Role of DNA Methylation in Modulating Transcription Factor Occupancy
Open accessAbstract
Although DNA methylation is commonly invoked as a mechanism for transcriptional repression, the extent to which it actively silences transcription factor (TF) occupancy sites in vivo is unknown. To study the role of DNA methylation in the active modulation of TF binding, we quantified the effect of DNA methylation depletion on the genomic occupancy patterns of CTCF, an abundant TF with known methylation sensitivity that is capable of autonomous binding to its target sites in chromatin. Here, we show that the vast majority (>98.5%) of the tens of thousands of unoccupied, methylated CTCF recognition sequences remain unbound upon abrogation of DNA methylation. The small fraction of sites that show methylation-dependent binding in vivo are in turn characterized by highly variable CTCF occupancy across cell types. Our results suggest that DNA methylation is not a primary groundskeeper of genomic TF landscapes, but rather a specialized mechanism for stabilizing intrinsically labile sites.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
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?
5mC affects CTCF binding only at a specific subset of recognition sequences.
“Intriguingly, 5mC only affects CTCF binding at a specific subset of recognition sequences (30).”
From Dynamic DNA methylation: In the right place at the right time (2018) · cites this paper as [30]
Functional analyses of 5mC have traditionally relied on pharmacological or genetic perturbations that affect 5mC levels genome-wide.
“Functional analyses of 5mC have traditionally relied on pharmacological or genetic perturbations that affect 5mC levels genome-wide (30, 32).”
From Dynamic DNA methylation: In the right place at the right time (2018) · cites this paper as [30]
Changes in DNA methylation are often associated with chromatin status, resulting in increased or decreased DNA accessibility.
“Changes in DNA methylation are often associated with chromatin status, resulting in increased or decreased DNA accessibility 96,97.”
From Transcription factors as readers and effectors of DNA methylation (2016) · cites this paper as [96]
Cites
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.
Langmead, B., Trapnell, C., Pop, M., & Salzberg, S. L. (2009) · Genome Biology · doi:10.1186/gb-2009-10-3-r25 · Cited by 21,849 · see citing works
An integrated encyclopedia of DNA elements in the human genome
The ENCODE Project Consortium (2012) · Nature · doi:10.1038/nature11247 · Cited by 18,072 · see citing works
Differential expression analysis for sequence count data
Anders, S., & Huber, W. (2010) · Genome Biology · doi:10.1186/gb-2010-11-10-r106 · Cited by 15,581 · see citing works
A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping
Rao, S. S. P., Huntley, M. H., Durand, N. C., Stamenova, E. K., Bochkov, I. D., Robinson, J. T., Sanborn, A. L., Machol, I., Omer, A. D., Lander, E. S., et al. (2014) · Cell · doi:10.1016/j.cell.2014.11.021 · Cited by 9,212 · see citing works
Functions of DNA methylation: islands, start sites, gene bodies and beyond
Jones, P. A. (2012) · Nature Reviews Genetics · doi:10.1038/nrg3230 · Cited by 6,061 · see citing works
Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications
Krueger, F., & Andrews, S. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr167 · Cited by 5,161 · see citing works
Human DNA methylomes at base resolution show widespread epigenomic differences
Lister, R., Pelizzola, M., Dowen, R. H., Hawkins, R. D., Hon, G., Tonti-Filippini, J., Nery, J. R., Lee, L., Ye, Z., Ngo, Q.-M., et al. (2009) · Nature · doi:10.1038/nature08514 · Cited by 4,673 · see citing works
Targeted mutation of the DNA methyltransferase gene results in embryonic lethality
