{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,24]],"date-time":"2026-09-24T21:13:03Z","timestamp":1790284383190,"version":"4.1.0"},"reference-count":109,"publisher":"Elsevier BV","issue":"9","license":[{"start":{"date-parts":[[2026,5,1]],"date-time":"2026-05-01T00:00:00Z","timestamp":1777593600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2026,5,1]],"date-time":"2026-05-01T00:00:00Z","timestamp":1777593600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2026,5,1]],"date-time":"2026-05-01T00:00:00Z","timestamp":1777593600000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-017"},{"start":{"date-parts":[[2026,5,1]],"date-time":"2026-05-01T00:00:00Z","timestamp":1777593600000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-037"},{"start":{"date-parts":[[2026,5,1]],"date-time":"2026-05-01T00:00:00Z","timestamp":1777593600000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-012"},{"start":{"date-parts":[[2026,5,1]],"date-time":"2026-05-01T00:00:00Z","timestamp":1777593600000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-029"},{"start":{"date-parts":[[2026,5,1]],"date-time":"2026-05-01T00:00:00Z","timestamp":1777593600000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-004"}],"funder":[{"DOI":"10.13039\/501100013290","name":"National Key Research and Development Program of China Stem Cell and Translational Research","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100013290","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100019018","name":"CAMS Innovation Fund for Medical Sciences","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100019018","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["cell.com","elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Molecular Cell"],"published-print":{"date-parts":[[2026,5]]},"DOI":"10.1016\/j.molcel.2026.03.031","type":"journal-article","created":{"date-parts":[[2026,4,21]],"date-time":"2026-04-21T14:59:29Z","timestamp":1776783569000},"page":"1723-1741.e11","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":7,"title":["Alu repeat-containing RNAs spatially organize actively transcribed genomic regions around nuclear speckles"],"prefix":"10.1016","volume":"86","author":[{"given":"Siqi","family":"Liu","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhongyang","family":"Chen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xinyan","family":"Shen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jie","family":"Gao","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jia","family":"Guo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yu","family":"Rong","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tangai","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fanqi","family":"Zhou","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yanmin","family":"Si","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hualu","family":"Zhao","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tao","family":"Cheng","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lihong","family":"Shi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jia","family":"Yu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yanni","family":"Ma","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.molcel.2026.03.031_bib1","doi-asserted-by":"crossref","first-page":"499","DOI":"10.1038\/416499a","article-title":"An extensive network of coupling among gene expression machines","volume":"416","author":"Maniatis","year":"2002","journal-title":"Nature"},{"key":"10.1016\/j.molcel.2026.03.031_bib2","doi-asserted-by":"crossref","first-page":"637","DOI":"10.1038\/nrm.2017.63","article-title":"Splicing and transcription touch base: co-transcriptional spliceosome assembly and function","volume":"18","author":"Herzel","year":"2017","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"10.1016\/j.molcel.2026.03.031_bib3","doi-asserted-by":"crossref","first-page":"464","DOI":"10.1038\/s41580-018-0010-5","article-title":"Born to run: control of transcription elongation by RNA polymerase II","volume":"19","author":"Chen","year":"2018","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"10.1016\/j.molcel.2026.03.031_bib4","doi-asserted-by":"crossref","first-page":"119","DOI":"10.1146\/annurev-biochem-052610-095910","article-title":"RNA polymerase II elongation control","volume":"81","author":"Zhou","year":"2012","journal-title":"Annu. Rev. Biochem."},{"key":"10.1016\/j.molcel.2026.03.031_bib5","doi-asserted-by":"crossref","first-page":"8583","DOI":"10.1021\/cr400105n","article-title":"RNA polymerase II transcription elongation control","volume":"113","author":"Guo","year":"2013","journal-title":"Chem. Rev."