The DOI matches its Crossref record; 27 of the 27 references it cites were found in a registry or an index.
Comparative analysis of metazoan chromatin organization
Open accessAbstract
A large collection of new modENCODE and ENCODE genome-wide chromatin data sets from cell lines and developmental stages in worm, fly and human are analysed; this reveals many conserved features of chromatin organization among the three organisms, as well as notable differences in the composition and locations of repressive chromatin. This study describes numerous new genome-wide chromatin data sets from cell lines and developmental stages of Homo sapiens, Drosophila melanogaster and Caenorhabditis elegans generated by the ENCODE and modENCODE consortia. The results point to many conserved features of chromatin organization among the three organisms, while identifying differences in the composition and locations of repressive chromatin. Genome function is dynamically regulated in part by chromatin, which consists of the histones, non-histone proteins and RNA molecules that package DNA. Studies in Caenorhabditis elegans and Drosophila melanogaster have contributed substantially to our understanding of molecular mechanisms of genome function in humans, and have revealed conservation of chromatin components and mechanisms1,2,3. Nevertheless, the three organisms have markedly different genome sizes, chromosome architecture and gene organization. On human and fly chromosomes, for example, pericentric heterochromatin flanks single centromeres, whereas worm chromosomes have dispersed heterochromatin-like regions enriched in the distal chromosomal ‘arms’, and centromeres distributed along their lengths4,5. To systematically investigate chromatin organization and associated gene regulation across species, we generated and analysed a large collection of genome-wide chromatin data sets from cell lines and developmental stages in worm, fly and human. Here we present over 800 new data sets from our ENCODE and modENCODE consortia, bringing the total to over 1,400. Comparison of combinatorial patterns of histone modifications, nuclear lamina-associated domains, organization of large-scale topological domains, chromatin environment at promoters and enhancers, nucleosome positioning, and DNA replication patterns reveals many conserved features of chromatin organization among the three organisms. We also find notable differences in the composition and locations of repressive chromatin. These data sets and analyses provide a rich resource for comparative and species-specific investigations of chromatin composition, organization and function.
Overview
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
Verification
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?
The cited source says what the claim attributes to it.
In the citing paper
“The obtained matrix was grouped using the k-means clustering approach and five distinct groups of TADs were identified similar to a previous classification of chromatin domains17,19,33. These groups comprised heterochromatin (61), low/quiescent (705), repressed (481), low-active (764) and active (365) domains (Fig. 4a, Supplementary Table 4).”
From Disruption of chromatin folding domains by somatic genomic rearrangements in human cancer (2020) · cites this paper as [19]
In the citing paper
“The median distance between the common boundaries was approximately 750 kb, consistent with the reported median TAD size in human cells4,19 (Extended Data Fig. 1e).”
From Disruption of chromatin folding domains by somatic genomic rearrangements in human cancer (2020) · cites this paper as [19]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
An integrated encyclopedia of DNA elements in the human genome
The ENCODE Project Consortium (2012) · Nature · doi:10.1038/nature11247 · Cited by 18,072
Self-citationTopological domains in mammalian genomes identified by analysis of chromatin interactions
