Long-range regulation of transcription scales with genomic distance in a gene-specific manner
Open accessPublished version of a preprint
Abstract
Although critical for tuning the timing and level of transcription, enhancer communication with distal promoters is not well understood. Here, we bypass the need for sequence-specific transcription factors (TFs) and recruit activators directly using a chimeric array of gRNA oligos to target dCas9 fused to the activator VP64-p65-Rta (CARGO-VPR). We show that this approach achieves effective activator recruitment to arbitrary genomic sites, even those inaccessible when targeted with a single guide. We utilize CARGO-VPR across the Prdm8-Fgf5 locus in mouse embryonic stem cells (mESCs), where neither gene is expressed. Although activator recruitment to any tested region results in the transcriptional induction of at least one gene, the expression level strongly depends on the genomic distance between the promoter and activator recruitment site. However, the expression-distance relationship for each gene scales distinctly in a manner not attributable to differences in 3D contact frequency, promoter DNA sequence, or the presence of repressive chromatin marks at the locus.
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?
The importance of genomic context for long-range regulatory effects is corroborated by the distinct scaling with genomic distance between Sox2 and Car2 and by observations at other loci.
“Long-range regulatory effects scaled distinctly with genomic distance between Sox2 and Car2, corroborating the importance of genomic context observed at other loci (56).”
From Synergy between regulatory elements can render cohesin dispensable for distal enhancer function (2026) · cites this paper as [56]
The Results report distinct expression–distance scaling for Prdm8 and Fgf5, and the Discussion concludes that genomic context beyond the promoter contributes to gene-specific scaling (page numbers unavailable). Our copy does not support the claim’s specific comparison between Sox2 and Car2. (LLM, conf=0.88)
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
ggplot2: Elegant Graphics for Data Analysis
Ginestet, C. E. (2011) · Journal of the Royal Statistical Society Series A (Statistics in Society) · doi:10.1111/j.1467-985x.2010.00676_9.x · Cited by 14,484 · see citing works
The Human Genome Browser at UCSC
Kent, W. J., Sugnet, C. W., Furey, T. S., Roskin, K. M., Pringle, T. H., Zahler, A. M., & Haussler, A. D. (2002) · Genome Research · doi:10.1101/gr.229102 · Cited by 10,400 · 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
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
Genome-scale transcriptional activation by an engineered CRISPR-Cas9 complex
Konermann, S., Brigham, M. D., Trevino, A. E., Joung, J., Abudayyeh, O. O., Barcena, C., Hsu, P. D., Habib, N., Gootenberg, J. S., Nishimasu, H., et al. (2015) · Nature · doi:10.1038/nature14136 · Cited by 2,825 · see citing works
Enhancements and modifications of primer design program Primer3
Kõressaar, T., & Remm, M. (2007) · Bioinformatics · doi:10.1093/bioinformatics/btm091 · Cited by 2,618 · see citing works
HiGlass: web-based visual exploration and analysis of genome interaction maps
Kerpedjiev, P., Abdennur, N. A., Lekschas, F., McCallum, C., Dinkla, K., Strobelt, H., Luber, J. M., Ouellette, S., Azhir, A., Kumar, N., et al. (2018) · Genome biology · doi:10.1186/s13059-018-1486-1 · Cited by 2,416 · see citing works
Derivation of completely cell culture-derived mice from early-passage embryonic stem cells.