},{"key":"10.1016\/j.molcel.2026.03.031_bib6","doi-asserted-by":"crossref","DOI":"10.1101\/cshperspect.a000711","article-title":"Biogenesis of nuclear bodies","volume":"2","author":"Dundr","year":"2010","journal-title":"Cold Spring Harb. Perspect. Biol."},{"key":"10.1016\/j.molcel.2026.03.031_bib7","doi-asserted-by":"crossref","first-page":"245","DOI":"10.1038\/nrm3965","article-title":"Three-dimensional genome architecture: players and mechanisms","volume":"16","author":"Pombo","year":"2015","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"10.1016\/j.molcel.2026.03.031_bib8","doi-asserted-by":"crossref","DOI":"10.1242\/jcs.235093","article-title":"The liquid nucleome - phase transitions in the nucleus at a glance","volume":"132","author":"Strom","year":"2019","journal-title":"J. Cell Sci."},{"key":"10.1016\/j.molcel.2026.03.031_bib9","doi-asserted-by":"crossref","first-page":"653","DOI":"10.1038\/s41580-021-00387-1","article-title":"Nuclear compartmentalization as a mechanism of quantitative control of gene expression","volume":"22","author":"Bhat","year":"2021","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"10.1016\/j.molcel.2026.03.031_bib10","doi-asserted-by":"crossref","first-page":"1052","DOI":"10.3724\/abbs.2023099","article-title":"Phase separation in gene transcription control","volume":"55","author":"Li","year":"2023","journal-title":"Acta Biochim. Biophys. Sin. (Shanghai)"},{"key":"10.1016\/j.molcel.2026.03.031_bib11","doi-asserted-by":"crossref","first-page":"437","DOI":"10.1038\/s41576-019-0128-0","article-title":"Long-range enhancer-promoter contacts in gene expression control","volume":"20","author":"Schoenfelder","year":"2019","journal-title":"Nat. Rev. Genet."},{"key":"10.1016\/j.molcel.2026.03.031_bib12","doi-asserted-by":"crossref","first-page":"381","DOI":"10.1038\/nature11049","article-title":"Spatial partitioning of the regulatory landscape of the X-inactivation centre","volume":"485","author":"Nora","year":"2012","journal-title":"Nature"},{"key":"10.1016\/j.molcel.2026.03.031_bib13","doi-asserted-by":"crossref","first-page":"744","DOI":"10.1016\/j.cell.2018.05.024","article-title":"Higher-Order Inter-chromosomal Hubs Shape 3D Genome Organization in the Nucleus","volume":"174","author":"Quinodoz","year":"2018","journal-title":"Cell"},{"key":"10.1016\/j.molcel.2026.03.031_bib14","doi-asserted-by":"crossref","first-page":"412","DOI":"10.1126\/science.aar4199","article-title":"Mediator and RNA polymerase II clusters associate in transcription-dependent condensates","volume":"361","author":"Cho","year":"2018","journal-title":"Science"},{"key":"10.1016\/j.molcel.2026.03.031_bib15","doi-asserted-by":"crossref","first-page":"1842","DOI":"10.1016\/j.cell.2018.10.042","article-title":"Transcription Factors Activate Genes through the Phase-Separation Capacity of Their Activation Domains","volume":"175","author":"Boija","year":"2018","journal-title":"Cell"},{"key":"10.1016\/j.molcel.2026.03.031_bib16","doi-asserted-by":"crossref","first-page":"543","DOI":"10.1038\/s41586-019-1464-0","article-title":"Pol II phosphorylation regulates a switch between transcriptional and splicing condensates","volume":"572","author":"Guo","year":"2019","journal-title":"Nature"},{"key":"10.1016\/j.molcel.2026.03.031_bib17","doi-asserted-by":"crossref","DOI":"10.1101\/cshperspect.a000646","article-title":"Nuclear speckles","volume":"3","author":"Spector","year":"2011","journal-title":"Cold Spring Harb. Perspect. Biol."},{"key":"10.1016\/j.molcel.2026.03.031_bib18","doi-asserted-by":"crossref","DOI":"10.1083\/jcb.201910207","article-title":"Tyramide signal amplification mass spectrometry (TSA-MS) ratio identifies nuclear speckle proteins","volume":"219","author":"Dopie","year":"2020","journal-title":"J. Cell Biol."},{"key":"10.1016\/j.molcel.2026.03.031_bib19","doi-asserted-by":"crossref","first-page":"3876","DOI":"10.1091\/mbc.e04-03-0253","article-title":"Proteomic analysis of interchromatin granule clusters","volume":"15","author":"Saitoh","year":"2004","journal-title":"Mol. Biol. Cell"},{"key":"10.1016\/j.molcel.2026.03.031_bib20","doi-asserted-by":"crossref","first-page":"305","DOI":"10.1073\/pnas.89.1.305","article-title":"U1 and U2 small nuclear RNAs are present in nuclear speckles","volume":"89","author":"Huang","year":"1992","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.molcel.2026.03.031_bib21","doi-asserted-by":"crossref","first-page":"111","DOI":"10.1017\/S1355838200991982","article-title":"The