Dixon, J. R., Selvaraj, S., Yue, F., Kim, A., Li, Y., Shen, Y., Hu, M., Liu, J. S., & Ren, B. (2012) · Nature · doi:10.1038/nature11082 · Cited by 6,829
Mapping and analysis of chromatin state dynamics in nine human cell types
Ernst, J., Kheradpour, P., Mikkelsen, T. S., Shoresh, N., Ward, L. D., Epstein, C. B., Zhang, X., Wang, L., Issner, R., Coyne, M., et al. (2011) · Nature · doi:10.1038/nature09906 · Cited by 2,898
Self-citationChIP-seq guidelines and practices of the ENCODE and modENCODE consortia
Landt, S. G., Marinov, G. K., Kundaje, A., Kheradpour, P., Pauli, F., Batzoglou, S., Bernstein, B. E., Bickel, P., Brown, J. B., Cayting, P., et al. (2012) · Genome Research · doi:10.1101/gr.136184.111 · Cited by 2,033
Self-citationThree-dimensional folding and functional organization principles of the Drosophila genome
Sexton, T., Yaffe, E., Kenigsberg, E., Bantignies, F., Leblanc, B., Hoichman, M., Parrinello, H., Tanay, A., & Cavalli, G. (2012) · Cell · doi:10.1016/j.cell.2012.01.010 · Cited by 1,983
Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE
Roy, S., Ernst, J., Kharchenko, P. V., Kheradpour, P., Nègre, N., Eaton, M. L., Landolin, J. M., Bristow, C. A., Ma, L., Lin, M. F., et al. (2010) · Science · doi:10.1126/science.1198374 · Cited by 1,242
Self-citationIntegrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project
Gerstein, M., Lu, Z. J., Nostrand, E. L. V., Cheng, C., Arshinoff, B. I., Liu, T., Yip, K. Y.-L., Robilotto, R., Rechtsteiner, A., Ikegami, K., et al. (2010) · Science · doi:10.1126/science.1196914 · Cited by 973
Self-citationComprehensive analysis of the chromatin landscape in Drosophila melanogaster
Kharchenko, P. V., Alekseyenko, A. A., Schwartz, Y. B., Minoda, A., Riddle, N. C., Ernst, J., Sabo, P. J., Larschan, E., Gorchakov, A. A., Gu, T., et al. (2010) · Nature · doi:10.1038/nature09725 · Cited by 893
Self-citationDistinct epigenomic landscapes of pluripotent and lineage-committed human cells
Hawkins, R. D., Hon, G. C., Lee, L. K., Ngo, Q., Lister, R., Pelizzola, M., Edsall, L. E., Kuan, S., Luu, Y., Klugman, S., et al. (2010) · Cell stem cell · doi:10.1016/j.stem.2010.03.018 · Cited by 806
Step-wise methylation of histone H3K9 positions heterochromatin at the nuclear periphery
Towbin, B. D., González-Aguilera, C., Sack, R., Gaidatzis, D., Kalck, V., Meister, P., Askjaer, P., & Gasser, S. M. (2012) · Cell · doi:10.1016/j.cell.2012.06.051 · Cited by 597
Cited by
Sorted by citations
Principles of genome folding into topologically associating domains
Szabo, Q., Bantignies, F., & Cavalli, G. (2019) · Science Advances · doi:10.1126/sciadv.aaw1668 · Cited by 631
Pioneer transcription factors in cell reprogrammingPreprint
Iwafuchi, M., & Zaret, K. S. (2014) · Genes & Development · doi:10.1101/gad.253443.114 · Cited by 613
ENCODE data at the ENCODE portal
Sloan, C. A., Chan, E. T., Davidson, J. M., Malladi, V. S., Strattan, J. S., Hitz, B. C., Gabdank, I., Narayanan, A. K., Ho, M., Lee, B. T., et al. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv1160 · Cited by 549
Ke, Y., Xu, Y., Chen, X., Feng, S., Liu, Z., Sun, Y., Yao, X., Li, F., Zhu, W. Z., Gao, L., et al. (2017) · Cell · doi:10.1016/j.cell.2017.06.029 · Cited by 531
WILDS: A Benchmark of in-the-Wild Distribution Shifts
Koh, P. W., Sagawa, S., Marklund, H., Xie, S. M., Zhang, M., Balsubramani, A., Hu, W., Yasunaga, M., Phillips, R. L., Gao, I., et al. (2020) · arXiv · doi:10.48550/arxiv.2012.07421 · Cited by 518
“…platforms have enabled systematic mapping of biochemical activity of genomes across diverse cellular contexts, populations, and species (Consortium et al., 2012; Ho et al., 2014; Kundaje et al., 2015; Aviv et al., 2017; Consortium et al., 2019; Moore et al., 2020; Consortium et al., 2020).”
Self-citationThe impact of structural variation on human gene expression
GTEx Consortium, Chiang, C., Scott, A. J., Davis, J. R., Tsang, E. K., Li, X., Kim, Y., Hadzic, T., Damani, F. N., Ganel, L., et al. (2017) · Nature Genetics · doi:10.1038/ng.3834 · Cited by 495