Nagy, A., Rossant, J., Nagy, R., Abramow-Newerly, W., & Roder, J. (1993) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.90.18.8424 · Cited by 2,328 · see citing works
Hilton, I. B., D’Ippolito, A. M., Vockley, C. M., Thakore, P. I., Crawford, G. E., Reddy, T. E., & Gersbach, C. A. (2015) · Nature Biotechnology · doi:10.1038/nbt.3199 · Cited by 1,879 · see citing works
Expression of a β-globin gene is enhanced by remote SV40 DNA sequences
Banerji, J., Rusconi, S., & Schaffner, W. (1981) · Cell · doi:10.1016/0092-8674(81)90413-x · Cited by 1,724 · see citing works
Lettice, L. A. (2003) · Human Molecular Genetics · doi:10.1093/hmg/ddg180 · Cited by 1,164 · see citing works
Bootstrap methods and their applications
Varga, L. (2018) · Eötvös Loránd Tudományegyetem · doi:10.15476/elte.2017.147 · Cited by 1,118 · see citing works
Activity-by-contact model of enhancer–promoter regulation from thousands of CRISPR perturbations
Fulco, C. P., Nasser, J., Jones, T. R., Munson, G., Bergman, D. T., Subramanian, V., Grossman, S. R., Anyoha, R., Doughty, B. R., Patwardhan, T. A., et al. (2019) · Nature Genetics · doi:10.1038/s41588-019-0538-0 · Cited by 1,111 · see citing works
Super-resolution chromatin tracing reveals domains and cooperative interactions in single cells
Bintu, B., Mateo, L. J., Su, J.-H., Sinnott-Armstrong, N. A., Parker, M., Kinrot, S., Yamaya, K., Boettiger, A. N., & Zhuang, X. (2018) · Science · doi:10.1126/science.aau1783 · Cited by 976 · see citing works
Self-citationEver-Changing Landscapes: Transcriptional Enhancers in Development and Evolution
Long, H. K., Prescott, S. L., & Wysocka, J. (2016) · Cell · doi:10.1016/j.cell.2016.09.018 · Cited by 945 · see citing works
Self-citationThe Transcriptional and Epigenomic Foundations of Ground State Pluripotency
Marks, H., Kalkan, T., Menafra, R., Denissov, S., Jones, K. A., Hofemeister, H., Nichols, J., Kranz, A., Stewart, A., Smith, A. G., et al. (2012) · Cell · doi:10.1016/j.cell.2012.03.026 · Cited by 881 · see citing works
Controlled expression of transgenes introduced by in vivo electroporation
Matsuda, T., & Cepko, C. L. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0610155104 · Cited by 666 · see citing works
Resolving the 3D Landscape of Transcription-Linked Mammalian Chromatin Folding
Hsieh, T.-H. S., Cattoglio, C., Slobodyanyuk, E., Hansen, A. S., Rando, O. J., Tjian, R., & Darzacq, X. (2020) · Molecular Cell · doi:10.1016/j.molcel.2020.03.002 · Cited by 661 · see citing works
Developmental enhancers and chromosome topology
Furlong, E. E. M., & Levine, M. (2018) · Science · doi:10.1126/science.aau0320 · Cited by 641 · see citing works
Targeting cells with single vectors using multiple-feature Boolean logic
Fenno, L. E., Mattis, J., Ramakrishnan, C., Hyun, M., Lee, S. Y., He, M., Tucciarone, J., Selimbeyoglu, A., Berndt, A., Grosenick, L., et al. (2014) · Nature Methods · doi:10.1038/nmeth.2996 · Cited by 557 · see citing works
Reorganization of enhancer patterns in transition from naive to primed pluripotency
Buecker, C., Srinivasan, R., Wu, Z., Calo, E., Acampora, D., Faial, T., Simeone, A., Tan, M., Swigut, T., & Wysocka, J. (2014) · Cell Stem Cell · doi:10.1016/j.stem.2014.04.003 · Cited by 507 · see citing works
Self-citationDynamic interplay between enhancer–promoter topology and gene activity
Chen, H., Levo, M., Barinov, L., Fujioka, M., Jaynes, J. B., & Gregor, T. (2018) · Nature Genetics · doi:10.1038/s41588-018-0175-z · Cited by 483 · see citing works
Functional and topological characteristics of mammalian regulatory domains
Symmons, O., Uslu, V. V., Tsujimura, T., Ruf, S., Nassari, S., Schwarzer, W., Ettwiller, L., & Spitz, F. (2014) · Genome Research · doi:10.1101/gr.163519.113 · Cited by 455 · see citing works