SRm160\/300 splicing coactivator subunits","volume":"6","author":"Blencowe","year":"2000","journal-title":"RNA"},{"key":"10.1016\/j.molcel.2026.03.031_bib22","doi-asserted-by":"crossref","first-page":"650","DOI":"10.1091\/mbc.e09-02-0126","article-title":"Son is essential for nuclear speckle organization and cell cycle progression","volume":"21","author":"Sharma","year":"2010","journal-title":"Mol. Biol. Cell"},{"key":"10.1016\/j.molcel.2026.03.031_bib23","doi-asserted-by":"crossref","DOI":"10.7554\/eLife.60579","article-title":"SON and SRRM2 are essential for nuclear speckle formation","volume":"9","author":"Ilik","year":"2020","journal-title":"eLife"},{"key":"10.1016\/j.molcel.2026.03.031_bib24","doi-asserted-by":"crossref","first-page":"727","DOI":"10.1038\/372727a0","article-title":"RNA processing. Splicing in space","volume":"372","author":"Mattaj","year":"1994","journal-title":"Nature"},{"key":"10.1016\/j.molcel.2026.03.031_bib25","doi-asserted-by":"crossref","first-page":"1385","DOI":"10.1126\/science.288.5470.1385","article-title":"Like attracts like: getting RNA processing together in the nucleus","volume":"288","author":"Lewis","year":"2000","journal-title":"Science"},{"key":"10.1016\/j.molcel.2026.03.031_bib26","doi-asserted-by":"crossref","first-page":"91","DOI":"10.1016\/j.gde.2019.06.008","article-title":"Genome organization around nuclear speckles","volume":"55","author":"Chen","year":"2019","journal-title":"Curr. Opin. Genet. Dev."},{"key":"10.1016\/j.molcel.2026.03.031_bib27","doi-asserted-by":"crossref","first-page":"1165","DOI":"10.1038\/s41586-024-07429-6","article-title":"Genome organization around nuclear speckles drives mRNA splicing efficiency","volume":"629","author":"Bhat","year":"2024","journal-title":"Nature"},{"key":"10.1016\/j.molcel.2026.03.031_bib28","doi-asserted-by":"crossref","first-page":"5775","DOI":"10.1016\/j.cell.2021.10.014","article-title":"RNA promotes the formation of spatial compartments in the nucleus","volume":"184","author":"Quinodoz","year":"2021","journal-title":"Cell"},{"key":"10.1016\/j.molcel.2026.03.031_bib29","doi-asserted-by":"crossref","first-page":"4025","DOI":"10.1083\/jcb.201807108","article-title":"Mapping 3D genome organization relative to nuclear compartments using TSA-Seq as a cytological ruler","volume":"217","author":"Chen","year":"2018","journal-title":"J. Cell Biol."},{"key":"10.1016\/j.molcel.2026.03.031_bib30","doi-asserted-by":"crossref","first-page":"424","DOI":"10.1038\/s41594-019-0226-x","article-title":"Constitutive splicing and economies of scale in gene expression","volume":"26","author":"Ding","year":"2019","journal-title":"Nat. Struct. Mol. Biol."},{"key":"10.1016\/j.molcel.2026.03.031_bib31","doi-asserted-by":"crossref","first-page":"1085","DOI":"10.1534\/genetics.110.124180","article-title":"A brief history of the status of transposable elements: from junk DNA to major players in evolution","volume":"186","author":"Bi\u00e9mont","year":"2010","journal-title":"Genetics"},{"key":"10.1016\/j.molcel.2026.03.031_bib32","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pgen.1002384","article-title":"Repetitive elements may comprise over two-thirds of the human genome","volume":"7","author":"de Koning","year":"2011","journal-title":"PLoS Genet."},{"key":"10.1016\/j.molcel.2026.03.031_bib33","doi-asserted-by":"crossref","first-page":"1626","DOI":"10.1126\/science.1089670","article-title":"Mobile elements: drivers of genome evolution","volume":"303","author":"Kazazian","year":"2004","journal-title":"Science"},{"key":"10.1016\/j.molcel.2026.03.031_bib34","doi-asserted-by":"crossref","first-page":"192","DOI":"10.1016\/j.cell.2008.09.028","article-title":"SnapShot: Vertebrate transposons","volume":"135","author":"Mandal","year":"2008","journal-title":"Cell"},{"key":"10.1016\/j.molcel.2026.03.031_bib35","doi-asserted-by":"crossref","first-page":"604","DOI":"10.1038\/284604a0","article-title":"Selfish DNA: the ultimate parasite","volume":"284","author":"Orgel","year":"1980","journal-title":"Nature"},{"key":"10.1016\/j.molcel.2026.03.031_bib36","doi-asserted-by":"crossref","first-page":"1154","DOI":"10.1038\/ng.917","article-title":"Transposon-mediated rewiring of gene regulatory networks contributed to the evolution of pregnancy in mammals","volume":"43","author":"Lynch","year":"2011","journal-title":"Nat. Genet."},{"key":"10.1016\/j.molcel.2026.03.031_bib37","doi-asserted-by":"crossref","first-page":"44","DOI":"10.1038\/ng.3449","article-title":"The primate-specific noncoding RNA HPAT5 regulates pluripotency during human preimplantation development and nuclear reprogramming","volume":"48","author":"Durruthy-Durruthy","year":"2016","journal-title":"Nat. Genet."