Li, E., Bestor, T. H., & Jaenisch, R. (1992) · Cell · doi:10.1016/0092-8674(92)90611-f · Cited by 3,984 · see citing works
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 · see citing works
Self-citationCpG islands and the regulation of transcription
Deaton, A. M., & Bird, A. (2011) · Genes & Development · doi:10.1101/gad.2037511 · Cited by 3,187 · see citing works
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 · see citing works
Self-citationCellular differentiation, cytidine analogs and DNA methylation
Jones, P. A., & Taylor, S. M. (1980) · Cell · doi:10.1016/0092-8674(80)90237-8 · Cited by 1,831 · see citing works
Methylation of a CTCF-dependent boundary controls imprinted expression of the Igf2 gene
Bell, A. C., & Felsenfeld, G. (2000) · Nature · doi:10.1038/35013100 · Cited by 1,746 · see citing works
DNMT3L connects unmethylated lysine 4 of histone H3 to de novo methylation of DNA
Ooi, S. K. T., Qiu, C., Bernstein, E., Li, K., Jia, D., Yang, Z., Erdjument‐Bromage, H., Tempst, P., Lin, S., Allis, C. D., et al. (2007) · Nature · doi:10.1038/nature05987 · Cited by 1,558 · see citing works
CTCF mediates methylation-sensitive enhancer-blocking activity at the H19/Igf2 locus
Hark, A. T., Schoenherr, C. J., Katz, D. J., Ingram, R. S., Levorse, J. M., & Tilghman, S. M. (2000) · Nature · doi:10.1038/35013106 · Cited by 1,547 · see citing works
CTCF: Master Weaver of the Genome
Phillips‐Cremins, J. E., & Corces, V. G. (2009) · Cell · doi:10.1016/j.cell.2009.06.001 · Cited by 1,540 · see citing works
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 · see citing works
Lewis, J. D., Meehan, R. R., Henzel, W. J., Maurer-Fogy, I., Jeppesen, P., Klein, F., & Bird, A. (1992) · Cell · doi:10.1016/0092-8674(92)90610-o · Cited by 1,371 · see citing works
DNMT1 and DNMT3b cooperate to silence genes in human cancer cells
Rhee, I. P., Bachman, K. E., Park, B. H., Jair, K.-W., Yen, R.-W. C., Schuebel, K. E., Cui, H., Feinberg, A. P., Christoph Lengauer, C., Kinzler, K. W., et al. (2002) · Nature · doi:10.1038/416552a · Cited by 1,243 · see citing works
Analysis of the Vertebrate Insulator Protein CTCF-Binding Sites in the Human Genome
Kim, T. H., Abdullaev, Z., Smith, A. D., Ching, K. A., Loukinov, D. I., Green, R. D., Zhang, M. Q., Lobanenkov, V. V., & Ren, B. (2007) · Cell · doi:10.1016/j.cell.2006.12.048 · Cited by 1,022 · see citing works
Measuring reproducibility of high-throughput experiments
Li, Q., Brown, J. B., Huang, H., & Bickel, P. J. (2011) · The Annals of Applied Statistics · doi:10.1214/11-aoas466 · Cited by 1,008 · see citing works
BEDOPS: high-performance genomic feature operations
Neph, S. J., Kuehn, M. S., Reynolds, A. P., Haugen, E., Thurman, R. E., Johnson, A., Rynes, E., Maurano, M. T., Vierstra, J. D., Thomas, S., et al. (2012) · Bioinformatics · doi:10.1093/bioinformatics/bts277 · Cited by 971 · see citing works
Self-citationChromatin 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
Self-citationDesign and analysis of ChIP-seq experiments for DNA-binding proteins
Kharchenko, P., Tolstorukov, M., & Park, P. J. (2008) · Nature Biotechnology · doi:10.1038/nbt.1508 · Cited by 950 · see citing works
Measuring reproducibility of high-throughput experiments
Li, Q., Brown, J. B., Huang, H., & Bickel, P. J. (2010) · UC Berkeley · Cited by 915 · see citing works
Comprehensive Genome-wide Protein-DNA Interactions Detected at Single-Nucleotide Resolution
Rhee, H. S., & Pugh, B. F. (2011) · Cell · doi:10.1016/j.cell.2011.11.013 · Cited by 760 · see citing works
An expansive human regulatory lexicon encoded in transcription factor footprints
Neph, S. J., Vierstra, J. D., Stergachis, A. B., Reynolds, A. P., Haugen, E., Vernot, B., Thurman, R. E., John, S., Sandstrom, R. S., Johnson, A., et al. (2012) · Nature · doi:10.1038/nature11212 · Cited by 746 · see citing works
