J. R., Hu, W., Yuan, B., Shi, J., Park, S. S., Gromatzky, A. A., van Oudenaarden, A., & Lodish, H. F. (2013) · Blood · doi:10.1182/blood-2013-10-530683 · Cited by 185 · see citing works
Lineage and species-specific long noncoding RNAs during erythro-megakaryocytic development
Paralkar, V. R., Mishra, T., Luan, J. Y., Yao, Y., Kossenkov, A. V., Anderson, S. M., Dunagin, M. C., Pimkin, M., Gore, M., Sun, D. K., et al. (2014) · Blood · doi:10.1182/blood-2013-12-544494 · Cited by 184 · see citing works
Self-citationBresnick, E. H., Katsumura, K. R., Lee, H., Johnson, K. D., & Perkins, A. S. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks281 · Cited by 177 · see citing works
Ldb1 complexes: the new master regulators of erythroid gene transcription
Love, P. E., Warzecha, C. C., & Li, L. (2013) · Trends in Genetics · doi:10.1016/j.tig.2013.10.001 · Cited by 126 · see citing works
Cyclin D3 coordinates the cell cycle during differentiation to regulate erythrocyte size and numberPreprint
Sankaran, V. G., Ludwig, L. S., Sicińska, E., Xu, J., Bauer, D. E., Eng, J. C., Patterson, H. C., Metcalf, R. A., Natkunam, Y., Orkin, S. H., et al. (2012) · Genes & Development · doi:10.1101/gad.197020.112 · Cited by 119 · see citing works
Genome accessibility is widely preserved and locally modulated during mitosisPreprint
Hsiung, C., Morrissey, C. S., Udugama, M., Frank, C. L., Keller, C. A., Baek, S., Giardine, B., Crawford, G. E., Sung, M.-H., Hardison, R., et al. (2015) · Genome Research · doi:10.1101/gr.180646.114 · Cited by 114 · see citing works
Self-citationA hyperactive transcriptional state marks genome reactivation at the mitosis–G1 transitionPreprint
Hsiung, C. C. ‐., Bartman, C., Huang, P., Ginart, P., Stonestrom, A. J., Keller, C. A., Face, C. J., Jahn, K. S., Evans, P., Sankaranarayanan, L., et al. (2016) · Genes & Development · doi:10.1101/gad.280859.116 · Cited by 105 · see citing works
Self-citationDogan, N., Wu, W., Morrissey, C. S., Chen, K.-B., Stonestrom, A., Long, M., Keller, C. A., Cheng, Y., Jain, D., Visel, A., et al. (2015) · Epigenetics & Chromatin · doi:10.1186/s13072-015-0009-5 · Cited by 114 · see citing works
Self-citationPimkin, M., Kossenkov, A., Mishra, T., Morrissey, C. S., Wu, W.-S., Keller, C. A., Blobel, G., Lee, D., Beer, M. A., Hardison, R., et al. (2014) · Genome Research · doi:10.1101/gr.164178.113 · Cited by 96 · see citing works
Self-citationFunctions of BET proteins in erythroid gene expression
Stonestrom, A. J., Hsu, S. C., Jahn, K. S., Huang, P., Keller, C. A., Giardine, B. M., Kadauke, S., Campbell, A. E., Evans, P., Hardison, R. C., et al. (2015) · Blood · doi:10.1182/blood-2014-10-607309 · Cited by 103 · see citing works
Self-citationCombinatorial regulation of tissue specification by GATA and FOG factors
Chlon, T. M., & Crispino, J. D. (2012) · Development · doi:10.1242/dev.080440 · Cited by 96 · see citing works
Interplay between chromatin state, regulator binding, and regulatory motifs in six human cell typesPreprint
Ernst, J., & Kellis, M. (2013) · Genome Research · doi:10.1101/gr.144840.112 · Cited by 95 · see citing works
Self-citationThe Chromatin Fingerprint of Gene Enhancer Elements
Zentner, G. E., & Scacheri, P. C. (2012) · Journal of Biological Chemistry · doi:10.1074/jbc.r111.296491 · Cited by 89 · see citing works
Transcriptional divergence and conservation of human and mouse erythropoiesis
