Chromatin immunoprecipitation and microarray-based analysis of protein location

Transcriptional Regulatory Networks in Saccharomyces cerevisiae

Lee, T. I., Rinaldi, N. J., Robert, F., Odom, D. T., Bar-Joseph, Z., Gerber, G. K., Hannett, N. M., Harbison, C. T., Thompson, C. M., Simon, I., et al. (2002) · Science · doi:10.1126/science.1075090 · Cited by 2,956

E2F integrates cell cycle progression with DNA repair, replication, and G 2 /M checkpoints

Ren, B., Cam, H., Takahashi, Y., Volkert, T., Terragni, J., Young, R. A., & Dynlacht, B. D. (2002) · Genes & Development · doi:10.1101/gad.949802 · Cited by 1,125

Microarray identification of FMRP-associated brain mRNAs and altered mRNA translational profiles in fragile X syndrome

Brown, V., Jin, P., Ceman, S., Darnell, J. C., O'Donnell, W. T., Tenenbaum, S. A., Jin, X., Feng, Y., Wilkinson, K. D., Keene, J. D., et al. (2001) · Cell · doi:10.1016/s0092-8674(01)00568-2 · Cited by 1,109

Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs

Cawley, S., Bekiranov, S., Ng, H. H., Kapranov, P., Sekinger, E. A., Kampa, D., Piccolboni, A., Sementchenko, V., Cheng, J., Williams, A. J., et al. (2004) · Cell · doi:10.1016/s0092-8674(04)00127-8 · Cited by 1,095

Genome-wide binding map of the histone deacetylase Rpd3 in yeast

Kurdistani, S. K., Robyr, D., Tavazoie, S., & Grunstein, M. (2002) · Nature Genetics · doi:10.1038/ng907 · Cited by 279

Suppression of inflammation by a synthetic histone mimic

Nicodeme, E., Jeffrey, K. L., Schaefer, U., Beinke, S., Dewell, S., Chung, C.-W., Chandwani, R., Marazzi, I., Wilson, P., Coste, H., et al. (2010) · Nature · doi:10.1038/nature09589 · Cited by 1,563

c-Myc Regulates Transcriptional Pause Release

Rahl, P. B., Lin, C. Y., Seila, A. C., Flynn, R. A., McCuine, S., Burge, C. B., Sharp, P. A., & Young, R. A. (2010) · Cell · doi:10.1016/j.cell.2010.03.030 · Cited by 1,279

Distinct Factors Control Histone Variant H3.3 Localization at Specific Genomic Regions

Goldberg, A. D., Banaszynski, L. A., Noh, K.-M., Lewis, P. W., Elsaesser, S. J., Stadler, S., Dewell, S., Law, M., Guo, X., Li, X., et al. (2010) · Cell · doi:10.1016/j.cell.2010.01.003 · Cited by 1,280

Senescence-associated reprogramming promotes cancer stemness

Milanovic, M., Fan, D. N. Y., Belenki, D., Däbritz, J. H. M., Zhao, Z., Yu, Y., Dörr, J. R., Dimitrova, L., Lenze, D., Monteiro Barbosa, I. A., et al. (2018) · Nature · doi:10.1038/nature25167 · Cited by 1,131

Activation of proto-oncogenes by disruption of chromosome neighborhoods

Hnisz, D., Weintraub, A. S., Day, D. S., Valton, A.-L., Bak, R. O., Li, C. H., Goldmann, J., Lajoie, B. R., Fan, Z. P., Sigova, A. A., et al. (2016) · Science · doi:10.1126/science.aad9024 · Cited by 1,042

YY1 Is a Structural Regulator of Enhancer-Promoter Loops

Weintraub, A. S., Li, C. H., Zamudio, A. V., Sigova, A. A., Hannett, N. M., Day, D. S., Abraham, B. J., Cohen, M. A., Nabet, B., Buckley, D. L., et al. (2017) · Cell · doi:10.1016/j.cell.2017.11.008 · Cited by 992

Densely Interconnected Transcriptional Circuits Control Cell States in Human Hematopoiesis

Novershtern, N., Subramanian, A., Lawton, L. N., Mak, R. H., Haining, W. N., McConkey, M. E., Habib, N., Yosef, N., Chang, C. Y., Shay, T., et al. (2011) · Cell · doi:10.1016/j.cell.2011.01.004 · Cited by 942

Braveheart, a Long Noncoding RNA Required for Cardiovascular Lineage Commitment

Klattenhoff, C. A., Scheuermann, J. C., Surface, L. E., Bradley, R. K., Fields, P. A., Steinhauser, M. L., Ding, H., Butty, V. L., Torrey, L., Haas, S., et al. (2013) · Cell · doi:10.1016/j.cell.2013.01.003 · Cited by 913