Visualizing DNA folding and RNA in embryos at single-cell resolution
Mateo, L. J., Murphy, S. E., Hafner, A., Cinquini, I. S., Walker, C. A., & Boettiger, A. N. (2019) · Nature · doi:10.1038/s41586-019-1035-4 · Cited by 446 · see citing works
Self-citationNucleosomes impede Cas9 access to DNA in vivo and in vitro
Horlbeck, M. A., Witkowsky, L. B., Guglielmi, B., Replogle, J. M., Gilbert, L. A., Villalta, J. E., Torigoe, S. E., Tjian, R., & Weissman, J. S. (2016) · eLife · doi:10.7554/elife.12677 · Cited by 415 · 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
Dorighi, K. M., Swigut, T., Henriques, T., Bhanu, N. V., Scruggs, B. S., Nady, N., Still, C. D., Garcia, B. A., Adelman, K., & Wysocka, J. (2017) · Molecular Cell · doi:10.1016/j.molcel.2017.04.018 · Cited by 403 · see citing works
Self-citationEpigenome characterization at single base-pair resolution
Henikoff, J. G., Belsky, J. A., Krassovsky, K., MacAlpine, D. M., & Henikoff, S. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1110731108 · Cited by 392 · see citing works
Transcription-coupled changes in nuclear mobility of mammalian cis-regulatory elements
Gu, B., Swigut, T., Spencley, A., Bauer, M. R., Chung, M., Meyer, T., & Wysocka, J. (2018) · Science · doi:10.1126/science.aao3136 · Cited by 363 · see citing works
Self-citationCombinatorial function of transcription factors and cofactors
Reiter, F., Wienerroither, S., & Stark, A. (2017) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2016.12.007 · Cited by 354 · see citing works
Live-cell imaging reveals enhancer-dependent Sox2 transcription in the absence of enhancer proximity
Alexander, J. M., Guan, J., Li, B., Maliskova, L., Song, M., Shen, Y., Huang, B., Lomvardas, S., & Weiner, O. D. (2019) · eLife · doi:10.7554/elife.41769 · Cited by 346 · see citing works
Decreased Enhancer-Promoter Proximity Accompanying Enhancer Activation
Benabdallah, N. S., Williamson, I., Illingworth, R. S., Kane, L., Boyle, S., Sengupta, D., Grimes, G. R., Therizols, P., & Bickmore, W. A. (2019) · Molecular Cell · doi:10.1016/j.molcel.2019.07.038 · Cited by 335 · see citing works
A Myc enhancer cluster regulates normal and leukaemic haematopoietic stem cell hierarchies
Bahr, C., von Paleske, L., Uslu, V. V., Remeseiro, S., Takayama, N., Ng, S. W., Murison, A., Langenfeld, K., Petretich, M., Scognamiglio, R., et al. (2018) · Nature · doi:10.1038/nature25193 · Cited by 328 · see citing works
Deciphering the multi-scale, quantitative cis-regulatory code
Kim, S., & Wysocka, J. (2023) · Molecular Cell · doi:10.1016/j.molcel.2022.12.032 · Cited by 282 · see citing works
Self-citationInterrogation of enhancer function by enhancer-targeting CRISPR epigenetic editing
Li, K., Liu, Y., Cao, H., Zhang, Y., Gu, Z., Liu, X., Yu, A., Kaphle, P., Dickerson, K. E., Ni, M., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-14362-5 · Cited by 247 · see citing works
Nucleosome breathing and remodeling constrain CRISPR-Cas9 function
Isaac, R. S., Jiang, F., Doudna, J. A., Lim, W. A., Narlikar, G. J., & Almeida, R. (2016) · eLife · doi:10.7554/elife.13450 · Cited by 234 · 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
Symmons, O., Pan, L., Remeseiro, S., Aktas, T., Klein, F., Huber, W., & Spitz, F. (2016) · Developmental Cell · doi:10.1016/j.devcel.2016.10.015 · Cited by 222 · see citing works
Histone H3 lysine 4 monomethylation modulates long-range chromatin interactions at enhancers
Yan, J., Chen, S.-A. A., Local, A., Liu, T., Qiu, Y., Lee, A. Y., Jung, I., Preißl, S., Rivera, C. M., Wang, C., et al. (2018) · Cell Research · doi:10.1038/cr.2018.1 · Cited by 198 · see citing works
Self-citationFuentes, D., Swigut, T., & Wysocka, J. (2018) · eLife · doi:10.7554/elife.35989 · Cited by 184 · see citing works