Pishesha, N., Thiru, P., Shi, J., Eng, J. C., Sankaran, V. G., & Lodish, H. F. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1401598111 · Cited by 86 · see citing works
Wu, W.-S., Morrissey, C. S., Keller, C. A., Mishra, T., Pimkin, M., Blobel, G. A., Weiss, M. J., & Hardison, R. C. (2014) · Genome Research · doi:10.1101/gr.164830.113 · Cited by 82 · see citing works
Self-citationMechanisms by which transcription factors gain access to target sequence elements in chromatin
Guertin, M. J., & Lis, J. (2012) · Current Opinion in Genetics and Development · doi:10.1016/j.gde.2012.11.008 · Cited by 84 · see citing works
Spatiotemporal clustering of the epigenome reveals rules of dynamic gene regulationPreprint
Yu, P., Shu Dong, X. I. A. O., Xin, X., Song, C., Huang, W., McDee, D., Tanaka, T. S., Wang, T., He, C., & Zhong, S. (2012) · Genome Research · doi:10.1101/gr.144949.112 · Cited by 78 · see citing works
Coordinated changes in gene expression kinetics underlie both mouse and human erythroid maturation
Barile, M., Imaz-Rosshandler, I., Inzani, I., Ghazanfar, S., Nichols, J., Marioni, J. C., Guibentif, C., & Göttgens, B. (2021) · Genome Biology · doi:10.1186/s13059-021-02414-y · Cited by 77 · see citing works
Dynamic enhancer–gene body contacts during transcription elongationPreprint
Lee, K., Hsiung, C. C. ‐., Huang, P., Raj, A., & Blobel, G. A. (2015) · Genes & Development · doi:10.1101/gad.255265.114 · Cited by 71 · see citing works
Self-citationChlon, T. M., Doré, L. C., & Crispino, J. D. (2012) · Molecular Cell · doi:10.1016/j.molcel.2012.05.051 · Cited by 73 · see citing works
Interrogating Histone Acetylation and BRD4 as Mitotic Bookmarks of Transcription
Behera, V., Stonestrom, A. J., Hamagami, N., Hsiung, C. C. ‐., Keller, C. A., Giardine, B. M., Sidoli, S., Yuan, Z., Bhanu, N. V., Werner, M. T., et al. (2019) · Cell Reports · doi:10.1016/j.celrep.2019.03.057 · Cited by 67 · see citing works
Self-citationGuertin, M. J., Zhang, X., Coonrod, S. A., & Hager, G. L. (2014) · Molecular Endocrinology · doi:10.1210/me.2014-1130 · Cited by 67 · see citing works
Kremsky, I., & Corces, V. G. (2020) · Genome biology · doi:10.1186/s13059-020-02036-w · Cited by 69 · see citing works
Ross, J., Mavoungou, L. O., Bresnick, E. H., & Milot, É. (2012) · Molecular and Cellular Biology · doi:10.1128/mcb.00163-12 · Cited by 64 · see citing works
Wakabayashi, A., Ulirsch, J. C., Ludwig, L. S., Fiorini, C., Yasuda, M., Choudhuri, A., McDonel, P. E., Zon, L. I., & Sankaran, V. G. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1521754113 · Cited by 59 · see citing works
jMOSAiCS: joint analysis of multiple ChIP-seq datasets
Zeng, X. W., Sanalkumar, R., Bresnick, E. H., Li, H., Chang, Q., & Keleş, S. (2013) · Genome biology · doi:10.1186/gb-2013-14-4-r38 · Cited by 61 · see citing works
Ikaros inhibits megakaryopoiesis through functional interaction with GATA-1 and NOTCH signaling
Malinge, S., Thiollier, C., Chlon, T. M., Doré, L. C., Diebold, L. P., Bluteau, O., Mabialah, V., Vainchenker, W., Dessen, P., Winandy, S., et al. (2013) · Blood · doi:10.1182/blood-2012-08-450627 · Cited by 61 · see citing works
Widespread and dynamic translational control of red blood cell development
Alvarez‐Dominguez, J. R., Zhang, X., & Hu, W. (2016) · Blood · doi:10.1182/blood-2016-09-741835 · Cited by 60 · see citing works
An effective statistical evaluation of ChIPseq dataset similarity
Chikina, M. D., & Troyanskaya, O. G. (2012) · Bioinformatics · doi:10.1093/bioinformatics/bts009 · Cited by 60 · see citing works
