CoChat
Sign Up
Cited by 66Genomics and Chromatin DynamicsChromatin Remodeling and CancerProtein Structure and Dynamics

Structural elements promote architectural stripe formation and facilitate ultra-long-range gene regulation at a human disease locus

Open access
Chen, Liang-Fu, Long, Hannah Katherine, Park, Minhee, Swigut, Tomek, Boettiger, Alistair Nicol, Wysocka, Joanna·2023·Molecular Cell
DOI 10.1016/j.molcel.2023.03.009PMC PMC13507663

Published version of a preprint

Open this paper in CoChat — free account

Abstract

Summary Enhancer clusters overlapping disease-associated mutations in Pierre Robin sequence (PRS) patients regulate SOX9 expression at genomic distances over 1.25 megabases. We applied optical reconstruction of chromatin architecture (ORCA) imaging to trace 3D locus topology during PRS-enhancer activation. While we observed pronounced changes in locus topology between cell-types, analysis of single chromatin fiber traces revealed that these ensemble-average differences arise not from the presence of cell-type unique conformations, but through changes in frequency of commonly sampled topologies. We further identified two CTCF-bound elements, internal to the SOX9 topologically associating domain, which are positioned near its 3D geometric center and bridge enhancer-promoter contacts in a series of chromatin loops. Ablation of these elements results in diminished SOX9 expression and altered domain-wide contacts. Polymer models with uniform loading across the domain and frequent cohesin collisions recapitulate this multiloop, centrally clustered geometry, suggesting a mechanism for gene regulation over ultralong ranges. Four short bullet points that convey the key message of the paper SOX9 domain topology dynamically changes during a developmental transition Structural elements promote TAD-wide interactions, stripe formation and transcription Structural elements are CTCF-dependent and situated centrally in the 3D TAD structure Polymer simulations of multi-loop model best recapitulate topological features

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.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1016/j.molcel.2023.03.009

Cites

16 of 16 references verified0 citation errors · 0 not checkable

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.

A few free checks a day · papers already verified open instantly · results are public

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 presence of so-called stripes or flames on Hi-C maps indicates that unidirectional extrusion from an enhancer is quite common.

    “The presence of so-called stripes or flames on Hi-C maps indicates that unidirectional extrusion from an enhancer is quite common [116,117,118].”

    From Enhancer Function in the 3D Genome (2023) · cites this paper as [118]

    In Results (“A multi-loop model better explains…”; page not provided), the paper says both targeted-loading and random-loading models produce stripes, so stripes do not establish extrusion from an enhancer. The Discussion favors random cohesin loading between loop barriers over the enhancer-loading reel-in model at the SOX9 locus; it does not present enhancer-origin extrusion as common. (LLM, conf=0.87)

    Checked by a reasoning model — may be wrong.