Self-citationRinzema, N. J., Sofiadis, K., Tjalsma, S. J. D., Verstegen, M. J. A. M., Oz, Y., Valdes-Quezada, C., Felder, A.-K., Filipovska, T., van der Elst, S., de Andrade dos Ramos, Z., et al. (2022) · Nature Structural & Molecular Biology · doi:10.1038/s41594-022-00787-7 · Cited by 166 · 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
Self-citationLoss of Extreme Long-Range Enhancers in Human Neural Crest Drives a Craniofacial Disorder
Long, H. K., Osterwalder, M., Welsh, I. C., Hansen, K. L., Davies, J. O. J., Liu, Y. E., Koska, M., Adams, A. T., Aho, R., Arora, N., et al. (2020) · Cell stem cell · doi:10.1016/j.stem.2020.09.001 · Cited by 160 · see citing works
Self-citationSingle-Molecule Nanoscopy Elucidates RNA Polymerase II Transcription at Single Genes in Live Cells
Li, J., Dong, A., Saydaminova, K., Chang, H., Wang, G., Ochiai, H., Yamamoto, T., & Pertsinidis, A. (2019) · Cell · doi:10.1016/j.cell.2019.05.029 · Cited by 154 · see citing works
Cohesin is required for long-range enhancer action at the Shh locus
Kane, L., Williamson, I., Flyamer, I. M., Kumar, Y., Hill, R. E., Lettice, L. A., & Bickmore, W. A. (2022) · Nature Structural & Molecular Biology · doi:10.1038/s41594-022-00821-8 · Cited by 153 · see citing works
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 · 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
Loop stacking organizes genome folding from TADs to chromosomes
Hafner, A., Park, M., Berger, S. E., Murphy, S. E., Nora, E. P., & Boettiger, A. N. (2023) · Molecular Cell · doi:10.1016/j.molcel.2023.04.008 · Cited by 120 · see citing works
Self-citationIdentification and functional characterization of transcriptional activators in human cells
Alerasool, N., Leng, H., Lin, Z.-Y., Gingras, A.-C., & Taipale, M. (2022) · Molecular Cell · doi:10.1016/j.molcel.2021.12.008 · Cited by 120 · see citing works
Stochastic motion and transcriptional dynamics of pairs of distal DNA loci on a compacted chromosome
Brückner, D. B., Chen, H., Barinov, L., Zoller, B., & Gregor, T. (2023) · Science · doi:10.1126/science.adf5568 · Cited by 112 · see citing works
Single-gene imaging links genome topology, promoter–enhancer communication and transcription control
Li, J., Hsu, A. M., Hua, Y., Wang, G., Cheng, L., Ochiai, H., Yamamoto, T., & Pertsinidis, A. (2020) · Nature Structural & Molecular Biology · doi:10.1038/s41594-020-0493-6 · Cited by 112 · see citing works
Thomas, H. F., Kotova, E., Jayaram, S., Pilz, A., Romeike, M., Lackner, A., Penz, T., Bock, C., Leeb, M., Halbritter, F., et al. (2021) · Molecular Cell · doi:10.1016/j.molcel.2020.12.047 · Cited by 98 · see citing works
Self-citationDNA Methylation Directs Polycomb-Dependent 3D Genome Re-organization in Naive Pluripotency
McLaughlin, K. A., Flyamer, I. M., Thomson, J. P., Mjoseng, H. K., Shukla, R., Williamson, I., Grimes, G. R., Illingworth, R. S., Adams, I. R., Pennings, S., et al. (2019) · Cell Reports · doi:10.1016/j.celrep.2019.10.031 · Cited by 95 · 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
Tracing DNA paths and RNA profiles in cultured cells and tissues with ORCA
Mateo, L. J., Sinnott-Armstrong, N., & Boettiger, A. N. (2021) · Nature Protocols · doi:10.1038/s41596-020-00478-x · Cited by 64 · see citing works
Self-citationHung, T.-C., Kingsley, D. M., & Boettiger, A. N. (2024) · Nature Genetics · doi:10.1038/s41588-023-01641-2 · Cited by 61 · see citing works
Self-citationCo-transcriptional genome surveillance by HUSH is coupled to termination machinery
Spencley, A. L., Bar, S., Swigut, T., Flynn, R. A., Lee, C. H., Chen, L., Bassik, M. C., & Wysocka, J. (2023) · Molecular Cell · doi:10.1016/j.molcel.2023.04.014 · Cited by 46 · see citing works
