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Connection

John Rinn to RNA, Long Noncoding

This is a "connection" page, showing publications John Rinn has written about RNA, Long Noncoding.

 
Connection Strength
  
 
 
17.495
  
  1. Much C, Lasda EL, Pereira IT, Vallery TK, Ramirez D, Lewandowski JP, Dowell RD, Smallegan MJ, Rinn JL. The temporal dynamics of lncRNA Firre-mediated epigenetic and transcriptional regulation. Nat Commun. 2024 Aug 09; 15(1):6821.
    View in: PubMed
    Score: 0.759
  2. Much C, Smallegan MJ, Hwang T, Hanson SD, Dumbovic G, Rinn JL. Evolutionary divergence of Firre localization and expression. RNA. 2022 06; 28(6):842-853.
    View in: PubMed
    Score: 0.642
  3. Andergassen D, Rinn JL. From genotype to phenotype: genetics of mammalian long non-coding RNAs in vivo. Nat Rev Genet. 2022 04; 23(4):229-243.
    View in: PubMed
    Score: 0.629
  4. Dumbovic G, Braunschweig U, Langner HK, Smallegan M, Biayna J, Hass EP, Jastrzebska K, Blencowe B, Cech TR, Caruthers MH, Rinn JL. Nuclear compartmentalization of TERT mRNA and TUG1 lncRNA is driven by intron retention. Nat Commun. 2021 06 03; 12(1):3308.
    View in: PubMed
    Score: 0.608
  5. Lewandowski JP, Dumbovic G, Watson AR, Hwang T, Jacobs-Palmer E, Chang N, Much C, Turner KM, Kirby C, Rubinstein ND, Groff AF, Liapis SC, Gerhardinger C, Bester A, Pandolfi PP, Clohessy JG, Hoekstra HE, Sauvageau M, Rinn JL. The Tug1 lncRNA locus is essential for male fertility. Genome Biol. 2020 09 07; 21(1):237.
    View in: PubMed
    Score: 0.578
  6. Rinn JL, Chang HY. Long Noncoding RNAs: Molecular Modalities to Organismal Functions. Annu Rev Biochem. 2020 06 20; 89:283-308.
    View in: PubMed
    Score: 0.569
  7. Andergassen D, Smith ZD, Lewandowski JP, Gerhardinger C, Meissner A, Rinn JL. In vivo Firre and Dxz4 deletion elucidates roles for autosomal gene regulation. Elife. 2019 11 18; 8.
    View in: PubMed
    Score: 0.547
  8. Lewandowski JP, Lee JC, Hwang T, Sunwoo H, Goldstein JM, Groff AF, Chang NP, Mallard W, Williams A, Henao-Meija J, Flavell RA, Lee JT, Gerhardinger C, Wagers AJ, Rinn JL. The Firre locus produces a trans-acting RNA molecule that functions in hematopoiesis. Nat Commun. 2019 11 13; 10(1):5137.
    View in: PubMed
    Score: 0.546
  9. Smallegan MJ, Rinn JL. Linking long noncoding RNA to drug resistance. Proc Natl Acad Sci U S A. 2019 10 29; 116(44):21963-21965.
    View in: PubMed
    Score: 0.543
  10. Raj A, Rinn JL. Illuminating Genomic Dark Matter with RNA Imaging. Cold Spring Harb Perspect Biol. 2019 05 01; 11(5).
    View in: PubMed
    Score: 0.526
  11. Mattioli K, Volders PJ, Gerhardinger C, Lee JC, Maass PG, Mel? M, Rinn JL. High-throughput functional analysis of lncRNA core promoters elucidates rules governing tissue specificity. Genome Res. 2019 03; 29(3):344-355.
    View in: PubMed
    Score: 0.517
  12. Groff AF, Barutcu AR, Lewandowski JP, Rinn JL. Enhancers in the Peril lincRNA locus regulate distant but not local genes. Genome Biol. 2018 12 11; 19(1):219.
    View in: PubMed
    Score: 0.512
  13. Maass PG, Barutcu AR, Rinn JL. Interchromosomal interactions: A genomic love story of kissing chromosomes. J Cell Biol. 2019 01 07; 218(1):27-38.
