Highly rearranged chromosomes reveal uncoupling between genome topology and gene expression
Open accessAbstract
Chromatin topology is intricately linked to gene expression, yet its functional requirement remains unclear. Here, we comprehensively assessed the interplay between genome topology and gene expression using highly rearranged chromosomes (balancers) spanning ~75% of the Drosophila genome. Using transheterozyte (balancer/wild-type) embryos, we measured allele-specific changes in topology and gene expression in cis, while minimizing trans effects. Through genome sequencing, we resolved eight large nested inversions, smaller inversions, duplications and thousands of deletions. These extensive rearrangements caused many changes to chromatin topology, disrupting long-range loops, topologically associating domains (TADs) and promoter interactions, yet these are not predictive of changes in expression. Gene expression is generally not altered around inversion breakpoints, indicating that mis-appropriate enhancer-promoter activation is a rare event. Similarly, shuffling or fusing TADs, changing intra-TAD connections and disrupting long-range inter-TAD loops does not alter expression for the majority of genes. Our results suggest that properties other than chromatin topology ensure productive enhancer-promoter interactions.
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
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?
Considerable TAD re-arrangements observed in Drosophila balancer chromosomes compared with wild-type result in changes in expression of only about 10% of genes.
“the considerable TAD re-arrangements observed in Drosophila balancer chromosomes compared with their wild-type counterparts result in changes in the expression of only ~ 10% of genes [449].”
From Transcriptional enhancers and their communication with gene promoters (2021) · cites this paper as [449]
The Results section reports that 512 of 5,357 testable genes (9.6%) differed in expression between balancer and wild-type haplotypes. But that figure covers the chromosomes’ extensive genomic rearrangements overall, not changes caused specifically by TAD rearrangements. The TAD analysis reports differential expression for 23 of 161 expressed genes in resized TADs and 29 of 237 testable genes near perturbed boundaries. (LLM, conf=0.88)
Experimental — accuracy not yet measuredBiochemical annotations fail to specify which gene(s) a putative enhancer regulates, let alone the degree of activation conferred.
“Third, biochemical annotations fail to specify which gene(s) a putative enhancer regulates, let alone the degree of activation conferred78,79.”
From Towards a comprehensive catalogue of validated and target-linked human enhancers (2020) · cites this paper as [78]
The Abstract and Discussion report that changes in chromatin topology do not reliably predict gene-expression changes. The Online Methods describe using DNase hypersensitivity and enhancer annotations, but our copy does not assess whether biochemical annotations identify an enhancer’s target genes or quantify the activation it confers. Searches for those specific points found no deciding passage; page numbers were unavailable in our copy. (LLM, conf=0.73)
Experimental — accuracy not yet measured
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
Love, M. I., Huber, W., & Anders, S. (2014) · Genome Biology · doi:10.1186/s13059-014-0550-8 · Cited by 95,106 · see citing works
HTSeq—a Python framework to work with high-throughput sequencing data
Anders, S., Pyl, P. T., & Huber, W. (2015) · Bioinformatics · doi:10.1093/bioinformatics/btu638 · Cited by 21,464 · 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
Primer3—new capabilities and interfaces
Untergasser, A., Cutcutache, I., Kõressaar, T., Ye, J., Faircloth, B., Remm, M., & Rozen, S. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks596 · Cited by 9,165 · see citing works
Topological 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 · see citing works
The Genome of Drosophila Melanogaster
Lindsley, D. L., & Zimm, G. G. (1992) · Cited by 3,090 · see citing works
Spatial partitioning of the regulatory landscape of the X-inactivation centre
Nora, E. P., Lajoie, B. R., Schulz, E. G., Giorgetti, L., Okamoto, I., Servant, N., Piolot, T., van Berkum, N. L., Meisig, J., Sedat, J., et al. (2012) · Nature · doi:10.1038/nature11049 · Cited by 2,895 · see citing works
DELLY: structural variant discovery by integrated paired-end and split-read analysis
Rausch, T., Zichner, T., Schlattl, A., Stütz, A. M., Beneš, V., & Korbel, J. O. (2012) · Bioinformatics · doi:10.1093/bioinformatics/bts378 · Cited by 2,384 · see citing works
Self-citationAn integrated map of structural variation in 2,504 human genomes
Sudmant, P. H., Rausch, T., Gardner, E. J., Handsaker, R. E., Abyzov, A., Huddleston, J., Zhang, Y., Ye, K., Jun, G., Hsi-Yang Fritz, M., et al. (2015) · Nature · doi:10.1038/nature15394 · Cited by 2,354 · see citing works
Self-citationTranscription factors: from enhancer binding to developmental control
