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Publications

|     2017   |     2016   |     2015   |     2014   |     2013   |     2012   |     2011 before  

2017

Litzenburger UM, Buenrostro JD, Wu B, Shen Y, Sheffield NC, Kathiria A, Greenleaf WJ, Chang HY.
Single-cell epigenomic variability reveals functional cancer heterogeneity.
Genome Biol. 2017 Jan 24;18(1):15. doi: 10.1186/s13059-016-1133-7.
Pubmed Genome Biol.   PDF

Xu J, Carter AC, Gendrel AV, Attia M, Loftus J, Greenleaf WJ, Tibshirani R, Heard E, Chang HY.
Landscape of monoallelic DNA accessibility in mouse embryonic stem cells and neural progenitor cells.
Nat Genet. 2017 Jan 23. doi: 10.1038/ng.3769
Pubmed Nat Genet.   PDF

Liu SJ,, Horlbeck MA, Cho SW, Birk HS, Malatesta M, He D, Attenello FJ, Villalta JE, Cho MY, Chen Y, Mandegar MA, Olvera MP, Gilbert LA, Conklin BR, Chang HY, Weissman JS, Lim DA.
CRISPRi-based genome-scale identification of functional long noncoding RNA loci in human cells.
Science. 2017 Jan 6;355(6320). pii: aah7111. doi: 10.1126/science.aah7111. Epub 2016 Dec 15.
Pubmed Science.   PDF

2016

Li L, Helms JA, Chang HY.
Comment on "Hotair Is Dispensable for Mouse Development".
PLoS Genet. 2016 Dec 15;12(12):e1006406. doi: 10.1371/journal.pgen.1006406. eCollection 2016.
Pubmed PLoS Genet.   PDF

Lee B, Flynn RA, Kadina A, Guo JK, Kool ET, Chang HY.
Comparison of SHAPE Reagents for Mapping RNA Structures Inside Living Cells.
RNA. 2016 Nov 22. pii: rna.058784.116.
Pubmed RNA.   PDF

Chen X, Shen Y, Draper W, Buenrostro JD, Litzenburger U, Cho SW, Satpathy AT, Carter AC, Ghosh RP, East-Seletsky A, Doudna JA, Greenleaf WJ, Liphardt JT, Chang HY.
ATAC-see reveals the accessible genome by transposase-mediated imaging and sequencing.
Nat Methods. 2016 Oct 17. doi: 10.1038/nmeth.4031
Pubmed Nat Methods.   PDF

Fazal FM, Chang HY.
lncRNA Structure: Message to the Heart.
Mol Cell. 2016 Oct 6;64(1):1-2. doi: 10.1016/j.molcel.2016.09.030.
Pubmed Mol Cell.   PDF

Schmitt AM, Garcia JT, Hung T, Flynn RA, Shen Y, Qu K, Payumo AY, Peres-da-Silva A, Broz DK, Baum R, Guo S, Chen JK, Attardi LD, Chang HY.
An inducible long noncoding RNA amplifies DNA damage signaling.
Nat Genet. 2016 Sep 26. doi: 10.1038/ng.3673
Pubmed Nat Genet.   PDF

Huang WH, Guenthner CJ, Xu J, Nguyen T, Schwarz LA, Wilkinson AW, Gozani O, Chang HY, Shamloo M, Luo L
Molecular and Neural Functions of Rai1, the Causal Gene for Smith-Magenis Syndrome.
Neuron. 2016 Sep 22. pii: S0896-6273(16)30578-5. doi: 10.1016/j.neuron.2016.09.019.
Pubmed Neuron.   PDF

Mumbach MR, Rubin AJ, Flynn RA, Dai C, Khavari PA, Greenleaf WJ, Chang HY.
HiChIP: efficient and sensitive analysis of protein-directed genome architecture.
Nat Methods. 2016 Sep 19. doi: 10.1038/nmeth.3999
Pubmed Nat Methods.   PDF