},{"key":"10.1016\/j.molcel.2026.03.031_bib38","doi-asserted-by":"crossref","first-page":"405","DOI":"10.1038\/nature13804","article-title":"Primate-specific endogenous retrovirus-driven transcription defines naive-like stem cells","volume":"516","author":"Wang","year":"2014","journal-title":"Nature"},{"key":"10.1016\/j.molcel.2026.03.031_bib39","doi-asserted-by":"crossref","first-page":"228","DOI":"10.1038\/nature25179","article-title":"Selective silencing of euchromatic L1s revealed by genome-wide screens for L1 regulators","volume":"553","author":"Liu","year":"2018","journal-title":"Nature"},{"key":"10.1016\/j.molcel.2026.03.031_bib40","doi-asserted-by":"crossref","first-page":"3296","DOI":"10.1016\/j.celrep.2020.02.048","article-title":"Genomic Repeats Categorize Genes with Distinct Functions for Orchestrated Regulation","volume":"30","author":"Lu","year":"2020","journal-title":"Cell Rep."},{"key":"10.1016\/j.molcel.2026.03.031_bib41","doi-asserted-by":"crossref","first-page":"613","DOI":"10.1038\/s41422-020-00466-6","article-title":"Homotypic clustering of L1 and B1\/Alu repeats compartmentalizes the 3D genome","volume":"31","author":"Lu","year":"2021","journal-title":"Cell Res."},{"key":"10.1016\/j.molcel.2026.03.031_bib42","doi-asserted-by":"crossref","first-page":"107","DOI":"10.1038\/nature25757","article-title":"Sequences enriched in Alu repeats drive nuclear localization of long RNAs in human cells","volume":"555","author":"Lubelsky","year":"2018","journal-title":"Nature"},{"key":"10.1016\/j.molcel.2026.03.031_bib43","doi-asserted-by":"crossref","DOI":"10.15252\/embr.201948068","article-title":"Differential contribution of steady-state RNA and active transcription in chromatin organization","volume":"20","author":"Barutcu","year":"2019","journal-title":"EMBO Rep."},{"key":"10.1016\/j.molcel.2026.03.031_bib44","doi-asserted-by":"crossref","first-page":"3509","DOI":"10.1016\/j.molcel.2021.07.004","article-title":"Nascent RNA scaffolds contribute to chromosome territory architecture and counter chromatin compaction","volume":"81","author":"Creamer","year":"2021","journal-title":"Mol. Cell"},{"key":"10.1016\/j.molcel.2026.03.031_bib45","doi-asserted-by":"crossref","first-page":"1240","DOI":"10.1126\/science.1252966","article-title":"RNA Function. RNA and dynamic nuclear organization","volume":"345","author":"Rinn","year":"2014","journal-title":"Science"},{"key":"10.1016\/j.molcel.2026.03.031_bib46","doi-asserted-by":"crossref","DOI":"10.1101\/cshperspect.a000638","article-title":"The nucleolus","volume":"3","author":"Pederson","year":"2011","journal-title":"Cold Spring Harb. Perspect. Biol."},{"key":"10.1016\/j.molcel.2026.03.031_bib47","doi-asserted-by":"crossref","DOI":"10.1126\/science.1237973","article-title":"The Xist lncRNA exploits three-dimensional genome architecture to spread across the X chromosome","volume":"341","author":"Engreitz","year":"2013","journal-title":"Science"},{"key":"10.1016\/j.molcel.2026.03.031_bib48","doi-asserted-by":"crossref","first-page":"1038","DOI":"10.1016\/j.molcel.2018.05.019","article-title":"Functional Domains of NEAT1 Architectural lncRNA Induce Paraspeckle Assembly through Phase Separation","volume":"70","author":"Yamazaki","year":"2018","journal-title":"Mol. Cell"},{"key":"10.1016\/j.molcel.2026.03.031_bib49","doi-asserted-by":"crossref","first-page":"53","DOI":"10.1038\/ng.496","article-title":"Preferential associations between co-regulated genes reveal a transcriptional interactome in erythroid cells","volume":"42","author":"Schoenfelder","year":"2010","journal-title":"Nat. Genet."},{"key":"10.1016\/j.molcel.2026.03.031_bib50","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.jmb.2009.10.031","article-title":"A model for all genomes: the role of transcription factories","volume":"395","author":"Cook","year":"2010","journal-title":"J. Mol. Biol."},{"key":"10.1016\/j.molcel.2026.03.031_bib51","doi-asserted-by":"crossref","first-page":"457","DOI":"10.1038\/nrg2592","article-title":"Transcription factories: gene expression in unions?","volume":"10","author":"Sutherland","year":"2009","journal-title":"Nat. Rev. Genet."},{"key":"10.1016\/j.molcel.2026.03.031_bib52","article-title":"USP52 acts as a deubiquitinase and promotes histone chaperone ASF1A stabilization","volume":"9","author":"Yang","year":"2018","journal-title":"Nat. Commun."