Spitz, F., & Furlong, E. E. M. (2012) · Nature Reviews Genetics · doi:10.1038/nrg3207 · Cited by 2,227 · see citing works
Self-citationDisruptions of Topological Chromatin Domains Cause Pathogenic Rewiring of Gene-Enhancer Interactions
Lupiáñez, D. G., Kraft, K., Heinrich, V., Krawitz, P., Brancati, F., Klopocki, E., Horn, D., Kayserili, H., Opitz, J. M., Laxova, R., et al. (2015) · Cell · doi:10.1016/j.cell.2015.04.004 · Cited by 2,132 · see citing works
Three-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 · see citing works
Cohesin Loss Eliminates All Loop Domains
Rao, S. S. P., Huang, S.-C., Glenn St Hilaire, B., Engreitz, J. M., Perez, E. M., Kieffer-Kwon, K.-R., Sanborn, A. L., Johnstone, S. E., Bascom, G. D., Bochkov, I. D., et al. (2017) · Cell · doi:10.1016/j.cell.2017.09.026 · Cited by 1,883 · see citing works
Nora, E. P., Goloborodko, A., Valton, A.-L., Gibcus, J. H., Uebersohn, A., Abdennur, N., Dekker, J., Mirny, L. A., & Bruneau, B. G. (2017) · Cell · doi:10.1016/j.cell.2017.05.004 · Cited by 1,709 · see citing works
Drosophila: A laboratory handbook
Ashburner, M. (1990) · Trends in Ecology & Evolution · doi:10.1016/0169-5347(90)90121-s · Cited by 1,703 · see citing works
The Drosophila melanogaster Genetic Reference Panel
Mackay, T., Richards, S., Stone, E. A., Barbadilla, A., Ayroles, J., Zhu, D., Casillas, S., Han, Y., Magwire, M., Cridland, J., et al. (2012) · Nature · doi:10.1038/nature10811 · Cited by 1,686 · see citing works
Insulator dysfunction and oncogene activation in IDH mutant gliomas
Flavahan, W. A., Drier, Y., Liau, B. B., Gillespie, S. M., Venteicher, A. S., Stemmer-Rachamimov, A. O., Suvà, M. L., & Bernstein, B. E. (2016) · Nature · doi:10.1038/nature16490 · Cited by 1,288 · see citing works
A high-resolution map of the three-dimensional chromatin interactome in human cells
Jin, F., Li, Y., Dixon, J. R., Selvaraj, S., Ye, Z., Lee, A. Y., Yen, C.-A., Schmitt, A. D., Espinoza, C. A., & Ren, B. (2013) · Nature · doi:10.1038/nature12644 · Cited by 1,208 · see citing works
Two independent modes of chromatin organization revealed by cohesin removal
Schwarzer, W., Abdennur, N., Goloborodko, A., Pekowska, A., Fudenberg, G., Loe-Mie, Y., Fonseca, N. A., Huber, W., Haering, C. H., Mirny, L., et al. (2017) · Nature · doi:10.1038/nature24281 · Cited by 1,196 · see citing works
Paired-End Mapping Reveals Extensive Structural Variation in the Human Genome
Korbel, J. O., Urban, A. E., Affourtit, J. P., Godwin, B., Grubert, F., Simons, J. F., Kim, P. M., Palejev, D., Carriero, N. J., Du, L., et al. (2007) · Science · doi:10.1126/science.1149504 · Cited by 1,163 · see citing works
Self-citationThe whole-genome landscape of medulloblastoma subtypes
Northcott, P. A., Buchhalter, I., Morrissy, A. S., Hovestadt, V., Weischenfeldt, J., Ehrenberger, T., Gröbner, S., Segura-Wang, M., Zichner, T., Rudneva, V. A., et al. (2017) · Nature · doi:10.1038/nature22973 · Cited by 1,112 · see citing works
Self-citationActivation 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 · see citing works
High-resolution TADs reveal DNA sequences underlying genome organization in flies
Ramírez, F., Bhardwaj, V., Arrigoni, L., Lam, K. C., Grüning, B. A., Villaveces, J. M., Habermann, B. H., Akhtar, A., & Manke, T. (2018) · Nature Communications · doi:10.1038/s41467-017-02525-w · Cited by 974 · see citing works
CRISPR Inversion of CTCF Sites Alters Genome Topology and Enhancer/Promoter Function
Guo, Y., Xu, Q., Canzio, D., Shou, J., Li, J., Gorkin, D. U., Jung, I., Wu, H., Zhai, Y., Tang, Y., et al. (2015) · Cell · doi:10.1016/j.cell.2015.07.038 · Cited by 958 · 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
Functional and Mechanistic Diversity of Distal Transcription Enhancers
Bulger, M., & Groudine, M. (2011) · Cell · doi:10.1016/j.cell.2011.01.024 · Cited by 803 · see citing works
fdrtool: a versatile R package for estimating local and tail area-based false discovery rates
Strimmer, K. (2008) · Bioinformatics · doi:10.1093/bioinformatics/btn209 · Cited by 723 · see citing works
Structural variation in the 3D genome
Spielmann, M., Lupiáñez, D. G., & Mundlos, S. (2018) · Nature Reviews Genetics · doi:10.1038/s41576-018-0007-0 · Cited by 719 · see citing works
CrossMap: a versatile tool for coordinate conversion between genome assemblies
Zhao, H., Sun, Z., Wang, J., Huang, H., Kocher, J., & Wang, L. (2013) · Bioinformatics · doi:10.1093/bioinformatics/btt730 · Cited by 718 · see citing works
CTCF mediates long-range chromatin looping and local histone modification in the β-globin locus
Splinter, E., Heath, H., Kooren, J., Palstra, R.-J., Klous, P., Grosveld, F., Galjart, N., & de Laat, W. (2006) · Genes & Development · doi:10.1101/gad.399506 · Cited by 677 · see citing works
Formation of new chromatin domains determines pathogenicity of genomic duplications
Franke, M., Ibrahim, D. M., Andrey, G., Schwarzer, W., Heinrich, V., Schöpflin, R., Kraft, K., Kempfer, R., Jerković, I., Chan, W.-L., et al. (2016) · Nature · doi:10.1038/nature19800 · Cited by 673 · see citing works
Phenotypic impact of genomic structural variation: insights from and for human disease