    View in: PubMed
    Score: 0.503
  14. Barutcu AR, Maass PG, Lewandowski JP, Weiner CL, Rinn JL. A TAD boundary is preserved upon deletion of the CTCF-rich Firre locus. Nat Commun. 2018 04 13; 9(1):1444.
    View in: PubMed
    Score: 0.489
  15. Shukla CJ, McCorkindale AL, Gerhardinger C, Korthauer KD, Cabili MN, Shechner DM, Irizarry RA, Maass PG, Rinn JL. High-throughput identification of RNA nuclear enrichment sequences. EMBO J. 2018 03 15; 37(6).
    View in: PubMed
    Score: 0.481
  16. Mel? M, Mattioli K, Mallard W, Shechner DM, Gerhardinger C, Rinn JL. Chromatin environment, transcriptional regulation, and splicing distinguish lincRNAs and mRNAs. Genome Res. 2017 01; 27(1):27-37.
    View in: PubMed
    Score: 0.446
  17. Groff AF, Sanchez-Gomez DB, Soruco MML, Gerhardinger C, Barutcu AR, Li E, Elcavage L, Plana O, Sanchez LV, Lee JC, Sauvageau M, Rinn JL. In?Vivo Characterization of Linc-p21 Reveals Functional cis-Regulatory DNA Elements. Cell Rep. 2016 08 23; 16(8):2178-2186.
    View in: PubMed
    Score: 0.436
  18. Mel? M, Rinn JL. "Cat's Cradling" the 3D Genome by the Act of LncRNA Transcription. Mol Cell. 2016 06 02; 62(5):657-64.
    View in: PubMed
    Score: 0.430
  19. Hacisuleyman E, Shukla CJ, Weiner CL, Rinn JL. Function and evolution of local repeats in the Firre locus. Nat Commun. 2016 Mar 24; 7:11021.
    View in: PubMed
    Score: 0.424
  20. Goff LA, Rinn JL. Linking RNA biology to lncRNAs. Genome Res. 2015 Oct; 25(10):1456-65.
    View in: PubMed
    Score: 0.411
  21. Goff LA, Groff AF, Sauvageau M, Trayes-Gibson Z, Sanchez-Gomez DB, Morse M, Martin RD, Elcavage LE, Liapis SC, Gonzalez-Celeiro M, Plana O, Li E, Gerhardinger C, Tomassy GS, Arlotta P, Rinn JL. Spatiotemporal expression and transcriptional perturbations by long noncoding RNAs in the mouse brain. Proc Natl Acad Sci U S A. 2015 Jun 02; 112(22):6855-62.
    View in: PubMed
    Score: 0.401
  22. Shechner DM, Hacisuleyman E, Younger ST, Rinn JL. Multiplexable, locus-specific targeting of long RNAs with CRISPR-Display. Nat Methods. 2015 Jul; 12(7):664-70.
    View in: PubMed
    Score: 0.401
  23. Rinn J, Guttman M. RNA Function. RNA and dynamic nuclear organization. Science. 2014 Sep 12; 345(6202):1240-1.
    View in: PubMed
    Score: 0.382
  24. Rinn JL. lncRNAs: linking RNA to chromatin. Cold Spring Harb Perspect Biol. 2014 Aug 01; 6(8).
    View in: PubMed
    Score: 0.379
  25. Younger ST, Rinn JL. 'Lnc'-ing enhancers to MYC regulation. Cell Res. 2014 Jun; 24(6):643-4.
    View in: PubMed
    Score: 0.372
  26. Hacisuleyman E, Goff LA, Trapnell C, Williams A, Henao-Mejia J, Sun L, McClanahan P, Hendrickson DG, Sauvageau M, Kelley DR, Morse M, Engreitz J, Lander ES, Guttman M, Lodish HF, Flavell R, Raj A, Rinn JL. Topological organization of multichromosomal regions by the long intergenic noncoding RNA Firre. Nat Struct Mol Biol. 2014 Feb; 21(2):198-206.