Self-citationEffects of DNA methylation on DNA-binding proteins and gene expression
Tate, P. H., & Bird, A. P. (1993) · Current Opinion in Genetics & Development · doi:10.1016/0959-437x(93)90027-m · Cited by 737 · see citing works
Spl elements protect a CpG island from de novo methylation
Brandeis, M., Frank, D., Keshet, I., Siegfried, Z., Mendelsohn, M. M., Names, A., Temper, V., Razin, A., & Cedar, H. (1994) · Nature · doi:10.1038/371435a0 · Cited by 705 · see citing works
Dynamic DNA methylation across diverse human cell lines and tissuesPreprint
Varley, K. E., Gertz, J., Bowling, K. M., Parker, S. L., Reddy, T. E., Pauli, F., Cross, M. K., Williams, B. A., Stamatoyannopoulos, J. A., Crawford, G. E., et al. (2013) · Genome Research · doi:10.1101/gr.147942.112 · Cited by 693 · see citing works
Self-citationCpG islands influence chromatin structure via the CpG-binding protein Cfp1
Thomson, J. P., Skene, P. J., Selfridge, J., Clouaire, T., Guy, J., Webb, S., Kerr, A. R. W., Deaton, A., Andrews, R., James, K. D., et al. (2010) · Nature · doi:10.1038/nature08924 · Cited by 625 · see citing works
Schmidt, D., Schwalie, P. C., Wilson, M. D., Ballester, B., Gonçalves, Â., Kutter, C., Brown, G. D., Marshall, A., Flicek, P., & Odom, D. T. (2012) · Cell · doi:10.1016/j.cell.2011.11.058 · Cited by 598 · see citing works
Sp1 sites in the mouse aprt gene promoter are required to prevent methylation of the CpG island.Preprint
Macleod, D., Charlton, J., Mullins, J. J., & Bird, A. P. (1994) · Genes & Development · doi:10.1101/gad.8.19.2282 · Cited by 596 · see citing works
CTCF is a uniquely versatile transcription regulator linked to epigenetics and disease
Ohlsson, R., Renkawitz, R., & Lobanenkov, V. (2001) · Trends in Genetics · doi:10.1016/s0168-9525(01)02366-6 · Cited by 591 · see citing works
Widespread plasticity in CTCF occupancy linked to DNA methylation
Wang, H., Maurano, M. T., Qu, H., Varley, K. E., Gertz, J., Pauli, F., Lee, K., Canfield, T., Weaver, M., Sandstrom, R., et al. (2012) · Genome Research · doi:10.1101/gr.136101.111 · Cited by 588 · see citing works
Self-citationRamirez-Carrozzi, V. R., Braas, D., Bhatt, D. M., Cheng, C. S., Hong, C., Doty, K. R., Black, J. C., Hoffmann, A., Carey, M., & Smale, S. T. (2009) · Cell · doi:10.1016/j.cell.2009.04.020 · Cited by 581 · see citing works
Filippova, G. N., Fagerlie, S. R., Klenova, E. M., Myers, C. D., Dehner, Y., Goodwin, G. H., Neiman, P. E., Collins, S. J., & Lobanenkov, V. V. (1996) · Molecular and Cellular Biology · doi:10.1128/mcb.16.6.2802 · Cited by 543 · see citing works
Epigenetic memory at embryonic enhancers identified in DNA methylation maps from adult mouse tissues
Hon, G. C., Rajagopal, N., Shen, Y., McCleary, D. F., Yue, F., Dang, M. D., & Ren, B. (2013) · Nature Genetics · doi:10.1038/ng.2746 · Cited by 457 · see citing works
Identification of genetic elements that autonomously determine DNA methylation states
Lienert, F., Wirbelauer, C., Som, I., Dean, A., Mohn, F., & Schübeler, D. (2011) · Nature Genetics · doi:10.1038/ng.946 · Cited by 385 · see citing works
Methylation-Dependent and -Independent Genomic Targeting Principles of the MBD Protein Family
Baubec, T., Ivánek, R., Lienert, F., & Schübeler, D. (2013) · Cell · doi:10.1016/j.cell.2013.03.011 · Cited by 365 · see citing works
DNA methylation presents distinct binding sites for human transcription factors
Hu, S., Wan, J., Su, Y., Song, Q., Zeng, Y., Nguyen, H. N., Shin, J., Cox, E., Rho, H. S., Woodard, C., et al. (2013) · eLife · doi:10.7554/elife.00726 · Cited by 349 · see citing works
CTCF-binding sites flank CTG/CAG repeats and form a methylation-sensitive insulator at the DM1 locus