The Role of Chromosome Domains in Shaping the Functional Genome
Sexton, T., & Cavalli, G. (2015) · Cell · doi:10.1016/j.cell.2015.02.040 · Cited by 427
Nuclear F-actin and myosins drive relocalization of heterochromatic breaks
Caridi, C. P., D’Agostino, C., Ryu, T., Zapotoczny, G., Delabaere, L., Li, X., Khodaverdian, V. Y., Amaral, N., Lin, E., Rau, A. R., et al. (2018) · Nature · doi:10.1038/s41586-018-0242-8 · Cited by 372
Andersson, L., Archibald, A. L., Bottema, C. D. K., Bräuning, R., Burgess, S. C., Burt, D. W., Casas, E., Cheng, H. H., Clarke, L., Couldrey, C., et al. (2015) · Genome biology · doi:10.1186/s13059-015-0622-4 · Cited by 361
Pioneer transcription factors, chromatin dynamics, and cell fate control
Zaret, K. S., & Mango, S. E. (2016) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2015.12.003 · Cited by 337
Cell fate control by pioneer transcription factors
Iwafuchi-Doi, M., & Zaret, K. S. (2016) · Development · doi:10.1242/dev.133900 · Cited by 304
Comparison of computational methods for Hi-C data analysis
Forcato, M., Nicoletti, C., Pal, K., Livi, C. M., Ferrari, F., & Bicciato, S. (2017) · Nature Methods · doi:10.1038/nmeth.4325 · Cited by 314
Self-citationSingle-cell epigenomics: techniques and emerging applications
Schwartzman, O., & Tanay, A. (2015) · Nature Reviews Genetics · doi:10.1038/nrg3980 · Cited by 291
Disruption of chromatin folding domains by somatic genomic rearrangements in human cancer
Akdemir, K. C., Le, V. T., Chandran, S., Li, Y., Verhaak, R. G., Beroukhim, R., Campbell, P. J., Chin, L., Dixon, J. R., Futreal, P. A., et al. (2020) · Nature Genetics · doi:10.1038/s41588-019-0564-y · Cited by 283
Self-citationMethods for ChIP-seq analysis: A practical workflow and advanced applications
Nakato, R., & Sakata, T. (2021) · Methods · doi:10.1016/j.ymeth.2020.03.005 · Cited by 267
Heterochromatic breaks move to the nuclear periphery to continue recombinational repair
Ryu, T., Spatola, B. N., Delabaere, L., Bowlin, K., Hopp, H., Kunitake, R. C., Karpen, G. H., & Chiolo, I. (2015) · Nature Cell Biology · doi:10.1038/ncb3258 · Cited by 248
Self-citationMNase titration reveals differences between nucleosome occupancy and chromatin accessibility
Mieczkowski, J., Cook, A., Bowman, S., Mueller, B., Alver, B. H., Kundu, S., Deaton, A. M., Urban, J. A., Larschan, E., Park, P. J., et al. (2016) · Nature Communications · doi:10.1038/ncomms11485 · Cited by 235
Self-citationThe Integrator Complex Attenuates Promoter-Proximal Transcription at Protein-Coding Genes
Elrod, N. D., Henriques, T., Huang, K.-L., Tatomer, D. C., Wilusz, J. E., Wagner, E. J., & Adelman, K. (2019) · Molecular Cell · doi:10.1016/j.molcel.2019.10.034 · Cited by 230
HiCPlotter integrates genomic data with interaction matrices
Akdemir, K. C., & Chin, L. (2015) · Genome biology · doi:10.1186/s13059-015-0767-1 · Cited by 216
The Dynamic Regulatory Genome of Capsaspora and the Origin of Animal Multicellularity
Sebé-Pedrós, A., Ballaré, C., Parra-Acero, H., Chiva, C., Tena, J. J., Sabidó, E., Gómez-Skármeta, J. L., Croce, L. D., & Ruiz‐Trillo, I. (2016) · Cell · doi:10.1016/j.cell.2016.03.034 · Cited by 191
Discovery and implications of polygenicity of common diseases
Visscher, P. M., Yengo, L., Cox, N. J., & Wray, N. R. (2021) · Science · doi:10.1126/science.abi8206 · Cited by 199
Chromatin accessibility dynamics reveal novel functional enhancers in C. elegansPreprint
Daugherty, A. C., Yeo, R. W., Buenrostro, J. D., Greenleaf, W. J., Kundaje, A. B., & Brunet, A. (2017) · Genome Research · doi:10.1101/gr.226233.117 · Cited by 177
Self-citationComparative Analysis of Gene Regulatory Networks: From Network Reconstruction to Evolution
Thompson, D. A., Regev, A., & Roy, S. (2015) · Annual Review of Cell and Developmental Biology · doi:10.1146/annurev-cellbio-100913-012908 · Cited by 178
Reprogramming of cell fate: epigenetic memory and the erasure of memories past
Nashun, B., Hill, P. W. S., & Hájková, P. (2015) · The EMBO Journal · doi:10.15252/embj.201490649 · Cited by 184
