DNA methylation and late replication probably aid cell memory, and type I DNA reeling could aid chromosome folding and enhancer function
Abstract
DNA methylation in mammals is reviewed, and it is concluded that one role of methylation is to aid cell memory, which is defined as the ability of mitotically derived progeny cells to remember and re-establish their proper cellular identity. Methylation of X-linked CpG-rich islands probably stabilizes X-chromosome inactivation, but other mechanisms appear to be involved. Late replication is discussed as a key ancestral mechanism for X inactivation, and it is emphasized that early and late replication domains may each be self perpetuating. Therefore, early-late replication timing becomes another strong candidate mechanism for cell memory. A chromosome-loop folding enigma is discussed, and it is concluded that special mechanisms are needed to explain the formation and maintenance of specific looped domains. DNA reeling, such as done by type I restriction-modification enzymes, is proposed to provide this special mechanism for folding. DNA reeling mechanisms can help to explain the cis-spreading of X-chromosome inactivation as well as long-range action by enhancers.
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?
The convergent rule and cohesin sliding favor a linear tracking mechanism known as the loop extrusion model.
“this favors a linear tracking mechanism,47 known as the “loop extrusion model”.8,9,48”
From Recent evidence that TADs and chromatin loops are dynamic structures (2018) · cites this paper as [47]
Cites
CpG-rich islands and the function of DNA methylation
Bird, A. P. (1986) · Nature · doi:10.1038/321209a0 · Cited by 3,777 · see citing works
DNA Methylation and Gene Function
Razin, A., & Riggs, A. D. (1980) · Science · doi:10.1126/science.6254144 · Cited by 2,076 · see citing works
Self-citationDNA Modification Mechanisms and Gene Activity During Development
Holliday, R., & Pugh, J. E. (1975) · Science · doi:10.1126/science.187.4173.226 · Cited by 1,973 · see citing works
How eukaryotic transcriptional activators work
Ptashne, M. (1988) · Nature · doi:10.1038/335683a0 · Cited by 1,828 · see citing works
X inactivation, differentiation, and DNA methylation
Riggs, A. D. (2008) · Cytogenetics and Cell Genetics · doi:10.1159/000130315 · Cited by 1,343 · see citing works
Self-citationBunz, U. H. F. (2005) · Science · doi:10.1126/science.1111098 · Cited by 1,252 · see citing works
DNA METHYLATION AND GENE ACTIVITY
Doerfler, W. (1983) · Annual Review of Biochemistry · doi:10.1146/annurev.bi.52.070183.000521 · Cited by 1,115 · see citing works
Monk, M., Boubelı́k, M., & Lehnert, S. A. (1987) · Development · doi:10.1242/dev.99.3.371 · Cited by 1,100 · see citing works
The Inheritance of Epigenetic Defects
Holliday, R. (1987) · Science · doi:10.1126/science.3310230 · Cited by 1,078 · see citing works
DNA methylation and gene activity
Cedar, H. (1988) · Cell · doi:10.1016/0092-8674(88)90479-5 · Cited by 907 · see citing works
Cockerill, P. N., & Garrard, W. T. (1986) · Cell · doi:10.1016/0092-8674(86)90761-0 · Cited by 881 · see citing works
van Holde, K. E. (1989) · Springer series in molecular biology · doi:10.1007/978-1-4612-3490-6 · Cited by 650 · see citing works
Watt, F., & Molloy, P. L. (1988) · Genes & Development · doi:10.1101/gad.2.9.1136 · Cited by 611 · see citing works
5-Methylcytosine, Gene Regulation, and Cancer
Riggs, A. D., & Jones, P. A. (1983) · Advances in cancer research · doi:10.1016/s0065-230x(08)60678-8 · Cited by 420 · see citing works
Self-citationA glimpse at chromosomal order
Gasser, S. M., & Laemmli, U. K. (1987) · Trends in Genetics · doi:10.1016/0168-9525(87)90156-9 · Cited by 416 · see citing works
Transcriptional elements as components of eukaryotic origins of DNA replication
DePamphilis, M. L. (1988) · Cell · doi:10.1016/0092-8674(88)90398-4 · Cited by 338 · see citing works
DNA methylation, biochemistry, and biological significance
Razin, A., Cedar, H., & Riggs, A. D. (1984) · Springer eBooks · Cited by 332 · see citing works
Self-citationThe replicative origin of the E. coli chromosome binds to cell membranes only when hemimethylated
Ogden, G. B., Pratt, M. J., & Schaechter, M. (1988) · Cell · doi:10.1016/0092-8674(88)90186-9 · Cited by 315 · see citing works
Sanford, J. P., Clark, H., Chapman, V. M., & Rossant, J. (1987) · Genes & Development · doi:10.1101/gad.1.10.1039 · Cited by 279 · see citing works
Role of replication time in the control of tissue-specific gene expression.
