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Items: 1 to 50 of 109

1.

Reorganization of inter-chromosomal interactions in the 2q37-deletion syndrome.

Maass PG, Weise A, Rittscher K, Lichtenwald J, Barutcu AR, Liehr T, Aydin A, Wefeld-Neuenfeld Y, Pölsler L, Tinschert S, Rinn JL, Luft FC, Bähring S.

EMBO J. 2018 Jun 19. pii: e96257. doi: 10.15252/embj.201696257. [Epub ahead of print]

PMID:
29921581
2.

An Integrated Genome-wide CRISPRa Approach to Functionalize lncRNAs in Drug Resistance.

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.

Cell. 2018 Apr 19;173(3):649-664.e20. doi: 10.1016/j.cell.2018.03.052.

PMID:
29677511
3.

A TAD boundary is preserved upon deletion of the CTCF-rich Firre locus.

Barutcu AR, Maass PG, Lewandowski JP, Weiner CL, Rinn JL.

Nat Commun. 2018 Apr 13;9(1):1444. doi: 10.1038/s41467-018-03614-0.

4.

A CLK3-HMGA2 Alternative Splicing Axis Impacts Human Hematopoietic Stem Cell Molecular Identity throughout Development.

Cesana M, Guo MH, Cacchiarelli D, Wahlster L, Barragan J, Doulatov S, Vo LT, Salvatori B, Trapnell C, Clement K, Cahan P, Tsanov KM, Sousa PM, Tazon-Vega B, Bolondi A, Giorgi FM, Califano A, Rinn JL, Meissner A, Hirschhorn JN, Daley GQ.

Cell Stem Cell. 2018 Apr 5;22(4):575-588.e7. doi: 10.1016/j.stem.2018.03.012.

PMID:
29625070
5.

Inter-chromosomal Contact Properties in Live-Cell Imaging and in Hi-C.

Maass PG, Barutcu AR, Weiner CL, Rinn JL.

Mol Cell. 2018 Apr 5;70(1):188-189. doi: 10.1016/j.molcel.2018.03.021. No abstract available.

6.

Inter-chromosomal Contact Properties in Live-Cell Imaging and in Hi-C.

Maass PG, Barutcu AR, Weiner CL, Rinn JL.

Mol Cell. 2018 Mar 15;69(6):1039-1045.e3. doi: 10.1016/j.molcel.2018.02.007. Epub 2018 Mar 8. Erratum in: Mol Cell. 2018 Apr 5;70(1):188-189.

PMID:
29526697
7.

Genetic determinants and epigenetic effects of pioneer-factor occupancy.

Donaghey J, Thakurela S, Charlton J, Chen JS, Smith ZD, Gu H, Pop R, Clement K, Stamenova EK, Karnik R, Kelley DR, Gifford CA, Cacchiarelli D, Rinn JL, Gnirke A, Ziller MJ, Meissner A.

Nat Genet. 2018 Feb;50(2):250-258. doi: 10.1038/s41588-017-0034-3. Epub 2018 Jan 22.

PMID:
29358654
8.

Spatiotemporal allele organization by allele-specific CRISPR live-cell imaging (SNP-CLING).

Maass PG, Barutcu AR, Shechner DM, Weiner CL, Melé M, Rinn JL.

Nat Struct Mol Biol. 2018 Feb;25(2):176-184. doi: 10.1038/s41594-017-0015-3. Epub 2018 Jan 8.

9.

High-throughput identification of RNA nuclear enrichment sequences.

Shukla CJ, McCorkindale AL, Gerhardinger C, Korthauer KD, Cabili MN, Shechner DM, Irizarry RA, Maass PG, Rinn JL.

EMBO J. 2018 Mar 15;37(6). pii: e98452. doi: 10.15252/embj.201798452. Epub 2018 Jan 15.

10.

Live-cell mapping of organelle-associated RNAs via proximity biotinylation combined with protein-RNA crosslinking.

Kaewsapsak P, Shechner DM, Mallard W, Rinn JL, Ting AY.

Elife. 2017 Dec 14;6. pii: e29224. doi: 10.7554/eLife.29224.

11.

p53 regulates enhancer accessibility and activity in response to DNA damage.

Younger ST, Rinn JL.