An integrative view of the regulatory and transcriptional landscapes in mouse hematopoiesisPreprint
Xiang, G., Keller, C. A., Heuston, E. F., Giardine, B. M., An, L., Wixom, A. Q., Miller, A., Cockburn, A., Sauria, M. E. G., Isaac, K. J., et al. (2020) · Genome Research · doi:10.1101/gr.255760.119 · Cited by 55 · see citing works
Self-citationLing, T., Birger, Y., Stankiewicz, M. J., Ben-Haim, N., Tomer Kalisky, C., Rein, A., Kugler, E., Chen, W., Fu, C., Zhang, K. X., et al. (2019) · Blood · doi:10.1182/blood.2019001234 · Cited by 54 · see citing works
Accurate Prediction of Inducible Transcription Factor Binding Intensities In Vivo
Guertin, M. J., Martins, A. L., Siepel, A., & Lis, J. (2012) · PLoS Genetics · doi:10.1371/journal.pgen.1002610 · Cited by 63 · see citing works
Bender, M. A., Ragoczy, T., Lee, J., Byron, R., Telling, A., Dean, A., & Groudine, M. (2012) · Blood · doi:10.1182/blood-2011-09-380485 · Cited by 53 · see citing works
Genome-wide Epigenetic Data Facilitate Understanding of Disease Susceptibility Association Studies
Hardison, R. C. (2012) · Journal of Biological Chemistry · doi:10.1074/jbc.r112.352427 · Cited by 53 · see citing works
Self-citationDirect targets of pSTAT5 signalling in erythropoiesis
Gillinder, K. R., Tuckey, H., Bell, C. C., Magor, G. W., Huang, S., Ilsley, M. D., & Perkins, A. C. (2017) · PLoS ONE · doi:10.1371/journal.pone.0180922 · Cited by 52 · see citing works
Cpeb4-Mediated Translational Regulatory Circuitry Controls Terminal Erythroid Differentiation
Hu, W., Yuan, B., & Lodish, H. F. (2014) · Developmental Cell · doi:10.1016/j.devcel.2014.07.008 · Cited by 51 · see citing works
Evolution of hemoglobin loci and their regulatory elements
Philipsen, S., & Hardison, R. C. (2018) · Blood Cells, Molecules, and Diseases · doi:10.1016/j.bcmd.2017.08.001 · Cited by 51 · see citing works
Self-citationO-GlcNAc homeostasis contributes to cell fate decisions during hematopoiesis
Zhang, Z., Parker, M. P., Graw, S., Novikova, L., Fedosyuk, H., Fontes, J. D., Koestler, D. C., Peterson, K. R., & Slawson, C. M. (2018) · Journal of Biological Chemistry · doi:10.1074/jbc.ra118.005993 · Cited by 51 · see citing works
Mar, D., Gharib, S. A., Zager, R. A., Johnson, A. C. M., Denisenko, O. N., & Bomsztyk, K. (2015) · Kidney International · doi:10.1038/ki.2015.164 · Cited by 49 · see citing works
Genome-wide organization of GATA1 and TAL1 determined at high resolution
Han, G. C., Vinayachandran, V., Bataille, A. R., Park, B., Chan-Salis, K. Y., Keller, C. A., Long, M., Mahony, S., Hardison, R. C., & Pugh, B. F. (2016) · Molecular and Cellular Biology · doi:10.1128/mcb.00806-15 · Cited by 48 · see citing works
Self-citationUlirsch, J., Lacy, J., An, X., Mohandas, N., Mikkelsen, T., & Sankaran, V. (2014) · PLoS Genetics · doi:10.1371/journal.pgen.1004890 · Cited by 51 · see citing works
Mechanism governing a stem cell-generating cis -regulatory element
Sanalkumar, R., Johnson, K. D., Gao, X., Boyer, M. E., Chang, Y., Hewitt, K. J., Zhang, J., & Bresnick, E. H. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1400065111 · Cited by 46 · see citing works
Chlon, T. M., McNulty, M., Goldenson, B., Rosinski, A., & Crispino, J. D. (2015) · Haematologica · doi:10.3324/haematol.2014.112714 · Cited by 46 · see citing works
Bottardi, S., Mavoungou, L. O., Pak, H., Daou, S., Bourgoin, V., Lakehal, Y. A., Affar, E. B., & Milot, É. (2014) · PLoS Genetics · doi:10.1371/journal.pgen.1004827 · Cited by 44 · see citing works