Holmquist, G. P. (1987) · PubMed · Cited by 249 · see citing works
MECHANISMS OF X-CHROMOSOME REGULATION
Grant, S. G., & Chapman, V. M. (1988) · Annual Review of Genetics · doi:10.1146/annurev.ge.22.120188.001215 · Cited by 219 · see citing works
Radial loops and helical coils coexist in metaphase chromosomes
Rattner, J. B., & LIN, C. (1985) · Cell · doi:10.1016/s0092-8674(85)80124-0 · Cited by 208 · see citing works
Molecular Biology of DNA Methylation
ADAMS, R. L. P., & Burdon, R. H. (1985) · Springer series in molecular biology · doi:10.1007/978-1-4612-5130-9 · Cited by 187 · see citing works
Lyon, M. F. (1988) · PubMed · Cited by 179 · see citing works
Kaslow, D. C., & Migeon, B. R. (1987) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.84.17.6210 · Cited by 173 · see citing works
Keith, D. H., Singer–Sam, J., & Riggs, A. D. (1986) · Molecular and Cellular Biology · doi:10.1128/mcb.6.11.4122 · Cited by 162 · see citing works
Self-citationMolecular biology of DNA methylation
(1987) · Comparative Biochemistry and Physiology Part A Physiology · doi:10.1016/0300-9629(87)90413-0 · Cited by 161 · see citing works
Model for how type I restriction enzymes select cleavage sites in DNA.
Studier, F. W., & Bandyopadhyay, P. K. (1988) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.85.13.4677 · Cited by 145 · see citing works
New beginnings in studies of eukaryotic DNA replication origins
Umek, R. M., Linskens, M. H. K., Kowalski, D., & Huberman, J. A. (1989) · Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression · doi:10.1016/0167-4781(89)90123-1 · Cited by 129 · see citing works
The chromatin domain as a unit of gene regulation
Goldman, M. A. (1988) · BioEssays · doi:10.1002/bies.950090204 · Cited by 125 · see citing works
DNA translocation by the restriction enzyme from E. coli K
Yuan, R. T., Hamilton, D. L., & Burckhardt, J. (1980) · Cell · doi:10.1016/0092-8674(80)90251-2 · Cited by 115 · see citing works
Toniolo, D., Martini, G., Migeon, B. R., & Rosana, D. (1988) · The EMBO Journal · doi:10.1002/j.1460-2075.1988.tb02827.x · Cited by 112 · see citing works
Mechanism of action of rat liver DNA methylase
Drahovský, D., & Morris, N. R. (1971) · Journal of Molecular Biology · doi:10.1016/0022-2836(71)90104-5 · Cited by 102 · see citing works
Methylation and the X chromosome
Monk, M. (1986) · BioEssays · doi:10.1002/bies.950040505 · Cited by 101 · see citing works
Hansen, R. S., Ellis, N. A., & Gartler, S. M. (1988) · Molecular and Cellular Biology · doi:10.1128/mcb.8.11.4692 · Cited by 89 · see citing works
Regulation of mouse satellite DNA replication time.
Selig, S., Ariel, M. S., Goitein, R., Marcus, M., & Cedar, H. (1988) · The EMBO Journal · doi:10.1002/j.1460-2075.1988.tb02829.x · Cited by 82 · see citing works
Singer, J., Roberts-Ems, J., Luthardt, F. W., & Riggs, A. D. (1979) · Nucleic Acids Research · doi:10.1093/nar/7.8.2369 · Cited by 82 · see citing works
Self-citationEffect of ageing on reactivation of the human X-linked HPRT locus
Migeon, B. R., Axelman, J., & Beggs, A. H. (1988) · Nature · doi:10.1038/335093a0 · Cited by 80 · see citing works
Jablonka, E., Goitein, R., Marcus, M., & Cedar, H. (1985) · Chromosoma · doi:10.1007/bf00293162 · Cited by 77 · see citing works
Achwal, C. W., Ganguly, P., & Chandra, H. S. (1984) · The EMBO Journal · doi:10.1002/j.1460-2075.1984.tb01795.x · Cited by 63 · see citing works
Endlich, B., & Linn, S. (1985) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(18)89082-2 · Cited by 57 · see citing works
Supercoiled loops and the organization of replication and transcription in eukaryotes
Zehnbauer, B. A., & Vogelstein, B. (1985) · BioEssays · doi:10.1002/bies.950020203 · Cited by 57 · see citing works
Razin, A., Cedar, H., & Riggs, A. D. (1984) · Springer series in molecular biology · doi:10.1007/978-1-4613-8519-6 · Cited by 54 · see citing works
Self-citationX-linked gene expression and X-chromosome inactivation: marsupials, mouse, and man compared.