Schotanus, K., Soyer, J. L., Connolly, L., Grandaubert, J., Happel, P., Smith, K., Freitag, M., & Stukenbrock, E. H. (2015) · Epigenetics & Chromatin · doi:10.1186/s13072-015-0033-5 · Cited by 173
FOXA1 Directs H3K4 Monomethylation at Enhancers via Recruitment of the Methyltransferase MLL3
Jozwik, K. M., Chernukhin, I. V., Sérandour, A. A., Nagarajan, S., & Carroll, J. S. (2016) · Cell Reports · doi:10.1016/j.celrep.2016.11.028 · Cited by 173
How the cell cycle impacts chromatin architecture and influences cell fate
Ma, Y., Kanakousaki, K., & Buttitta, L. (2015) · Frontiers in Genetics · doi:10.3389/fgene.2015.00019 · Cited by 166
Histone Methylation by SET Domain Proteins in Fungi
Freitag, M. (2017) · Annual Review of Microbiology · doi:10.1146/annurev-micro-102215-095757 · Cited by 169
Stable Chromosome Condensation Revealed by Chromosome Conformation Capture
Eagen, K. P., Hartl, T. A., & Kornberg, R. D. (2015) · Cell · doi:10.1016/j.cell.2015.10.026 · Cited by 151
Quantitative MNase-seq accurately maps nucleosome occupancy levels
Chereji, R. V., Bryson, T. D., & Henikoff, S. (2019) · Genome biology · doi:10.1186/s13059-019-1815-z · Cited by 147
Editing the Epigenome: Reshaping the Genomic Landscape
Holtzman, L., & Gersbach, C. A. (2018) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev-genom-083117-021632 · Cited by 147
Dai, X., Bai, Y., Zhao, L., Dou, X., Liu, Y., Wang, L., Li, Y., Li, W., Hui, Y., Huang, X., et al. (2017) · Molecular Plant · doi:10.1016/j.molp.2017.09.007 · Cited by 133
Shaping the cellular landscape with Set2/SETD2 methylation
McDaniel, S. L., & Strahl, B. D. (2017) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-017-2517-x · Cited by 130
Nuclear actin filaments in DNA repair dynamics
Caridi, C. P., Plessner, M., Grosse, R., & Chiolo, I. (2019) · Nature Cell Biology · doi:10.1038/s41556-019-0379-1 · Cited by 127
Transcriptional cofactors display specificity for distinct types of core promoters
Haberle, V., Arnold, C. D., Pagani, M., Rath, M., Schernhuber, K., & Stark, A. (2019) · Nature · doi:10.1038/s41586-019-1210-7 · Cited by 123
An Abundant Class of Non-coding DNA Can Prevent Stochastic Gene Silencing in the C. elegans Germline
Frøkjær‐Jensen, C., Jain, N., Hansen, L. L., Davis, M. W., Li, Y., Zhao, D., Rébora, K., Millet, J. R., Liu, X., Kim, S. K., et al. (2016) · Cell · doi:10.1016/j.cell.2016.05.072 · Cited by 121
Self-citationThe Need for a Human Pangenome Reference Sequence
Miga, K. H., & Wang, T. (2021) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev-genom-120120-081921 · Cited by 137
Resolving Heart Regeneration by Replacement Histone Profiling
Goldman, J., Kuzu, G., Lee, N., Karasik, J., Gemberling, M. P., Foglia, M. J., Karra, R., Dickson, A. L., Sun, F., Tolstorukov, M. Y., et al. (2017) · Developmental Cell · doi:10.1016/j.devcel.2017.01.013 · Cited by 121
Self-citationRepressive Chromatin in Caenorhabditis elegans: Establishment, Composition, and Function
Ahringer, J., & Gasser, S. M. (2018) · Genetics · doi:10.1534/genetics.117.300386 · Cited by 121
Self-citationRegulatory analysis of the C. elegans genome with spatiotemporal resolution
Araya, C. L., Kawli, T., Kundaje, A. B., Jiang, L., Wu, B., Vafeados, D. K., Terrell, R., Weisdepp, P., Gevirtzman, L., Mace, D., et al. (2014) · Nature · doi:10.1038/nature13497 · Cited by 119
Self-citationSimultaneous profiling of multiple chromatin proteins in the same cells
Gopalan, S., Wang, Y., Harper, N. W., Garber, M. G., & Fazzio, T. G. (2021) · Molecular Cell · doi:10.1016/j.molcel.2021.09.019 · Cited by 112
Lewis, S. H., Ross, L., Bain, S. A., Pahita, E., Smith, S. A., Cordaux, R., Miska, E. A., Lenhard, B., Jiggins, F. M., & Sarkies, P. (2020) · PLoS Genetics · doi:10.1371/journal.pgen.1008864 · Cited by 103
Prediction of histone post-translational modification patterns based on nascent transcription data