Nucleic Acids Res. 2017 Sep 29;45(17):9889-9900. doi: 10.1093/nar/gkx577.

12.

Group 1 Innate Lymphoid Cell Lineage Identity Is Determined by a cis-Regulatory Element Marked by a Long Non-coding RNA.

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.

Immunity. 2017 Sep 19;47(3):435-449.e8. doi: 10.1016/j.immuni.2017.08.012.

PMID:
28930659
13.

lncRNA requirements for mouse acute myeloid leukemia and normal differentiation.

Delás 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.

Elife. 2017 Sep 6;6. pii: e25607. doi: 10.7554/eLife.25607.

14.

Chromatin environment, transcriptional regulation, and splicing distinguish lincRNAs and mRNAs.

Melé M, Mattioli K, Mallard W, Shechner DM, Gerhardinger C, Rinn JL.

Genome Res. 2017 Jan;27(1):27-37. doi: 10.1101/gr.214205.116. Epub 2016 Dec 7.

15.

LINC00520 is induced by Src, STAT3, and PI3K and plays a functional role in breast cancer.

Henry WS, Hendrickson DG, Beca F, Glass B, Lindahl-Allen M, He L, Ji Z, Struhl K, Beck AH, Rinn JL, Toker A.

Oncotarget. 2016 Dec 13;7(50):81981-81994. doi: 10.18632/oncotarget.11962.

16.

In vivo Ebola virus infection leads to a strong innate response in circulating immune cells.

Caballero IS, Honko AN, Gire SK, Winnicki SM, Melé M, Gerhardinger C, Lin AE, Rinn JL, Sabeti PC, Hensley LE, Connor JH.

BMC Genomics. 2016 Sep 5;17:707. doi: 10.1186/s12864-016-3060-0.

17.

The long non-coding RNA Morrbid regulates Bim and short-lived myeloid cell lifespan.

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.

Nature. 2016 Sep 8;537(7619):239-243. doi: 10.1038/nature19346. Epub 2016 Aug 15.

18.

In Vivo Characterization of Linc-p21 Reveals Functional cis-Regulatory DNA Elements.

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.

Cell Rep. 2016 Aug 23;16(8):2178-2186. doi: 10.1016/j.celrep.2016.07.050. Epub 2016 Aug 11.

19.

"Cat's Cradling" the 3D Genome by the Act of LncRNA Transcription.

Melé M, Rinn JL.

Mol Cell. 2016 Jun 2;62(5):657-64. doi: 10.1016/j.molcel.2016.05.011. Review.

20.

Basset: learning the regulatory code of the accessible genome with deep convolutional neural networks.

Kelley DR, Snoek J, Rinn JL.

Genome Res. 2016 Jul;26(7):990-9. doi: 10.1101/gr.200535.115. Epub 2016 May 3.

21.

A distant trophoblast-specific enhancer controls HLA-G expression at the maternal-fetal interface.

Ferreira LM, Meissner TB, Mikkelsen TS, Mallard W, O'Donnell CW, Tilburgs T, Gomes HA, Camahort R, Sherwood RI, Gifford DK, Rinn JL, Cowan CA, Strominger JL.

Proc Natl Acad Sci U S A. 2016 May 10;113(19):5364-9. doi: 10.1073/pnas.1602886113. Epub 2016 Apr 13.

22.

Function and evolution of local repeats in the Firre locus.

Hacisuleyman E, Shukla CJ, Weiner CL, Rinn JL.

Nat Commun. 2016 Mar 24;7:11021. doi: 10.1038/ncomms11021.

23.

Integrative analyses reveal a long noncoding RNA-mediated sponge regulatory network in prostate cancer.

Du Z, Sun T, Hacisuleyman E, Fei T, Wang X, Brown M, Rinn JL, Lee MG, Chen Y, Kantoff PW, Liu XS.

Nat Commun. 2016 Mar 15;7:10982. doi: 10.1038/ncomms10982.

24.

Widespread RNA binding by chromatin-associated proteins.

G Hendrickson D, Kelley DR, Tenen D, Bernstein B, Rinn JL.

Genome Biol. 2016 Feb 16;17:28. doi: 10.1186/s13059-016-0878-3.

25.

Mechanisms of Long Non-coding RNAs in Mammalian Nervous System Development, Plasticity, Disease, and Evolution.

