NUCLEASE HYPERSENSITIVE SITES IN CHROMATIN

An integrated encyclopedia of DNA elements in the human genome

The ENCODE Project Consortium (2012) · Nature · doi:10.1038/nature11247 · Cited by 18,072

Systematic Localization of Common Disease-Associated Variation in Regulatory DNA

Maurano, M. T., Humbert, R., Rynes, E., Thurman, R. E., Haugen, E., Wang, H., Reynolds, A. P., Sandstrom, R., Qu, H., Brody, J., et al. (2012) · Science · doi:10.1126/science.1222794 · Cited by 3,716

ATAC-seq: a method for assaying chromatin accessibility genome-wide

Buenrostro, J. D., Wu, B., Chang, H. Y., & Greenleaf, W. J. (2015) · Current Protocols in Molecular Biology · doi:10.1002/0471142727.mb2129s109 · Cited by 3,289

Histone acetylation in chromatin structure and transcription

Grunstein, M. (1997) · Nature · doi:10.1038/38664 · Cited by 2,884

The accessible chromatin landscape of the human genome

Thurman, R. E., Rynes, E., Humbert, R., Vierstra, J., Maurano, M. T., Haugen, E., Sheffield, N. C., Stergachis, A. B., Wang, H., Vernot, B., et al. (2012) · Nature · doi:10.1038/nature11232 · Cited by 2,679

Tissue-Resident Macrophage Enhancer Landscapes Are Shaped by the Local Microenvironment

Lavin, Y., Winter, D., Blecher-Gonen, R., David, E., Keren-Shaul, H., Merad, M., Jung, S., & Amit, I. (2014) · Cell · doi:10.1016/j.cell.2014.11.018 · Cited by 2,167

High-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

Modification of Enhancer Chromatin: What, How, and Why?

Calo, E., & Wysocka, J. (2013) · Molecular Cell · doi:10.1016/j.molcel.2013.01.038 · Cited by 1,457

DNA-binding factors shape the mouse methylome at distal regulatory regions

Stadler, M. B., Murr, R., Burger, L., Ivanek, R., Lienert, F., Schöler, A., Nimwegen, E. V., Wirbelauer, C., Oakeley, E. J., Gaidatzis, D., et al. (2011) · Nature · doi:10.1038/nature10716 · Cited by 1,383

Activity-by-contact model of enhancer–promoter regulation from thousands of CRISPR perturbations

Fulco, C. P., Nasser, J., Jones, T. R., Munson, G., Bergman, D. T., Subramanian, V., Grossman, S. R., Anyoha, R., Doughty, B. R., Patwardhan, T. A., et al. (2019) · Nature Genetics · doi:10.1038/s41588-019-0538-0 · Cited by 1,111

Microglia development follows a stepwise program to regulate brain homeostasis

Matcovitch-Natan, O., Winter, D. R., Giladi, A., Vargas Aguilar, S., Spinrad, A., Sarrazin, S., Ben-Yehuda, H., David, E., Zelada González, F., Perrin, P., et al. (2016) · Science · doi:10.1126/science.aad8670 · Cited by 1,180

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

Transcriptional Regulatory Elements in the Human Genome

Maston, G. A., Evans, S. K., & Green, M. R. (2006) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev.genom.7.080505.115623 · Cited by 937

Latent Enhancers Activated by Stimulation in Differentiated Cells

Ostuni, R., Piccolo, V., Barozzi, I., Polletti, S., Termanini, A., Bonifacio, S., Curina, A., Prosperini, E., Ghisletti, S., & Natoli, G. (2013) · Cell · doi:10.1016/j.cell.2012.12.018 · Cited by 867

Functional and Mechanistic Diversity of Distal Transcription Enhancers

Bulger, M., & Groudine, M. (2011) · Cell · doi:10.1016/j.cell.2011.01.024 · Cited by 803

Regulation of macrophage development and function in peripheral tissues

Lavin, Y., Mortha, A., Rahman, A., & Merad, M. (2015) · Nature Reviews Immunology · doi:10.1038/nri3920 · Cited by 680

Global mapping of protein-DNA interactions in vivo by digital genomic footprinting

Hesselberth, J. R., Chen, X., Zhang, Z., Sabo, P. J., Sandstrom, R., Reynolds, A. P., Thurman, R. E., Neph, S., Kuehn, M. S., Noble, W. S., et al. (2009) · Nature Methods · doi:10.1038/nmeth.1313 · Cited by 559

Towards a comprehensive catalogue of validated and target-linked human enhancers

Gasperini, M., Tome, J. M., & Shendure, J. (2020) · Nature Reviews Genetics · doi:10.1038/s41576-019-0209-0 · Cited by 396

Retroviral DNA integration: viral and cellular determinants of target-site selection

Lewinski, M. K., Yamashita, M., Emerman, M., Ciuffi, A., Marshall, H., Crawford, G., Collins, F., Shinn, P., Leipzig, J., Hannenhalli, S., et al. (2006) · PLoS Pathogens · doi:10.1371/journal.ppat.0020060 · Cited by 364

Heritable Individual-Specific and Allele-Specific Chromatin Signatures in Humans

McDaniell, R., Lee, B.-K., Song, L., Liu, Z., Boyle, A. P., Erdos, M. R., Scott, L. J., Morken, M. A., Kucera, K. S., Battenhouse, A., et al. (2010) · Science · doi:10.1126/science.1184655 · Cited by 308

Index and biological spectrum of human DNase I hypersensitive sites

Meuleman, W., Muratov, A., Rynes, E., Halow, J., Lee, K., Bates, D., Diegel, M., Dunn, D., Neri, F., Teodosiadis, A., et al. (2020) · Nature · doi:10.1038/s41586-020-2559-3 · Cited by 331