    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

Flagged first, then by citations

Research works printed but not linked: 63

  1. [1]Furlong E.E.M. Levine M. Developmental enhancers and chromosome topology Science 361 2018 1341 1345 10.1126/science.aau0320 30262496 PMC6986801 · DOI · Paper page
  2. [2]Long H.K. Prescott S.L. Wysocka J. Ever-changing landscapes: transcriptional enhancers in development and evolution Cell 167 2016 1170 1187 10.1016/j.cell.2016.09.018 27863239 PMC5123704 · DOI · Paper page
  3. [3]Dixon J.R. Selvaraj S. Yue F. Kim A. Li Y. Shen Y. Hu M. Liu J.S. Ren B. Topological domains in mammalian genomes identified by analysis of chromatin interactions Nature 485 2012 376 380 10.1038/nature11082 22495300 PMC3356448 · DOI · Paper page
  4. [5]Hsieh T.-H.S. Cattoglio C. Slobodyanyuk E. Hansen A.S. Rando O.J. Tjian R. Darzacq X. Resolving the 3D landscape of transcription-linked mammalian chromatin folding Mol. Cell 78 2020 10.1016/j.molcel.2020.03.002 539–553.e8 PMC7703524 32213323 · DOI · Paper page
  5. [7]Bintu B. Mateo L.J. Su J.H. Sinnott-Armstrong N.A. Parker M. Kinrot S. Yamaya K. Boettiger A.N. Zhuang X. Super-resolution chromatin tracing reveals domains and cooperative interactions in single cells Science 362 2018 eaau1783 10.1126/science.aau1783 30361340 PMC6535145 · DOI · Paper page
  6. [8]Cheng R.R. Contessoto V.G. Lieberman Aiden E. Wolynes P.G. Di Pierro M. Onuchic J.N. Exploring chromosomal structural heterogeneity across multiple cell lines eLife 9 2020 e60312 10.7554/eLife.60312 33047670 PMC7593087 · DOI
  7. [9]Finn E.H. Pegoraro G. Brandão H.B. Valton A.L. Oomen M.E. Dekker J. Mirny L. Misteli T. Extensive heterogeneity and intrinsic variation in spatial genome organization Cell 176 2019 10.1016/j.cell.2019.01.020 1502–1515.e10 PMC6408223 30799036 · DOI · Paper page
  8. [12]Takei Y. Yun J. Zheng S. Ollikainen N. Pierson N. White J. Shah S. Thomassie J. Suo S. Eng C.-H.L. Integrated spatial genomics reveals global architecture of single nuclei Nature 590 2021 344 350 10.1038/s41586-020-03126-2 33505024 PMC7878433 · DOI
  9. [13]Welch L.R. Baugher C. Zhang Y. Davis T. Marzluff W.F. Welch J.D. Pombo A. Single-cell analysis of the 3D topologies of genomic loci using genome architecture mapping 2020 10.1101/2020.02.10.941047 · DOI
  10. [14]Anderson E. Devenney P.S. Hill R.E. Lettice L.A. Mapping the Shh long-range regulatory domain Development 141 2014 3934 3943 10.1242/dev.108480 25252942 PMC4197689 · DOI
  11. [15]Symmons O. Uslu V.V. Tsujimura T. Ruf S. Nassari S. Schwarzer W. Ettwiller L. Spitz F. Functional and topological characteristics of mammalian regulatory domains Genome Res. 24 2014 390 400 10.1101/gr.163519.113 24398455 PMC3941104 · DOI · Paper page
  12. [16]Bruijn de S.E. Fiorentino A. Ottaviani D. Fanucchi S. Melo U.S. Corral-Serrano J.C. Mulders T. Georgiou M. Rivolta C. Pontikos N. Structural variants create new topological-associated domains and ectopic retinal enhancer-gene contact in dominant retinitis pigmentosa Am. J. Hum. Genet. 107 2020 802 814 10.1016/j.ajhg.2020.09.002 33022222 PMC7675008 · DOI
  13. [18]Laugsch M. Bartusel M. Rehimi R. Alirzayeva H. Karaolidou A. Crispatzu G. Zentis P. Nikolic M. Bleckwehl T. Kolovos P. Modeling the pathological long-range regulatory effects of human structural variation with patient-specific hiPSCs Cell Stem Cell 24 2019 10.1016/j.stem.2019.03.004 736–752.e12 30982769 · DOI
  14. [24]Nora E.P. Caccianini L. Fudenberg G. So K. Kameswaran V. Nagle A. Uebersohn A. Hajj B. Saux A.L. Coulon A. Molecular basis of CTCF binding polarity in genome folding Nat. Commun. 11 2020 5612 10.1038/s41467-020-19283-x 33154377 PMC7645679 · DOI
  15. [25]Wutz G. Ladurner R. St Hilaire B.G. Stocsits R.R. Nagasaka K. Pignard B. Sanborn A. Tang W. Várnai C. Ivanov M.P. ESCO1 and CTCF enable formation of long chromatin loops by protecting cohesinSTAG1 from WAPL eLife 9 2020 e52091 10.7554/eLife.52091 32065581 PMC7054000 · DOI