    View in: PubMed
    Score: 0.365
  27. Sauvageau M, Goff LA, Lodato S, Bonev B, Groff AF, Gerhardinger C, Sanchez-Gomez DB, Hacisuleyman E, Li E, Spence M, Liapis SC, Mallard W, Morse M, Swerdel MR, D'Ecclessis MF, Moore JC, Lai V, Gong G, Yancopoulos GD, Frendewey D, Kellis M, Hart RP, Valenzuela DM, Arlotta P, Rinn JL. Multiple knockout mouse models reveal lincRNAs are required for life and brain development. Elife. 2013 Dec 31; 2:e01749.
    View in: PubMed
    Score: 0.364
  28. Sun L, Goff LA, Trapnell C, Alexander R, Lo KA, Hacisuleyman E, Sauvageau M, Tazon-Vega B, Kelley DR, Hendrickson DG, Yuan B, Kellis M, Lodish HF, Rinn JL. Long noncoding RNAs regulate adipogenesis. Proc Natl Acad Sci U S A. 2013 Feb 26; 110(9):3387-92.
    View in: PubMed
    Score: 0.342
  29. Kelley D, Rinn J. Transposable elements reveal a stem cell-specific class of long noncoding RNAs. Genome Biol. 2012 Nov 26; 13(11):R107.
    View in: PubMed
    Score: 0.337
  30. Hasenbein TP, Hoelzl S, Smith ZD, Gerhardinger C, Gonner MOC, Aguilar-Pimentel A, Amarie OV, Becker L, Calzada-Wack J, Dragano NRV, da Silva-Buttkus P, Garrett L, H?lter SM, Kraiger M, ?stereicher MA, Rathkolb B, Sanz-Moreno A, Spielmann N, Wurst W, Gailus-Durner V, Fuchs H, Hrabe de Angelis M, Meissner A, Engelhardt S, Rinn JL, Andergassen D. X-linked deletion of Crossfirre, Firre, and Dxz4 in vivo uncovers diverse phenotypes and combinatorial effects on autosomes. Nat Commun. 2024 12 05; 15(1):10631.
    View in: PubMed
    Score: 0.194
  31. Santus L, Sopena-Rios M, Garc?a-P?rez R, Lin AE, Adams GC, Barnes KG, Siddle KJ, Wohl S, Reverter F, Rinn JL, Bennett RS, Hensley LE, Sabeti PC, Mel? M. Single-cell profiling of lncRNA expression during Ebola virus infection in rhesus macaques. Nat Commun. 2023 06 30; 14(1):3866.
    View in: PubMed
    Score: 0.176
  32. Landshammer A, Bolondi A, Kretzmer H, Much C, Buschow R, Rose A, Wu HJ, Mackowiak SD, Braendl B, Giesselmann P, Tornisiello R, Parsi KM, Huey J, Mielke T, Meierhofer D, Maehr R, Hnisz D, Michor F, Rinn JL, Meissner A. T-REX17 is a transiently expressed non-coding RNA essential for human endoderm formation. Elife. 2023 01 31; 12.
    View in: PubMed
    Score: 0.171
  33. Mattick JS, Amaral PP, Carninci P, Carpenter S, Chang HY, Chen LL, Chen R, Dean C, Dinger ME, Fitzgerald KA, Gingeras TR, Guttman M, Hirose T, Huarte M, Johnson R, Kanduri C, Kapranov P, Lawrence JB, Lee JT, Mendell JT, Mercer TR, Moore KJ, Nakagawa S, Rinn JL, Spector DL, Ulitsky I, Wan Y, Wilusz JE, Wu M. Long non-coding RNAs: definitions, functions, challenges and recommendations. Nat Rev Mol Cell Biol. 2023 06; 24(6):430-447.
    View in: PubMed
    Score: 0.170
  34. Broadwell LJ, Smallegan MJ, Rigby KM, Navarro-Arriola JS, Montgomery RL, Rinn JL, Leinwand LA. Myosin 7b is a regulatory long noncoding RNA (lncMYH7b) in the human heart. J Biol Chem. 2021 Jan-Jun; 296:100694.