VandeBerg, J. L., Robinson, E. S., Samollow, P. B., & Johnston, P. G. (1987) · PubMed · Cited by 53 · see citing works
DNA methylation and cell memory
Riggs, A. D. (1989) · Cell Biophysics · doi:10.1007/bf02991574 · Cited by 50 · see citing works
Self-citationMarsupials and Mechanisms of X-Chromosome Inactivation
Riggs, A. D. (1989) · Australian Journal of Zoology · doi:10.1071/zo9890419 · Cited by 44 · see citing works
Self-citationEvolution of Mammalian X-chromosome Inactivation: Sex Chromatin in Monotremes and Marsupials
McKay, L. M., Wrigley, J. M., & Graves, J. A. M. (1987) · Australian Journal of Biological Sciences · doi:10.1071/bi9870397 · Cited by 25 · see citing works
Type I and Type III Restriction-Modification Enzymes
Yuan, R. T., & Hamilton, D. L. (1984) · Springer series in molecular biology · doi:10.1007/978-1-4613-8519-6_2 · Cited by 16 · see citing works
Comparative Aspects of Chromosome Replication in Drosophila and Mammals
Raman, R., & Lakhotia, S. C. (1990) · Springer eBooks · doi:10.1007/978-3-662-10621-1_6 · Cited by 6 · see citing works
Ellis, G. C., Grobler, A., Hough, F. S., & Bester, A. J. (1988) · Biochemical and Biophysical Research Communications · doi:10.1016/s0006-291x(88)80277-8 · Cited by 5 · see citing works
Flagged first, then by citations
Cited by
Sorted by citations
Alterations in DNA Methylation: A Fundamental Aspect of Neoplasia
Baylln, S. B., Herman, J. G., Graff, J. R., Vertino, P. M., & Issa, J. J. (1997) · Advances in cancer research · doi:10.1016/s0065-230x(08)60702-2 · Cited by 1,913 · see citing works
Brown, C. J., Hendrich, B., Rupert, J. L., Lafrenière, R. G., Xing, Y., Lawrence, J. B., & Willard, H. F. (1992) · Cell · doi:10.1016/0092-8674(92)90520-m · Cited by 1,310 · see citing works
Wutz, G., Várnai, C., Nagasaka, K., Cisneros, D. A., Stocsits, R. R., Tang, W., Schoenfelder, S., Jessberger, G., Muhar, M., Hossain, M. J., et al. (2017) · The EMBO Journal · doi:10.15252/embj.201798004 · Cited by 864 · see citing works
A pathway for mitotic chromosome formation
Gibcus, J. H., Samejima, K., Goloborodko, A. A., Samejima, I., Naumova, N., Nuebler, J., Kanemaki, M. T., Xie, L., Paulson, J. R., Earnshaw, W. C., et al. (2018) · Science · doi:10.1126/science.aao6135 · Cited by 709 · see citing works
Chromatin organization by an interplay of loop extrusion and compartmental segregation
Nuebler, J., Fudenberg, G., Imakaev, M., Abdennur, N. A., & Mirny, L. A. (2018) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1717730115 · Cited by 617 · see citing works
Genome folding through loop extrusion by SMC complexes
Davidson, I. F., & Peters, J. (2021) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-021-00349-7 · Cited by 507 · see citing works
On the existence and functionality of topologically associating domains
Beagan, J. A., & Phillips‐Cremins, J. E. (2020) · Nature Genetics · doi:10.1038/s41588-019-0561-1 · Cited by 357 · see citing works
Over- and under-representation of short oligonucleotides in DNA sequences.