  16. [28]Dowen J.M. Fan Z.P. Hnisz D. Ren G. Abraham B.J. Zhang L.N. Weintraub A.S. Schujiers J. Lee T.I. Zhao K. Young R.A. Control of cell identity genes occurs in insulated neighborhoods in mammalian chromosomes Cell 159 2014 374 387 10.1016/j.cell.2014.09.030 25303531 PMC4197132 · DOI · Paper page
  17. [29]Kubo N. Ishii H. Xiong X. Bianco S. Meitinger F. Hu R. Hocker J.D. Conte M. Gorkin D. Yu M. Promoter-proximal CTCF binding promotes distal enhancer-dependent gene activation Nat. Struct. Mol. Biol. 28 2021 152 161 10.1038/s41594-020-00539-5 33398174 PMC7913465 · DOI · Paper page
  18. [30]Schuijers J. Manteiga J.C. Weintraub A.S. Day D.S. Zamudio A.V. Hnisz D. Lee T.I. Young R.A. Transcriptional dysregulation of MYC reveals common enhancer-docking mechanism Cell Rep. 23 2018 349 360 10.1016/j.celrep.2018.03.056 29641996 PMC5929158 · DOI
  19. [31]Benko S. Fantes J.A. Amiel J. Kleinjan D.J. Thomas S. Ramsay J. Jamshidi N. Essafi A. Heaney S. Gordon C.T. Highly conserved non-coding elements on either side of SOX9 associated with Pierre Robin sequence Nat. Genet. 41 2009 359 364 10.1038/ng.329 19234473 · DOI
  20. [32]Croft B. Ohnesorg T. Hewitt J. Bowles J. Quinn A. Tan J. Corbin V. Pelosi E. van den Bergen J. Sreenivasan R. Human sex reversal is caused by duplication or deletion of core enhancers upstream of SOX9 Nat. Commun. 9 2018 5319 10.1038/s41467-018-07784-9 30552336 PMC6293998 · DOI
  21. [33]Gonen N. Quinn A. O’Neill H.C. Koopman P. Lovell-Badge R. Normal levels of Sox9 expression in the developing mouse testis depend on the TES/TESCO enhancer, but this does not act alone PLoS Genet. 13 2017 e1006520 10.1371/journal.pgen.1006520 28045957 PMC5207396 · DOI
  22. [34]Kurth I. Klopocki E. Stricker S. van Oosterwijk J. Vanek S. Altmann J. Santos H.G. van Harssel J.J.T. de Ravel T. Wilkie A.O.M. Duplications of noncoding elements 5′ of SOX9 are associated with brachydactyly-anonychia Nat. Genet. 41 2009 862 863 10.1038/ng0809-862 19639023 · DOI
  23. [35]Yao B. Wang Q. Liu C.F. Bhattaram P. Li W. Mead T.J. Crish J.F. Lefebvre V. The SOX9 upstream region prone to chromosomal aberrations causing campomelic dysplasia contains multiple cartilage enhancers Nucleic Acids Res. 43 2015 5394 5408 10.1093/nar/gkv426 25940622 PMC4477657 · DOI
  24. [36]Long H.K. Osterwalder M. Welsh I.C. Hansen K. Davies J.O.J. Liu Y.E. Koska M. Adams A.T. Aho R. Arora N. Loss of extreme long-range enhancers in human neural crest drives a craniofacial disorder Cell Stem Cell 27 2020 765 783.e14 10.1016/j.stem.2020.09.001 32991838 PMC7655526 · DOI
  25. [37]Logjes R.J.H. Breugem C.C. Van Haaften G. Paes E.C. Sperber G.H. van den Boogaard M.-J.H. Farlie P.G. The ontogeny of Robin sequence Am. J. Med. Genet. A 176 2018 1349 1368 10.1002/ajmg.a.38718 29696787 · DOI
  26. [38]Bronner M.E. LeDouarin N.M. Development and evolution of the neural crest: an overview Dev. Biol. 366 2012 2 9 10.1016/j.ydbio.2011.12.042 22230617 PMC3351559 · DOI
  27. [40]Akgol Oksuz B. Yang L. Abraham S. Venev S.V. Krietenstein N. Parsi K.M. Ozadam H. Oomen M.E. Nand A. Mao H. Systematic evaluation of chromosome conformation capture assays Nat. Methods 18 2021 1046 1055 10.1038/s41592-021-01248-7 34480151 PMC8446342 · DOI
  28. [41]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. Aiden E.L. A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping Cell 159 2014 1665 1680 10.1016/j.cell.2014.11.021 25497547 PMC5635824 · DOI · Paper page
  29. [42]Amarillo I.E. Dipple K.M. Quintero-Rivera F. Familial microdeletion of 17q24.3 upstream of SOX9 is associated with isolated Pierre Robin sequence due to position effect Am. J. Med. Genet. A 161A 2013 1167 1172 10.1002/ajmg.a.35847 23532965 · DOI
  30. [43]Gordon C.T. Attanasio C. Bhatia S. Benko S. Ansari M. Tan T.Y. Munnich A. Pennacchio L.A. Abadie V. Temple I.K. Identification of novel craniofacial regulatory domains located far upstream of SOX9 and disrupted in Pierre Robin sequence Hum. Mutat. 35 2014 1011 1020 10.1002/humu.22606 24934569 PMC4389788 · DOI