The role of chromatin dynamics in immune cell development
Winter, D. R., & Amit, I. (2014) · Immunological Reviews · doi:10.1111/imr.12200 · Cited by 43 · see citing works
Fawal, M.-A., Jungas, T., Kischel, A., Audouard, C., Iacovoni, J. S., & Davy, A. (2018) · Cell Reports · doi:10.1016/j.celrep.2018.05.005 · Cited by 45 · see citing works
Behera, V., Evans, P., Face, C. J., Hamagami, N., Sankaranarayanan, L., Keller, C. A., Giardine, B. M., Tan, K., Hardison, R. C., Shi, J., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-03082-6 · Cited by 45 · see citing works
Self-citationTranscriptional Mechanisms Underlying Hemoglobin SynthesisPreprint
Katsumura, K. R., DeVilbiss, A., Pope, N. J., Johnson, K. D., & Bresnick, E. H. (2013) · Cold Spring Harbor Perspectives in Medicine · doi:10.1101/cshperspect.a015412 · Cited by 43 · see citing works
Hematopoietic Signaling Mechanism Revealed From a Stem/Progenitor Cell Cistrome
Hewitt, K., Kim, D.-H., Devadas, P., Prathibha, R., Zuo, C., Sanalkumar, R., Johnson, K. D., Kang, Y.-A., Kim, J.-S., Dewey, C., et al. (2015) · Molecules and Cells · doi:10.1016/j.molcel.2015.05.020 · Cited by 42 · see citing works
Xu, P., Scott, D. C., Xu, B., Yao, Y., Feng, R., Cheng, L., Mayberry, K. D., Wang, Y., Bi, W., Palmer, L. E., et al. (2020) · Blood · doi:10.1182/blood.2020007809 · Cited by 43 · see citing works
Self-citationGATA Factor-Mediated Gene Regulation in Human Erythropoiesis
Romano, O., Petiti, L., Félix, T., Meneghini, V., Portafax, M., Antoniani, C., Amendola, M., Bicciato, S., Peano, C., & Miccio, A. (2020) · iScience · doi:10.1016/j.isci.2020.101018 · Cited by 40 · see citing works
AIAP: A Quality Control and Integrative Analysis Package to Improve ATAC-Seq Data Analysis
Liu, S., Li, D., Lyu, C., Gontarz, P. M., Miao, B., Madden, P. A. F., Wang, T., & Zhang, B. (2021) · Genomics Proteomics & Bioinformatics · doi:10.1016/j.gpb.2020.06.025 · Cited by 41 · see citing works
GATA factor transcriptional activity: Insights from genome‐wide binding profiles
Romano, O., & Miccio, A. (2020) · IUBMB Life - A Journal of the International Union of Biochemistry and Molecular Biology · doi:10.1002/iub.2169 · Cited by 32 · see citing works
Acetylation of histone deacetylase 1 regulates NuRD corepressor complex activity
Yang, T., Jian, W., Luo, Y., Fu, X., Noguchi, C., Bungert, J., Huang, S., & Qiu, Y. (2012) · Journal of Biological Chemistry · doi:10.1074/jbc.m112.349704 · Cited by 35 · see citing works
Sedley, L. (2020) · Epigenetics Insights · doi:10.1177/2516865720981924 · Cited by 29 · see citing works
Regulation of RNA polymerase II activity is essential for terminal erythroid maturation
Murphy, Z. C., Murphy, K. E., Myers, J., Getman, M. R., Couch, T. A., Schulz, V., Lezon-Geyda, K., Palumbo, C. D., Yan, H., Mohandas, N., et al. (2021) · Blood · doi:10.1182/blood.2020009903 · Cited by 29 · see citing works
Hagey, D. W., Zaouter, C., Combeau, G., Andersson‐Lendahl, M., Andersson, O., Huss, M., & Muhr, J. (2016) · Genome Research · doi:10.1101/gr.203513.115 · Cited by 29 · see citing works
Identification of mammalian transcription factors that bind to inaccessible chromatin
Pop, R. T., Pisante, A., Nagy, D., Martin, P. C. N., Mikheeva, L. A., Hayat, A., Ficz, G., & Zabet, N. R. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkad614 · Cited by 28 · see citing works