An oncogenic super-enhancer formed through somatic mutation of a noncoding intergenic element

Mansour, M. R., Abraham, B. J., Anders, L., Berezovskaya, A., Gutierrez, A., Durbin, A. D., Etchin, J., Lawton, L., Sallan, S. E., Silverman, L. B., et al. (2014) · Science · doi:10.1126/science.1259037 · Cited by 801

HSF1 Drives a Transcriptional Program Distinct from Heat Shock to Support Highly Malignant Human Cancers

Mendillo, M. L., Santagata, S., Koeva, M., Bell, G. W., Hu, R., Tamimi, R. M., Fraenkel, E., Ince, T. A., Whitesell, L., & Lindquist, S. (2012) · Cell · doi:10.1016/j.cell.2012.06.031 · Cited by 694

CDK7 Inhibition Suppresses Super-Enhancer-Linked Oncogenic Transcription in MYCN-Driven Cancer

Chipumuro, E., Marco, E., Christensen, C. L., Kwiatkowski, N., Zhang, T., Hatheway, C. M., Abraham, B. J., Sharma, B., Yeung, C., Altabef, A., et al. (2014) · Cell · doi:10.1016/j.cell.2014.10.024 · Cited by 631

Lamin B1 depletion in senescent cells triggers large-scale changes in gene expression and the chromatin landscape

Shah, P. P., Donahue, G., Otte, G. L., Capell, B. C., Nelson, D. M., Cao, K., Aggarwala, V., Cruickshanks, H. A., Rai, T. S., McBryan, T., et al. (2013) · Genes & Development · doi:10.1101/gad.223834.113 · Cited by 550

ChIP-seq: Using high-throughput sequencing to discover protein–DNA interactions

Schmidt, D., Wilson, M. D., Spyrou, C., Brown, G. D., Hadfield, J., & Odom, D. T. (2009) · Methods · doi:10.1016/j.ymeth.2009.03.001 · Cited by 525

Rescue of Fragile X Syndrome Neurons by DNA Methylation Editing of the FMR1 Gene

Liu, X. S., Wu, H., Krzisch, M., Wu, X., Graef, J., Muffat, J., Hnisz, D., Li, C. H., Yuan, B., Xu, C., et al. (2018) · Cell · doi:10.1016/j.cell.2018.01.012 · Cited by 512

A Regulatory Archipelago Controls Hox Genes Transcription in Digits

Montavon, T., Soshnikova, N., Mascrez, B., Joye, E., Thevenet, L., Splinter, E., de Laat, W., Spitz, F., & Duboule, D. (2011) · Cell · doi:10.1016/j.cell.2011.10.023 · Cited by 477

H3K4me3 Interactions with TAF3 Regulate Preinitiation Complex Assembly and Selective Gene Activation

Lauberth, S. M., Nakayama, T., Wu, X., Ferris, A. L., Tang, Z., Hughes, S. H., & Roeder, R. G. (2013) · Cell · doi:10.1016/j.cell.2013.01.052 · Cited by 473

Therapeutic targeting of polycomb and BET bromodomain proteins in diffuse intrinsic pontine gliomas

Piunti, A., Hashizume, R., Morgan, M. A., Bartom, E. T., Horbinski, C. M., Marshall, S. A., Rendleman, E. J., Ma, Q., Takahashi, Y.-H., Woodfin, A. R., et al. (2017) · Nature Medicine · doi:10.1038/nm.4296 · Cited by 445

CDK7-Dependent Transcriptional Addiction in Triple-Negative Breast Cancer

Wang, Y., Zhang, T., Kwiatkowski, N., Abraham, B. J., Lee, T. I., Xie, S., Yuzugullu, H., Von, T., Li, H., Lin, Z., et al. (2015) · Cell · doi:10.1016/j.cell.2015.08.063 · Cited by 465

Annotating non-coding regions of the genome.