  31. [44]Blayney J. Francis H. Camellato B. Mitchell L. Stolper R. Boeke J. Higgs D. Kassouf M. Super-enhancers require a combination of classical enhancers and novel facilitator elements to drive high levels of gene expression 2022 10.1101/2022.06.20.496856 · DOI
  32. [45]Batut P.J. Bing X.Y. Sisco Z. Raimundo J. Levo M. Levine M.S. Genome organization controls transcriptional dynamics during development Science 375 2022 566 570 10.1126/science.abi7178 35113722 PMC10368186 · DOI
  33. [46]Barrington C. Georgopoulou D. Pezic D. Varsally W. Herrero J. Hadjur S. Enhancer accessibility and CTCF occupancy underlie asymmetric TAD architecture and cell type specific genome topology Nat. Commun. 10 2019 2908 10.1038/s41467-019-10725-9 31266948 PMC6606583 · DOI · Paper page
  34. [47]Kraft K. Magg A. Heinrich V. Riemenschneider C. Schöpflin R. Markowski J. Ibrahim D.M. Acuna-Hidalgo R. Despang A. Andrey G. Serial genomic inversions induce tissue-specific architectural stripes, gene misexpression and congenital malformations Nat. Cell Biol. 21 2019 305 310 10.1038/s41556-019-0273-x 30742094 · DOI
  35. [48]Brackey C.A. Marenduzzo D. Gilbert N. Mechanistic modeling of chromatin folding to understand function Nat. Methods 17 2020 767 775 10.1038/s41592-020-0852-6 32514111 · DOI
  36. [49]Conte M. Irani E. Chiariello A.M. Abraham A. Bianco S. Esposito A. Nicodemi M. Loop-extrusion and polymer phase-separation can co-exist at the single-molecule level to shape chromatin folding Nat. Commun. 13 2022 4070 10.1038/s41467-022-31856-6 35831310 PMC9279381 · DOI
  37. [50]Mirny L.A. Imakaev M. Abdennur N. Two major mechanisms of chromosome organization Curr. Opin. Cell Biol. 58 2019 142 152 10.1016/j.ceb.2019.05.001 31228682 PMC6800258 · DOI
  38. [51]Valton A.-L. Venev S.V. Mair B. Khokhar E. Tong A.H.Y. Usaj M. Chan K.S.K. Pai A.A. Moffat J. Dekker J. A cohesin traffic pattern genetically linked to gene regulation Nat. Struct. Mol. Biol. 29 2021 1239 1251 10.1101/2021.07.29.454218 PMC10228515 36482254 · DOI
  39. [54]Phillips-Cremins J.E. Sauria M.E.G. Sanyal A. Gerasimova T.I. Lajoie B.R. Bell J.S.K. Ong C.-T. Hookway T.A. Guo C. Sun Y. Architectural protein subclasses shape 3D organization of genomes during lineage commitment Cell 153 2013 1281 1295 10.1016/j.cell.2013.04.053 23706625 PMC3712340 · DOI · Paper page
  40. [55]Smith E.M. Lajoie B.R. Jain G. Dekker J. Invariant TAD boundaries constrain cell-type-specific looping interactions between promoters and distal elements around the CFTR locus Am. J. Hum. Genet. 98 2016 185 201 10.1016/j.ajhg.2015.12.002 26748519 PMC4716690 · DOI
  41. [56]Hafner A. Park M. Berger S.E. Nora E.P. Boettiger A.N. Loop stacking organizes genome folding from TADs to chromosomes 2022 10.1101/2022.07.13.499982 PMC10167645 37146570 · DOI
  42. [57]Banigan E.J. Tang W. Berg van den A.A. Stocsits R.R. Wutz G. Brandão H.B. Busslinger G.A. Peters J.-M. Mirny L.A. Transcription shapes 3D chromatin organization by interacting with loop extrusion 2022 10.1101/2022.01.07.475367 PMC10089175 36897969 · DOI
  43. [59]Gabriele M. Brandão H.B. Grosse-Holz S. Jha A. Dailey G.M. Cattoglio C. Hsieh T.-H.S. Mirny L. Zechner C. Hansen A.S. Dynamics of CTCF- and cohesin-mediated chromatin looping revealed by live-cell imaging Science 376 2022 496 501 10.1126/science.abn6583 35420890 PMC9069445 · DOI · Paper page
  44. [60]Gassler J. Brandão H.B. Imakaev M. Flyamer I.M. Ladstätter S. Bickmore W.A. Peters J.M. Mirny L.A. Tachibana K. A mechanism of cohesin-dependent loop extrusion organizes zygotic genome architecture EMBO J. 36 2017 3600 3618 10.15252/embj.201798083 29217590 PMC5730859 · DOI
  45. [61]Ortabozkoyun H. Huang P.Y. Cho H. Narendra V. LeRoy G. Gonzalez-Buendia E. Skok J.A. Tsirigos A. Mazzoni E.O. Reinberg D. CRISPR and biochemical screens identify MAZ as a cofactor in CTCF-mediated insulation at Hox clusters Nat. Genet. 54 2022 202 212 10.1038/s41588-021-01008-5 35145304 PMC8837555 · DOI