Wang, Z., Chivu, A. G., Choate, L. A., Rice, E. J., Miller, D. C., Chu, T., Chou, S., Kingsley, N. B., Petersen, J. L., Finno, C. J., et al. (2022) · Nature Genetics · doi:10.1038/s41588-022-01026-x · Cited by 114
HMMRATAC: a Hidden Markov ModeleR for ATAC-seq
Tarbell, E., & Liu, T. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz533 · Cited by 98
Self-citationJost, D., & Vaillant, C. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky009 · Cited by 84
Frapporti, A., Miró-Pina, C., Arnaiz, O., Holoch, D., Kawaguchi, T., Humbert, A., Eleftheriou, E., Lombard, B., Loew, D., Sperling, L., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-10648-5 · Cited by 104
Replication Stress Shapes a Protective Chromatin Environment across Fragile Genomic Regions
Kim, J., Sturgill, D. M., Sebastian, R., Khurana, S., Tran, A. D., Edwards, G. B., Kruswick, A., Burkett, S. S., Hosogane, E. K., Hannon, W. W., et al. (2017) · Molecular Cell · doi:10.1016/j.molcel.2017.11.021 · Cited by 98
Self-citationPavlov, D. A., Lorber, D., Bajpai, G., Reuveny, A., Roncato, F., Alon, R., Safran, S. A., & Volk, T. (2021) · Science Advances · doi:10.1126/sciadv.abf6251 · Cited by 99
OnTAD: hierarchical domain structure reveals the divergence of activity among TADs and boundaries
An, L., Yang, T., Yang, J., Nuebler, J., Xiang, G., Hardison, R. C., Li, Q., & Zhang, Y. (2019) · Genome biology · doi:10.1186/s13059-019-1893-y · Cited by 91
Ghosh, S. K., & Jost, D. (2018) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1006159 · Cited by 94
Sato, Y., Hilbert, L., Oda, H., Wan, Y., Heddleston, J. M., Chew, T., Zaburdaev, V., Keller, P., Lionnet, T., Vastenhouw, N. L., et al. (2019) · Development · doi:10.1242/dev.179127 · Cited by 95
Macqueen, D. J., Primmer, C. R., Houston, R. D., Nowak, B. F., Bernatchez, L., Bergseth, S., Davidson, W. S., Gallardo‐Escárate, C., Goldammer, T., Guiguen, Y., et al. (2017) · BMC Genomics · doi:10.1186/s12864-017-3862-8 · Cited by 95
A phylogenetic and proteomic reconstruction of eukaryotic chromatin evolution
Grau‐Bové, X., Navarrete, C., Chiva, C., Pribasnig, T., Antó, M., Torruella, G., Galindo, L. J., Lang, B. F., Moreira, D., López‐García, P., et al. (2022) · Nature Ecology & Evolution · doi:10.1038/s41559-022-01771-6 · Cited by 87
Nuclear Dynamics of Heterochromatin Repair
Amaral, N., Ryu, T., Li, X., & Chiolo, I. (2017) · Trends in Genetics · doi:10.1016/j.tig.2016.12.004 · Cited by 95
Evans, K. J., Huang, N., Stempor, P., Chesney, M. A., Down, T. A., & Ahringer, J. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1608162113 · Cited by 89
Self-citationBAP1 constrains pervasive H2AK119ub1 to control the transcriptional potential of the genomePreprint
Fursova, N. A., Turberfield, A. H., Blackledge, N. P., Findlater, E. L., Lastuvkova, A., Huseyin, M. K., Dobrinić, P., & Klose, R. J. (2021) · Genes & Development · doi:10.1101/gad.347005.120 · Cited by 91
Yao, B., Li, Y., Wang, Z., Chen, L., Poidevin, M., Zhang, C., Li, L., Wang, F., Bao, H., Jiao, B., et al. (2018) · Molecular Cell · doi:10.1016/j.molcel.2018.07.005 · Cited by 86
Skalska, L., Stojnic, R., Li, J., Fischer, B., Cerda‐Moya, G., Sakai, H., Tajbakhsh, S., Russell, S. R. H., Adryan, B., & Bray, S. J. (2015) · The EMBO Journal · doi:10.15252/embj.201489923 · Cited by 86
Polycomb complexes PRC1 and their function in hematopoiesis
Vidal, M., & Starowicz, K. (2017) · Experimental Hematology · doi:10.1016/j.exphem.2016.12.006 · Cited by 90
Libbrecht, M. W., Ay, F., Hoffman, M. M., Gilbert, D. M., Bilmes, J. A., & Noble, W. S. (2015) · Genome Research · doi:10.1101/gr.184341.114 · Cited by 84
Self-citationAbsence of canonical marks of active chromatin in developmentally regulated genes
Pérez-Lluch, S., Blanco, E., Tilgner, H., Curado, J., Ruiz‐Romero, M., Corominas, M., & Guigó, R. (2015) · Nature Genetics · doi:10.1038/ng.3381 · Cited by 84
Coordinated control of terminal differentiation and restriction of cellular plasticity
Patel, T., & Hobert, O. (2017) · eLife · doi:10.7554/elife.24100 · Cited by 80
ASH1-catalyzed H3K36 methylation drives gene repression and marks H3K27me2/3-competent chromatin