},{"key":"10.1016\/j.molcel.2026.03.031_bib53","doi-asserted-by":"crossref","first-page":"767","DOI":"10.1016\/j.molcel.2009.05.027","article-title":"Shifts in replication timing actively affect histone acetylation during nucleosome reassembly","volume":"34","author":"Lande-Diner","year":"2009","journal-title":"Mol. Cell"},{"key":"10.1016\/j.molcel.2026.03.031_bib54","doi-asserted-by":"crossref","first-page":"503","DOI":"10.1038\/s41576-019-0135-1","article-title":"Chromatin-associated RNAs as facilitators of functional genomic interactions","volume":"20","author":"Li","year":"2019","journal-title":"Nat. Rev. Genet."},{"key":"10.1016\/j.molcel.2026.03.031_bib55","doi-asserted-by":"crossref","first-page":"1035","DOI":"10.1016\/j.molcel.2021.12.010","article-title":"Systematic mapping of nuclear domain-associated transcripts reveals speckles and lamina as hubs of functionally distinct retained introns","volume":"82","author":"Barutcu","year":"2022","journal-title":"Mol. Cell"},{"key":"10.1016\/j.molcel.2026.03.031_bib56","doi-asserted-by":"crossref","first-page":"798","DOI":"10.1038\/s41586-025-09568-w","article-title":"Collective homeostasis of condensation-prone proteins via their mRNAs","volume":"647","author":"Faraway","year":"2025","journal-title":"Nature"},{"key":"10.1016\/j.molcel.2026.03.031_bib57","doi-asserted-by":"crossref","first-page":"1963","DOI":"10.1182\/blood-2018-07-862003","article-title":"Fetal gamma-globin genes are regulated by the BGLT3 long noncoding RNA locus","volume":"132","author":"Ivaldi","year":"2018","journal-title":"Blood"},{"key":"10.1016\/j.molcel.2026.03.031_bib58","doi-asserted-by":"crossref","first-page":"667","DOI":"10.1016\/j.molcel.2011.08.027","article-title":"Genomic maps of long noncoding RNA occupancy reveal principles of RNA-chromatin interactions","volume":"44","author":"Chu","year":"2011","journal-title":"Mol. Cell"},{"key":"10.1016\/j.molcel.2026.03.031_bib59","doi-asserted-by":"crossref","first-page":"1384","DOI":"10.1101\/gad.242990.114","article-title":"A double-edged sword: R loops as threats to genome integrity and powerful regulators of gene expression","volume":"28","author":"Skourti-Stathaki","year":"2014","journal-title":"Genes Dev."},{"key":"10.1016\/j.molcel.2026.03.031_bib60","doi-asserted-by":"crossref","first-page":"619","DOI":"10.1126\/science.1234848","article-title":"R-loop stabilization represses antisense transcription at the Arabidopsis FLC locus","volume":"340","author":"Sun","year":"2013","journal-title":"Science"},{"key":"10.1016\/j.molcel.2026.03.031_bib61","doi-asserted-by":"crossref","DOI":"10.7554\/eLife.28306","article-title":"Defining the location of promoter-associated R-loops at near-nucleotide resolution using bisDRIP-seq","volume":"6","author":"Dumelie","year":"2017","journal-title":"eLife"},{"key":"10.1016\/j.molcel.2026.03.031_bib62","doi-asserted-by":"crossref","first-page":"626","DOI":"10.1016\/j.molcel.2015.10.001","article-title":"LncRNA Khps1 Regulates Expression of the Proto-oncogene SPHK1 via Triplex-Mediated Changes in Chromatin Structure","volume":"60","author":"Postepska-Igielska","year":"2015","journal-title":"Mol. Cell"},{"key":"10.1016\/j.molcel.2026.03.031_bib63","doi-asserted-by":"crossref","DOI":"10.1038\/ncomms8743","article-title":"MEG3 long noncoding RNA regulates the TGF-beta pathway genes through formation of RNA-DNA triplex structures","volume":"6","author":"Mondal","year":"2015","journal-title":"Nat. Commun."},{"key":"10.1016\/j.molcel.2026.03.031_bib64","doi-asserted-by":"crossref","first-page":"1325","DOI":"10.1016\/j.chembiol.2016.09.011","article-title":"RNA-DNA Triplex Formation by Long Noncoding RNAs","volume":"23","author":"Li","year":"2016","journal-title":"Cell Chem. Biol."},{"key":"10.1016\/j.molcel.2026.03.031_bib65","doi-asserted-by":"crossref","first-page":"583","DOI":"10.1038\/nrg3961","article-title":"R loops: new modulators of genome dynamics and function","volume":"16","author":"Santos-Pereira","year":"2015","journal-title":"Nat. Rev. Genet."},{"key":"10.1016\/j.molcel.2026.03.031_bib66","doi-asserted-by":"crossref","first-page":"1734","DOI":"10.1038\/s41596-019-0159-1","article-title":"High-resolution, strand-specific R-loop mapping via S9.6-based DNA-RNA immunoprecipitation and high-throughput sequencing","volume":"14","author":"Sanz","year":"2019","journal-title":"Nat. Protoc."},{"key":"10.1016\/j.molcel.2026.03.031_bib67","doi-asserted-by":"crossref","first-page":"1063","DOI":"10.1101\/gr.219394.116","article-title":"RNA-DNA hybrid (R-loop) immunoprecipitation mapping: an analytical workflow to evaluate inherent biases","volume":"27","author":"Hal\u00e1sz","year":"2017","journal-title":"Genome Res."