  46. [62]Annunziatella C. Chiariello A.M. Esposito A. Bianco S. Fiorillo L. Nicodemi M. Molecular Dynamics simulations of the Strings and Binders Switch model of chromatin Methods 142 2018 81 88 10.1016/j.ymeth.2018.02.024 29522804 · DOI
  47. [63]Prescott S.L. Srinivasan R. Marchetto M.C. Grishina I. Narvaiza I. Selleri L. Gage F.H. Swigut T. Wysocka J. Enhancer divergence and cis-regulatory evolution in the human and chimp neural crest Cell 163 2015 68 83 10.1016/j.cell.2015.08.036 26365491 PMC4848043 · DOI
  48. [64]Adams D.C. Otárola-Castillo E. Geomorph: an R package for the collection and analysis of geometric morphometric shape data Methods Ecol. Evol. 4 2013 393 399 10.1111/2041-210X.12035 · DOI
  49. [65]Jiang H. Lei R. Ding S.W. Zhu S. Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads BMC Bioinformatics 15 2014 182 10.1186/1471-2105-15-182 24925680 PMC4074385 · DOI
  50. [66]Langmead B. Salzberg S.L. Fast gapped-read alignment with Bowtie 2 Nat. Methods 9 2012 357 359 10.1038/nmeth.1923 22388286 PMC3322381 · DOI · Paper page
  51. [67]Quinlan A.R. Hall I.M. BEDTools: a flexible suite of utilities for comparing genomic features Bioinformatics 26 2010 841 842 10.1093/bioinformatics/btq033 20110278 PMC2832824 · DOI · Paper page
  52. [68]Kent W.J. Zweig A.S. Barber G. Hinrichs A.S. Karolchik D. BigWig and BigBed: enabling browsing of large distributed datasets Bioinformatics 26 2010 2204 2207 10.1093/bioinformatics/btq351 20639541 PMC2922891 · DOI
  53. [69]Zhang Y. Liu T. Meyer C.A. Eeckhoute J. Johnson D.S. Bernstein B.E. Nusbaum C. Myers R.M. Brown M. Li W. Liu X.S. Model-based analysis of ChIP-seq (MACS) Genome Biol. 9 2008 R137 10.1186/gb-2008-9-9-r137 18798982 PMC2592715 · DOI · Paper page
  54. [70]Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads EMBnet.journal 17 2011 10 12 10.14806/ej.17.1.200 · DOI · Paper page
  55. [71]Liao Y. Smyth G.K. Shi W. FeatureCounts: an efficient general purpose program for assigning sequence reads to genomic features Bioinformatics 30 2014 923 930 10.1093/bioinformatics/btt656 24227677 · DOI · Paper page
  56. [72]Liu T. Ortiz J.A. Taing L. Meyer C.A. Lee B. Zhang Y. Shin H. Wong S.S. Ma J. Lei Y. Cistrome: an integrative platform for transcriptional regulation studies Genome Biol. 12 2011 R83 10.1186/gb-2011-12-8-r83 21859476 PMC3245621 · DOI
  57. [73]Wagih O. Ggseqlogo: a versatile R package for drawing sequence logos Bioinformatics 33 2017 3645 3647 10.1093/bioinformatics/btx469 29036507 · DOI
  58. [74]Wickham H. ggplot2: Elegant Graphics for Data Analysis 2016 Springer-Verl
  59. [75]Kent W.J. Sugnet C.W. Furey T.S. Roskin K.M. Pringle T.H. Zahler A.M. Haussler D. The human genome browser at UCSC Genome Res. 12 2002 996 1006 10.1101/gr.229102 12045153 PMC186604 · DOI · Paper page
  60. [76]Li H. Handsaker B. Wysoker A. Fennell T. Ruan J. Homer N. Marth G. Abecasis G. Durbin R. 1000 Genome Project Data Processing Subgroup The sequence alignment/map format and SAMtools Bioinformatics 25 2009 2078 2079 10.1093/bioinformatics/btp352 19505943 PMC2723002 · DOI · Paper page
  61. [77]Mateo L.J. Sinnott-Armstrong N. Boettiger A.N. Tracing DNA paths and RNA profiles in cultured cells and tissues with ORCA Nat. Protoc. 16 2021 1647 1713 10.1038/s41596-020-00478-x 33619390 PMC8525907 · DOI
  62. [78]Nuebler J. Fudenberg G. Imakaev M. Abdennur N. Mirny L.A. Chromatin organization by an interplay of loop extrusion and compartmental segregation Proc. Natl. Acad. Sci. USA 115 2018 E6697 E6706 10.1073/pnas.1717730115 29967174 PMC6055145 · DOI
  63. [79]Eastman P. Swails J. Chodera J.D. McGibbon R.T. Zhao Y. Beauchamp K.A. Wang L.P. Simmonett A.C. Harrigan M.P. Stern C.D. OpenMM 7: rapid development of high performance algorithms for molecular dynamics PLoS Comput. Biol. 13 2017 e1005659 10.1371/journal.pcbi.1005659 28746339 PMC5549999 · DOI · Paper page