Weischenfeldt, J., Symmons, O., Spitz, F., & Korbel, J. O. (2013) · Nature Reviews Genetics · doi:10.1038/nrg3373 · Cited by 648 · see citing works
Self-citationEnhancer hijacking activates GFI1 family oncogenes in medulloblastoma
Northcott, P. A., Lee, C., Zichner, T., Stütz, A. M., Erkek, S., Kawauchi, D., Shih, D. J. H., Hovestadt, V., Zapatka, M., Sturm, D., et al. (2014) · Nature · doi:10.1038/nature13379 · Cited by 642 · see citing works
Self-citationDevelopmental enhancers and chromosome topology
Furlong, E. E. M., & Levine, M. (2018) · Science · doi:10.1126/science.aau0320 · Cited by 641 · see citing works
Self-citationHuang, W., Massouras, A., Inoue, Y., Peiffer, J., Ràmia, M., Tarone, A. M., Turlapati, L., Zichner, T., Zhu, D., Lyman, R. F., et al. (2014) · Genome Research · doi:10.1101/gr.171546.113 · Cited by 578 · see citing works
Self-citationNarendra, V., Rocha, P. P., An, D., Raviram, R., Skok, J. A., Mazzoni, E. O., & Reinberg, D. (2015) · Science · doi:10.1126/science.1262088 · Cited by 535 · see citing works
Bonn, S., Zinzen, R. P., Girardot, C., Gustafson, E. H., Perez-Gonzalez, A., Delhomme, N., Ghavi-Helm, Y., Wilczyński, B., Riddell, A., & Furlong, E. E. M. (2012) · Nature Genetics · doi:10.1038/ng.1064 · Cited by 502 · see citing works
Self-citationTranscriptional Enhancers in Animal Development and Evolution
Levine, M. (2010) · Current Biology · doi:10.1016/j.cub.2010.06.070 · Cited by 449 · see citing works
CHiCAGO: robust detection of DNA looping interactions in Capture Hi-C data
Cairns, J., Freire-Pritchett, P., Wingett, S. W., Várnai, C., Dimond, A., Plagnol, V., Zerbino, D., Schoenfelder, S., Javierre, B.-M., Osborne, C., et al. (2016) · Genome Biology · doi:10.1186/s13059-016-0992-2 · Cited by 417 · see citing works
Weischenfeldt, J., Dubash, T., Drainas, A. P., Mardin, B. R., Chen, Y., Stütz, A. M., Waszak, S. M., Bosco, G., Halvorsen, A. R., Raeder, B., et al. (2017) · Nature Genetics · doi:10.1038/ng.3722 · Cited by 404 · see citing works
Self-citationCombinatorial binding predicts spatio-temporal cis-regulatory activity
Zinzen, R. P., Girardot, C., Gagneur, J., Braun, M. M., & Furlong, E. E. M. (2009) · Nature · doi:10.1038/nature08531 · Cited by 397 · see citing works
Self-citationUnified representation of genetic variants
Tan, A. K. S., Abecasis, G. R., & Kang, H. M. (2015) · Bioinformatics · doi:10.1093/bioinformatics/btv112 · Cited by 388 · see citing works
The cis-regulatory dynamics of embryonic development at single-cell resolution
Cusanovich, D. A., Reddington, J. P., Garfield, D. A., Daza, R. M., Aghamirzaie, D., Marco-Ferreres, R., Pliner, H. A., Christiansen, L., Qiu, X., Steemers, F. J., et al. (2018) · Nature · doi:10.1038/nature25981 · Cited by 363 · see citing works
Self-citationMultiplexed analysis of chromosome conformation at vastly improved sensitivity
Davies, J. O. J., Telenius, J. M., McGowan, S. J., Roberts, N. A., Taylor, S., Higgs, D. R., & Hughes, J. R. (2016) · Nature Methods · doi:10.1038/nmeth.3664 · Cited by 268 · see citing works
Creating a functional single-chromosome yeast
Shao, Y., Lü, N., Wu, Z., Cai, C., Wang, S., Zhang, L.-L., Zhou, F., Xiao, S., Liu, L., Zeng, X., et al. (2018) · Nature · doi:10.1038/s41586-018-0382-x · Cited by 265 · see citing works
Polycomb-Dependent Chromatin Looping Contributes to Gene Silencing during Drosophila Development
Ogiyama, Y., Schuettengruber, B., Papadopoulos, G. L., Chang, J., & Cavalli, G. (2018) · Molecular Cell · doi:10.1016/j.molcel.2018.05.032 · Cited by 242 · see citing works
Deep functional analysis of synII, a 770-kilobase synthetic yeast chromosome.
Shen, Y., Wang, Y., Chen, T., Gao, F., Gong, J., Abramczyk, D., Walker, R., Zhao, H., Chen, S., Liu, W., et al. (2017) · Science · doi:10.1126/science.aaf4791 · Cited by 202 · see citing works
Dynamic reprogramming of chromatin accessibility during Drosophilaembryo development
Thomas, S., Li, X., Sabo, P. J., Sandstrom, R. S., Thurman, R. E., Canfield, T. K., Giste, E., Fisher, W., Hammonds, A. S., Celniker, S., et al. (2011) · Genome biology · doi:10.1186/gb-2011-12-5-r43 · Cited by 176 · see citing works
Rodríguez-Carballo, E., Lopez‐Delisle, L., Zhan, Y., Fabre, P. J., Beccari, L. L., El-Idrissi, I., Huynh, T. H. N., Özadam, H., Dekker, J., & Duboule, D. (2017) · Genes & Development · doi:10.1101/gad.307769.117 · Cited by 174 · see citing works
A cell‐based model system links chromothripsis with hyperploidy
Mardin, B. R., Drainas, A. P., Waszak, S. M., Weischenfeldt, J., Isokane, M., Stütz, A. M., Raeder, B., Efthymiopoulos, T., Buccitelli, C., Segura‐Wang, M., et al. (2015) · Molecular Systems Biology · doi:10.15252/msb.20156505 · Cited by 140 · see citing works
Self-citationEnhancer-adoption as a mechanism of human developmental disease
Lettice, L. A., Daniels, S. L., Sweeney, E., Venkataraman, S., Devenney, P. S., Gautier, P. E., Morrison, H., Fantes, J. A., Hill, R. E., & FitzPatrick, D. R. (2011) · Human Mutation · doi:10.1002/humu.21615 · Cited by 107 · see citing works