Alexander, R. P., Fang, G., Rozowsky, J., Snyder, M., & Gerstein, M. B. (2010) · Nature Reviews Genetics · doi:10.1038/nrg2814 · Cited by 464

Target Genes of the MADS Transcription Factor SEPALLATA3: Integration of Developmental and Hormonal Pathways in the Arabidopsis Flower

Kaufmann, K., Muiño, J. M., Jauregui, R., Airoldi, C. A., Smaczniak, C., Krajewski, P., & Angenent, G. C. (2009) · PLoS Biology · doi:10.1371/journal.pbio.1000090 · Cited by 458

An epithelial circadian clock controls pulmonary inflammation and glucocorticoid action

Gibbs, J., Ince, L., Matthews, L., Mei, J., Bell, T., Yang, N., Saer, B., Begley, N., Poolman, T., Pariollaud, M., et al. (2014) · Nature Medicine · doi:10.1038/nm.3599 · Cited by 455

Mbd3/NURD Complex Regulates Expression of 5-Hydroxymethylcytosine Marked Genes in Embryonic Stem Cells

Yildirim, O., Li, R., Hung, J.-H., Chen, P. B., Dong, X., Ee, L.-S., Weng, Z., Rando, O. J., & Fazzio, T. G. (2011) · Cell · doi:10.1016/j.cell.2011.11.054 · Cited by 450

ATR-X Syndrome Protein Targets Tandem Repeats and Influences Allele-Specific Expression in a Size-Dependent Manner

Law, M. J., Lower, K. M., Voon, H. P. J., Hughes, J. R., Garrick, D., Viprakasit, V., Mitson, M., De Gobbi, M., Marra, M., Morris, A., et al. (2010) · Cell · doi:10.1016/j.cell.2010.09.023 · Cited by 444

The MLL3/MLL4 Branches of the COMPASS Family Function as Major Histone H3K4 Monomethylases at Enhancers

Hu, D., Gao, X., Morgan, M. A., Herz, H.-M., Smith, E. R., & Shilatifard, A. (2013) · Molecular and Cellular Biology · doi:10.1128/mcb.01181-13 · Cited by 439

The Rhino-Deadlock-Cutoff Complex Licenses Noncanonical Transcription of Dual-Strand piRNA Clusters in Drosophila

Mohn, F., Sienski, G., Handler, D., & Brennecke, J. (2014) · Cell · doi:10.1016/j.cell.2014.04.031 · Cited by 414

A zebrafish melanoma model reveals emergence of neural crest identity during melanoma initiation

Kaufman, C. K., Mosimann, C., Fan, Z. P., Yang, S., Thomas, A. J., Ablain, J., Tan, J. L., Fogley, R. D., van Rooijen, E., Hagedorn, E. J., et al. (2016) · Science · doi:10.1126/science.aad2197 · Cited by 398

Establishment of porcine and human expanded potential stem cells

Gao, X., Nowak-Imialek, M., Chen, X., Chen, D., Herrmann, D., Ruan, D., Chen, A. C. H., Eckersley-Maslin, M. A., Ahmad, S., Lee, Y. L., et al. (2019) · Nature Cell Biology · doi:10.1038/s41556-019-0333-2 · Cited by 389

The Reprogramming of Tumor Stroma by HSF1 Is a Potent Enabler of Malignancy

Scherz-Shouval, R., Santagata, S., Mendillo, M. L., Sholl, L. M., Ben-Aharon, I., Beck, A. H., Dias-Santagata, D., Koeva, M., Stemmer, S. M., Whitesell, L., et al. (2014) · Cell · doi:10.1016/j.cell.2014.05.045 · Cited by 386

Relief of Feedback Inhibition of HER3 Transcription by RAF and MEK Inhibitors Attenuates Their Antitumor Effects in BRAF -Mutant Thyroid Carcinomas

Montero-Conde, C., Ruiz-Llorente, S., Dominguez, J. M., Knauf, J. A., Viale, A., Sherman, E. J., Ryder, M., Ghossein, R. A., Rosen, N., & Fagin, J. A. (2013) · Cancer Discovery · doi:10.1158/2159-8290.cd-12-0531 · Cited by 382

Core Transcriptional Regulatory Circuit Controlled by the TAL1 Complex in Human T Cell Acute Lymphoblastic Leukemia

Sanda, T., Lawton, L. N., Barrasa, M. I., Fan, Z. P., Kohlhammer, H., Gutierrez, A., Ma, W., Tatarek, J., Ahn, Y., Kelliher, M. A., et al. (2012) · Cancer Cell · doi:10.1016/j.ccr.2012.06.007 · Cited by 334

Using formaldehyde-assisted isolation of regulatory elements (FAIRE) to isolate active regulatory DNA

Simon, J. M., Giresi, P. G., Davis, I. J., & Lieb, J. D. (2012) · Nature Protocols · doi:10.1038/nprot.2011.444 · Cited by 329

Lineage Regulators Direct BMP and Wnt Pathways to Cell-Specific Programs during Differentiation and Regeneration

Trompouki, E., Bowman, T. V., Lawton, L. N., Fan, Z. P., Wu, D.-C., DiBiase, A., Martin, C. S., Cech, J. N., Sessa, A. K., Leblanc, J. L., et al. (2011) · Cell · doi:10.1016/j.cell.2011.09.044 · Cited by 310