Self-citationTemporal and Spatial Epigenome Editing Allows Precise Gene Regulation in Mammalian Cells
Kuscu, C., Mammadov, R., Czikora, Á., Unlu, H., Tufan, T., Fischer, N. L., Arslan, Ş., Bekiranov, S., Kanemaki, M. T., & Adli, M. (2018) · Journal of Molecular Biology · doi:10.1016/j.jmb.2018.08.001 · Cited by 42 · see citing works
Physical mechanisms behind the large scale features of chromatin organization
Pombo, A., & Nicodemi, M. (2014) · Transcription · doi:10.4161/trns.28447 · Cited by 15 · see citing works
Functional chromatin signatures premark future lineage-specific enhancers
Pulecio, J., Tayyebi, Z., Liu, D., Wong, W., Luo, R., Damodaran, J. R., Kaplan, S. J., Hu, N., Cho, H., Yan, J., et al. (2026) · Cell Genomics · doi:10.1016/j.xgen.2026.101189 · Cited by 5 · see citing works
Boulos, J., Golov, A. K., Keren, N., Erlich, I., Shehadeh, N., Avidan, N., Kariti, H., Sadeh, O., Haimovich-Caspi, L., Helms, A. S., et al. (2025) · iScience · doi:10.1016/j.isci.2025.114040 · Cited by 4 · see citing works
Flagged first, then by citations
1 of the 62 references couldn’t be matched to a known paper.
Research works printed but not linked: 2
- [40]Pulecio J, Tayyebi Z, Liu D, Wong W, Luo R, Damodaran JR, Kaplan S, Cho H, Yan J, Murphy D, (2023). Discovery of Competent Chromatin Regions in Human Embryonic Stem Cells. bioRxiv.
- [54]Nagy A, Rossant J, Nagy R, Abramow-Newerly W, and Roder JC (1993). by STANFORD UNIVERSITY SERIALS DEPARTMENT on December 30. Dev. Biol 90, 8424– 8428. PMC47369 8378314
Cited by
Sorted by citations
Enhancer cooperativity can compensate for loss of activity over large genomic distances
Antonović, M., Feng, S., Haslhofer, F., Huber, M., Gallardo, M. G., Loubiere, V., Vanina, D., Pitasi, M., Stark, A., & Buecker, C. (2024) · Molecular Cell · doi:10.1016/j.molcel.2024.11.008 · Cited by 50 · see citing works
Synergy between regulatory elements can render cohesin dispensable for distal enhancer function
Hansen, K. L., Adachi, A. S., Braccioli, L., Kadvani, S., Boileau, R. M., Martinovic, M., Pokorny, B., Shah, R., Anderson, E. C., Zhang, K., et al. (2026) · Science · doi:10.1126/science.adt4221 · Cited by 29 · see citing works
Genetic factors mediating long-range enhancer–promoter communication in mammalian development
Bower, G., & Kvon, E. Z. (2024) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2024.102282 · Cited by 26 · see citing works
Tünnermann, J., Roth, G., Cramard, J., & Giorgetti, L. (2026) · Nature Genetics · doi:10.1038/s41588-026-02676-x · Cited by 10 · see citing works
Zhu, T., Li, C., & Chu, X. (2025) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2513371122 · Cited by 8 · see citing works
Redefining enhancer action: Insights from structural, genomic, and single-molecule perspectives
Llères, D., Gizzi, A. M. C., & Nöllmann, M. (2025) · Current Opinion in Cell Biology · doi:10.1016/j.ceb.2025.102527 · Cited by 8 · see citing works
Loop extrusion creates rare, long-lived encounters underlying enhancer-promoter communicationPreprint
Ubertini, M. A., Louafi, N., Landry, K., Kos, P. I., Roth, G., Marchi, E., Cramard, J., Tiana, G., & Giorgetti, L. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.09.24.678119 · Cited by 8 · see citing works
Enhancer cooperativity in the folded genome
Friman, E. T., & Bickmore, W. A. (2025) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2025.102416 · Cited by 7 · see citing works
Exploring the interplay between enhancer–promoter interactions and transcription
Kittle, R., & Levo, M. (2025) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2024.102303 · Cited by 7 · see citing works
Configuring the Code: Enhancer-Promoter Arrangement and Transcriptional Regulation