Corces MR, Buenrostro JD, Wu B, Greenside PG, Chan SM, Koenig J, Snyder MP, Pritchard JK, Kundaje A, Greenleaf WJ, Majeti R, Chang HY.
Lineage-specific and single-cell chromatin accessibility charts human hematopoiesis and leukemia evolution.
Nat Genet. 2016 Aug 15. doi: 10.1038/ng.3646.
Pubmed Nat Genet.   PDF

Giorgetti L, Lajoie BR, Carter AC, Attia M, Zhan Y, Xu J, Chen CJ, Kaplan N, Chang HY, Heard E,, Dekker J,.
Structural organization of the inactive X chromosome in the mouse.
Nature. 2016 Jul 18. doi: 10.1038/nature18589.
Pubmed Nature.   PDF

Atianand MK, Hu W, Satpathy AT, Shen Y, Ricci EP, Alvarez-Dominguez JR, Bhatta A, Schattgen SA, McGowan JD, Blin J, Braun JE, Gandhi P, Moore MJ, Chang HY, Lodish HF, Caffrey DR, Fitzgerald KA.
A Long Noncoding RNA lincRNA-EPS Acts as a Transcriptional Brake to Restrain Inflammation.
Cell. 2016 Jun 16;165(7):1672-85. doi: 10.1016/j.cell.2016.05.075.
Pubmed Cell   PDF

Sadik H, Korangath P, Nguyen N, Győrffy B, Kumar R, Hedayati M, Teo WW, Park S, Panday H, Gonzalez Munoz T, Menyhart O, Shah N, Pandita RK, Chang JC, DeWeese TL, Chang HY, Pandita TK, Sukumar S.
HOXC10 expression supports the development of chemotherapy resistance by fine tuning DNA repair in breast cancer cells.
Cancer Res. 2016 Jun 14. pii: canres.0774.2016
Pubmed Cancer Res.   PDF

Lu Z, Zhang QC, Lee B, Flynn RA, Smith MA, Robinson JT, Davidovich C, Gooding AR, Goodrich KJ, Mattick JS, Mesirov JP, Cech TR, Chang HY
RNA Duplex Map in Living Cells Reveals Higher-Order Transcriptome Structure.
Cell. 2016 May 11. pii: S0092-8674(16)30422-6. doi: 10.1016/j.cell.2016.04.028.
Pubmed Cell Cover PDF

Arda HE, Li L, Tsai J, Torre EA, Rosli Y, Peiris H, Spitale RC, Dai C, Gu X, Qu K, Wang P, Wang J, Grompe M, Scharfmann R, Snyder MS, Bottino R, Powers AC, Chang HY, Kim SK10.
Age-Dependent Pancreatic Gene Regulation Reveals Mechanisms Governing Human β Cell Function.
Cell Metab. 2016 May 10;23(5):909-20. doi: 10.1016/j.cmet.2016.04.002. Epub 2016 Apr 28.
Pubmed Cell Metab.   PDF

Zarnegar BJ, Flynn RA, Shen Y, Do BT, Chang HY, Khavari PA.
irCLIP platform for efficient characterization of protein-RNA interactions.
Nat Methods. 2016 Apr 25. doi: 10.1038/nmeth.3840
Pubmed Nat Methods..   PDF

Ma Q, Chang HY
Single-cell profiling of lncRNAs in the developing human brain.
Genome Biol. 2016 Apr 14;17(1):68. doi: 10.1186/s13059-016-0933-0.
Pubmed Genome Biol.   PDF

Schmitt AM, Chang HY.
Long Noncoding RNAs in Cancer Pathways.
Cancer Cell. 2016 Apr 11;29(4):452-63. doi: 10.1016/j.ccell.2016.03.010.
Pubmed Cancer Cell   PDF