},{"key":"10.1016\/j.molcel.2026.03.031_bib68","doi-asserted-by":"crossref","first-page":"833","DOI":"10.1016\/j.molcel.2022.01.014","article-title":"HOTTIP-dependent R-loop formation regulates CTCF boundary activity and TAD integrity in leukemia","volume":"82","author":"Luo","year":"2022","journal-title":"Mol. Cell"},{"key":"10.1016\/j.molcel.2026.03.031_bib69","article-title":"Triptolide (TPL) inhibits global transcription by inducing proteasome-dependent degradation of RNA polymerase II (Pol II)","volume":"6","author":"Wang","year":"2011","journal-title":"PLoS One"},{"key":"10.1016\/j.molcel.2026.03.031_bib70","doi-asserted-by":"crossref","first-page":"702","DOI":"10.1016\/j.devcel.2021.01.015","article-title":"N6-methyladenosine modification of MALAT1 promotes metastasis via reshaping nuclear speckles","volume":"56","author":"Wang","year":"2021","journal-title":"Dev. Cell"},{"key":"10.1016\/j.molcel.2026.03.031_bib71","doi-asserted-by":"crossref","DOI":"10.1242\/jcs.226563","article-title":"Nuclear speckle fusion via long-range directional motion regulates speckle morphology after transcriptional inhibition","volume":"132","author":"Kim","year":"2019","journal-title":"J. Cell Sci."},{"key":"10.1016\/j.molcel.2026.03.031_bib72","doi-asserted-by":"crossref","first-page":"288","DOI":"10.1038\/s41580-022-00558-8","article-title":"A guide to membraneless organelles and their various roles in gene regulation","volume":"24","author":"Hirose","year":"2023","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"10.1016\/j.molcel.2026.03.031_bib73","doi-asserted-by":"crossref","first-page":"478","DOI":"10.1016\/j.devcel.2020.12.019","article-title":"Genome-wide analysis of pseudogenes reveals HBBP1\u2019s human-specific essentiality in erythropoiesis and implication in \u03b2-thalassemia","volume":"56","author":"Ma","year":"2021","journal-title":"Dev. Cell"},{"key":"10.1016\/j.molcel.2026.03.031_bib74","doi-asserted-by":"crossref","first-page":"188","DOI":"10.1016\/j.cell.2014.08.018","article-title":"RNA-RNA interactions enable specific targeting of noncoding RNAs to nascent Pre-mRNAs and chromatin sites","volume":"159","author":"Engreitz","year":"2014","journal-title":"Cell"},{"key":"10.1016\/j.molcel.2026.03.031_bib75","doi-asserted-by":"crossref","DOI":"10.3389\/fcell.2021.735527","article-title":"Emerging Roles of Repetitive and Repeat-Containing RNA in Nuclear and Chromatin Organization and Gene Expression","volume":"9","author":"Trigiante","year":"2021","journal-title":"Front. Cell Dev. Biol."},{"key":"10.1016\/j.molcel.2026.03.031_bib76","doi-asserted-by":"crossref","first-page":"33","DOI":"10.3390\/genes5010033","article-title":"The past, present, and future of human centromere genomics","volume":"5","author":"Aldrup-Macdonald","year":"2014","journal-title":"Genes (Basel)"},{"key":"10.1016\/j.molcel.2026.03.031_bib77","doi-asserted-by":"crossref","first-page":"407","DOI":"10.1002\/wrna.1220","article-title":"Telomeric noncoding RNA: telomeric repeat-containing RNA in telomere biology","volume":"5","author":"Cusanelli","year":"2014","journal-title":"Wiley Interdiscip. Rev., RNA"},{"key":"10.1016\/j.molcel.2026.03.031_bib78","doi-asserted-by":"crossref","DOI":"10.1126\/science.aam5439","article-title":"Response to Comment on \u201cXist recruits the X chromosome to the nuclear lamina to enable chromosome-wide silencing\u201d","volume":"356","author":"Chen","year":"2017","journal-title":"Science"},{"key":"10.1016\/j.molcel.2026.03.031_bib79","doi-asserted-by":"crossref","first-page":"90","DOI":"10.3389\/fmolb.2017.00090","article-title":"Function by Structure: Spotlights on Xist Long Non-coding RNA","volume":"4","author":"Pintacuda","year":"2017","journal-title":"Front. Mol. Biosci."},{"key":"10.1016\/j.molcel.2026.03.031_bib80","doi-asserted-by":"crossref","DOI":"10.12688\/f1000research.21362.1","article-title":"The B-side of Xist","volume":"9","author":"Monfort","year":"2020","journal-title":"F1000Res"},{"key":"10.1016\/j.molcel.2026.03.031_bib81","doi-asserted-by":"crossref","first-page":"423","DOI":"10.1093\/nar\/gkm1056","article-title":"Transcription of Satellite III non-coding RNAs is a general stress response in human cells","volume":"36","author":"Valgardsdottir","year":"2008","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.molcel.2026.03.031_bib82","doi-asserted-by":"crossref","first-page":"1513","DOI":"10.1016\/j.bbadis.2016.05.015","article-title":"Nuclear speckles are detention centers for transcripts containing