Ten-Eleven Translocation-2 (TET2) Is a Master Regulator of Smooth Muscle Cell Plasticity

Liu, R., Jin, Y., Tang, W. H., Qin, L., Zhang, X., Tellides, G., Hwa, J., Yu, J., & Martin, K. A. (2013) · Circulation · doi:10.1161/circulationaha.113.002887 · Cited by 294

Whole-genome ChIP–chip analysis of Dorsal, Twist, and Snail suggests integration of diverse patterning processes in the Drosophila embryo

Zeitlinger, J., Zinzen, R. P., Stark, A., Kellis, M., Zhang, H., Young, R. A., & Levine, M. (2007) · Genes & Development · doi:10.1101/gad.1509607 · Cited by 286

A rapid micro chromatin immunoprecipitation assay (ChIP)

Dahl, J. A., & Collas, P. (2008) · Nature Protocols · doi:10.1038/nprot.2008.68 · Cited by 283

A heterochromatin-dependent transcription machinery drives piRNA expression

Andersen, P. R., Tirian, L., Vunjak, M., & Brennecke, J. (2017) · Nature · doi:10.1038/nature23482 · Cited by 280

The pluripotency factor Oct4 interacts with Ctcf and also controls X-chromosome pairing and counting

Donohoe, M. E., Silva, S. S., Pinter, S. F., Xu, N., & Lee, J. T. (2009) · Nature · doi:10.1038/nature08098 · Cited by 276

Next is now: new technologies for sequencing of genomes, transcriptomes, and beyond

Lister, R., Gregory, B. D., & Ecker, J. R. (2009) · Current Opinion in Plant Biology · doi:10.1016/j.pbi.2008.11.004 · Cited by 274

Distinct transcriptional MYCN/c-MYC activities are associated with spontaneous regression or malignant progression in neuroblastomas

Westermann, F., Muth, D., Benner, A., Bauer, T., Henrich, K.-O., Oberthuer, A., Brors, B., Beissbarth, T., Vandesompele, J., Pattyn, F., et al. (2008) · Genome Biology · doi:10.1186/gb-2008-9-10-r150 · Cited by 264

PAF1, a Molecular Regulator of Promoter-Proximal Pausing by RNA Polymerase II

Chen, F. X., Woodfin, A. R., Gardini, A., Rickels, R. A., Marshall, S. A., Smith, E. R., Shiekhattar, R., & Shilatifard, A. (2015) · Cell · doi:10.1016/j.cell.2015.07.042 · Cited by 253

Changes in regeneration-responsive enhancers shape regenerative capacities in vertebrates

Wang, W., Hu, C.-K., Zeng, A., Alegre, D., Hu, D., Gotting, K., Ortega Granillo, A., Wang, Y., Robb, S., Schnittker, R., et al. (2020) · Science · doi:10.1126/science.aaz3090 · Cited by 210

Silencio/CG9754 connects the Piwi-piRNA complex to the cellular heterochromatin machinery

Sienski, G., Batki, J., Senti, K.-A., Dönertas, D., Tirian, L., Meixner, K., & Brennecke, J. (2015) · Genes & Development · doi:10.1101/gad.271908.115 · Cited by 185

Preformed chromatin topology assists transcriptional robustness of Shh during limb development

Paliou, C., Guckelberger, P., Schöpflin, R., Heinrich, V., Esposito, A., Chiariello, A. M., Bianco, S., Annunziatella, C., Helmuth, J., Haas, S., et al. (2019) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1900672116 · Cited by 163

MicroRNA-223 is a crucial mediator of PPARγ-regulated alternative macrophage activation

Ying, W., Tseng, A., Chang, R. C.-A., Morin, A., Brehm, T., Triff, K., Nair, V., Zhuang, G., Song, H., Kanameni, S., et al. (2015) · Journal of Clinical Investigation · doi:10.1172/jci81656 · Cited by 144

Convergent evolution of complex regulatory landscapes and pleiotropy at Hox loci

Lonfat, N., Montavon, T., Darbellay, F., Gitto, S., & Duboule, D. (2014) · Science · doi:10.1126/science.1257493 · Cited by 113

CREB-activity and nmnat2 transcription are down-regulated prior to neurodegeneration, while NMNAT2 over-expression is neuroprotective, in a mouse model of human tauopathy

Ljungberg, M. C., Ali, Y. O., Zhu, J., Wu, C.-S., Oka, K., Zhai, R. G., & Lu, H.-C. (2012) · Human Molecular Genetics · doi:10.1093/hmg/ddr492 · Cited by 107