Zichner, T., Garfield, D. A., Rausch, T., Stütz, A. M., Cannavò, E., Braun, M. M., Furlong, E. E. M., & Korbel, J. O. (2012) · Genome Research · doi:10.1101/gr.142646.112 · Cited by 75 · see citing works
Self-citationTsujimura, T., Klein, F. A., Langenfeld, K., Glaser, J., Huber, W. K., & Spitz, F. (2015) · PLoS Genetics · doi:10.1371/journal.pgen.1004897 · Cited by 64 · see citing works
Effects of Gene Dose, Chromatin, and Network Topology on Expression in Drosophila melanogaster
Lee, H., Cho, D.-Y., Whitworth, C., Eisman, R. C., Phelps, M., Roote, J., Kaufman, T. C., Cook, K. R., Russell, S. R. H., Przytycka, T. M., et al. (2016) · PLoS Genetics · doi:10.1371/journal.pgen.1006295 · Cited by 41 · see citing works
Miller, D. E., Cook, K. R., Arvanitakis, A. V., & Hawley, R. S. (2016) · G3 Genes Genomes Genetics · doi:10.1534/g3.116.029330 · Cited by 33 · see citing works
Neighbourhood Continuity Is Not Required for Correct Testis Gene Expression in Drosophila
Meadows, L. A., Chan, Y. S., Roote, J., & Russell, S. R. H. (2010) · PLoS Biology · doi:10.1371/journal.pbio.1000552 · Cited by 30 · see citing works
The Molecular and Genetic Characterization of Second Chromosome Balancers in Drosophila melanogaster
Miller, D. E., Cook, K. R., Hemenway, E. A., Fang, V., Miller, A. L., Hales, K. G., & Hawley, R. S. (2018) · G3 Genes Genomes Genetics · doi:10.1534/g3.118.200021 · Cited by 18 · see citing works
Flagged first, then by citations
Research works printed but not linked: 2
- [58]Ramírez F High-resolution TADs reveal DNA sequences underlying genome organization in flies Nat Commun 2018 9 189 29335486 PMC5768762
- [62]Thomas S Dynamic reprogramming of chromatin accessibility during Drosophila embryo development Genome Biol 2011 12 R43 21569360 PMC3219966
Cited by
Sorted by citations
The Self-Organizing Genome: Principles of Genome Architecture and Function
Misteli, T. (2020) · Cell · doi:10.1016/j.cell.2020.09.014 · Cited by 706 · see citing works
Nonlinear control of transcription through enhancer–promoter interactions
Zuin, J., Roth, G., Zhan, Y., Cramard, J., Redolfi, J., Piskadlo, E., Mach, P., Kryzhanovska, M., Tihanyi, G., Kohler, H., et al. (2022) · Nature · doi:10.1038/s41586-022-04570-y · Cited by 415 · see citing works
Advances in Targeting ‘Undruggable’ transcription Factors With Small Molecules
Henley, M. J., & Koehler, A. N. (2021) · Nature Reviews Drug Discovery · doi:10.1038/s41573-021-00199-0 · Cited by 409 · see citing works
Towards a comprehensive catalogue of validated and target-linked human enhancers
Gasperini, M., Tome, J. M., & Shendure, J. (2020) · Nature Reviews Genetics · doi:10.1038/s41576-019-0209-0 · Cited by 396 · see citing works
Understanding 3D genome organization by multidisciplinary methods
Jerković, I., & Cavalli, G. (2021) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-021-00362-w · Cited by 389 · 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
The Mediator complex as a master regulator of transcription by RNA polymerase II
Richter, W. F., Nayak, S., Iwasa, J., & Taatjes, D. J. (2022) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-022-00498-3 · Cited by 312 · see citing works
The relationship between genome structure and function
Oudelaar, A. M., & Higgs, D. R. (2021) · Nature Reviews Genetics · doi:10.1038/s41576-020-00303-x · Cited by 304 · see citing works
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 · see citing works
Self-citationMolecular basis and biological function of variability in spatial genome organization
Finn, E. H., & Misteli, T. (2019) · Science · doi:10.1126/science.aaw9498 · Cited by 270 · see citing works
Genome organization controls transcriptional dynamics during development
Batut, P. J., Bing, X., Sisco, Z., Raimundo, J., Levo, M., & Levine, M. (2022) · Science · doi:10.1126/science.abi7178 · Cited by 226 · see citing works
McCord, R. P., Kaplan, N., & Giorgetti, L. (2020) · Molecular Cell · doi:10.1016/j.molcel.2019.12.021 · Cited by 204 · see citing works
McArthur, E., & Capra, J. A. (2021) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2021.01.001 · Cited by 200 · see citing works
Sequence determinants of human gene regulatory elements
Sahu, B., Hartonen, T., Pihlajamaa, P., Wei, B., Dave, K., Zhu, F., Kaasinen, E., Lidschreiber, K., Lidschreiber, M., Daub, C. O., et al. (2022) · Nature Genetics · doi:10.1038/s41588-021-01009-4 · Cited by 198 · see citing works
Deeply conserved synteny and the evolution of metazoan chromosomes
Simakov, O., Bredeson, J., Berkoff, K., Marletaz, F., Mitros, T., Schultz, D. T., O’Connell, B. L., Dear, P., Martinez, D. E., Steele, R. E., et al. (2022) · Science Advances · doi:10.1126/sciadv.abi5884 · Cited by 197 · see citing works
The road ahead in genetics and genomics
McGuire, A. L., Gabriel, S., Tishkoff, S. A., Wonkam, A., Chakravarti, A., Furlong, E. E. M., Treutlein, B., Meissner, A., Chang, H. Y., López-Bigas, N., et al. (2020) · Nature Reviews Genetics · doi:10.1038/s41576-020-0272-6 · Cited by 188 · see citing works
Self-citationEnhancers in disease: molecular basis and emerging treatment strategies
