Show simple item record

dc.contributor.authorShuaib, Muhammad
dc.contributor.authorParsi, Krishna Mohan
dc.contributor.authorKawaji, Hideya
dc.contributor.authorThimma, Manjula
dc.contributor.authorAdroub, Sabir
dc.contributor.authorFort, Alexandre
dc.contributor.authorGhosheh, Yanal
dc.contributor.authorYamazaki, Tomohiro
dc.contributor.authorMannen, Taro
dc.contributor.authorSeridi, Loqmane
dc.contributor.authorFallatah, Bodor
dc.contributor.authorAlbawardi, Waad
dc.contributor.authorRavasi, Timothy
dc.contributor.authorCarninci, Piero
dc.contributor.authorHirose, Tetsuro
dc.contributor.authorOrlando, Valerio
dc.date.accessioned2019-12-09T12:04:59Z
dc.date.available2019-12-09T12:04:59Z
dc.date.issued2019-01-21
dc.identifier.citationShuaib, M., Parsi, K. M., Kawaji, H., Thimma, M., Adroub, S. A., Fort, A., … Orlando, V. (2019). AGO1 in association with NEAT1 lncRNA contributes to nuclear and 3D chromatin architecture in human cells. doi:10.1101/525527
dc.identifier.doi10.1101/525527
dc.identifier.urihttp://hdl.handle.net/10754/660475
dc.description.abstractAside from their roles in the cytoplasm, RNA-interference components have been reported to localize also in the nucleus of human cells. In particular, AGO1 associates with active chromatin and appears to influence global gene expression. However, the mechanistic aspects remain elusive. Here, we identify AGO1 as a paraspeckle component that in combination with the NEAT1 lncRNA maintains 3D genome architecture. We demonstrate that AGO1 interacts with NEAT1 lncRNA and its depletion affects NEAT1 expression and the formation of paraspeckles. By Hi-C analysis in AGO1 knockdown cells, we observed global changes in chromatin organization, including TADs configuration, and A/B compartment mixing. Consistently, distinct groups of genes located within the differential interacting loci showed altered expression upon AGO1 depletion. NEAT1 knockout cells displayed similar changes in TADs and higher-order A/B compartmentalization. We propose that AGO1 in association with NEAT1 lncRNA can act as a scaffold that bridges chromatin and nuclear bodies to regulate genome organization and gene expression in human cells.
dc.description.sponsorshipWe are grateful to Hakan Ozadamand Johan Gibcus from Job Dekker group (University of Massachusetts Medical School, USA) for initial help in Hi-C analysis; Riccardo Aiese Cigliano (Sequentia Biotech) for help in bioinformatic analysis; Ana Maria Suzuki (RIKEN) for help in CAGE-seq; Heno Hwang (scientific illustrator) at KAUST for his help in drawing the image (Figure-8); Christian Froekjaer Jensen for critical reading of the manuscript; KAUST Bioscience Core Lab for providing sequencing facility. The work was supported by EPIGEN-CNR (Italian Ministry of University and Research) and King Abdullah University of Science and Technology (KAUST) to V.O. The grants from the MEXT of Japan to TH (26113002 and 17H03630). The grant for Joint Research Program of IGM, Hokkaido University.
dc.publisherCold Spring Harbor Laboratory
dc.relation.urlhttp://biorxiv.org/lookup/doi/10.1101/525527
dc.relation.urlhttps://www.biorxiv.org/content/biorxiv/early/2019/01/20/525527.full.pdf
dc.rightsArchived with thanks to Cold Spring Harbor Laboratory
dc.rights.urihttp://creativecommons.org/licenses/by-nc/4.0/
dc.titleAGO1 in association with NEAT1 lncRNA contributes to nuclear and 3D chromatin architecture in human cells
dc.typePreprint
dc.contributor.departmentBiological and Environmental Sciences and Engineering (BESE) Division
dc.contributor.departmentComputer Science Program
dc.contributor.departmentApplied Mathematics and Computational Science Program
dc.contributor.departmentBioscience Program
dc.contributor.departmentKAUST Environmental Epigenetics Program
dc.eprint.versionPre-print
dc.contributor.institutionIRCSS Fondazione Santa Lucia, Epigenetics and Genome Reprogramming, Rome, Italy.
dc.contributor.institutionRIKEN Center for Life Science Technologies, Division of Genomic Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
dc.contributor.institutionInstitute for Genetic Medicine, Hokkaido University, Sapporo 060-0815, Japan
kaust.personShuaib, Muhammad
kaust.personThimma, Manjula
kaust.personAdroub, Sabir
kaust.personGhosheh, Yanal
kaust.personSeridi, Loqmane
kaust.personFallatah, Bodor Khalid Abdulrahman
kaust.personAlbawardi, Waad
kaust.personRavasi, Timothy
kaust.personOrlando, Valerio
dc.relation.issupplementedbybioproject:PRJNA398595
refterms.dateFOA2019-12-09T12:07:06Z
display.relations<b>Is Supplemented By:</b><br/> <ul><li><i>[Bioproject]</i> <br/> Title: Studying the role of nuclear AGO1 in Chromatin OrganisationPublication Date: 2017-08-17. bioproject: <a href="https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA398595" >PRJNA398595</a> Handle: <a href="http://hdl.handle.net/10754/666483" >10754/666483</a></a></li></ul>
kaust.acknowledged.supportUnitKAUST Bioscience Core Lab
kaust.acknowledged.supportUnitscientific illustrator


Files in this item

Thumbnail
Name:
Preprintfile1.pdf
Size:
5.119Mb
Format:
PDF
Description:
Pre-print

This item appears in the following Collection(s)

Show simple item record

Archived with thanks to Cold Spring Harbor Laboratory
Except where otherwise noted, this item's license is described as Archived with thanks to Cold Spring Harbor Laboratory