    View in: PubMed
    Score: 0.151
  35. Ruan X, Li P, Ma Y, Jiang CF, Chen Y, Shi Y, Gupta N, Seifuddin F, Pirooznia M, Ohnishi Y, Yoneda N, Nishiwaki M, Dumbovic G, Rinn JL, Higuchi Y, Kawai K, Suemizu H, Cao H. Identification of human long noncoding RNAs associated with nonalcoholic fatty liver disease and metabolic homeostasis. J Clin Invest. 2021 01 04; 131(1).
    View in: PubMed
    Score: 0.148
  36. Fang H, Bonora G, Lewandowski JP, Thakur J, Filippova GN, Henikoff S, Shendure J, Duan Z, Rinn JL, Deng X, Noble WS, Disteche CM. Trans- and cis-acting effects of Firre on epigenetic features of the inactive X chromosome. Nat Commun. 2020 11 27; 11(1):6053.
    View in: PubMed
    Score: 0.147
  37. Elling R, Robinson EK, Shapleigh B, Liapis SC, Covarrubias S, Katzman S, Groff AF, Jiang Z, Agarwal S, Motwani M, Chan J, Sharma S, Hennessy EJ, FitzGerald GA, McManus MT, Rinn JL, Fitzgerald KA, Carpenter S. Genetic Models Reveal cis and trans Immune-Regulatory Activities for lincRNA-Cox2. Cell Rep. 2018 11 06; 25(6):1511-1524.e6.
    View in: PubMed
    Score: 0.127
  38. Bester AC, Lee JD, Chavez A, Lee YR, Nachmani D, Vora S, Victor J, Sauvageau M, Monteleone E, Rinn JL, Provero P, Church GM, Clohessy JG, Pandolfi PP. An Integrated Genome-wide CRISPRa Approach to Functionalize lncRNAs in Drug Resistance. Cell. 2018 04 19; 173(3):649-664.e20.
    View in: PubMed
    Score: 0.122
  39. Mowel WK, McCright SJ, Kotzin JJ, Collet MA, Uyar A, Chen X, DeLaney A, Spencer SP, Virtue AT, Yang E, Villarino A, Kurachi M, Dunagin MC, Pritchard GH, Stein J, Hughes C, Fonseca-Pereira D, Veiga-Fernandes H, Raj A, Kambayashi T, Brodsky IE, O'Shea JJ, Wherry EJ, Goff LA, Rinn JL, Williams A, Flavell RA, Henao-Mejia J. Group 1 Innate Lymphoid Cell Lineage Identity Is Determined by a cis-Regulatory Element Marked by a Long Non-coding RNA. Immunity. 2017 09 19; 47(3):435-449.e8.
    View in: PubMed
    Score: 0.118
  40. Del?s MJ, Sabin LR, Dolzhenko E, Knott SR, Munera Maravilla E, Jackson BT, Wild SA, Kovacevic T, Stork EM, Zhou M, Erard N, Lee E, Kelley DR, Roth M, Barbosa IA, Zuber J, Rinn JL, Smith AD, Hannon GJ. lncRNA requirements for mouse acute myeloid leukemia and normal differentiation. Elife. 2017 09 06; 6.
    View in: PubMed
    Score: 0.117
  41. Mello SS, Sinow C, Raj N, Mazur PK, Bieging-Rolett K, Broz DK, Imam JFC, Vogel H, Wood LD, Sage J, Hirose T, Nakagawa S, Rinn J, Attardi LD. Neat1 is a p53-inducible lincRNA essential for transformation suppression. Genes Dev. 2017 06 01; 31(11):1095-1108.
    View in: PubMed
    Score: 0.115
  42. Henry WS, Hendrickson DG, Beca F, Glass B, Lindahl-Allen M, He L, Ji Z, Struhl K, Beck AH, Rinn JL, Toker A. LINC00520 is induced by Src, STAT3, and PI3K and plays a functional role in breast cancer. Oncotarget. 2016 Dec 13; 7(50):81981-81994.
    View in: PubMed
    Score: 0.112
  43. Kotzin JJ, Spencer SP, McCright SJ, Kumar DBU, Collet MA, Mowel WK, Elliott EN, Uyar A, Makiya MA, Dunagin MC, Harman CCD, Virtue AT, Zhu S, Bailis W, Stein J, Hughes C, Raj A, Wherry EJ, Goff LA, Klion AD, Rinn JL, Williams A, Flavell RA, Henao-Mejia J. The long non-coding RNA Morrbid regulates Bim and short-lived myeloid cell lifespan. Nature. 2016 09 08; 537(7619):239-243.
