The DOI matches its Crossref record; 87 of the 92 references it cites were found in a registry or an index.
RNA polymerases as moving barriers to condensin loop extrusion
Open accessPublished version of a preprint
Abstract
To separate replicated sister chromatids during mitosis, eukaryotes and prokaryotes have structural maintenance of chromosome (SMC) condensin complexes that were recently shown to organize chromosomes by a process known as DNA loop extrusion. In rapidly dividing bacterial cells, the process of separating sister chromatids occurs concomitantly with ongoing transcription. How transcription interferes with the condensin loop-extrusion process is largely unexplored, but recent experiments have shown that sites of high transcription may directionally affect condensin loop extrusion. We quantitatively investigate different mechanisms of interaction between condensin and elongating RNA polymerases (RNAPs) and find that RNAPs are likely steric barriers that can push and interact with condensins. Supported by chromosome conformation capture and chromatin immunoprecipitation for cells after transcription inhibition and RNAP degradation, we argue that translocating condensins must bypass transcribing RNAPs within ∼1 to 2 s of an encounter at rRNA genes and within ∼10 s at protein-coding genes. Thus, while individual RNAPs have little effect on the progress of loop extrusion, long, highly transcribed operons can significantly impede the extrusion process. Our data and quantitative models further suggest that bacterial condensin loop extrusion occurs by 2 independent, uncoupled motor activities; the motors translocate on DNA in opposing directions and function together to enlarge chromosomal loops, each independently bypassing steric barriers in their path. Our study provides a quantitative link between transcription and 3D genome organization and proposes a mechanism of interactions between SMC complexes and elongating transcription machinery relevant from bacteria to higher eukaryotes.
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“although RNAP can act as a moving barrier that significantly impedes SMC extrusion at highly transcribed operons.60”
From Bringing the genetically minimal cell to life on a computer in 4D (2026) · cites this paper as [60]
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Citations
Cites
Formation of chromosomal domains by loop extrusion
Fudenberg, G., Imakaev, M., Lu, C., Goloborodko, A., Abdennur, N., & Mirny, L. A. (2016) · Cell Reports · doi:10.1016/j.celrep.2016.04.085 · Cited by 2,003
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
Formation of Chromosomal Domains by Loop Extrusion
Fudenberg, G., Imakaev, M., Lu, C. W., Goloborodko, A., Abdennur, N. A., & Mirny, L. (2015) · bioRxiv · doi:10.1101/024620 · Cited by 1,858
Self-citationSanborn, A. L., Rao, S. S. P., Huang, S.-C., Durand, N. C., Huntley, M. H., Jewett, A. I., Bochkov, I. D., Chinnappan, D., Cutkosky, A., Li, J., et al. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1518552112 · Cited by 1,730 · cited 2×
“, trapped at transcription start sites by rifampicin) are directional barriers to condensin translocation, akin to CTCFs as directional barriers to cohesin in eukaryotes (4), or an RNAPindependent mechanism generates the “baseline asymmetry” of chromosome juxtaposition at loci outside of rRNA operons.”
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 · cited 6×
“One can hypothesize that RNAP has a directional effect on condensin translocation, like the effect of CTCF proteins on cohesin in eukaryotes (4).”
InfluentialSelf-citation遺伝子の分子生物学 = Molecular biology of the gene
Watson, J. D., Hopkins, N., Roberts, J. W., Steitz, J., Weiner, A., 松原, 謙., 中村, 桂., 三浦, 謹., 今成, 啓., 菊池, 京., et al. (1970) · doi:10.1016/0378-1119(88)90351-4 · Cited by 1,486 · cited 2×
“…do not have coupled transcription and translation, there is transcription-coupled splicing, and the spliceosome is of similar size to the ribosome (58), making the whole complex of a globular diameter > 70 nm. Future experiments will be needed to test whether SMCs can bypass steric barriers…”
InfluentialCodling, E. A., Plank, M. J., & Benhamou, S. (2008) · Journal of The Royal Society Interface · doi:10.1098/rsif.2008.0014 · Cited by 1,482 · cited 2×
“Rudner [2], Leonid A.”
BackgroundReal-Time Kinetics of Gene Activity in Individual Bacteria
Golding, I., Paulsson, J., Zawilski, S. M., & Cox, E. C. (2005) · Cell · doi:10.1016/j.cell.2005.09.031 · Cited by 1,468 · cited 1×
“tclockwise(i) = tclockwise,operon(i) + tclockwise,rRNA(i) + tclockwise,tRNA(i) (3)”
Iterative correction of Hi-C data reveals hallmarks of chromosome organization
Imakaev, M., Fudenberg, G., McCord, R. P., Naumova, N., Goloborodko, A., Lajoie, B. R., Dekker, J., & Mirny, L. A. (2012) · Nature Methods · doi:10.1038/nmeth.2148 · Cited by 1,423 · cited 4×
“4A, right), when a translocating condensin encounters a transcribing RNAP, condensin is stalled and pushed back to the transcription termination site (condensin has a very low stall force measured in vitro (10) compared to RNAP (50)).”