Buitrago, N., Vidal, J. A., & Lim, B. (2025) · Journal of Molecular Biology · doi:10.1016/j.jmb.2025.169417 · Cited by 6 · see citing works
Kribelbauer-Swietek, J. F., Gardeux, V., Llimos, G., Faltejsková, K., Russeil, J., Grenningloh, N., Levassor, L., Steiner, C., Vondrášek, J., & Deplancke, B. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.12.08.627402 · Cited by 6 · see citing works
Cohesin bridging as a physical principle of enhancer-promoter communicationPreprint
Földes, T., Hansen, K. L., Imakaev, M., Pinholt, H. D., Abdennur, N. A., Fudenberg, G., Carel, I., Handal, T., Vargas-Romero, F., Nora, E. P., et al. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.05.07.723561 · Cited by 6 · see citing works
Promoter strength and position govern promoter competition through transcript-dependent insulation
Koska, M., Nagano, M., Swigut, T., Boettiger, A. N., Hansen, A. S., & Wysocka, J. (2026) · Nature Genetics · doi:10.1038/s41588-026-02691-y · Cited by 5 · see citing works
Self-citationBoulos, J., Golov, A. K., Keren, N., Erlich, I., Shehadeh, N., Avidan, N., Kariti, H., Sadeh, O., Haimovich-Caspi, L., Helms, A. S., et al. (2025) · iScience · doi:10.1016/j.isci.2025.114040 · Cited by 4 · see citing works
Photoactivation/regulation of CRISPR systems: From in vitro diagnosis to in vivo gene manipulation
Jiang, H., Deng, Y., Yang, J., Li, A., Li, X., & Lv, X. (2025) · TrAC Trends in Analytical Chemistry · doi:10.1016/j.trac.2025.118477 · Cited by 3 · see citing works
Synthetic genomic dissection of enhancer context sensitivity and synergyPreprint
Ordóñez, R., Ribeiro-dos-Santos, A. M., Mcloughlin, C., Ellis, G., Ashe, H. J., Berastegui, N., Brosh, R., Majewski, M., Barriball, K., Camellato, B. R., et al. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.08.13.669251 · Cited by 3 · see citing works
FISH Omics Format: a standard enabling FAIR chromatin tracing data sharing across repositoriesPreprint
Navelkar, R., Cosolo, A., Porto, I. M., Bintu, B., Cheng, Y., Gardeux, V., Gutnik, S., Fujimori, T., Hafner, A., Jay, A., et al. (2025) · PubMed · doi:10.48550/arxiv.2508.13255 · Cited by 3 · see citing works
Self-citationDistal enhancers loop to proximal enhancers, not to promoters
Struhl, K. (2025) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-025-00889-2 · Cited by 2 · see citing works
Haydar, S., Bednarz, R., Laurette, P., Sobitov, I., Pedrosa, N. D. I., Videm, P., Lueneburg, T., Kuß, S., Lahm, H. W., Dreßen, M., et al. (2026) · Nature Communications · doi:10.1038/s41467-025-67220-7 · Cited by 2 · see citing works
Modeling periodic transcriptions in tandem gene systems
Wu, W., Tan, S., Tang, M., & Sun, Q. (2026) · Mathematical Biosciences · doi:10.1016/j.mbs.2026.109648 · Cited by 2 · see citing works
A mathematical model clarifies the ABC Score formula used in enhancer-gene predictionPreprint
Nasser, J., Nam, K.-M., & Gunawardena, J. (2025) · eLife · doi:10.7554/elife.105740.1 · Cited by 2 · see citing works
Cellular plasticity of cancer: roles of biomolecular condensates and ecDNA
Sugimoto, Y., Zhang, Y., Kachi, T., Ogami, K., & Suzuki, H. I. (2026) · Japanese Journal of Clinical Oncology · doi:10.1093/jjco/hyag065 · Cited by 1 · see citing works
A mathematical model clarifies the ABC Score formula used in enhancer-gene predictionPreprint
Nasser, J., Nam, K.-M., & Gunawardena, J. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.11.29.626072
Bridging the gap: How enhancers cooperate to regulate gene expression over large genomic distances
Tsouraki, D., & Oudelaar, A. M. (2025) · Molecular Cell · doi:10.1016/j.molcel.2024.12.001
Nuc3DMap delineates finer nucleosome-based three-dimensional chromatin architecturePreprint