    View in: PubMed
    Score: 0.109
  44. Du Z, Sun T, Hacisuleyman E, Fei T, Wang X, Brown M, Rinn JL, Lee MG, Chen Y, Kantoff PW, Liu XS. Integrative analyses reveal a long noncoding RNA-mediated sponge regulatory network in prostate cancer. Nat Commun. 2016 Mar 15; 7:10982.
    View in: PubMed
    Score: 0.106
  45. G Hendrickson D, Kelley DR, Tenen D, Bernstein B, Rinn JL. Widespread RNA binding by chromatin-associated proteins. Genome Biol. 2016 Feb 16; 17:28.
    View in: PubMed
    Score: 0.105
  46. Stojic L, Niemczyk M, Orjalo A, Ito Y, Ruijter AE, Uribe-Lewis S, Joseph N, Weston S, Menon S, Odom DT, Rinn J, Gergely F, Murrell A. Transcriptional silencing of long noncoding RNA GNG12-AS1 uncouples its transcriptional and product-related functions. Nat Commun. 2016 Feb 02; 7:10406.
    View in: PubMed
    Score: 0.105
  47. Broadbent KM, Broadbent JC, Ribacke U, Wirth D, Rinn JL, Sabeti PC. Strand-specific RNA sequencing in Plasmodium falciparum malaria identifies developmentally regulated long non-coding RNA and circular RNA. BMC Genomics. 2015 Jun 13; 16:454.
    View in: PubMed
    Score: 0.101
  48. Lai KM, Gong G, Atanasio A, Rojas J, Quispe J, Posca J, White D, Huang M, Fedorova D, Grant C, Miloscio L, Droguett G, Poueymirou WT, Auerbach W, Yancopoulos GD, Frendewey D, Rinn J, Valenzuela DM. Diverse Phenotypes and Specific Transcription Patterns in Twenty Mouse Lines with Ablated LincRNAs. PLoS One. 2015; 10(4):e0125522.
    View in: PubMed
    Score: 0.100
  49. Younger ST, Kenzelmann-Broz D, Jung H, Attardi LD, Rinn JL. Integrative genomic analysis reveals widespread enhancer regulation by p53 in response to DNA damage. Nucleic Acids Res. 2015 May 19; 43(9):4447-62.
    View in: PubMed
    Score: 0.099
  50. Cabili MN, Dunagin MC, McClanahan PD, Biaesch A, Padovan-Merhar O, Regev A, Rinn JL, Raj A. Localization and abundance analysis of human lncRNAs at single-cell and single-molecule resolution. Genome Biol. 2015 Jan 29; 16:20.
    View in: PubMed
    Score: 0.098
  51. Dunagin M, Cabili MN, Rinn J, Raj A. Visualization of lncRNA by single-molecule fluorescence in situ hybridization. Methods Mol Biol. 2015; 1262:3-19.
    View in: PubMed
    Score: 0.097
  52. Molyneaux BJ, Goff LA, Brettler AC, Chen HH, Hrvatin S, Rinn JL, Arlotta P. DeCoN: genome-wide analysis of in vivo transcriptional dynamics during pyramidal neuron fate selection in neocortex. Neuron. 2015 Jan 21; 85(2):275-288.
    View in: PubMed
    Score: 0.097
  53. Maamar H, Cabili MN, Rinn J, Raj A. linc-HOXA1 is a noncoding RNA that represses Hoxa1 transcription in cis. Genes Dev. 2013 Jun 01; 27(11):1260-71.
    View in: PubMed
    Score: 0.087
  54. Chew GL, Pauli A, Rinn JL, Regev A, Schier AF, Valen E. Ribosome profiling reveals resemblance between long non-coding RNAs and 5' leaders of coding RNAs. Development. 2013 Jul; 140(13):2828-34.