Claringbould, A., & Zaugg, J. B. (2021) · Trends in Molecular Medicine · doi:10.1016/j.molmed.2021.07.012 · Cited by 171 · see citing works
Espinola, S. M., Götz, M., Bellec, M., Messina, O., Fiche, J.-B., Houbron, C., Dejean, M., Reim, I., Cardozo Gizzi, A. M., Lagha, M., et al. (2021) · Nature Genetics · doi:10.1038/s41588-021-00816-z · Cited by 174 · see citing works
How subtle changes in 3D structure can create large changes in transcription
Xiao, J. Y., Hafner, A., & Boettiger, A. N. (2021) · eLife · doi:10.7554/elife.64320 · Cited by 162 · see citing works
Independence of chromatin conformation and gene regulation during Drosophila dorsoventral patterning
Ing-Simmons, E., Vaid, R., Bing, X. Y., Levine, M., Mannervik, M., & Vaquerizas, J. M. (2021) · Nature Genetics · doi:10.1038/s41588-021-00799-x · Cited by 159 · see citing works
Stik, G., Vidal, E., Barrero, M., Cuartero, S., Vila-Casadesús, M., Mendieta-Esteban, J., Tian, T. V., Choi, J., Berenguer, C., Abad, A., et al. (2020) · Nature Genetics · doi:10.1038/s41588-020-0643-0 · Cited by 139 · see citing works
Evidence for and against Liquid-Liquid Phase Separation in the Nucleus
Peng, A., & Weber, S. C. (2019) · Non-Coding RNA · doi:10.3390/ncrna5040050 · Cited by 144 · see citing works
Carullo, N. V. N., Phillips, R. A., III, Simon, R. C., Soto, S. A. R., Hinds, J. E., Salisbury, A. J., Revanna, J. S., Bunner, K. D., Ianov, L., Sultan, F. A., et al. (2020) · Nucleic Acids Research · doi:10.1093/nar/gkaa671 · Cited by 128 · see citing works
CTCF shapes chromatin structure and gene expression in health and disease
Dehingia, B., Milewska, M., Janowski, M., & Pękowska, A. (2022) · EMBO Reports · doi:10.15252/embr.202255146 · Cited by 128 · see citing works
Aljahani, A., Hua, P., Karpinska, M. A., Quililan, K., Davies, J. O. J., & Oudelaar, A. M. (2022) · Nature Communications · doi:10.1038/s41467-022-29696-5 · Cited by 121 · see citing works
Chakraborty, S., Kopitchinski, N., Zuo, Z., Eraso, A., Awasthi, P., Chari, R., Mitra, A., Tobias, I. C., Moorthy, S. D., Dale, R. K., et al. (2023) · Nature Genetics · doi:10.1038/s41588-022-01295-6 · Cited by 120 · see citing works
Transposable elements in mammalian chromatin organization
Lawson, H. A., Liang, Y., & Wang, T. (2023) · Nature Reviews Genetics · doi:10.1038/s41576-023-00609-6 · Cited by 121 · see citing works
Pachano, T., Sánchez-Gaya, V., Ealo, T., Mariner-Faulí, M., Bleckwehl, T., Asenjo, H. G., Respuela, P., Cruz-Molina, S., Muñoz-San Martín, M., Haro, E., et al. (2021) · Nature Genetics · doi:10.1038/s41588-021-00888-x · Cited by 116 · see citing works
Chromatin topology, condensates and gene regulation: shifting paradigms or just a phase?
Mir, M., Bickmore, W. A., Furlong, E. E. M., & Narlikar, G. J. (2019) · Development · doi:10.1242/dev.182766 · Cited by 109 · see citing works
Self-citationTo loop or not to loop: what is the role of TADs in enhancer function and gene regulation?
Cavalheiro, G. R., Pollex, T., & Furlong, E. E. M. (2021) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2020.12.015 · Cited by 101 · see citing works
Self-citationKaushal, A., Mohana, G., Dorier, J., Özdemir, İ., Omer, A., Cousin, P., Semenova, A. I., Taschner, M., Dergai, O., Marzetta, F., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-21366-2 · Cited by 99 · see citing works
Structural variants drive context-dependent oncogene activation in cancer
Xu, Z., Lee, D.-S., Chandran, S., Le, V. T., Bump, R., Yasis, J., Dallarda, S., Marcotte, S., Clock, B., Haghani, N. K., et al. (2022) · Nature · doi:10.1038/s41586-022-05504-4 · Cited by 97 · 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
Visualizing the Role of Boundary Elements in Enhancer-Promoter Communication
Yokoshi, M., Kazuma, S., & Fukaya, T. (2020) · Molecular Cell · doi:10.1016/j.molcel.2020.02.007 · Cited by 89 · 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
Chromoanagenesis: a piece of the macroevolution scenario
Pellestor, F., & Gâtinois, V. (2020) · Molecular Cytogenetics · doi:10.1186/s13039-020-0470-0 · Cited by 90 · see citing works
The 3D architecture of the pepper genome and its relationship to function and evolution
Liao, Y., Wang, J., Zhu, Z., Liu, Y., Chen, J., Zhou, Y., Liu, F., Lei, J., Gaut, B. S., Cao, B., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-31112-x · Cited by 92 · see citing works
Bravo González‐Blas, C., Quan, X., Duran‐Romaña, R., Taskiran, I. I., Koldere, D., Davie, K., Christiaens, V., Makhzami, S., Hulselmans, G., de Waegeneer, M., et al. (2020) · Molecular Systems Biology · doi:10.15252/msb.20209438 · Cited by 88 · see citing works
Determinants of transcription factor regulatory range
Chen, C.-H., Zheng, R., Tokheim, C., Dong, X., Fan, J., Wan, C., Tang, Q., Brown, M., Liu, J. S., Meyer, C. A., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-16106-x · Cited by 85 · see citing works
Pollex, T., Rabinowitz, A. H., Gambetta, M. C., Marco-Ferreres, R., Viales, R. R., Jankowski, A., Schaub, C., & Furlong, E. E. M. (2024) · Nature Genetics · doi:10.1038/s41588-024-01678-x · Cited by 82 · see citing works
Self-citationTranscriptional enhancers and their communication with gene promoters