Fang, K., Choppavarapu, L., Liu, T., Knight, P. A., & Jin, V. X. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.04.03.647017
A mathematical model clarifies the ABC Score formula used in enhancer-gene predictionPreprint
Nasser, J., Nam, K.-M., & Gunawardena, J. (2025) · eLife · doi:10.7554/elife.105740
Ng, H. L., Glaser, T. L., Zhu, J., Robinson, M. E., Cosgun, K. N., Malysheva, V., Deniz, Ö., Crump, N. T., Helian, K., Innes, A. J., et al. (2026) · Advanced Science · doi:10.1002/advs.202517231
Maltoni, F., Wang, S., Steketee, M., Gómez-Martín, C., Drees, E. E. E., Morelli, F., Bosch, L., van Eijndhoven, M. A. J., Timmers, G.-J., Houtenbos, I., et al. (2026) · Journal of Extracellular Vesicles · doi:10.1002/jev2.70259
Synthetic chromosomes for 3D functional genomics: from principles to AI-guided design
Perrot, M., Serizay, J., & Koszul, R. (2026) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2026.102471
Connecting multiway enhancer-promoter interactions to changes in gene expression in cancerPreprint
Kumari, K., Shin, S., Shi, G., Reed, K. S. M., Misteli, T., & Thirumalai, D. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.04.25.720760
Zhao, W., Mihelich, B., Fan, B., Glass, E. B., & Chaufty, J. A. (2026) · Cytotherapy · doi:10.1016/j.jcyt.2026.102908
Telang, A. C., Wan, M., Orbán, S., Stahlecker, J., Ference-Salo, J. T., Delker, D. A., Shillingford, J. M., McElliott, M. C., Laszczyk, A. M., Vashi, R. N., et al. (2026) · Journal of Biological Chemistry · doi:10.1016/j.jbc.2026.113305
Zan, T., Wen, Z., Jia, H., Dong, X., & Shen, N. (2026) · Cardiovascular Diabetology · doi:10.1186/s12933-026-03309-7
Temporal regulation of a spatial patterning factor in Drosophila neurogenesisPreprint
Coyne, R., Kamulegeya, F., Lake, C. M., Rajesh, R., Treese, M., Chen, Y., Troutwine, B., Zeitlinger, J., & Özel, M. N. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.08.11.744200
Mechanisms and functional implications of long-range enhancer-dependent gene regulation
Iliadou, M., Haro, E., & Rada-Iglesias, Á. (2026) · Nature Genetics · doi:10.1038/s41588-026-02721-9
What Is the Role of Cohesin in Transcription Regulation?
Ulianov, S. V., & Razin, S. V. (2026) · Biochemistry (Moscow) · doi:10.1134/s0006297926602285
Fibroblast growth factor in pancreatic development, homeostasis, and disease
Dou, Z., Jian, Y., Liu, X., Liu, Z., 刘会生, Lin, H., & Guo, Y. (2026) · Cytokine & Growth Factor Reviews · doi:10.1016/j.cytogfr.2026.101535
- Authors
- Jensen, C. L., Chen, L.-F., Swigut, T., Crocker, O. J., Yao, D., Bassik, M. C., Ferrell, J. E., Boettiger, A. N., & Wysocka, J.
- Affiliations
- Stanford University (US)
- Stanford Medicine (US)
- Howard Hughes Medical Institute (US)
- Corresponding author
- Wysocka, Joanna
- ORCID
- Venue
- Molecular Cell
- Publisher
- Elsevier BV
- Published
- 2025-01
- Volume
- 85
- Issue
- 2
- Pages
- 347-361.e7
- ISSN
- 1097-2765 (ISSN-L)
- PMC
- PMC11741922
- OpenAlex
- W4404919685
- Cited by
- 39
- References
- 62
- Citations by year
- 2026: 16 · 2025: 18 · 2024: 5
- FWCI
- 5.31
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Molecular Cell (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
- PubMed (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed Central (submittedVersion)
- Funders
- National Institutes of Health Office of the Director
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › CRISPR and Genetic Engineering
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chromatin Remodeling and Cancer
- Keywords
- long-range transcriptional regulation, enhancer-promoter interactions, genomic distance, gene-specific regulation, dCas9, mouse embryonic stem cells, repressive chromatin, transcriptional induction
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