Burge, C., Campbell, A., & Karlin, S. (1992) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.89.4.1358 · Cited by 368 · see citing works
Organization of Chromosomal DNA by SMC Complexes
Yatskevich, S., Rhodes, J., & Nasmyth, K. (2019) · Annual Review of Genetics · doi:10.1146/annurev-genet-112618-043633 · Cited by 337 · see citing works
X-chromosome inactivation and cell memory
Riggs, A. D., & Pfeifer, G. P. (1992) · Trends in Genetics · doi:10.1016/0168-9525(92)90219-t · Cited by 328 · see citing works
Self-citationEmerging Evidence of Chromosome Folding by Loop ExtrusionPreprint
Fudenberg, G., Abdennur, N. A., Imakaev, M., Goloborodko, A. A., & Mirny, L. A. (2017) · Cold Spring Harbor Symposia on Quantitative Biology · doi:10.1101/sqb.2017.82.034710 · Cited by 287 · see citing works
The condensin complex is a mechanochemical motor that translocates along DNA
Terakawa, T., Bisht, S., Eeftens, J., Dekker, C., Haering, C., & Greene, E. (2017) · Science · doi:10.1126/science.aan6516 · Cited by 269 · see citing works
Recent evidence that TADs and chromatin loops are dynamic structures
Hansen, A. S., Cattoglio, C., Darzacq, X., & Tjian, R. (2018) · Nucleus · doi:10.1080/19491034.2017.1389365 · Cited by 266 · see citing works
Isolation and characterization of the cDNA encoding human DNA methyltransferase
Yen, R.-W. C., Vertino, P. M., Nelkin, B. D., Yu, J. J., El‐Deiry, W. S., Cumaraswamy, A., Lennon, G. G., Trask, B. J., Celano, P., & Baylin, S. B. (1992) · Nucleic Acids Research · doi:10.1093/nar/20.9.2287 · Cited by 256 · see citing works
Pfeifer, G. P., Tanguay, R. L., Steigerwald, S. D., & Riggs, A. D. (1990) · Genes & Development · doi:10.1101/gad.4.8.1277 · Cited by 238 · see citing works
Self-citationTwo major mechanisms of chromosome organization
Mirny, L. A., Imakaev, M., & Abdennur, N. A. (2019) · Current Opinion in Cell Biology · doi:10.1016/j.ceb.2019.05.001 · Cited by 222 · see citing works
Pfeifer, G. P., & Riggs, A. D. (1991) · Genes & Development · doi:10.1101/gad.5.6.1102 · Cited by 188 · see citing works
Self-citationHaaf, T. (1995) · Pharmacology & Therapeutics · doi:10.1016/0163-7258(94)00053-6 · Cited by 175 · see citing works
The Role of DNA Methylation in Invertebrates: Developmental Regulation or Genome Defense?
Regev, A., Lamb, M. J., & Jablonka, E. (1998) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a025992 · Cited by 173 · see citing works
Human Condensin I and II Drive Extensive ATP-Dependent Compaction of Nucleosome-Bound DNA
Kong, M., Cutts, E., Pan, D., Beuron, F., Kaliyappan, T., Xue, C., Morris, E. P., Musacchio, A., Vannini, A., & Greene, E. C. (2020) · Molecular Cell · doi:10.1016/j.molcel.2020.04.026 · Cited by 156 · see citing works
Towards a unified Model of SMC Complex Function
Hassler, M., Shaltiel, I. A., & Haering, C. (2018) · Current Biology · doi:10.1016/j.cub.2018.08.034 · Cited by 162 · see citing works
Loop extrusion: theory meets single-molecule experiments
Banigan, E. J., & Mirny, L. A. (2020) · Current Opinion in Cell Biology · doi:10.1016/j.ceb.2020.04.011 · Cited by 160 · see citing works
MCM complexes are barriers that restrict cohesin-mediated loop extrusion
Dequeker, B. J. H., Scherr, M. J., Brandão, H. B., Gassler, J., Powell, S. T., Gáspár, I., Flyamer, I. M., Lalic, A., Tang, W., Stocsits, R. R., et al. (2022) · Nature · doi:10.1038/s41586-022-04730-0 · Cited by 149 · see citing works
Chromosome organization by one-sided and two-sided loop extrusion
Banigan, E. J., van den Berg, A. A., Brandão, H. B., Marko, J. F., & Mirny, L. A. (2020) · eLife · doi:10.7554/elife.53558 · Cited by 146 · see citing works
“The SMC complex progressively enlarges the loop by reeling chromatin from outside the loop into the growing loop (Alipour and Marko, 2012; Nasmyth, 2001; Riggs, 1990).”