Ray-Jones, H., & Spivakov, M. (2021) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-021-03903-w · Cited by 81 · see citing works
Chromosome-level organization of the regulatory genome in the Drosophila nervous system
Mohana, G., Dorier, J., Li, X., Mouginot, M., Smith, R. C., Malek, H., Leleu, M., Rodríguez, D., Khadka, J., Rosa, P., et al. (2023) · Cell · doi:10.1016/j.cell.2023.07.008 · Cited by 76 · see citing works
Self-citationNoack, F., Vangelisti, S., Raffl, G., Carido, M., Diwakar, J., Chong, F., & Bonev, B. (2022) · Nature Neuroscience · doi:10.1038/s41593-021-01002-4 · Cited by 74 · see citing works
Recurrent inversion toggling and great ape genome evolution
Porubsky, D., Sanders, A. D., Höps, W., Hsieh, P., Sulovari, A., Li, R., Mercuri, L., Sorensen, M., Murali, S. C., Gordon, D., et al. (2020) · Nature Genetics · doi:10.1038/s41588-020-0646-x · Cited by 72 · see citing works
Self-citationSpecialized functions of cohesins STAG1 and STAG2 in 3D genome architecture
Cuadrado, A., & Losada, A. (2020) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2020.02.024 · Cited by 74 · see citing works
Liao, Y., Zhang, X., Chakraborty, M., & Emerson, J. J. (2021) · Genome Research · doi:10.1101/gr.266130.120 · Cited by 71 · see citing works
Franke, M., de la Calle‐Mustienes, E., Neto, A., Almuedo‐Castillo, M., Irastorza-Azcárate, I., Acemel, R. D., Tena, J. J., Santos-Pereira, J. M., & Gómez-Skármeta, J. L. (2021) · Nature Communications · doi:10.1038/s41467-021-25604-5 · Cited by 69 · see citing works
Anopheles mosquitoes reveal new principles of 3D genome organization in insects
Lukyanchikova, V., Nuriddinov, M., Belokopytova, P. S., Taskina, A., Liang, J., Reijnders, M. J. M. F., Ruzzante, L., Feron, R., Waterhouse, R. M., Wu, Y., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-29599-5 · Cited by 73 · see citing works
The maternal-to-zygotic transition: reprogramming of the cytoplasm and nucleus
Kojima, M. L., Hoppe, C., & Giráldez, A. J. (2024) · Nature Reviews Genetics · doi:10.1038/s41576-024-00792-0 · Cited by 77 · see citing works
Mechanisms of Enhancer-Promoter Interactions in Higher Eukaryotes
Georgiev, P. G., & Kyrchanova, O. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms22020671 · Cited by 68 · see citing works
The regulatory landscapes of developmental genes
Bolt, C. C., & Duboule, D. (2020) · Development · doi:10.1242/dev.171736 · Cited by 60 · see citing works
Three-dimensional chromatin in disease: What holds us together and what drives us apart?
Ibrahim, D. M., & Mundlos, S. (2020) · Current Opinion in Cell Biology · doi:10.1016/j.ceb.2020.01.003 · Cited by 66 · see citing works
Nonlinear control of transcription through enhancer-promoter interactions
Zuin, J., Roth, G., Zhan, Y., Cramard, J., Redolfi, J., Piskadlo, E., Mach, P., Kryzhanovska, M., Tihanyi, G., Kohler, H., et al. (2021) · doi:10.1101/2021.04.22.440891 · Cited by 67 · see citing works
A TAD Skeptic: Is 3D Genome Topology Conserved?
Eres, I. E., & Gilad, Y. (2020) · Trends in Genetics · doi:10.1016/j.tig.2020.10.009 · Cited by 66 · see citing works
Cohesin: behind dynamic genome topology and gene expression reprogramming
Perea-Resa, C., Wattendorf, L., Marzouk, S., & Blower, M. D. (2021) · Trends in Cell Biology · doi:10.1016/j.tcb.2021.03.005 · Cited by 63 · see citing works
Capture-C: A modular and flexible approach for high-resolution chromosome conformation capture
Downes, D., Smith, A. L., Karpińska, M. A., Velychko, T., Rue-Albrecht, K., Sims, D., Milne, T., Davies, J., Oudelaar, A. M., & Hughes, J. (2022) · Nature Protocols · doi:10.1038/s41596-021-00651-w · Cited by 52 · see citing works
Spatial Organization of Chromatin: Emergence of Chromatin Structure During Development
Ghosh, R. P., & Meyer, B. J. (2021) · Annual Review of Cell and Developmental Biology · doi:10.1146/annurev-cellbio-032321-035734 · Cited by 56 · see citing works
Sigalova, O. M., Shaeiri, A., Forneris, M., Furlong, E. E. M., & Zaugg, J. B. (2020) · Molecular Systems Biology · doi:10.15252/msb.20209539 · Cited by 60 · see citing works
Self-citationAnalysis of muntjac deer genome and chromatin architecture reveals rapid karyotype evolution
Mudd, A. B., Bredeson, J. V., Baum, R., Hockemeyer, D. F., & Rokhsar, D. S. (2020) · Communications Biology · doi:10.1038/s42003-020-1096-9 · Cited by 61 · see citing works
Full circle: a brief history of cohesin and the regulation of gene expression
Horsfield, J. A. (2022) · FEBS Journal · doi:10.1111/febs.16362 · Cited by 55 · see citing works
Viets, K., Sauria, M. E. G., Chernoff, C., Viales, R. R., Echterling, M., Anderson, C., Tran, S., Dove, A., Goyal, R., Voortman, L., et al. (2019) · Developmental Cell · doi:10.1016/j.devcel.2019.09.007 · Cited by 58 · see citing works
Self-citationEnhancer-gene specificity in development and disease
Pachano, T., Haro, E., & Rada-Iglesias, Á. (2022) · Development · doi:10.1242/dev.186536 · Cited by 55 · see citing works
Beyond Drosophila: resolving the rapid radiation of schizophoran flies with phylotranscriptomics