expanded CAG repeats","volume":"1862","author":"Urbanek","year":"2016","journal-title":"Biochim. Biophys. Acta"},{"key":"10.1016\/j.molcel.2026.03.031_bib83","doi-asserted-by":"crossref","first-page":"10350","DOI":"10.1093\/nar\/gkx759","article-title":"Nuclear speckles: molecular organization, biological function and role in disease","volume":"45","author":"Galganski","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.molcel.2026.03.031_bib84","doi-asserted-by":"crossref","first-page":"738","DOI":"10.1261\/rna.028639.111","article-title":"Identification of cis- and trans-acting factors involved in the localization of MALAT-1 noncoding RNA to nuclear speckles","volume":"18","author":"Miyagawa","year":"2012","journal-title":"RNA"},{"key":"10.1016\/j.molcel.2026.03.031_bib85","doi-asserted-by":"crossref","first-page":"10842","DOI":"10.1073\/pnas.1903808116","article-title":"Imaging-based pooled CRISPR screening reveals regulators of lncRNA localization","volume":"116","author":"Wang","year":"2019","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.molcel.2026.03.031_bib86","doi-asserted-by":"crossref","first-page":"925","DOI":"10.1016\/j.molcel.2010.08.011","article-title":"The nuclear-retained noncoding RNA MALAT1 regulates alternative splicing by modulating SR splicing factor phosphorylation","volume":"39","author":"Tripathi","year":"2010","journal-title":"Mol. Cell"},{"key":"10.1016\/j.molcel.2026.03.031_bib87","doi-asserted-by":"crossref","first-page":"814","DOI":"10.1016\/j.molcel.2012.01.017","article-title":"R-loop formation is a distinctive characteristic of unmethylated human CpG island promoters","volume":"45","author":"Ginno","year":"2012","journal-title":"Mol. Cell"},{"key":"10.1016\/j.molcel.2026.03.031_bib88","doi-asserted-by":"crossref","first-page":"167","DOI":"10.1016\/j.molcel.2016.05.032","article-title":"Prevalent, Dynamic, and Conserved R-Loop Structures Associate with Specific Epigenomic Signatures in Mammals","volume":"63","author":"Sanz","year":"2016","journal-title":"Mol. Cell"},{"key":"10.1016\/j.molcel.2026.03.031_bib89","doi-asserted-by":"crossref","first-page":"5785","DOI":"10.1073\/pnas.1421197112","article-title":"Head-to-head antisense transcription and R-loop formation promotes transcriptional activation","volume":"112","author":"Boque-Sastre","year":"2015","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.molcel.2026.03.031_bib90","doi-asserted-by":"crossref","first-page":"115","DOI":"10.1016\/j.molcel.2012.04.009","article-title":"R loops: from transcription byproducts to threats to genome stability","volume":"46","author":"Aguilera","year":"2012","journal-title":"Mol. Cell"},{"key":"10.1016\/j.molcel.2026.03.031_bib91","doi-asserted-by":"crossref","first-page":"523","DOI":"10.1038\/387523a0","article-title":"The dynamics of a pre-mRNA splicing factor in living cells","volume":"387","author":"Misteli","year":"1997","journal-title":"Nature"},{"key":"10.1016\/j.molcel.2026.03.031_bib92","doi-asserted-by":"crossref","first-page":"387","DOI":"10.1038\/s41586-022-05365-x","article-title":"Subtype-specific 3D genome alteration in acute myeloid leukaemia","volume":"611","author":"Xu","year":"2022","journal-title":"Nature"},{"key":"10.1016\/j.molcel.2026.03.031_bib93","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1093\/bioinformatics\/bts635","article-title":"STAR: ultrafast universal RNA-seq aligner","volume":"29","author":"Dobin","year":"2013","journal-title":"Bioinformatics"},{"key":"10.1016\/j.molcel.2026.03.031_bib94","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1038\/nmeth.1923","article-title":"Fast gapped-read alignment with Bowtie 2","volume":"9","author":"Langmead","year":"2012","journal-title":"Nat. Methods"},{"key":"10.1016\/j.molcel.2026.03.031_bib95","doi-asserted-by":"crossref","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","article-title":"Trimmomatic: a flexible trimmer for Illumina sequence data","volume":"30","author":"Bolger","year":"2014","journal-title":"Bioinformatics"},{"key":"10.1016\/j.molcel.2026.03.031_bib96","doi-asserted-by":"crossref","DOI":"10.1186\/gb-2013-14-4-r36","article-title":"TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions","volume":"14","author":"Kim","year":"2013","journal-title":"Genome Biol."