Tan JL, Fogley RD, Flynn RA, Ablain J, Yang S, Saint-André V, Fan ZP, Do BT, Laga AC, Fujinaga K, Santoriello C, Greer CB, Kim YJ, Clohessy JG, Bothmer A, Pandell N, Avagyan S, Brogie JE, van Rooijen E, Hagedorn EJ, Shyh-Chang N, White RM, Price DH, Pandolfi PP, Peterlin BM, Zhou Y, Kim TH, Asara JM1, Chang HY, Young RA, Zon LI.
Stress from Nucleotide Depletion Activates the Transcriptional Regulator HEXIM1 to Suppress Melanoma.
Mol Cell. 2016 Apr 7;62(1):34-46. doi: 10.1016/j.molcel.2016.03.013.
Pubmed Mol Cell.   PDF

Oh S, Flynn RA, Floor SN, Purzner J, Martin L, Do BT, Schubert S, Vaka D, Morrissy S, Li Y, Kool M, Hovestadt V, Jones DT, Northcott PA, Risch T, Warnatz HJ, Yaspo ML, Adams CM, Leib RD, Breese M, Marra MA, Malkin D, Lichter P, Doudna JA, Pfister SM, Taylor MD, Chang HY, Cho YJ
Medulloblastoma-associated DDX3 variant selectively alters the translational response to stress.
Oncotarget. 2016 Apr 5. doi: 10.18632/oncotarget.8612
Pubmed Oncotarget.   PDF

Lu Z, Chang HY.
Decoding the RNA structurome.
Curr Opin Struct Biol. 2016 Feb;36:142-8. doi: 10.1016/j.sbi.2016.01.007. Epub 2016 Feb 26.
Pubmed Genome Biol.   PDF

Flynn RA, Do BT, Rubin AJ, Calo E, Lee B, Kuchelmeister H, Rale M, Chu C, Kool ET, Wysocka J, Khavari PA, Chang HY.
7SK-BAF axis controls pervasive transcription at enhancers.
Nat Struct Mol Biol. 2016 Feb 15. doi: 10.1038/nsmb.3176.
Pubmed Nat Struct Mol Biol.   PDF

Flynn RA, Zhang QC, Spitale RC, Lee B, Mumbach MR, Chang HY.
Transcriptome-wide interrogation of RNA secondary structure in living cells with icSHAPE.
Nat Protoc. 2016 Feb;11(2):273-90. doi: 10.1038/nprot.2016.011. Epub 2016 Jan 14.
Pubmed Nat Protoc.   PDF

Lee Y, Shin JH, Longmire M, Wang H, Kohrt HE, Chang HY, Sunwoo JB.
CD44+ cells in head and neck squamous cell carcinoma suppress T cell-mediated immunity by selective constitutive and inducible expression of PD-L1.
Clin Cancer Res. 2016 Feb 10. pii: clincanres.2665.2015.
Pubmed Clin Cancer Res..   PDF

Qu K, Garamszegi S, Wu F, Thorvaldsdottir H, Liefeld T, Ocana M, Borges-Rivera D, Pochet N, Robinson JT, Demchak B, Hull T, Ben-Artzi G, Blankenberg D, Barber GP, Lee BT, Kuhn RM, Nekrutenko A, Segal E, Ideker T, Reich M, Regev A, Chang HY, Mesirov JP.
Integrative genomic analysis by interoperation of bioinformatics tools in GenomeSpace.
Nat Methods. 2016 Jan 18. doi: 10.1038/nmeth.3732.
Pubmed Nat Methods.   PDF

Quinn JJ, Zhang QC, Georgiev P, Ilik IA, Akhtar A, Chang HY.
Rapid evolutionary turnover underlies conserved lncRNA-genome interactions.
Genes Dev. 2016 Jan 15;30(2):191-207. doi: 10.1101/gad.272187.115.
Pubmed Genes Dev. Cover PDF

2015

Huang W, Thomas B, Flynn RA, Gavzy SJ, Wu L1, Kim SV, Hall JA, Miraldi ER, Ng CP, Rigo FW, Meadows S, Montoya NR, Herrera NG, Domingos AI, Rastinejad F, Myers RM, Fuller-Pace FV, Bonneau R, Chang HY, Acuto O, Littman DR.
DDX5 and its associated lncRNA Rmrp modulate TH17 cell effector functions.
Nature. 2015 Dec 24;528(7583):517-22. doi: 10.1038/nature16193. Epub 2015 Dec 16.
Pubmed Nature.   PDF