Bicocca, V. T., Ormsby, T., Adhvaryu, K. K., Honda, S., & Selker, E. U. (2018) · eLife · doi:10.7554/elife.41497 · Cited by 86
Iwafuchi, M., Cuesta, I., Donahue, G., Takenaka, N., Osipovich, A. B., Magnuson, M. A., Röder, H., Seeholzer, S. H., Santisteban, P., & Zaret, K. S. (2020) · Nature Genetics · doi:10.1038/s41588-020-0591-8 · Cited by 85
IC-Finder: inferring robustly the hierarchical organization of chromatin folding
Haddad, N., Vaillant, C., & Jost, D. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx036 · Cited by 81
Gaiti, F., Jindrich, K., Fernández-Valverde, S. L., Roper, K. E., Degnan, B. M., & Tanurdžić, M. (2017) · eLife · doi:10.7554/elife.22194 · Cited by 84
Morris, S. A. (2016) · Development · doi:10.1242/dev.138263 · Cited by 85
Deciphering Hi-C: from 3D genome to function
Kong, S., & Zhang, Y. (2019) · Cell Biology and Toxicology · doi:10.1007/s10565-018-09456-2 · Cited by 85
Camacho, J., Truong, L., Kurt, Z., Chen, Y.-W., Morselli, M., Gutierrez, G., Pellegrini, M., Yang, X., & Allard, P. (2018) · Cell Reports · doi:10.1016/j.celrep.2018.04.078 · Cited by 72
Evidence for the implication of the histone code in building the genome structure
Prakash, K., & Fournier, D. (2017) · Biosystems · doi:10.1016/j.biosystems.2017.11.005 · Cited by 82
Mesoscale phase separation of chromatin in the nucleus
Bajpai, G., Pavlov, D. A., Lorber, D., Volk, T., & Safran, S. A. (2021) · eLife · doi:10.7554/elife.63976 · Cited by 77
Garrigues, J. M., Sidoli, S., Garcia, B. A., & Strome, S. (2014) · Genome Research · doi:10.1101/gr.180489.114 · Cited by 72
Self-citationMapping the dsRNA WorldPreprint
Reich, D. P., & Bass, B. (2019) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a035352 · Cited by 74
Three-Dimensional Genome Organization and Function in Drosophila
Schwartz, Y. B., & Cavalli, G. (2017) · Genetics · doi:10.1534/genetics.115.185132 · Cited by 77
Self-citationRecruitment of RNA polymerase II by the pioneer transcription factor PHA-4
Hsu, H.-T., Chen, H. ‐., Yang, Z., Wang, J., Lee, N. K., Burger, A., Zaret, K. S., Liu, T., Levine, E., & Mango, S. E. (2015) · Science · doi:10.1126/science.aab1223 · Cited by 72
Self-citationHaddad, N., Jost, D., & Vaillant, C. (2017) · Chromosome Research · doi:10.1007/s10577-016-9548-2 · Cited by 75
Nucleosome and ubiquitin position Set2 to methylate H3K36
Bilokapić, S., & Halić, M. (2019) · Nature Communications · doi:10.1038/s41467-019-11726-4 · Cited by 72
Benton, M. L., Talipineni, S. C., Kostka, D., & Capra, J. A. (2019) · BMC Genomics · doi:10.1186/s12864-019-5779-x · Cited by 70
Nucleosome positioning: resources and tools online
Teif, V. B. (2015) · Briefings Bioinform. · doi:10.1093/bib/bbv086 · Cited by 66
Structural insights into p300 regulation and acetylation-dependent genome organisation
Ibrahim, Z., Wang, T., Destaing, O., Salvi, N., Hoghoughi, N., Chabert, C., Rusu, A., Gao, J., Feletto, L., Reynoird, N., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-35375-2 · Cited by 64
The interdependence of gene-regulatory elements and the 3D genome
Vermunt, M. W., Zhang, D., & Blobel, G. A. (2018) · The Journal of Cell Biology · doi:10.1083/jcb.201809040 · Cited by 72
Kang, H. A., Jung, Y. L., McElroy, K. A., Zee, B. M., Wallace, H. A., Woolnough, J. L., Park, P. J., & Kuroda, M. I. (2017) · Genes & Development · doi:10.1101/gad.305987.117 · Cited by 67
Self-citationEstablishment and evolution of heterochromatin
Liu, J., Ali, M., & Zhou, Q. (2020) · Annals of the New York Academy of Sciences · doi:10.1111/nyas.14303 · Cited by 74
Tabuchi, T. M., Rechtsteiner, A., Jeffers, T. E., Egelhofer, T. A., Murphy, C. T., & Strome, S. (2018) · Nature Communications · doi:10.1038/s41467-018-06236-8 · Cited by 72
Self-citationPourkarimi, E., Bellush, J. M., & Whitehouse, I. (2016) · eLife · doi:10.7554/elife.21728 · Cited by 64
Fortuny, A., Chansard, A., Caron, P., Chevallier, O., Leroy, O., Renaud, O., & Polo, S. E. (2021) · Nature Communications · doi:10.1038/s41467-021-22575-5 · Cited by 66