Briggs JA, Wolvetang EJ, Mattick JS, Rinn JL, Barry G.

Neuron. 2015 Dec 2;88(5):861-877. doi: 10.1016/j.neuron.2015.09.045. Review.

26.

Silent pericentromeric repeats speak out.

Younger ST, Rinn JL.

Proc Natl Acad Sci U S A. 2015 Dec 8;112(49):15008-9. doi: 10.1073/pnas.1520341112. Epub 2015 Nov 18. No abstract available.

27.

A comparison of genetically matched cell lines reveals the equivalence of human iPSCs and ESCs.

Choi J, Lee S, Mallard W, Clement K, Tagliazucchi GM, Lim H, Choi IY, Ferrari F, Tsankov AM, Pop R, Lee G, Rinn JL, Meissner A, Park PJ, Hochedlinger K.

Nat Biotechnol. 2015 Nov;33(11):1173-81. doi: 10.1038/nbt.3388. Epub 2015 Oct 26.

28.

Linking RNA biology to lncRNAs.

Goff LA, Rinn JL.

Genome Res. 2015 Oct;25(10):1456-65. doi: 10.1101/gr.191122.115. Review.

29.

Genome-wide RNA-Seq of Human Motor Neurons Implicates Selective ER Stress Activation in Spinal Muscular Atrophy.

Ng SY, Soh BS, Rodriguez-Muela N, Hendrickson DG, Price F, Rinn JL, Rubin LL.

Cell Stem Cell. 2015 Nov 5;17(5):569-84. doi: 10.1016/j.stem.2015.08.003. Epub 2015 Aug 27.

30.

Integrative Analyses of Human Reprogramming Reveal Dynamic Nature of Induced Pluripotency.

Cacchiarelli D, Trapnell C, Ziller MJ, Soumillon M, Cesana M, Karnik R, Donaghey J, Smith ZD, Ratanasirintrawoot S, Zhang X, Ho Sui SJ, Wu Z, Akopian V, Gifford CA, Doench J, Rinn JL, Daley GQ, Meissner A, Lander ES, Mikkelsen TS.

Cell. 2015 Jul 16;162(2):412-424. doi: 10.1016/j.cell.2015.06.016.

31.

Strand-specific RNA sequencing in Plasmodium falciparum malaria identifies developmentally regulated long non-coding RNA and circular RNA.

Broadbent KM, Broadbent JC, Ribacke U, Wirth D, Rinn JL, Sabeti PC.

BMC Genomics. 2015 Jun 13;16:454. doi: 10.1186/s12864-015-1603-4.

32.

Spatiotemporal expression and transcriptional perturbations by long noncoding RNAs in the mouse brain.

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.

Proc Natl Acad Sci U S A. 2015 Jun 2;112(22):6855-62.

33.

Multiplexable, locus-specific targeting of long RNAs with CRISPR-Display.

Shechner DM, Hacisuleyman E, Younger ST, Rinn JL.

Nat Methods. 2015 Jul;12(7):664-70. doi: 10.1038/nmeth.3433. Epub 2015 Jun 1.

34.

Integrative genomic analysis reveals widespread enhancer regulation by p53 in response to DNA damage.

Younger ST, Kenzelmann-Broz D, Jung H, Attardi LD, Rinn JL.

Nucleic Acids Res. 2015 May 19;43(9):4447-62. doi: 10.1093/nar/gkv284. Epub 2015 Apr 16.

35.

Targeted disruption of DNMT1, DNMT3A and DNMT3B in human embryonic stem cells.

Liao J, Karnik R, Gu H, Ziller MJ, Clement K, Tsankov AM, Akopian V, Gifford CA, Donaghey J, Galonska C, Pop R, Reyon D, Tsai SQ, Mallard W, Joung JK, Rinn JL, Gnirke A, Meissner A.

Nat Genet. 2015 May;47(5):469-78. doi: 10.1038/ng.3258. Epub 2015 Mar 30.

36.

Localization and abundance analysis of human lncRNAs at single-cell and single-molecule resolution.

Cabili MN, Dunagin MC, McClanahan PD, Biaesch A, Padovan-Merhar O, Regev A, Rinn JL, Raj A.