BackgroundRNA polymerases as moving barriers to condensin loop extrusion
Brandão, H. B., Paul, P., van den Berg, A. A., Rudner, D. Z., Wang, X., & Mirny, L. A. (2019) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1907009116 · Cited by 143 · see citing works
SMC complexes differentially compact mitotic chromosomes according to genomic context
Schalbetter, S. A., Goloborodko, A. A., Fudenberg, G., Belton, J.-M., Miles, C., Yu, M., Dekker, J., Mirny, L. A., & Baxter, J. (2017) · Nature Cell Biology · doi:10.1038/ncb3594 · Cited by 137 · see citing works
Liquid chromatin Hi-C characterizes compartment-dependent chromatin interaction dynamics
Belaghzal, H., Borrman, T. M., Stephens, A. D., Lafontaine, D. L. J., Venev, S. V., Weng, Z., Marko, J. F., & Dekker, J. (2021) · Nature Genetics · doi:10.1038/s41588-021-00784-4 · Cited by 132 · see citing works
Cohesin-mediated loop anchors confine the locations of human replication origins
Emerson, D. J., Zhao, P. A., Cook, A. L., Barnett, R. J., Klein, K. N., Saulebekova, D., Ge, C., Zhou, L., Simándi, Z., Minsk, M. K., et al. (2022) · Nature · doi:10.1038/s41586-022-04803-0 · Cited by 129 · see citing works
Revisiting the genomic hypomethylation hypothesis of aging
Unnikrishnan, A., Hadad, N., Masser, D. R., Jackson, J., Freeman, W. M., & Richardson, A. (2018) · Annals of the New York Academy of Sciences · doi:10.1111/nyas.13533 · Cited by 113 · see citing works
The chromosome folding problem and how cells solve it
Dekker, J., & Mirny, L. A. (2024) · Cell · doi:10.1016/j.cell.2024.10.026 · Cited by 112 · see citing works
Mechanisms of Chromosome Folding and Nuclear Organization: Their Interplay and Open QuestionsPreprint
Mirny, L. A., & Dekker, J. (2021) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a040147 · Cited by 102 · see citing works
Calling differentially methylated regions from whole genome bisulphite sequencing with DMRcate
Peters, T. J., Buckley, M. J., Chen, Y., Smyth, G. K., Goodnow, C. C., & Clark, S. J. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkab637 · Cited by 108 · see citing works
Mechanisms of X-chromosome inactivation
Samuel, C. C. (2006) · Frontiers in bioscience · doi:10.2741/1842 · Cited by 108 · see citing works
CTCF as a boundary factor for cohesin-mediated loop extrusion: evidence for a multi-step mechanism
Hansen, A. S. (2020) · Nucleus · doi:10.1080/19491034.2020.1782024 · Cited by 101 · see citing works
SOME MILESTONES IN THE HISTORY OF X-CHROMOSOME INACTIVATION
Lyon, M. F. (1992) · Annual Review of Genetics · doi:10.1146/annurev.ge.26.120192.000313 · Cited by 105 · see citing works
Looping the Genome with SMC Complexes
Kim, E., Barth, R., & Dekker, C. (2023) · Annual Review of Biochemistry · doi:10.1146/annurev-biochem-032620-110506 · Cited by 96 · see citing works
Popay, T. M., & Dixon, J. R. (2022) · Journal of Biological Chemistry · doi:10.1016/j.jbc.2022.102117 · Cited by 94 · see citing works
Hansen, R. S., Canfield, T. K., Fjeld, A. D., Mumm, S. R., Laird, C. D., & Gartler, S. M. (1997) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.94.9.4587 · Cited by 94 · see citing works
Paulson, J. R., Hudson, D. F., Cisneros-Soberanis, F., & Earnshaw, W. C. (2021) · Seminars in Cell and Developmental Biology · doi:10.1016/j.semcdb.2021.03.014 · Cited by 89 · see citing works
Do We Understand Somaclonal Variation?
Phillips, R. L., Kaeppler, S. M., & Peschke, V. M. (1990) · Current plant science and biotechnology in agriculture · doi:10.1007/978-94-009-2103-0_19 · Cited by 82 · see citing works
Multi-contact 3C reveals that the human genome during interphase is largely not entangled
Tavares-Cadete, F., Norouzi, D., Dekker, B., Liu, Y., & Dekker, J. (2020) · Nature Structural & Molecular Biology · doi:10.1038/s41594-020-0506-5 · Cited by 78 · see citing works
Cohesion and cohesin-dependent chromatin organization
Nishiyama, T. (2018) · Current Opinion in Cell Biology · doi:10.1016/j.ceb.2018.11.006 · Cited by 79 · see citing works
A stochastic epigenetic switch controls the dynamics of T-cell lineage commitment
Ng, K. K. H., Yui, M. A., Mehta, A., Siu, S., Irwin, B., Pease, S., Hirose, S., Elowitz, M. B., Rothenberg, E. V., & Kueh, H. Y. (2018) · eLife · doi:10.7554/elife.37851 · Cited by 77 · see citing works
Epigenetic inheritance in mammals
Lyon, M. F. (1993) · Trends in Genetics · doi:10.1016/0168-9525(93)90206-w · Cited by 79 · see citing works
X chromosome inactivation and DNA methylation.