Bayless, K. M., Trautwein, M., Meusemann, K., Shin, S., Petersen, M., Donath, A., Podsiadłowski, L., Mayer, C., Niehuis, O., Peters, R. S., et al. (2021) · BMC Biology · doi:10.1186/s12915-020-00944-8 · Cited by 59 · see citing works
Molecular architecture of enhancer–promoter interaction
Hamamoto, K., & Fukaya, T. (2022) · Current Opinion in Cell Biology · doi:10.1016/j.ceb.2022.01.003 · Cited by 55 · see citing works
Cavalheiro, G. R., Girardot, C., Viales, R. R., Feng, S., Pollex, T., Cao, T. B. N., Lacour, P., Rabinowitz, A. H., & Furlong, E. E. M. (2023) · Science Advances · doi:10.1126/sciadv.ade1085 · Cited by 56 · see citing works
Self-citationDong, P., Tu, X., Liang, Z., Kang, B., & Zhong, S. (2020) · Journal of Experimental Botany · doi:10.1093/jxb/eraa220 · Cited by 59 · see citing works
Topologically Associating Domains and Regulatory Landscapes in Development, Evolution and Disease
Tena, J. J., & Santos-Pereira, J. M. (2021) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2021.702787 · Cited by 55 · see citing works
Renschler, G., Richard, G., Valsecchi, C. I. K., Toscano, S., Arrigoni, L., Ramírez, F., & Akhtar, A. (2019) · Genes & Development · doi:10.1101/gad.328971.119 · Cited by 54 · see citing works
A model of active transcription hubs that unifies the roles of active promoters and enhancers
Zhu, I., Song, W., Ovcharenko, I., & Landsman, D. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkab235 · Cited by 55 · see citing works
TGFβ promotes widespread enhancer chromatin opening and operates on genomic regulatory domains
Guerrero-Martínez, J. A., Ceballos-Chávez, M., Koehler, F., Peiró, S., & Reyes, J. (2020) · Nature Communications · doi:10.1038/s41467-020-19877-5 · Cited by 44 · see citing works
The stochastic nature of genome organization and function
Sood, V., & Misteli, T. (2021) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2021.10.004 · Cited by 56 · see citing works
Nanopore sequencing of DNA concatemers reveals higher-order features of chromatin structurePreprint
Ulahannan, N., Pendleton, M., Deshpande, A. S., Schwenk, S., Behr, J. M., Dai, X., Tyer, C., Rughani, P., Kudman, S., Adney, E. M., et al. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/833590 · Cited by 48 · see citing works
Schöpflin, R., Melo, U. S., Moeinzadeh, H., Heller, D., Laupert, V., Hertzberg, J., Holtgrewe, M., Alavi, N., Klever, M.-K., Jungnitsch, J., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-34053-7 · Cited by 51 · see citing works
Range extender mediates long-distance enhancer activity
Bower, G., Hollingsworth, E. W., Jacinto, S. H., Alcantara, J. A., Clock, B., Cao, K., Liu, M., Dziulko, A., Alcaina-Caro, A., Xu, Q., et al. (2025) · Nature · doi:10.1038/s41586-025-09221-6 · Cited by 49 · see citing works
Sebestyén, E., Marullo, F., Lucini, F., Petrini, C., Bianchi, A., Valsoni, S., Olivieri, I., Antonelli, L., Gregoretti, F., Oliva, G., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-20048-9 · Cited by 49 · see citing works
3D genome evolution and reorganization in the Drosophila melanogaster species group
Torosin, N. S., Anand, A., Golla, T. R., Cao, W., & Ellison, C. E. (2020) · PLoS Genetics · doi:10.1371/journal.pgen.1009229 · Cited by 46 · see citing works
The role of insulators and transcription in 3D chromatin organization of fliesPreprint
Chathoth, K. T., Mikheeva, L. A., Crevel, G., Wolfe, J. C., Hunter, I., Beckett-Doyle, S., Cotterill, S., Dai, H., Harrison, A., & Zabet, N. R. (2022) · Genome Research · doi:10.1101/gr.275809.121 · Cited by 46 · see citing works
Evolution of 3D chromatin organization at different scales
Acemel, R. D., & Lupiáñez, D. G. (2023) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2022.102019 · Cited by 48 · see citing works
Wu, B. M., Yu, Q., Deng, Z., Duan, Y., Luo, F., & Gmitter, F. G. (2022) · Horticulture Research · doi:10.1093/hr/uhac247 · Cited by 47 · see citing works
Miller, D. E., Cook, K. R., & Hawley, R. S. (2019) · PLoS Genetics · doi:10.1371/journal.pgen.1008421 · Cited by 46 · see citing works
Integrative prediction of gene expression with chromatin accessibility and conformation data
Schmidt, F., Kern, F., & Schulz, M. H. (2020) · Epigenetics & Chromatin · doi:10.1186/s13072-020-0327-0 · Cited by 46 · see citing works
Repression and 3D-restructuring resolves regulatory conflicts in evolutionarily rearranged genomes
Ringel, A. R., Szabo, Q., Chiariello, A. M., Chudzik, K., Schöpflin, R., Rothe, P., Mattei, A. L., Zehnder, T., Harnett, D., Laupert, V., et al. (2022) · Cell · doi:10.1016/j.cell.2022.09.006 · Cited by 45 · see citing works
Transcriptional bursting: stochasticity in deterministic development
Porello, E. A. L., Trudeau, R. T., & Lim, B. (2023) · Development · doi:10.1242/dev.201546 · Cited by 43 · see citing works
Chromatin gene-gene loops support the cross-regulation of genes with related function
Pollex, T., Marco-Ferreres, R., Ciglar, L., Ghavi-Helm, Y., Rabinowitz, A. H., Viales, R. R., Schaub, C., Jankowski, A., Girardot, C., & Furlong, E. E. M. (2023) · Molecular Cell · doi:10.1016/j.molcel.2023.12.023 · Cited by 45 · see citing works