Animal Transcription Networks as Highly Connected, Quantitative Continua

Biggin, M. D. (2011) · Developmental Cell · doi:10.1016/j.devcel.2011.09.008 · Cited by 308

Nucleosomes, DNA-binding proteins, and DNA sequence modulate retroviral integration target site selection

Pryciak, P. M., & Varmus, H. E. (1992) · Cell · doi:10.1016/0092-8674(92)90289-o · Cited by 273

Single-molecule regulatory architectures captured by chromatin fiber sequencing

Stergachis, A. B., Debo, B. M., Haugen, E., Churchman, L. S., & Stamatoyannopoulos, J. A. (2020) · Science · doi:10.1126/science.aaz1646 · Cited by 257

Locus control regions of mammalian β-globin gene clusters: combining phylogenetic analyses and experimental results to gain functional insights

Hardison, R., Slightom, J. L., Gumucio, D. L., Goodman, M., Stojanovic, N., & Miller, W. (1997) · Gene · doi:10.1016/s0378-1119(97)00474-5 · Cited by 230

The role of chromatin accessibility in directing the widespread, overlapping patterns of Drosophila transcription factor binding

Li, X.-Y., Thomas, S., Sabo, P. J., Eisen, M. B., Stamatoyannopoulos, J. A., & Biggin, M. D. (2011) · Genome Biology · doi:10.1186/gb-2011-12-4-r34 · Cited by 217

The influence of DNA and nucleosome structure on integration events directed by HIV integrase

Pruss, D., Reeves, R., Bushman, F. D., & Wolffe, A. P. (1994) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(17)31494-1 · Cited by 173

Evaluation of chromatin accessibility in prefrontal cortex of individuals with schizophrenia

Bryois, J., Garrett, M. E., Song, L., Safi, A., Giusti-Rodriguez, P., Johnson, G. D., Shieh, A. W., Buil, A., Fullard, J. F., Roussos, P., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-05379-y · Cited by 167

Two distinct auto-regulatory loops operate at the PU.1 locus in B cells and myeloid cells

Leddin, M., Perrod, C., Hoogenkamp, M., Ghani, S., Assi, S., Heinz, S., Wilson, N. K., Follows, G., Schönheit, J., Vockentanz, L., et al. (2011) · Blood · doi:10.1182/blood-2010-08-302976 · Cited by 131

Dynamics of the epigenetic landscape during erythroid differentiation after GATA1 restoration

Wu, W., Cheng, Y., Keller, C. A., Ernst, J., Kumar, S. A., Mishra, T., Morrissey, C., Dorman, C. M., Chen, K.-B., Drautz, D., et al. (2011) · Genome Research · doi:10.1101/gr.125088.111 · Cited by 118

CaMK activation during exercise is required for histone hyperacetylation and MEF2A binding at the MEF2 site on the Glut4 gene

Smith, J. A. H., Kohn, T. A., Chetty, A. K., & Ojuka, E. O. (2008) · American Journal of Physiology-Endocrinology and Metabolism · doi:10.1152/ajpendo.00747.2007 · Cited by 115

Histone acetylation and globin gene switching

Hebbes, T. R., Thorne, A. W., Clayton, A. L., & Crane-Robinson, C. (1992) · Nucleic Acids Research · doi:10.1093/nar/20.5.1017 · Cited by 113

A novel enhancer in the immunoglobulin lambda locus is duplicated and functionally independent of NF kappa B.

Hagman, J., Rudin, C. M., Haasch, D., Chaplin, D., & Storb, U. (1990) · Genes & Development · doi:10.1101/gad.4.6.978 · Cited by 100

Non-coding Transcripts from Enhancers: New Insights into Enhancer Activity and Gene Expression Regulation

Chen, H., Du, G., Song, X., & Li, L. (2017) · Genomics, Proteomics & Bioinformatics · doi:10.1016/j.gpb.2017.02.003 · Cited by 85

Transcription termination and polyadenylation in retroviruses

Guntaka, R. V. (1993) · Microbiological Reviews · doi:10.1128/mr.57.3.511-521.1993 · Cited by 52

Mouse β-Globin DNA-Binding Protein B1 is Identical to a Proto-Oncogene, the Transcription Factor Spi-1 /PU.1, and is Restricted in Expression to Hematopoietic Cells and the Testis

Galson, D. L., Hensold, J. O., Bishop, T. R., Schalling, M., D'Andrea, A. D., Jones, C., Auron, P. E., & Housman, D. E. (1993) · Molecular and Cellular Biology · doi:10.1128/mcb.13.5.2929-2941.1993 · Cited by 45

DNA Methylation and Chromatin Structure Regulate PU.1 Expression

Amaravadi, L., & Klemsz, M. J. (1999) · DNA and Cell Biology · doi:10.1089/104454999314737 · Cited by 44

The HNF-4/HNF-1α transactivation cascade regulates gene activity and chromatin structure of the human serine protease inhibitor gene cluster at 14q32.1

Rollini, P., & Fournier, R. E. K. (1999) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.96.18.10308 · Cited by 42

A novel virus-inducible enhancer of the interferon-β gene with tightly linked promoter and enhancer activities

Banerjee, A. R., Kim, Y. J., & Kim, T. H. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku1018 · Cited by 39

Evaluation of chromatin accessibility in prefrontal cortex of schizophrenia cases and controls

Bryois, J., Garrett, M. E., Song, L., Safi, A., Giusti-Rodriguez, P., Johnson, G. D., Demur, A. B., Fullard, J. F., Roussos, P., Sklar, P., et al. (2017) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/141986 · Cited by 7