BackgroundInfluentialSelf-citationTwo 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
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Items 101–122 of 122
Emerging Roles for Transcription Factors During Mitosis
Flashner, S. P., & Azizkhan‐Clifford, J. (2025) · Cells · doi:10.3390/cells14040263 · Cited by 2
“Further, transcription slows condensin translocation and loop extrusion in bacteria and yeast [118,119].”
SMC translocation is unaffected by an excess of nucleoid associated proteins in vivo
Ren, Z., Way, L. E., & Wang, X. (2025) · Scientific Reports · doi:10.1038/s41598-025-86946-4 · Cited by 3
“For instance, simulations on Hi-C results suggested that RNA polymerases slow down B. subtilis SMC complex and human cohesin in vivo 27,61 ; the human minichromosome maintenance (MCM) complex was found to impede cohesin movement both in vivo and in vitro 62 ; single-molecule experiments showed that…”
Self-citationUnique territorial and compartmental organization of chromosomes in the holocentric silkmothPreprint
Gil, J., Navarrete, E., Rosin, L. F., Chowdhury, N., Abraham, S., Cornilleau, G., Lei, E. P., Mozziconacci, J., Mirny, L., Muller, H., et al. (2024) · Research Square · doi:10.21203/rs.3.rs-4732646/v1 · Cited by 2
“The presence of dots, stripes, and nested domains with insulation indicate the presence of extrusion barriers, similar to CTCF in vertebrate systems 75 , RNA and DNA polymerases 76,83 , and MCM complexes 84 .”
BackgroundSelf-citationZhegalova, I., Ulianov, S., Galitsyna, A., Pletenev, I., Tsoy, O., Luzhin, A. V., Vasiluev, P., Bulavko, E. S., Ivankov, D., Gavrilov, A., et al. (2024) · bioRxiv · doi:10.1101/2024.06.12.598618 · Cited by 2
“Finally, recent studies across various organisms, including bacteria 32 , dinoflagellates 33,34 , fission and budding yeast 30,35,36 , and mammals 37,38 , suggest that transcribed genes can be barriers to loop extrusion.”
BackgroundMethodInfluentialA functional overlap between actively transcribed genes and chromatin insulator elements
Cornell, L., Harrold, C. L., Holliman, S., Tsang, F. H., Gosden, M. E., Hanssen, L. E., Stolper, R. J., Downes, D. J., Biggs, D., Preece, C., et al. (2026) · The EMBO Journal · doi:10.1038/s44318-026-00730-2 · Cited by 3
“In the tracking model, highly transcribed genes may form a partial barrier to loop extrusion, due to the accumulation of large amounts of transcriptional machinery and regulatory factors (Brandão et al, 2019).”
Endless forms – how genome organization underlies evolution and development
Edwards, A. N., & Finn, E. H. (2026) · Journal of Cell Science · doi:10.1242/jcs.264059 · Cited by 1
Unique territorial and compartmental organization of chromosomes in the holocentric silkworm
Gil, J., Navarrete, E., Hockens, C. B., Chowdhury, N., Abraham, S., Cornilleau, G., Lei, E. P., Mozziconacci, J., Banigan, E. J., Rosin, L. F., et al. (2026) · The EMBO Journal · doi:10.1038/s44318-026-00694-3 · Cited by 7
“…SMC complexes in yeast (Lengronne et al, 2004; Gullerova and Proudfoot, 2008; Glynn et al, 2004; Bausch et al, 2007) and bacteria (Tran et al, 2017; Brandão et al, 2019) were foundational for subsequent studies explaining the nature of SMC-RNA Polymerase interactions in mammals (Busslinger et al,…”
Self-citationTsukamoto, S., & Mofrad, M. R. K. (2025) · Journal of Chemical Physics · doi:10.1063/5.0232328 · Cited by 1
Multicontact statistics distinguish models of chromosome organization
Harju, J., Messelink, J. J. B., & Broedersz, C. P. (2025) · Physical review. E · doi:10.1103/physreve.111.014403 · Cited by 1
“Loop-extruder simulations [27, 7] are conducted by updating the locations of moving condensins on a polymer, and letting the polymer configuration relax given the constraints.”
RNA Pol II antagonises mitotic chromatin folding and chromosome segregation by condensinPreprint
Lebreton, J., Colin, L., Chatre, E., & Bernard, P. (2023) · bioRxiv · doi:10.1101/2023.08.08.552486 · Cited by 1
Physical models for chromosome organization to predict multi-contact statisticsPreprint
Harju, J., Messelink, J. J. B., & Broedersz, C. P. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.05.17.492279 · Cited by 1
Chervinskaya, A., Gelfand, M. S., Metzler, R., & Polovnikov, K. (2026) · bioRxiv · doi:10.64898/2026.08.20.745948
“CTCF is the best-characterized sequence-specific barrier to cohesin, with blocking strongly dependent on CTCF orientation [3–8], but extrusion is also affected by other chromatin-bound proteins and by collisions with neighbouring cohesins [9, 10].”