Self-citationIn situ dissection of domain boundaries affect genome topology and gene transcription in Drosophila
Arzate-Mejía, R. G., Cerecedo-Castillo, A. J., Guerrero, G., Furlan-Magaril, M., & Recillas-Targa, F. (2019) · Nature Communications · doi:10.1038/s41467-020-14651-z · Cited by 36 · see citing works
The multiscale effects of polycomb mechanisms on 3D chromatin folding
Cheutin, T., & Cavalli, G. (2019) · Critical Reviews in Biochemistry and Molecular Biology · doi:10.1080/10409238.2019.1679082 · Cited by 43 · see citing works
Transcriptional Enhancers in Drosophila
Small, S., & Arnosti, D. N. (2020) · Genetics · doi:10.1534/genetics.120.301370 · Cited by 41 · see citing works
Chromosome structural variation in tumorigenesis: mechanisms of formation and carcinogenesis
Wang, W., Li, L., & Cui, J. (2020) · Epigenetics & Chromatin · doi:10.1186/s13072-020-00371-7 · Cited by 44 · see citing works
Tralamazza, S. M., Gluck‐Thaler, E., Feurtey, A., & Croll, D. (2024) · Nature Communications · doi:10.1038/s41467-024-49913-7 · Cited by 43 · see citing works
Regulatory mechanisms ensuring coordinated expression of functionally related genes
Zinani, O. Q. H., Keseroǧlu, K., & Özbudak, E. M. (2021) · Trends in Genetics · doi:10.1016/j.tig.2021.07.008 · Cited by 43 · see citing works
Sanalkumar, R., Dong, R., Lee, L., Xing, Y.-H., Iyer, S., Letovanec, I., Rosa, S. L., Finzi, G., Musolino, E., Papait, R., et al. (2023) · Science Advances · doi:10.1126/sciadv.abo3789 · Cited by 32 · see citing works
Genetics of premature ovarian insufficiency and the association with X-autosome translocations
Di‐Battista, A., Moysés‐Oliveira, M., & Melaragno, M. I. (2020) · Reproduction · doi:10.1530/rep-20-0338 · Cited by 42 · see citing works
The Stochastic Genome and Its Role in Gene ExpressionPreprint
Bohrer, C. H., & Larson, D. R. (2021) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a040386 · Cited by 42 · see citing works
Dissection of a CTCF topological boundary uncovers principles of enhancer-oncogene regulation
Kim, K. L., Rahme, G. J., Goel, V. Y., Farran, C. A. E., Hansen, A. S., & Bernstein, B. (2024) · Molecular Cell · doi:10.1016/j.molcel.2024.02.007 · Cited by 40 · see citing works
Balasubramanian, D., Pinto, P. B., Grasso, A., Vincent, S., Tarayre, H., Lajoignie, D., & Ghavi-Helm, Y. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkad1183 · Cited by 37 · see citing works
Self-citationPujadas-Liwag, E. M., Wei, X., Acosta, N., Carter, L. M., Yang, J., Almassalha, L. M., Jain, S., Daneshkhah, A., Rao, S. S. P., Seker-Polat, F., et al. (2024) · Genome biology · doi:10.1186/s13059-024-03212-y · Cited by 38 · see citing works
Zhang, X., Pandey, M. K., Wang, J., Zhao, K., Ma, X., Li, Z., Zhao, K. X., Gong, F., Guo, B. Z., Varshney, R. K., et al. (2021) · Genome biology · doi:10.1186/s13059-021-02520-x · Cited by 38 · see citing works
Randomizing the human genome by engineering recombination between repeat elements
Koeppel, J., Ferreira, R., Vanderstichele, T., Riedmayr, L. M., Peets, E. M., Girling, G., Weller, J., Murat, P., Liberante, F. G., Ellis, T., et al. (2025) · Science · doi:10.1126/science.ado3979 · Cited by 37 · see citing works
Detecting chromosomal interactions in Capture Hi-C data with CHiCAGO and companion tools
Freire-Pritchett, P., Ray-Jones, H., Rosa, M. D., Eijsbouts, C., Orchard, W. R., Wingett, S., Wallace, C., Cairns, J. M., Spivakov, M., & Malysheva, V. (2021) · Nature Protocols · doi:10.1038/s41596-021-00567-5 · Cited by 34 · see citing works
Shi, G., & Thirumalai, D. (2023) · Nature Communications · doi:10.1038/s41467-023-36412-4 · Cited by 34 · see citing works
- Authors
- Ghavi-Helm, Y., Jankowski, A., Meiers, S., Viales, R. R., Korbel, J. O., & Furlong, E. E. M.
- Affiliations
- Lyon 1 Université (FR)
- European Molecular Biology Laboratory (DE)
- Corresponding author
- Ghavi-Helm, Yad
- Korbel, Jan O.
- Furlong, Eileen E. M.
- ORCID
- Venue
- Nature Genetics
- Published
- 2019-07-15
- Volume
- 51
- Issue
- 8
- Pages
- 1272-1282
- ISSN
- 1061-4036 (ISSN-L)
- 1546-1718
- PMC
- PMC7116017
- OpenAlex
- W2958578938
- Cited by
- 354
- References
- 57
- Citations by year
- 2026: 16 · 2025: 33 · 2024: 41 · 2023: 54 · 2022: 60 · 2021: 74 · 2020: 56 · 2019: 19
- FWCI
- 17.94
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Nature Genetics (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- HAL (submittedVersion)
- Funders
- Nature
- Topics
- 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
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chromatin Remodeling and Cancer
- Keywords
- chromatin topology, gene expression, balancer chromosomes, chromosomal inversions, topologically associating domains, enhancer-promoter interactions, cis effect, Drosophila, chromosomal duplication, chromosomal deletion
- MeSH terms
- Animals, Chromatin, Chromosome Mapping, Drosophila melanogaster, Enhancer Elements, Genetic, Female, Gene Expression Regulation, Male, Promoter Regions, Genetic, Gene Rearrangement, Genome, Insect, Chromosomes, Insect
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