Filippova, G. N., Thienes, C. P., Penn, B. H., Cho, D. H., Hu, Y. J., Moore, J. M., Klesert, T. R., Lobanenkov, V. V., & Tapscott, S. J. (2001) · Nature Genetics · doi:10.1038/ng570 · Cited by 332 · see citing works
A Genome-wide Map of CTCF Multivalency Redefines the CTCF Code
Nakahashi, H., Kieffer, K.-R., Resch, W., Vian, L., Dose, M., Stavreva, D. A., Hakim, O., Pruett, N. D., Nelson, S., Yamane, A., et al. (2013) · Cell Reports · doi:10.1016/j.celrep.2013.04.024 · Cited by 306 · see citing works
Akalin, A., Garrett-Bakelman, F. E., Kormaksson, M., Busuttil, J., Zhang, L., Khrebtukova, I., Milne, T. A., Huang, Y., Biswas, D., Hess, J. L., et al. (2012) · PLoS Genetics · doi:10.1371/journal.pgen.1002781 · Cited by 296 · see citing works
Exonic Transcription Factor Binding Directs Codon Choice and Affects Protein Evolution
Stergachis, A. B., Haugen, E., Shafer, A., Fu, W., Vernot, B., Reynolds, A. P., Raubitschek, A., Ziegler, S. F., LeProust, E. M., Akey, J. M., et al. (2013) · Science · doi:10.1126/science.1243490 · Cited by 280 · see citing works
Self-citationDNA methylation status predicts cell type‐specific enhancer activity
Wiench, M., John, S., Baek, S., Johnson, T. A., Sung, M., Escobar, T., Simmons, C. A., Pearce, K. H., Biddie, S. C., Sabo, P. J., et al. (2011) · The EMBO Journal · doi:10.1038/emboj.2011.210 · Cited by 245 · see citing works
Self-citationReddington, J. P., Perricone, S. M., Nestor, C. E., Reichmann, J., Youngson, N. A., Suzuki, M., Reinhardt, D., Dunican, D. S., Prendergast, J. G., Mjoseng, H., et al. (2013) · Genome Biology · doi:10.1186/gb-2013-14-3-r25 · Cited by 240 · see citing works
Witcher, M., & Emerson, B. M. (2009) · Molecular Cell · doi:10.1016/j.molcel.2009.04.001 · Cited by 235 · see citing works
Transcription Factor Occupancy Can Mediate Active Turnover of DNA Methylation at Regulatory Regions
Feldmann, A., Ivánek, R., Murr, R., Gaidatzis, D., Burger, L., & Schübeler, D. (2013) · PLoS Genetics · doi:10.1371/journal.pgen.1003994 · Cited by 215 · see citing works
Does CTCF mediate between nuclear organization and gene expression?
OHLSSON, R. I., Lobanenkov, V. V., & Klenova, E. M. (2009) · BioEssays · doi:10.1002/bies.200900118 · Cited by 165 · see citing works
Hagemann, S., Heil, O., Lyko, F., & Brueckner, B. (2011) · PLoS ONE · doi:10.1371/journal.pone.0017388 · Cited by 152 · see citing works
Critical DNA Binding Interactions of the Insulator Protein CTCF
Renda, M., Baglivo, I., Burgess-Beusse, B. L., Esposito, S., Fattorusso, R., Felsenfeld, G., & Pedone, P. V. (2007) · Journal of Biological Chemistry · doi:10.1074/jbc.m706213200 · Cited by 152 · see citing works
5-azacytidine treatment reorganizes genomic histone modification patterns
Komashko, V., & Farnham, P. (2010) · Epigenetics · doi:10.4161/epi.5.3.11409 · Cited by 122 · see citing works
Groudine, M. T., & Conklin, K. F. (1985) · Science · doi:10.1126/science.2986289 · Cited by 115 · see citing works
The role of DNA methylation in directing the functional organization of the cancer epigenomePreprint
Lay, F. D., Liu, Y., Kelly, T. K., Witt, H. N., Farnham, P., Jones, P. A., & Berman, B. P. (2015) · Genome Research · doi:10.1101/gr.183368.114 · Cited by 109 · see citing works
An embryonic demethylation mechanism involving binding of transcription factors to replicating DNA
Matsuo, K., Silke, J., Georgiev, O., Marti, P., Giovannini, N., & Rungger, D. (1998) · The EMBO Journal · doi:10.1093/emboj/17.5.1446 · Cited by 104 · see citing works
Effects of DNA methylation on nucleosome stability
Collings, C. K., Waddell, P. J., & Anderson, J. N. (2013) · Nucleic Acids Research · doi:10.1093/nar/gks893 · Cited by 97 · see citing works
Soto‐Reyes, E., & Targa, F. R. (2010) · Oncogene · doi:10.1038/onc.2009.509 · Cited by 95 · see citing works
Functional DNA demethylation is accompanied by chromatin accessibility