Singer-Sam, J., & Riggs, A. D. (1993) · EXS · doi:10.1007/978-3-0348-9118-9_16 · Cited by 76 · see citing works
Self-citationMinárovits, J. (2009) · Acta Microbiologica et Immunologica Hungarica · doi:10.1556/amicr.56.2009.1.1 · Cited by 73 · see citing works
Chromatin jets define the properties of cohesin-driven in vivo loop extrusion.
Guo, Y., Al-Jibury, E., Garcia-Millan, R., Ntagiantas, K., King, J. W. D., Nash, A. J., Galjart, N., Lenhard, B., Rueckert, D., Fisher, A., et al. (2022) · Molecules and Cells · doi:10.1016/j.molcel.2022.09.003 · Cited by 69 · see citing works
Subramanian, P. S., Nelson, D. L., & Chinault, A. C. (1996) · PubMed Central · Cited by 70 · see citing works
Vertino, P. M., Issa, J. J., Pereira‐Smith, O. M., & Baylin, S. B. (1994) · PubMed · Cited by 68 · see citing works
Mammalian X Chromosome Inactivation
Gartler, S. M., Dyer, K. A., & Goldman, M. A. (1992) · Elsevier eBooks · doi:10.1016/b978-0-12-462002-5.50010-8 · Cited by 57 · see citing works
Tollefsbol, T. O., & Hutchison, C. A. (1995) · Journal of Biological Chemistry · doi:10.1074/jbc.270.31.18543 · Cited by 52 · see citing works
Imprinting and X-Chromosome Inactivation
Lyon, M. F. (1999) · Results and problems in cell differentiation · doi:10.1007/978-3-540-69111-2_4 · Cited by 48 · see citing works
YY1-controlled regulatory connectivity and transcription are influenced by the cell cycle
Lam, J. C., Aboreden, N. G., Midla, S. C., Wang, S., Huang, A., Keller, C. A., Giardine, B. M., Henderson, K. A., Hardison, R. C., Zhang, H., et al. (2024) · Nature Genetics · doi:10.1038/s41588-024-01871-y · Cited by 45 · see citing works
The macro and micro of chromosome conformation capture
Goel, V. Y., & Hansen, A. S. (2020) · Wiley Interdisciplinary Reviews Developmental Biology · doi:10.1002/wdev.395 · Cited by 46 · see citing works
DNA methylation and cellular ageing
Catania, J., & Fairweather, D. S. (1991) · Mutation Research/DNAging · doi:10.1016/0921-8734(91)90019-8 · Cited by 46 · see citing works
Riggs, A. D. (2002) · Cytogenetic and Genome Research · doi:10.1159/000071569 · Cited by 44 · see citing works
Self-citationChoppakatla, P., Dekker, B., Cutts, E., Vannini, A., Dekker, J., & Funabiki, H. (2021) · eLife · doi:10.7554/elife.68918 · Cited by 42 · see citing works
A tethered-inchworm model of SMC DNA translocation
Nichols, M. H., & Corces, V. G. (2018) · Nature Structural & Molecular Biology · doi:10.1038/s41594-018-0135-4 · Cited by 41 · see citing works
Expression of NR1 and NR2A/B subunits of the NMDA receptor in cortical astrocytes
Conti, F., Debiasi, S., Minelli, A., & Melone, M. (1996) · Glia · doi:10.1002/(sici)1098-1136(199607)17:3 · Cited by 143 · see citing works
Replication asynchrony between homologs 15q11.2: Cytogenetic evidence for genomic imprinting
Izumikawa, Y., Naritomi, K., & Hirayama, K. (1991) · Human Genetics · doi:10.1007/bf01213082 · Cited by 40 · see citing works
DNA sequence-dependent chromatin architecture and nuclear hubs formation
Jabbari, K., Chakraborty, M., & Wiehe, T. (2019) · Scientific Reports · doi:10.1038/s41598-019-51036-9 · Cited by 38 · see citing works
Chromatin organization by an interplay of loop extrusion and compartmental segregationPreprint
Nuebler, J., Fudenberg, G., Imakaev, M., Abdennur, N. A., & Mirny, L. A. (2017) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/196261 · Cited by 37 · see citing works
Computational methods for analyzing and modeling genome structure and organization
Lin, D., Bonora, G., Yardımcı, G. G., & Noble, W. S. (2018) · WIREs Systems Biology and Medicine · doi:10.1002/wsbm.1435 · Cited by 35 · see citing works
How DNA loop extrusion mediated by cohesin enables V(D)J recombination
Peters, J. (2021) · Current Opinion in Cell Biology · doi:10.1016/j.ceb.2020.11.007 · Cited by 34 · see citing works
Alteration of DNA methylation levels in MRL lupus mice