Al-Kurdi, B., Hernandez, J. A., Lewis, A. H., Snyder, L. M., Markus, S. M., & Swygert, S. G. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.07.10.737861
Chromosome segregation in a minimal bacterial cell driven by SMC protein complexes
Maytin, A. K., Gilbert, B. R., & Luthey-Schulten, Z. (2026) · Protein Science · doi:10.1002/pro.70604
Chen, L.-Y., Zhang, Z.-Q., Wang, Z.-H., Yu, X.-C., & Zhang, J.-J. (2026) · Journal of Theoretical Biology · doi:10.1016/j.jtbi.2026.112472
The Role of Spatial Organization of the Genome in the Regulation of Transcription
Razin, S. V. (2025) · Russian Journal of Genetics · doi:10.1134/s1022795425700917
“RNA polymerase or liquid-phase condensates assembled on promoters also represent a barrier to moving extrusion complexes [37, 60–62].”
Unique territorial and compartmental organization of chromosomes in the holocentric silkworm
Gil, J., Navarrete, E., Hockens, C., Chowdhury, N., Abraham, S., Cornilleau, G., Lei, E. P., Mozziconacci, J., Banigan, E., Rosin, L. F., et al. (2023) · bioRxiv · doi:10.1101/2023.09.14.557757
“For example, observations of SMC complexes in yeast 52–55 and bacteria 56,57 were foundational for subsequent studies explaining the nature of SMC-RNA Polymerase interactions in mammals 58,59 .”
Self-citationGhosh, D., Evans, B. A., & Vivekanandan, P. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.07.11.548559
Liang, Z., Zhao, L.-J., Ye, A. Y., Lin, S. G., Zhang, Y., Guo, C.-G., Dai, H.-Q., Ba, Z.-Q., & Alt, F. (2023) · bioRxiv · doi:10.1101/2023.04.21.537836
An SNF2 helicase-like protein links mitotic transcription termination to sister chromatid resolutionPreprint
Carmo, C., Coelho, J., Silva, R. D., Tavares, A., Boavida, A., Gaetani, P., Martinho, R., & Oliveira, R. A. (2022) · bioRxiv · doi:10.1101/2022.11.21.517340
“Genotype of the fly strains used in this study Microinjections Embryos were prepared for imaging and microinjected as previously described (Carmo et al, 2019).”
MethodBækkedal, C. S., Kahlke, T., & Haugen, P. (2020) · doi:10.21203/rs.3.rs-34687/v1
Abramo, K. (2020) · The Journal of the American Medical Association (JAMA) Network (American Medical Association) · doi:10.13028/a9gd-gw44
“Different organisms have revealed different dependencies on transcription and the formation of TADs, suggesting that domains investigated could be formed by distinct mechanisms (Davidson et al., 2016; Ulianov et al., 2016; Busslinger et al., 2017; Brandao et al., 2019; Rowley et al., 2019).”
Background
Metadata
- Authors
- Brandão, H. B., Paul, P., van den Berg, A. A., Rudner, D. Z., Wang, X., & Mirny, L. A.
- Affiliations
- Harvard University (US)
- Indiana University Bloomington (US)
- Massachusetts Institute of Technology (US)
- Corresponding author
- Wang, Xindan
- Mirny, Leonid A.
- Venue
- Proceedings of the National Academy of Sciences
- Publisher
- National Academy of Sciences
- Published
- 2019-09-23
- Volume
- 116
- Issue
- 41
- Pages
- 20489-20499
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- PMC
- PMC6789630
- OpenAlex
- W2975167630
- Cited by
- 143
- References
- 92
- Citations by year
- 2026: 15 · 2025: 20 · 2024: 14 · 2023: 28 · 2022: 23 · 2021: 21 · 2020: 14 · 2019: 7
- FWCI
- 5.38
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Proceedings of the National Academy of Sciences (publishedVersion, cc-by-nc-nd)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- PubMed Central (publishedVersion, cc-by-nc-nd)
- PubMed (publishedVersion)
- DSpace@MIT (Massachusetts Institute of Technology) (submittedVersion, cc-by-nc)
- Funders
- HHS | National Institutes of Health (GM086466, GM073831, GM114190)
- IU | Indiana University Bloomington (Start-up funds)
- Gouvernement du Canada | Natural Sciences and Engineering Research Council of Canada (PGS-D)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA Repair Mechanisms
- Keywords
- condensin, DNA loop extrusion, RNA polymerase, sister chromatid separation, SMC complex, steric barrier, transcription, 3D genome organization, ribosomal DNA, operon, chromosome conformation capture, chromatin immunoprecipitation
- MeSH terms
- Adenosine Triphosphatases, Bacillus subtilis, Bacterial Proteins, Chromosomes, Bacterial, DNA-Binding Proteins, Protein Binding, DNA-Directed RNA Polymerases, RNA, Ribosomal, Transcription, Genetic, Genome, Bacterial, Multiprotein Complexes
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