Pandiyan, K., You, J. S., Yang, X., Dai, C., Zhou, X. J., Baylin, S. B., Jones, P. A., & Liang, G. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt077 · Cited by 86 · see citing works
Comparative genome-wide DNA methylation analysis of colorectal tumor and matched normal tissues
Simmer, F., Brinkman, A. B., Assenov, Y., et al. (2012) · Epigenetics · doi:10.4161/epi.22562 · Cited by 84 · see citing works
Qiu, X., Hother, C., Ralfkiær, U., Helbo, A. S., Lu, Q., Workman, C. T., Liang, G., Jones, P. A., & Grønbæk, K. (2010) · PLoS ONE · doi:10.1371/journal.pone.0012994 · Cited by 68 · see citing works
Gaidatzis, D., Burger, L., Murr, R., Lerch, A., Dessus-Babus, S., Schübeler, D., & Stadler, M. B. (2014) · PLoS Genetics · doi:10.1371/journal.pgen.1004143 · Cited by 66 · see citing works
CTCF is a DNA methylation-sensitive positive regulator of the INK/ARF locus
Rodríguez, C., Borgel, J., Court, F., Cathala, G., Forné, T., & Piette, J. (2010) · Biochemical and Biophysical Research Communications · doi:10.1016/j.bbrc.2009.12.159 · Cited by 65 · see citing works
Butcher, D. T., Mancini‐DiNardo, D., Archer, T., & Rodenhiser, D. I. (2004) · International Journal of Cancer · doi:10.1002/ijc.20324 · Cited by 64 · see citing works
Modulation of DNA Binding Protein Affinity Directly Affects Target Site Demethylation
Lin, I. G., Tomzynski, T. J., Ou, Q., & Hsieh, C. (2000) · Molecular and Cellular Biology · doi:10.1128/mcb.20.7.2343-2349.2000 · Cited by 64 · see citing works
Widespread Site-Dependent Buffering of Human Regulatory Polymorphism
Maurano, M. T., Wang, H., Kutyavin, T. V., & Stamatoyannopoulos, J. A. (2012) · PLoS Genetics · doi:10.1371/journal.pgen.1002599 · Cited by 61 · see citing works
Self-citationDing, Z., Ni, Y., Timmer, S. W., Lee, B., Battenhouse, A. M., Louzada, S., Yang, F., Dunham, I., Crawford, G. E., Lieb, J. D., et al. (2014) · PLoS Genetics · doi:10.1371/journal.pgen.1004798 · Cited by 55 · see citing works
Bowers, S. R., Mirabella, F., Calero‐Nieto, F. J., Valeaux, S., Hadjur, S., Baxter, E. W., Merkenschlager, M., & Cockerill, P. N. (2009) · Molecular and Cellular Biology · doi:10.1128/mcb.01411-08 · Cited by 33 · see citing works
Gain of DNA methylation is enhanced in the absence of CTCF at the human retinoblastoma gene promoter
Dávalos-Salas, M., Furlan-Magaril, M., González-Buendía, E., Valdes‐Quezada, C., Ayala-Ortega, E., & Targa, F. R. (2011) · BMC Cancer · doi:10.1186/1471-2407-11-232 · Cited by 31 · see citing works
Flagged first, then by citations
Cited by
Sorted by citations
Dynamic DNA methylation: In the right place at the right time
Luo, C., Hajkova, P., & Ecker, J. R. (2018) · Science · doi:10.1126/science.aat6806 · Cited by 668 · see citing works
Transcription factors as readers and effectors of DNA methylation
Zhu, H., Wang, G., & Qian, J. (2016) · Nature Reviews Genetics · doi:10.1038/nrg.2016.83 · Cited by 649 · see citing works
Competition between DNA methylation and transcription factors determines binding of NRF1
Domcke, S., Bardet, A. F., Adrian Ginno, P., Hartl, D., Burger, L., & Schübeler, D. (2015) · Nature · doi:10.1038/nature16462 · Cited by 508 · see citing works
Sensitivity of transcription factors to DNA methylation
Héberlé, É., & Bardet, A. F. (2019) · Essays in Biochemistry · doi:10.1042/ebc20190033 · Cited by 347 · see citing works
YY1 and CTCF orchestrate a 3D chromatin looping switch during early neural lineage commitment
Beagan, J. A., Duong, M. T., Titus, K. R., Zhou, L., Cao, Z., Ma, J., Lachanski, C. V., Gillis, D. R., & Phillips-Cremins, J. E. (2017) · Genome Research · doi:10.1101/gr.215160.116 · Cited by 299 · see citing works
“Genome-wide CTCF occupancy patterns have been mapped across more than 100 mammalian cell types (Kim et al. 2007; Chen et al. 2008; Cuddapah et al. 2009; Wang et al. 2012; Maurano et al. 2015).”