Mizugaki, M., Yamaguchi, T., Ishiwata, S., Shindo, H., Hishinuma, T., 野崎, 征., & Nose, M. (1997) · Clinical & Experimental Immunology · doi:10.1111/j.1365-2249.1997.tb08326.x · Cited by 35 · see citing works
Limits of Chromosome Compaction by Loop-Extruding Motors
Banigan, E. J., & Mirny, L. A. (2019) · Physical Review X · doi:10.1103/physrevx.9.031007 · Cited by 35 · see citing works
Cytosine methylation in gene-silencing mechanisms
Chomet, P. S. (1991) · Current Opinion in Cell Biology · doi:10.1016/0955-0674(91)90071-6 · Cited by 33 · see citing works
Galupa, R., & Heard, É. (2017) · Cold Spring Harbor Symposia on Quantitative Biology · doi:10.1101/sqb.2017.82.035030 · Cited by 29 · see citing works
Eukaryotic replication origins: control in space and time
Diller, J. D., & Raghuraman, M. K. (1994) · Trends in Biochemical Sciences · doi:10.1016/0968-0004(94)90070-1 · Cited by 32 · see citing works
Instability of Retroviral DNA Methylation in Embryonic Stem Cells
Minoguchi, S., & Iba, H. (2008) · Stem Cells · doi:10.1634/stemcells.2007-1106 · Cited by 31 · see citing works
Epigenetic characteristics of the mitotic chromosome in 1D and 3D
Oomen, M. E., & Dekker, J. (2017) · Critical Reviews in Biochemistry and Molecular Biology · doi:10.1080/10409238.2017.1287160 · Cited by 30 · see citing works
Levings, P. P., Zhou, Z., Vieira, K. F., Crusselle‐Davis, V. J., & Bungert, J. (2006) · FEBS Journal · doi:10.1111/j.1742-4658.2005.05107.x · Cited by 29 · see citing works
Hershkovitz, M. A., & Riggs, A. D. (1995) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.92.6.2379 · Cited by 29 · see citing works
Self-citationNavigating the crowd: visualizing coordination between genome dynamics, structure, and transcription
Shaban, H. A., Barth, R., & Bystricky, K. (2020) · Genome biology · doi:10.1186/s13059-020-02185-y · Cited by 28 · see citing works
The Importance Of Epigenetic Alterations In The Development Of Epstein-Barr Virus-Related Lymphomas
Takács, M., Segesdi, J., Bánáti, F., Koroknai, A., Wolf, H. J., Niller, H. H., & Minárovits, J. (2009) · Mediterranean Journal of Hematology and Infectious Diseases · doi:10.4084/mjhid.2009.012 · Cited by 27 · see citing works
Methylation of the rat glial fibrillary acidic protein gene shows tissue‐specific domains
Teter, B., Osterburg, H., Anderson, C. P., & Finch, C. (1994) · Journal of Neuroscience Research · doi:10.1002/jnr.490390609 · Cited by 29 · see citing works
Piper, A. A., Bennett, A. M., Noyce, L., Swanton, M., & Cooper, D. W. (1993) · Somatic Cell and Molecular Genetics · doi:10.1007/bf01233530 · Cited by 25 · see citing works
Molecular and Genetic Studies of Human X Chromosome Inactivation
Brown, C. J., & Willard, H. F. (1993) · Advances in developmental biology · doi:10.1016/s1566-3116(08)60026-2 · Cited by 24 · see citing works
Mechanisms for methylation-mediated gene silencing and aging
Tollefsbol, T. O., & Andrews, L. G. (1993) · Medical Hypotheses · doi:10.1016/0306-9877(93)90040-w · Cited by 24 · see citing works
Henikoff, S. (1995) · Current topics in microbiology and immunology · doi:10.1007/978-3-642-79145-1_13 · Cited by 24 · see citing works
The interplay between asymmetric and symmetric DNA loop extrusion
Banigan, E., & Mirny, L. (2020) · bioRxiv · doi:10.7554/elife.63528 · Cited by 19 · see citing works
Genome organization via loop extrusion, insights from polymer physics models
Ghosh, S. K., & Jost, D. (2019) · Briefings in Functional Genomics · doi:10.1093/bfgp/elz023 · Cited by 24 · see citing works
DNA's secret weapon against knots and tangles
Dolgin, E. (2017) · Nature · doi:10.1038/544284a · Cited by 18 · see citing works
Fernandez, L. R., Gilgenast, T. G., & Phillips‐Cremins, J. E. (2020) · Genome biology · doi:10.1186/s13059-020-02061-9 · Cited by 17 · see citing works
Hempel, K., & Strätling, W. H. (1996) · Journal of Cell Science · doi:10.1242/jcs.109.6.1459 · Cited by 17 · see citing works