Papadopoulos, G. L., Karkoulia, E., Tsamardinos, I., Porcher, C., Ragoussis, J., Bungert, J., & Strouboulis, J. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt167 · Cited by 28 · see citing works
Gregoricchio, S., Polit, L., Esposito, M., Berthelet, J., Delestré, L., Evanno, E., Diop, M., Gallais, I., Aleth, H., Poplineau, M., et al. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac613 · Cited by 27 · see citing works
Leonards, K., Almosailleakh, M., Tauchmann, S., Bagger, F. O., Thirant, C., Juge, S., Bock, T., Méreau, H., Bezerra, M. F., Tzankov, A., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-16179-8 · Cited by 27 · see citing works
Integrative view on how erythropoietin signaling controls transcription patterns in erythroid cells
Perreault, A. A., & Venters, B. J. (2018) · Current Opinion in Hematology · doi:10.1097/moh.0000000000000415 · Cited by 27 · see citing works
Merryweather‐Clarke, A. T., Tipping, A. J., Lamikanra, A., Fa, R., Abu‐Jamous, B., Tsang, H. P., Carpenter, L., Robson, K., Nandi, A. K., & Roberts, D. J. (2016) · BMC Genomics · doi:10.1186/s12864-016-3134-z · Cited by 25 · see citing works
miR-181a regulates erythroid enucleation via the regulation of Xpo7 expression
Figueroa, A. A., Fasano, J. D., Martínez-Morilla, S., Venkatesan, S., Kupfer, G. M., & Hattangadi, S. M. (2018) · Haematologica · doi:10.3324/haematol.2017.171785 · Cited by 25 · see citing works
Li, D., Zhao, X., Zhou, S., Hu, Q., Wu, F., & Lee, H. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkad468 · Cited by 23 · see citing works
Epigenetic and Transcriptional Control of Erythropoiesis
Wells, M., & Steiner, L. A. (2022) · Frontiers in Genetics · doi:10.3389/fgene.2022.805265 · Cited by 23 · see citing works
Zwifelhofer, N. M., Cai, X., Liao, R., Mao, B., Conn, D. J., Mehta, C., Keleş, S., Xia, Y., & Bresnick, E. H. (2020) · PLoS Genetics · doi:10.1371/journal.pgen.1009286 · Cited by 21 · see citing works
Biology of Erythropoiesis, Erythroid Differentiation, and Maturation
Papayannopoulou, T., & Migliaccio, A. R. (2017) · Elsevier eBooks · doi:10.1016/b978-0-323-35762-3.00026-3 · Cited by 21 · see citing works
Deep modeling of gene expression regulation in an Erythropoiesis model
Denas, O. (2015) · Cited by 17 · see citing works
Ludwig, L. S., Cho, H., Wakabayashi, A., Eng, J. C., Ulirsch, J. C., Fleming, M. D., Lodish, H. F., & Sankaran, V. G. (2015) · American Journal of Hematology · doi:10.1002/ajh.23952 · Cited by 16 · see citing works
A statistical framework for power calculations in ChIP-seq experiments
Zuo, C., & Keleş, S. (2013) · Bioinformatics · doi:10.1093/bioinformatics/btt200 · Cited by 15 · see citing works
Gene silencing dynamics are modulated by transiently active regulatory elements
Vermunt, M. W., Luan, J. Y., Zhang, Z., Thrasher, A. J., Huang, A., Saari, M. S., Khandros, E., Beagrie, R. A., Zhang, S., Vemulamada, P., et al. (2023) · Molecular Cell · doi:10.1016/j.molcel.2023.02.006 · Cited by 16 · see citing works
Self-citationHEXIM1 is an essential transcription regulator during human erythropoiesis
Lv, X., Murphy, K. E., Murphy, Z. C., Getman, M. R., Rahman, N. F., Nakamura, Y., Blanc, L., Gallagher, P. G., Palis, J., Mohandas, N., et al. (2023) · Blood · doi:10.1182/blood.2022019495 · Cited by 15 · see citing works
Chung, D., Park, D. M., Myers, K. S., Grass, J., Kiley, P. J., Landick, R. C., & Keleş, S. (2013) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1003246 · Cited by 15 · see citing works
Epigenetic memories: structural marks or active circuits?