Meiotic recombination and the crossover assurance checkpoint in Caenorhabditis elegans
Yu, Z., Kim, Y., & Dernburg, A. F. (2016) · Seminars in Cell and Developmental Biology · doi:10.1016/j.semcdb.2016.03.014 · Cited by 62
Self-citationCell Biology of theCaenorhabditis elegansNucleus
Cohen‐Fix, O., & Askjaer, P. (2017) · Genetics · doi:10.1534/genetics.116.197160 · Cited by 56
GBshape: a genome browser database for DNA shape annotations
Chiu, T.-P., Yang, L., Zhou, T., Main, B. J., Parker, S. C. J., Nuzhdin, S. V., Tullius, T. D., & Rohs, R. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku977 · Cited by 62
Self-citationCaenorhabditis elegans as an emerging model system in environmental epigenetics
Weinhouse, C., Truong, L., Meyer, J. N., & Allard, P. (2018) · Environmental and Molecular Mutagenesis · doi:10.1002/em.22203 · Cited by 64
Beurton, F., Stempor, P., Caron, M. J., Appert, A., Yan, D., Chen, R. A.-J., Cluet, D., Couté, Y., Herbette, M., Huang, N., et al. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz880 · Cited by 52
Self-citationDistinctive regulatory architectures of germline-active and somatic genes in C. elegansPreprint
Serizay, J., Dong, Y., Jänes, J., Chesney, M. A., Cerrato, C., & Ahringer, J. (2020) · Genome Research · doi:10.1101/gr.265934.120 · Cited by 56
Self-citationMouridi, S. E., Alkhaldi, F., & Frøkjær‐Jensen, C. (2022) · G3 Genes Genomes Genetics · doi:10.1093/g3journal/jkac184 · Cited by 48
Lü, L., Chen, X., Sanders, D., Qian, S., & Zhong, X. (2015) · Epigenetics · doi:10.1080/15592294.2015.1104446 · Cited by 58
Endres, T., Solvie, D., Heidelberger, J. B., Andrioletti, V., Baluapuri, A., Ade, C. P., Muhar, M., Eilers, U., Vos, S. M., Cramer, P., et al. (2021) · Molecular Cell · doi:10.1016/j.molcel.2020.12.035 · Cited by 57
Decorating chromatin for enhanced genome editing using CRISPR-Cas9
Chen, E., Lin-Shiao, E., Trinidad, M. I., Doost, M. S., Colognori, D., & Doudna, J. A. (2022) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2204259119 · Cited by 57
Genome-wide repeat landscapes in cancer and cell-free DNA
Annapragada, A. V., Niknafs, N., White, J. R., Bruhm, D. C., Cherry, C., Medina, J. E., Adleff, V., Hruban, C., Mathios, D., Foda, Z. H., et al. (2024) · Science Translational Medicine · doi:10.1126/scitranslmed.adj9283 · Cited by 60
Brown, J., & Celniker, S. (2015) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev-genom-090413-025448 · Cited by 51
Carlton, P. M., Davis, R. E., & Ahmed, S. C. (2022) · Genetics · doi:10.1093/genetics/iyac014 · Cited by 49
Developmental Dynamics of X-Chromosome Dosage Compensation by the DCC and H4K20me1 in C. elegans
Kramer, M., Kranz, A.-L., Su, A., Winterkorn, L. H., Albritton, S. E., & Ercan, S. (2015) · PLoS Genetics · doi:10.1371/journal.pgen.1005698 · Cited by 48
Self-citation
Metadata
- Authors
- Ho, J. W. K., Jung, Y. L., Liu, T., Alver, B. H., Lee, S., Ikegami, K., Sohn, K.-A., Minoda, A., Tolstorukov, M. Y., Appert, A., Parker, S. C. J., Gu, T., Kundaje, A., Riddle, N. C., Bishop, E., Egelhofer, T. A., Hu, S. S., Alekseyenko, A. A., Rechtsteiner, A., Asker, D., Belsky, J. A., Bowman, S. K., Chen, Q. B., Chen, R. A.-J., Day, D. S., Dong, Y., Dose, A. C., Duan, X., Epstein, C. B., Ercan, S., Feingold, E. A., Ferrari, F., Garrigues, J. M., Gehlenborg, N., Good, P. J., Haseley, P., He, D., Herrmann, M., Hoffman, M. M., Jeffers, T. E., Kharchenko, P. V., Kolasinska-Zwierz, P., Kotwaliwale, C. V., Kumar, N., Langley, S. A., Larschan, E. N., Latorre, I., Libbrecht, M. W., Lin, X., Park, R., Pazin, M. J., Pham, H. N., Plachetka, A., Qin, B., Schwartz, Y. B., Shoresh, N., Stempor, P., Vielle, A., Wang, C., Whittle, C. M., Xue, H., Kingston, R. E., Kim, J. H., Bernstein, B. E., Dernburg, A. F., Pirrotta, V., Kuroda, M. I., Noble, W. S., Tullius, T. D., Kellis, M., MacAlpine, D. M., Strome, S., Elgin, S. C. R., Liu, X. S., Lieb, J. D., Ahringer, J., Karpen, G. H., & Park, P. J.