Castiglione, M. R., Frediani, M., Venora, G., & Cremonini, R. (2008) · PROTOPLASMA · doi:10.1007/s00709-008-0296-9 · Cited by 15 · see citing works
Structure-function relationships of SMC protein complexes for DNA loop extrusion
Lee, H., Noh, H., & Ryu, J. (2021) · Korean Society for Structural Biology · doi:10.34184/kssb.2021.9.1.1 · Cited by 15 · see citing works
Chong, S., Kontaraki, J. E., Bonifer, C., & Riggs, A. D. (2002) · Molecular and Cellular Biology · doi:10.1128/mcb.22.13.4667-4676.2002 · Cited by 15 · see citing works
Self-citationHirano, T. (2025) · The Journal of Cell Biology · doi:10.1083/jcb.202504075 · Cited by 12 · see citing works
Hu, L., Užameckis, D., Hedborg, F., & Blomberg, J. (2016) · Apmis · doi:10.1111/apm.12494 · Cited by 14 · see citing works
Analysis of high-resolution 3D intrachromosomal interactions aided by Bayesian network modeling
Zhang, X., Branciamore, S., Gogoshin, G., Rodin, A. S., & Riggs, A. D. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1620425114 · Cited by 12 · see citing works
Self-citationAberrant DNA Methylation of Genomic Regions Translocated in Myeloid Malignancies
Litz, C. E., & Etzell, J. E. (1998) · Leukemia & lymphoma/Leukemia and lymphoma · doi:10.3109/10428199809050924 · Cited by 13 · see citing works
Molecular genetics of X-chromosome inactivation
Lyon, M. F. (1996) · Advances in genome biology · doi:10.1016/s1067-5701(96)80006-4 · Cited by 12 · see citing works
DNA packaging by molecular motors: from bacteriophage to human chromosomes
Prevo, B., & Earnshaw, W. C. (2024) · Nature reviews genetics · doi:10.1038/s41576-024-00740-y · Cited by 14 · see citing works
Rusková, R., & Račko, D. (2021) · Biology · doi:10.3390/biology10020130 · Cited by 12 · see citing works
SMC-mediated chromosome organization: Does loop extrusion explain it all?
Hirano, T., & Kinoshita, K. (2024) · Current Opinion in Cell Biology · doi:10.1016/j.ceb.2024.102447 · Cited by 10 · see citing works
Cells use loop extrusion to weave and tie the genome
Mirny, L. A. (2021) · Nature · doi:10.1038/d41586-021-00351-1 · Cited by 10 · see citing works
Deobagkar, D. D. (2018) · Journal of Genetics · doi:10.1007/s12041-018-0937-5 · Cited by 8 · see citing works
Goldman, M. A. (1992) · Nature Genetics · doi:10.1038/ng1192-169 · Cited by 8 · see citing works
Genome organization across scales: mechanistic insights from in vitro reconstitution studies
Oberbeckmann, E., & Oudelaar, A. M. (2024) · Biochemical Society Transactions · doi:10.1042/bst20230883 · Cited by 7 · see citing works
- Authors
- Riggs, A. D.
- Affiliations
- City Of Hope National Medical Center (US)
- Corresponding author
- Riggs, A. D.
- ORCID
- Riggs, A. D.
- Venue
- Philosophical Transactions of the Royal Society of London. B, Biological Sciences
- Publisher
- The Royal Society
- Published
- 1990-01-30
- Volume
- 326
- Issue
- 1235
- Pages
- 285-297
- ISSN
- 0080-4622 (ISSN-L)
- 2054-0280
- OpenAlex
- W2029630391
- Cited by
- 126
- References
- 50
- Citations by year
- 2025: 3 · 2024: 10 · 2023: 5 · 2022: 6 · 2021: 12 · 2020: 11 · 2019: 8 · 2018: 9 · 2017: 13 · 2016: 1
- FWCI
- 2.67
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Philosophical transactions of the Royal Society of London. Series B, Biological sciences (publishedVersion)
- PubMed (publishedVersion)
- 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 › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
- Keywords
- DNA methylation, cellular memory, X chromosome inactivation, chromatin looping, chromosome folding, enhancer function, CpG islands, cell identity
- MeSH terms
- Animals, Base Sequence, Cell Physiological Phenomena, Chromosomes, DNA, DNA Replication, Gene Expression Regulation, Methylation, Models, Structural, Nucleic Acid Conformation, Transcription, Genetic, X Chromosome, Dinucleoside Phosphates
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