    View in: PubMed
    Score: 0.087
  55. Mar?n-B?jar O, Marchese FP, Athie A, S?nchez Y, Gonz?lez J, Segura V, Huang L, Moreno I, Navarro A, Monz? M, Garc?a-Foncillas J, Rinn JL, Guo S, Huarte M. Pint lincRNA connects the p53 pathway with epigenetic silencing by the Polycomb repressive complex 2. Genome Biol. 2013; 14(9):R104.
    View in: PubMed
    Score: 0.085
  56. Yoon JH, Abdelmohsen K, Kim J, Yang X, Martindale JL, Tominaga-Yamanaka K, White EJ, Orjalo AV, Rinn JL, Kreft SG, Wilson GM, Gorospe M. Scaffold function of long non-coding RNA HOTAIR in protein ubiquitination. Nat Commun. 2013; 4:2939.
    View in: PubMed
    Score: 0.085
  57. Kretz M, Siprashvili Z, Chu C, Webster DE, Zehnder A, Qu K, Lee CS, Flockhart RJ, Groff AF, Chow J, Johnston D, Kim GE, Spitale RC, Flynn RA, Zheng GX, Aiyer S, Raj A, Rinn JL, Chang HY, Khavari PA. Control of somatic tissue differentiation by the long non-coding RNA TINCR. Nature. 2013 Jan 10; 493(7431):231-5.
    View in: PubMed
    Score: 0.084
  58. Lee YH, Hass EP, Campodonico W, Lee YK, Lasda E, Shah JS, Rinn JL, Hwang T. Massively parallel dissection of RNA in RNA-protein interactions in vivo. Nucleic Acids Res. 2024 Jun 10; 52(10):e48.
    View in: PubMed
    Score: 0.047
  59. Cable J, Heard E, Hirose T, Prasanth KV, Chen LL, Henninger JE, Quinodoz SA, Spector DL, Diermeier SD, Porman AM, Kumar D, Feinberg MW, Shen X, Unfried JP, Johnson R, Chen CK, Wilusz JE, Lempradl A, McGeary SE, Wahba L, Pyle AM, Hargrove AE, Simon MD, Marcia M, Przanowska RK, Chang HY, Jaffrey SR, Contreras LM, Chen Q, Shi J, Mendell JT, He L, Song E, Rinn JL, Lalwani MK, Kalem MC, Chuong EB, Maquat LE, Liu X. Noncoding RNAs: biology and applications-a Keystone Symposia report. Ann N Y Acad Sci. 2021 12; 1506(1):118-141.
    View in: PubMed
    Score: 0.039
  60. Andergassen D, Smith ZD, Kretzmer H, Rinn JL, Meissner A. Diverse epigenetic mechanisms maintain parental imprints within the embryonic and extraembryonic lineages. Dev Cell. 2021 11 08; 56(21):2995-3005.e4.
    View in: PubMed
    Score: 0.039
  61. Haswell JR, Mattioli K, Gerhardinger C, Maass PG, Foster DJ, Peinado P, Wang X, Medina PP, Rinn JL, Slack FJ. Genome-wide CRISPR interference screen identifies long non-coding RNA loci required for differentiation and pluripotency. PLoS One. 2021; 16(11):e0252848.
    View in: PubMed
    Score: 0.039
  62. Holmes ZE, Hamilton DJ, Hwang T, Parsonnet NV, Rinn JL, Wuttke DS, Batey RT. The Sox2 transcription factor binds RNA. Nat Commun. 2020 04 14; 11(1):1805.
    View in: PubMed
    Score: 0.035
  63. Tay Y, Rinn J, Pandolfi PP. The multilayered complexity of ceRNA crosstalk and competition. Nature. 2014 Jan 16; 505(7483):344-52.
    View in: PubMed
    Score: 0.023
  64. Kretz M, Webster DE, Flockhart RJ, Lee CS, Zehnder A, Lopez-Pajares V, Qu K, Zheng GX, Chow J, Kim GE, Rinn JL, Chang HY, Siprashvili Z, Khavari PA. Suppression of progenitor differentiation requires the long noncoding RNA ANCR. Genes Dev. 2012 Feb 15; 26(4):338-43.
    View in: PubMed
    Score: 0.020
Connection Strength

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Publication scores are based on many factors, including how long ago they were written and whether the person is a first or senior author.

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