Nicol‐Benoit, F., Goff, P. L., Dréan, Y. L., Demay, F., Pakdel, F., Flouriot, G., & Michel, D. (2012) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-012-0923-7 · Cited by 15 · see citing works
Epo reprograms the epigenome of erythroid cells
Perreault, A. A., Benton, M. L., Koury, M. J., Brandt, S. J., & Venters, B. J. (2017) · Experimental Hematology · doi:10.1016/j.exphem.2017.03.004 · Cited by 16 · see citing works
The DEK Oncoprotein Is a Critical Component of the EKLF/KLF1 Enhancer in Erythroid Cells
Lohmann, F., Dangeti, M., Soni, S., Chen, X., Planutis, A., Baron, M. H., Choi, K., & Bieker, J. J. (2015) · Molecular and Cellular Biology · doi:10.1128/mcb.00382-15 · Cited by 14 · see citing works
Genetic screens reveal CCDC115 as a modulator of erythroid iron and heme trafficking
Sobh, A., Loguinov, A. V., Zhou, J., Jenkitkasemwong, S., Zeidan, R. S., Ahmadie, N. E., Tagmount, A., Knutson, M. D., Fraenkel, P. G., & Vulpe, C. D. (2020) · American Journal of Hematology · doi:10.1002/ajh.25899 · Cited by 12 · see citing works
Jain, D., Mishra, T., Giardine, B. M., Keller, C. A., Morrissey, C. S., Magargee, S. F., Dorman, C. M., Long, M., Weiss, M. J., & Hardison, R. C. (2015) · Genomics Data · doi:10.1016/j.gdata.2015.01.008 · Cited by 12 · see citing works
Self-citationRNA-regulatory exosome complex confers cellular survival to promote erythropoiesis
Mehta, C., de Andrade, I. F., Matson, D. R., Dewey, C. N., & Bresnick, E. H. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkab367 · Cited by 12 · see citing works
Zhao, H., Zhang, G., Pang, L., Lan, Y., Wang, L., Yu, F., Hu, J. R., Li, F., Zhao, T., Xiao, Y., et al. (2016) · Biochimica et Biophysica Acta (BBA) - General Subjects · doi:10.1016/j.bbagen.2016.04.008 · Cited by 11 · see citing works
Dynamics of gene expression with positive feedback to histone modifications at bivalent domains
Huang, R., & Lei, J. (2017) · International Journal of Modern Physics B · doi:10.1142/s0217979218500753 · Cited by 12 · see citing works
Hardison, R. C., Zhang, Y., Keller, C. A., Xiang, G., Heuston, E. F., An, L., Lichtenberg, J., Giardine, B. M., Bodine, D. M., Mahony, S., et al. (2019) · IUBMB Life · doi:10.1002/iub.2195 · Cited by 10 · see citing works
Self-citationImproving ATAC-seq Data Analysis with AIAP, a Quality Control and Integrative Analysis PackagePreprint
Liu, S., Li, D., Lyu, C., Gontarz, P. M., Miao, B., Madden, P. A. F., Wang, T., & Zhang, B. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/686808 · Cited by 10 · see citing works
Computational and experimental methods to decipher the epigenetic code
de Pretis, S., & Pelizzola, M. (2014) · Frontiers in Genetics · doi:10.3389/fgene.2014.00335 · Cited by 8 · see citing works
Lu, X., Zhao, Z., Wang, X., Zhang, X., Zhai, Y., Deng, W., Yi, Z., & Li, L. (2018) · Biology Open · doi:10.1242/bio.032508 · Cited by 8 · see citing works
dCaP: detecting differential binding events in multiple conditions and proteins
Chen, K.-B., Hardison, R. C., & Zhang, Y. (2014) · BMC Genomics · doi:10.1186/1471-2164-15-s9-s12 · Cited by 8 · see citing works