InfluentialGenome-wide DNA-methylation landscape defines specialization of regulatory T cells in tissues
Delacher, M., Imbusch, C. D., Weichenhan, D., Breiling, A., Hotz-Wagenblatt, A., Träger, U., Hofer, A.-C., Kägebein, D., Wang, Q., Frauhammer, F., et al. (2017) · Nature Immunology · doi:10.1038/ni.3799 · Cited by 282 · see citing works
Structural Basis for the Versatile and Methylation-Dependent Binding of CTCF to DNA
Hashimoto, H., Wang, D., Horton, J. R., Zhang, X., Corces, V. G., & Cheng, X. (2017) · Molecular Cell · doi:10.1016/j.molcel.2017.05.004 · Cited by 268 · see citing works
El Khattabi, L., Zhao, H., Kalchschmidt, J., Young, N., Jung, S., Van Blerkom, P., Kieffer-Kwon, P., Kieffer-Kwon, K.-R., Park, S., Wang, X., et al. (2019) · Cell · doi:10.1016/j.cell.2019.07.011 · Cited by 244 · see citing works
Pflueger, C., Tan, D., Swain, T., Nguyen, T., Pflueger, J., Nefzger, C., Polo, J. M., Ford, E., & Lister, R. (2018) · Genome Research · doi:10.1101/gr.233049.117 · Cited by 188 · see citing works
Crossed wires: 3D genome misfolding in human disease
Norton, H. K., & Phillips-Cremins, J. E. (2017) · Journal of Cell Biology · doi:10.1083/jcb.201611001 · Cited by 57 · see citing works
- Authors
- Maurano, M. T., Wang, H., John, S., Shafer, A., Canfield, T., Lee, K., & Stamatoyannopoulos, J. A.
- Affiliations
- University of Washington (US)
- Corresponding author
- Maurano, Matthew T.
- Stamatoyannopoulos, John A.
- Venue
- Cell Reports
- Publisher
- Elsevier BV
- Published
- 2015-08
- Volume
- 12
- Issue
- 7
- Pages
- 1184-1195
- ISSN
- 2211-1247 (ISSN-L)
- OpenAlex
- W1699926620
- Cited by
- 281
- References
- 69
- Citations by year
- 2026: 6 · 2025: 14 · 2024: 33 · 2023: 20 · 2022: 32 · 2021: 34 · 2020: 30 · 2019: 26 · 2018: 35 · 2017: 26 · 2016: 21 · 2015: 4
- FWCI
- 12.44
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Cell Reports (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- National Institutes of Health
- National Institute of Mental Health (F31MH094073)
- National Human Genome Research Institute (U54HG004592, U54HG007010)
- National Institute of Environmental Health Sciences (U01ES017156)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chromatin Remodeling and Cancer
- Keywords
- DNA methylation, transcription factor occupancy, CTCF, transcriptional repression, chromatin binding, cell type variation, epigenetic regulation of transcription
- MeSH terms
- Chromatin, Humans, Protein Binding, Transcription Factors, DNA Methylation, Cell Line, Tumor
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