- Affiliations
- Brigham and Women's Hospital (US)
- Harvard University (US)
- University of North Carolina at Chapel Hill (US)
- Seoul National University (KR)
- Lawrence Berkeley National Laboratory (US)
- University of Cambridge (GB)
- National Institutes of Health (US)
- Washington University in St. Louis (US)
- Broad Institute (US)
- Victor Chang Cardiac Research Institute (AU)
- Boston University (US)
- University of California, Santa Cruz (US)
- Rutgers, The State University of New Jersey (US)
- Duke Medical Center (US)
- Tongji University (CN)
- University of California, Berkeley (US)
- Princess Margaret Cancer Centre (CA)
- Howard Hughes Medical Institute (US)
- Brown University (US)
- University of Washington (US)
- Corresponding author
- MacAlpine, David M.
- Strome, Susan
- Elgin, Sarah C. R.
- Liu, Xiaole Shirley
- Lieb, Jason D.
- Ahringer, Julie
- Karpen, Gary H.
- Park, Peter J.
- ORCID
- Ho, Joshua W. K.
- Jung, Youngsook L.
- Liu, Tao
- Lee, Soohyun
- Ikegami, Kohta
- Sohn, Kyung-Ah
- Minoda, Aki
- Tolstorukov, Michael Y.
- Parker, Stephen C. J.
- Gu, Tingting
- Kundaje, Anshul
- Riddle, Nicole C.
- Rechtsteiner, Andreas
- Asker, Dalal
- Belsky, Jason A.
- Chen, Q. Brent
- Chen, Ron A.-J.
- Epstein, Charles B.
- Ferrari, Francesco
- Garrigues, Jacob M.
- Gehlenborg, Nils
- He, Daniel
- Hoffman, Michael M.
- Jeffers, Tess E.
- Kharchenko, Peter V.
- Langley, Sasha A.
- Larschan, Erica N.
- Latorre, Isabel
- Libbrecht, Maxwell W.
- Lin, Xueqiu
- Pazin, Michael J.
- Qin, Bo
- Schwartz, Yuri B.
- Vielle, Anne
- Wang, Chengyang
- Xue, Huiling
- Kingston, Robert E.
- Kim, Ju Han
- Bernstein, Bradley E.
- Dernburg, Abby F.
- Kuroda, Mitzi I.
- Noble, William S.
- Tullius, Thomas D.
- Kellis, Manolis
- MacAlpine, David M.
- Strome, Susan
- Elgin, Sarah C. R.
- Ahringer, Julie
- Karpen, Gary H.
- Park, Peter J.
- Venue
- Nature
- Published
- 2014-08-27
- Volume
- 512
- Issue
- 7515
- Pages
- 449-452
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC4227084
- OpenAlex
- W1981516407
- Cited by
- 390
- References
- 27
- Citations by year
- 2026: 6 · 2025: 13 · 2024: 21 · 2023: 30 · 2022: 25 · 2021: 58 · 2020: 24 · 2019: 42 · 2018: 31 · 2017: 45 · 2016: 35 · 2015: 49 · 2014: 11
- FWCI
- 19.12
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Nature (publishedVersion, cc-by-nc-sa)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Open Scholarship Institutional Repository (Washington University in St. Louis) (submittedVersion, cc-by-nc-sa)
- RePEc: Research Papers in Economics (submittedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- Funders
- National Science Foundation (1122374, 0000994)
- Howard Hughes Medical Institute
- Wellcome Trust (101863, 54523, 101863/Z/13/Z, 092096)
- National Natural Science Foundation of China (31028011, 1122374)
- National Institutes of Health (5u54hg004570-04, 1122374, U54-CA121852)
- National Human Genome Research Institute (U01HG004258, U01HG004270, K99HG006259, U01HG004279, U01HG004695, U54HG006991, U54-HG004570, R01HG004037, T32HG002295)
- National Cancer Institute (U54CA121852)
- National Institute of General Medical Sciences (T32GM071340, R01GM098461, R37GM048405)
- National Institute of Biomedical Imaging and Bioengineering (RL9EB008539)
- 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 › Genetics › Chromosomal and Genetic Variations
- Keywords
- chromatin organization, comparative genomics, histone modifications, repressive chromatin, heterochromatin, topologically associating domains, nucleosome positioning, DNA replication, enhancers, promoter, Caenorhabditis elegans, Drosophila melanogaster, human, modENCODE, ENCODE
- MeSH terms
- Animals, Cell Line, Centromere, Chromatin, DNA Replication, Drosophila melanogaster, Enhancer Elements, Genetic, Heterochromatin, Histones, Humans, Nucleosomes, Promoter Regions, Genetic, Species Specificity, Caenorhabditis elegans, Nuclear Lamina, Chromatin Assembly and Disassembly, Epigenesis, Genetic, Molecular Sequence Annotation
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