Self-citationAn integrative view of the regulatory and transcriptional landscapes in mouse hematopoiesisPreprint
Xiang, G., Keller, C. A., Heuston, E. F., Giardine, B. M., An, L., Wixom, A. Q., Miller, A., Cockburn, A., Sauria, M. E. G., Weaver, K., et al. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/731729 · Cited by 8 · see citing works
Self-citation
- Authors
- Wu, W., Cheng, Y., Keller, C. A., Ernst, J., Kumar, S. A., Mishra, T., Morrissey, C., Dorman, C. M., Chen, K.-B., Drautz, D., Giardine, B., Shibata, Y., Song, L., Pimkin, M., Crawford, G. E., Furey, T. S., Kellis, M., Miller, W., Taylor, J., Schuster, S. C., Zhang, Y., Chiaromonte, F., Blobel, G. A., Weiss, M. J., & Hardison, R. C.
- Affiliations
- Pennsylvania State University (US)
- Broad Institute (US)
- Duke University (US)
- University of North Carolina at Chapel Hill (US)
- Emory University (US)
- Children's Hospital of Philadelphia (US)
- ORCID
- Venue
- Genome Research
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 2011-07-27
- Volume
- 21
- Issue
- 10
- Pages
- 1659-1671
- ISSN
- 1088-9051 (ISSN-L)
- PMC
- PMC3202283
- OpenAlex
- W4299645797
- Cited by
- 118
- References
- 63
- Citations by year
- 2025: 1 · 2023: 4 · 2022: 3 · 2021: 8 · 2020: 10 · 2019: 9 · 2018: 7 · 2017: 7 · 2016: 8 · 2015: 11 · 2014: 16 · 2013: 11 · 2012: 22
- Type
- posted content
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Genome Research (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Carolina Digital Repository (University of North Carolina at Chapel Hill) (submittedVersion)
- DSpace@MIT (Massachusetts Institute of Technology) (submittedVersion, cc-by-nc)
- HighWire Press Open Archive (submittedVersion)
- UNC Libraries
- Funders
- National Science Foundation (0821527, 0905968)
- Gordon and Betty Moore Foundation
- Leukemia and Lymphoma Society
- University of Pennsylvania
- Pennsylvania State University (OCI-0821527)
- National Institutes of Health
- National Human Genome Research Institute (R01HG004718, RC2HG005573, RC1HG005334, RC2HG005639, R01HG004037, R01HG002238)
- National Institute of Diabetes and Digestive and Kidney Diseases (R01DK065806, R01DK058044, R01DK054937)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chromatin Remodeling and Cancer
- Keywords
- erythroid differentiation, GATA-1, chromatin accessibility, histone modifications, transcription factor occupancy, chromatin state, lineage commitment, epigenetic landscape, transcriptional regulation
- MeSH terms
- T-Cell Acute Lymphocytic Leukemia Protein 1, Animals, Cell Differentiation, Cell Line, Erythropoiesis, Estradiol, Peptide Hydrolases, Protein Binding, Proto-Oncogene Proteins, Receptors, Estrogen, Recombinant Proteins, Regulatory Sequences, Nucleic Acid, Multivariate Analysis, Gene Silencing, Gene Expression Profiling, Chromatin Assembly and Disassembly, Epigenesis, Genetic, Chromatin Immunoprecipitation, GATA1 Transcription Factor, GATA2 Transcription Factor, Mice, Basic Helix-Loop-Helix Proteins
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