ERβ- and Prostaglandin E2-Regulated Pathways Integrate Cell Proliferation via Ras-like and Estrogen-Regulated Growth Inhibitor in Endometriosis

Monsivais, D., Dyson, M. T., Yin, P., Coon, J. S., Navarro, A., Feng, G., Malpani, S. S., Ono, M., Ercan, C. M., Wei, J. J., et al. (2014) · Molecular Endocrinology · doi:10.1210/me.2013-1421 · Cited by 91

BRCA mutational status shapes the stromal microenvironment of pancreatic cancer linking clusterin expression in cancer associated fibroblasts with HSF1 signaling

Shaashua, L., Ben-Shmuel, A., Pevsner-Fischer, M., Friedman, G., Levi-Galibov, O., Nandakumar, S., Barki, D., Nevo, R., Brown, L. E., Zhang, W., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-34081-3 · Cited by 79

Chromatin kinases act on transcription factors and histone tails in regulation of inducible transcription

Josefowicz, S. Z., Shimada, M., Armache, A., Li, C. H., Miller, R. M., Lin, S., Yang, A., Dill, B. D., Molina, H., Park, H.-S., et al. (2016) · Molecular Cell · doi:10.1016/j.molcel.2016.09.026 · Cited by 84

Estrogen receptor β regulates endometriotic cell survival through serum and glucocorticoid–regulated kinase activation

Monsivais, D., Dyson, M. T., Yin, P., Navarro, A., Coon, J. S., Pavone, M. E., & Bulun, S. E. (2016) · Fertility and Sterility · doi:10.1016/j.fertnstert.2016.01.012 · Cited by 62

Genome-wide analysis of Pax8 binding provides new insights into thyroid functions

Ruiz-Llorente, S., de Pau, E. C. S., Sastre-Perona, A., Montero-Conde, C., Gómez-López, G., Fagin, J. A., Valencia, A., Pisano, D. G., & Santisteban, P. (2012) · BMC Genomics · doi:10.1186/1471-2164-13-147 · Cited by 51

IFN Regulatory Factor 8 Regulates MDM2 in Germinal Center B Cells

Zhou, J. X., Lee, C. H., Qi, C. F., Wang, H., Naghashfar, Z., Abbasi, S., & Morse, H. C. (2009) · The Journal of Immunology · doi:10.4049/jimmunol.0803693 · Cited by 47

Prenatal zinc deficiency-dependent epigenetic alterations of mouse metallothionein-2 gene

Kurita, H., Ohsako, S., Hashimoto, S.-I., Yoshinaga, J., & Tohyama, C. (2013) · The Journal of Nutritional Biochemistry · doi:10.1016/j.jnutbio.2012.05.013 · Cited by 45

EZH2 inhibitors restore epigenetically silenced CD58 expression in B-cell lymphomas

Otsuka, Y., Nishikori, M., Arima, H., Izumi, K., Kitawaki, T., Hishizawa, M., & Takaori-Kondo, A. (2020) · Molecular Immunology · doi:10.1016/j.molimm.2020.01.006 · Cited by 40

Aberrant expression and localization of deoxyribonucleic acid methyltransferase 3B in endometriotic stromal cells

Dyson, M. T., Kakinuma, T., Pavone, M. E., Monsivais, D., Navarro, A., Malpani, S. S., Ono, M., & Bulun, S. E. (2015) · Fertility and Sterility · doi:10.1016/j.fertnstert.2015.06.046 · Cited by 37

Bufalin inhibits hepatitis B virus-associated hepatocellular carcinoma development through androgen receptor dephosphorylation and cell cycle-related kinase degradation

Yu, Z., Feng, H., Zhuo, Y., Li, M., Zhu, X., Huang, L., Zhang, X., Zhou, Z., Zheng, C., Jiang, Y., et al. (2020) · Cellular Oncology · doi:10.1007/s13402-020-00546-0 · Cited by 27

Transient histone deacetylase inhibition induces cellular memory of gene expression and 3D genome folding

Paldi, F., Szalay, M.-F., Dufau, S., Di Stefano, M., Reboul, H., Jost, D., Bantignies, F., & Cavalli, G. (2026) · Nature Genetics · doi:10.1038/s41588-025-02489-4 · Cited by 18

Evolutionary Adaptation of an HP1-protein Chromodomain Integrates Chromatin and DNA Sequence Signals

Baumgartner, L., Ipsaro, J. J., Hohmann, U., Handler, D., Schleiffer, A., Duchek, P., & Brennecke, J. (2023) · doi:10.1101/2023.09.29.560096 · Cited by 2