ManuscriptsubmittedtoeLife Super resolution imaging of a 1 distinct chromatin loop in human 2 lymphoblastoid cells 3 Jacqueline Jufen Zhu 1,2* , Zofia Parteka 3,4* , Byoungkoo Lee 1 , Przemyslaw Szalaj 3,5,6 , 4 Ping Wang 1 , Karolina Jodkowska 3 , Jesse Aaron 7 , Teng-Leong Chew 7 , Dariusz 5 Plewczynski 3,4† , Yijun Ruan 1,2,8† 6 *For correspondence: d.plewczynski@cent.uw.edu.pl (DMP); Yijun.Ruan@jax.org (YR) * Theseauthorscontributedequally tothiswork † Theseauthorsalsocontributed equallytothiswork Present address: § Department, Institute,Country; ¶ Department, Institute,Country 1 TheJacksonLaboratoryforGenomicMedicine,10DiscoveryDrive,Farmington,CT 7 06030,USA; 2 DepartmentofGeneticsandGenomeSciences,UniversityofConnecticut 8 HealthCenter,400FarmingtonAvenue,Farmington,CT06030,USA; 3 CentreofNew 9 Technologies,UniversityofWarsaw,S.Banacha2c,02-097Warsaw,Poland; 4 Facultyof 10 Mathematicsand InformationScience,WarsawUniversityofTechnology,Warsaw,Poland; 11 5 CenterforBioinformaticsandDataAnalysis,MedicalUniversityofBialystok,Jana 12 Kilinskiego1,15-089Bialystok,Poland; 6 I-BioStat,HasseltUniversity,AgoralaanD,3590 13 Diepenbeek,Belgium; 7 Advanced ImagingCenter,JaneliaResearchCampus,Howard 14 HughesMedical Institute,19700HelixDrive,Ashburn,VA20147,USA; 8 Nationalkey 15 laboratoryofcropgeneticimprovement,CollegeofLifeSciencesandTechnology, 16 HuazhongAgriculturalUniversity,Wuhan,Hubei430070,China 17 18 Abstract Thethree-dimensionalgenomestructureplaysafundamentalroleingeneregulation 19 andcellularfunctions.Recentstudiesingenomicsbasedonsequencingtechnologiesinferredthe 20 verybasicfunctionalchromatinfoldingstructuresofthegenomeknownaschromatinloops,the 21 long-rangechromatininteractionsthatareoftenmediatedbyproteinfactors.Tovisualizethe 22 loopingstructureofchromatinweappliedsuper-resolutionmicroscopyiPALMtoimageaspecific 23 chromatinloopinGM12878cells.Totally,wehavegeneratedsiximagesofthetargetchromatin 24 regionatthesinglemoleculeresolution.Toinferthechromatinstructuresfromthecaptured 25 images,wemodeledthemasloopingconformationsusingdifferentcomputationalalgorithmsand 26 thenevaluatedthemodelsbycomparingwithHi-Cdatatoexaminetheconcordance.Theresults 27 showedagoodcorrelationbetweentheimagingdataandsequencingdata,suggestingthe 28 visualizationofhigher-orderchromatinstructuresfortheveryshortgenomicsegmentscanbe 29 realizedbymicroscopicimaging. 30 31 Introduction 32 Howchromatinisorganizedincellnucleusisahistoricallymysteriousquestion. Itisknownthat 33 DNAispackedindifferentlevelstoallowmeters-longlinearDNAtobecondensedinmicrometers- 34 sizednucleus.Boundbyhistoneproteins,146basepairs(bp)ofDNAformnucleosomes(Luger 35 et al., 1997; Tsunaka et al., 2005)thatareconnectedbydozensofbpoflinkerDNA,appearingas 36 a “beadsonastring” structure(Olins and Olins, 1974; Kornberg, 1974; Oudet et al., 1975; Finch 37 and Klug, 1976; Bustin et al., 1976; Leuba et al., 1994).The10nm “beadsonastring” DNA fiberis 38 thenfoldedintohigher-orderchromatinstructuresforfurtherchromatincompaction.However, 39 1of13 . CC-BY 4.0 International license certified by peer review) is the author/funder. It is made available under a The copyright holder for this preprint (which was not this version posted April 29, 2019. . https://doi.org/10.1101/621920 doi: bioRxiv preprint