Cited by

Sorted by citations

Authors
Chen, L.-F., Long, H. K., Park, M., Swigut, T., Boettiger, A. N., & Wysocka, J.
Affiliations
  • Stanford Medicine (US)
  • Howard Hughes Medical Institute (US)
Corresponding author
  • Boettiger, Alistair Nicol
  • Wysocka, Joanna
ORCID
Venue
Molecular Cell
Publisher
Elsevier BV
Published
2023-05
Volume
83
Issue
9
Pages
1446-1461.e6
ISSN
1097-2765 (ISSN-L)
DOI
10.1016/j.molcel.2023.03.009
PMC
PMC13507663
OpenAlex
W4361283111
Cited by
66
References
16
Citations by year
2026: 12 · 2025: 20 · 2024: 23 · 2023: 11
FWCI
5.88
Type
journal article
Language
en
Open access
Licence
Locations
  • Molecular Cell (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
  • PubMed (publishedVersion)
  • PubMed Central (publishedVersion, cc-by)
  • Edinburgh Research Explorer (University of Edinburgh) (submittedVersion, cc-by)
Funders
  • HHMI (R35 GM131757, U01 DK127419)
  • Damon Runyon Cancer Research Foundation
  • Wellcome Trust (106051/Z/14/Z)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chromatin Remodeling and Cancer
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
Keywords
3D genome organization, SOX9, Pierre Robin sequence, enhancer clusters, topologically associating domains, chromatin looping, enhancer-promoter interactions, cohesin, polymer models
MeSH terms
CCCTC-Binding Factor, Chromatin, Enhancer Elements, Genetic, Gene Expression Regulation, Humans, Promoter Regions, Genetic, Regulatory Sequences, Nucleic Acid, Genome, Cell Cycle Proteins

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