Genome Biol. 2015 Jan 29;16:20. doi: 10.1186/s13059-015-0586-4.

37.

Transposable elements modulate human RNA abundance and splicing via specific RNA-protein interactions.

Kelley DR, Hendrickson DG, Tenen D, Rinn JL.

Genome Biol. 2014 Dec 3;15(12):537. doi: 10.1186/s13059-014-0537-5.

38.

Discovery and annotation of long noncoding RNAs.

Mattick JS, Rinn JL.

Nat Struct Mol Biol. 2015 Jan;22(1):5-7. doi: 10.1038/nsmb.2942.

PMID:
25565026
39.

DeCoN: genome-wide analysis of in vivo transcriptional dynamics during pyramidal neuron fate selection in neocortex.

Molyneaux BJ, Goff LA, Brettler AC, Chen HH, Hrvatin S, Rinn JL, Arlotta P.

Neuron. 2015 Jan 21;85(2):275-288. doi: 10.1016/j.neuron.2014.12.024. Epub 2014 Dec 31. Erratum in: Neuron. 2016 Jan 6;89(1):235.

40.

lncRNAs: linking RNA to chromatin.

Rinn JL.

Cold Spring Harb Perspect Biol. 2014 Aug 1;6(8). pii: a018614. doi: 10.1101/cshperspect.a018614. Review.

41.

Gene co-regulation by Fezf2 selects neurotransmitter identity and connectivity of corticospinal neurons.

Lodato S, Molyneaux BJ, Zuccaro E, Goff LA, Chen HH, Yuan W, Meleski A, Takahashi E, Mahony S, Rinn JL, Gifford DK, Arlotta P.

Nat Neurosci. 2014 Aug;17(8):1046-54. doi: 10.1038/nn.3757. Epub 2014 Jul 6.

42.

'Lnc'-ing enhancers to MYC regulation.

Younger ST, Rinn JL.

Cell Res. 2014 Jun;24(6):643-4. doi: 10.1038/cr.2014.54. Epub 2014 Apr 29.

43.

The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells.

Trapnell C, Cacchiarelli D, Grimsby J, Pokharel P, Li S, Morse M, Lennon NJ, Livak KJ, Mikkelsen TS, Rinn JL.

Nat Biotechnol. 2014 Apr;32(4):381-386. doi: 10.1038/nbt.2859. Epub 2014 Mar 23.

44.

'Oming in on RNA-protein interactions.

Rinn JL, Ule J.

Genome Biol. 2014 Jan 31;15(1):401. doi: 10.1186/gb4158. No abstract available.

45.

Topological organization of multichromosomal regions by the long intergenic noncoding RNA Firre.

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.

Nat Struct Mol Biol. 2014 Feb;21(2):198-206. doi: 10.1038/nsmb.2764. Epub 2014 Jan 26.

46.

RNase-mediated protein footprint sequencing reveals protein-binding sites throughout the human transcriptome.

Silverman IM, Li F, Alexander A, Goff L, Trapnell C, Rinn JL, Gregory BD.

Genome Biol. 2014 Jan 7;15(1):R3. doi: 10.1186/gb-2014-15-1-r3.

47.

Multiple knockout mouse models reveal lincRNAs are required for life and brain development.

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.

Elife. 2013 Dec 31;2:e01749. doi: 10.7554/eLife.01749.

48.

Scaffold function of long non-coding RNA HOTAIR in protein ubiquitination.

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.

Nat Commun. 2013;4:2939. doi: 10.1038/ncomms3939.

49.

Poly-combing the genome for RNA.

Goff LA, Rinn JL.

Nat Struct Mol Biol. 2013 Dec;20(12):1344-6. doi: 10.1038/nsmb.2728.

PMID:
24304912
50.

DNMT1-interacting RNAs block gene-specific DNA methylation.

Di Ruscio A, Ebralidze AK, Benoukraf T, Amabile G, Goff LA, Terragni J, Figueroa ME, De Figueiredo Pontes LL, Alberich-Jorda M, Zhang P, Wu M, D'Alò F, Melnick A, Leone G, Ebralidze KK, Pradhan S, Rinn JL, Tenen DG.

Nature. 2013 Nov 21;503(7476):371-6. doi: 10.1038/nature12598. Epub 2013 Oct 9.

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