},{"key":"10.1016\/j.molcel.2026.03.031_bib97","doi-asserted-by":"crossref","first-page":"166","DOI":"10.1093\/bioinformatics\/btu638","article-title":"HTSeq--a Python framework to work with high-throughput sequencing data","volume":"31","author":"Anders","year":"2015","journal-title":"Bioinformatics"},{"key":"10.1016\/j.molcel.2026.03.031_bib98","doi-asserted-by":"crossref","first-page":"923","DOI":"10.1093\/bioinformatics\/btt656","article-title":"featureCounts: an efficient general purpose program for assigning sequence reads to genomic features","volume":"30","author":"Liao","year":"2014","journal-title":"Bioinformatics"},{"key":"10.1016\/j.molcel.2026.03.031_bib99","doi-asserted-by":"crossref","DOI":"10.1186\/gb-2008-9-9-r137","article-title":"Model-based analysis of ChIP-Seq (MACS)","volume":"9","author":"Zhang","year":"2008","journal-title":"Genome Biol."},{"key":"10.1016\/j.molcel.2026.03.031_bib100","doi-asserted-by":"crossref","first-page":"29","DOI":"10.1007\/978-1-61779-603-6_2","article-title":"Using and understanding RepeatMasker","volume":"859","author":"Tempel","year":"2012","journal-title":"Methods Mol. Biol."},{"key":"10.1016\/j.molcel.2026.03.031_bib101","doi-asserted-by":"crossref","first-page":"291","DOI":"10.1038\/nm.3101","article-title":"Lysine-specific demethylase 1 is a therapeutic target for fetal hemoglobin induction","volume":"19","author":"Shi","year":"2013","journal-title":"Nat. Med."},{"key":"10.1016\/j.molcel.2026.03.031_bib102","doi-asserted-by":"crossref","first-page":"45","DOI":"10.1007\/978-1-4939-6716-2_3","article-title":"GRO-seq, A Tool for Identification of Transcripts Regulating Gene Expression","volume":"1543","author":"Lopes","year":"2017","journal-title":"Methods Mol. Biol."},{"key":"10.1016\/j.molcel.2026.03.031_bib103","doi-asserted-by":"crossref","DOI":"10.1038\/s41467-019-09982-5","article-title":"CUT&Tag for efficient epigenomic profiling of small samples and single cells","volume":"10","author":"Kaya-Okur","year":"2019","journal-title":"Nat. Commun."},{"key":"10.1016\/j.molcel.2026.03.031_bib104","doi-asserted-by":"crossref","first-page":"576","DOI":"10.1016\/j.molcel.2010.05.004","article-title":"Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities","volume":"38","author":"Heinz","year":"2010","journal-title":"Mol. Cell"},{"key":"10.1016\/j.molcel.2026.03.031_bib105","doi-asserted-by":"crossref","first-page":"550","DOI":"10.1186\/s13059-014-0550-8","article-title":"Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2","volume":"15","author":"Love","year":"2014","journal-title":"Genome Biol."},{"key":"10.1016\/j.molcel.2026.03.031_bib106","doi-asserted-by":"crossref","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"The Sequence Alignment\/Map format and SAMtools","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"10.1016\/j.molcel.2026.03.031_bib107","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","article-title":"Basic local alignment search tool","volume":"215","author":"Altschul","year":"1990","journal-title":"J. Mol. Biol."},{"key":"10.1016\/j.molcel.2026.03.031_bib108","doi-asserted-by":"crossref","first-page":"W160","DOI":"10.1093\/nar\/gkw257","article-title":"deepTools2: a next generation web server for deep-sequencing data analysis","volume":"44","author":"Ram\u00edrez","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.molcel.2026.03.031_bib109","article-title":"Metascape provides a biologist-oriented resource for the analysis of systems-level datasets","volume":"10","author":"Zhou","year":"2019","journal-title":"Nat. Commun."}],"container-title":["Molecular Cell"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1097276526002078?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1097276526002078?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2026,7,3]],"date-time":"2026-07-03T05:38:12Z","timestamp":1783057092000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S1097276526002078"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,5]]},"references-count":109,"journal-issue":{"issue":"9","published-print":{"date-parts":[[2026,5]]}},"alternative-id":["S1097276526002078"],"URL":"https:\/\/doi.org\/10.1016\/j.molcel.2026.03.031","relation":{},"ISSN":["1097-2765"],"issn-type":[{"value":"1097-2765","type":"print"}],"subject":[],"published":{"date-parts":[[2026,5]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Alu repeat-containing RNAs spatially organize actively transcribed genomic regions around nuclear speckles","name":"articletitle","label":"Article Title"},{"value":"Molecular Cell","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.molcel.2026.03.031","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2026 Elsevier Inc. All rights are reserved, including those for text and data mining, AI training, and similar technologies.","name":"copyright","label":"Copyright"}]}}