Cheloufi S, Elling U, Hopfgartner B, Jung YL, Murn J, Ninova M, Hubmann M, Badeaux AI, Euong Ang C, Tenen D, Wesche DJ, Abazova N, Hogue M, Tasdemir N, Brumbaugh J, Rathert P, Jude J, Ferrari F, Blanco A, Fellner M, Wenzel D, Zinner M, Vidal SE, Bell O, Stadtfeld M, Chang HY, Almouzni G, Lowe SW, Rinn J, Wernig M, Aravin A, Shi Y, Park PJ, Penninger JM, Zuber J, Hochedlinger K
The histone chaperone CAF-1 safeguards somatic cell identity.
Nature. 2015 Dec 10;528(7581):218-24. doi: 10.1038/nature15749.
Pubmed Nature.   PDF

Quinn JJ, Chang HY.
Unique features of long non-coding RNA biogenesis and function.
Nat Rev Genet. 2015 Dec 15;17(1):47-62. doi: 10.1038/nrg.2015.10.
Pubmed Nat Rev Genet.   PDF

Bao X, Rubin AJ, Qu K, Zhang J, Giresi PG, Chang HY, Khavari PA
A novel ATAC-seq approach reveals lineage-specific reinforcement of the open chromatin landscape via cooperation between BAF and p63.
Genome Biol. 2015 Dec 18;16(1):284. doi: 10.1186/s13059-015-0840-9.
Pubmed Genome Biol.   PDF

Carlson HL, Quinn JJ, Yang YW, Thornburg CK, Chang HY, Stadler HS.
LncRNA-HIT Functions as an Epigenetic Regulator of Chondrogenesis through Its Recruitment of p100/CBP Complexes.
PLoS Genet. 2015 Dec 3;11(12):e1005680. doi: 10.1371/journal.pgen.1005680. eCollection 2015.
Pubmed PLoS Genet.   PDF

Mazumdar C, Shen Y, Xavy S, Zhao F, Reinisch A, Li R, Corces MR, Flynn RA, Buenrostro JD, Chan SM, Thomas D, Koenig JL, Hong WJ, Chang HY, Majeti R.
Leukemia-Associated Cohesin Mutants Dominantly Enforce Stem Cell Programs and Impair Human Hematopoietic Progenitor Differentiation.
Cell Stem Cell 2015 Oct 20. pii: S1934-5909(15)00424-5. doi: 10.1016/j.stem.2015.09.017.
Pubmed Cell Stem Cell   PDF

Qu K, Zaba LC, Giresi PG, Li R, Longmire M, Kim YH, Greenleaf WJ, Chang HY.
Individuality and variation of personal regulomes in primary human T cells.
Cell Syst. 2015 Jul 29;1(1):51-61.
Pubmed Cell Syst. News PDF

Buenrostro JD, Wu B, Litzenburger UM, Ruff D, Gonzales ML, Snyder MP, Chang HY, Greenleaf WJ.
Single-cell chromatin accessibility reveals principles of regulatory variation.
Nature. 2015 Jun 17. doi: 10.1038/nature14590.
Pubmed Nature   PDF

Satpathy AT, Chang HY.
Long Noncoding RNA in Hematopoiesis and Immunity.
Immunity. 2015 May 19;42(5):792-804. doi: 10.1016/j.immuni.2015.05.004.
Pubmed Immunity   PDF

Grow EJ, Flynn RA, Chavez SL, Bayless NL, Wossidlo M5, Wesche DJ, Martin L, Ware CB, Blish CA, Chang HY, Reijo Pera RA, Wysocka J.
Intrinsic retroviral reactivation in human preimplantation embryos and pluripotent cells.
Nature. 2015 Apr 20. doi: 10.1038/nature14308.
Pubmed Nature News PDF

Chu C, Zhang QC, da Rocha ST, Flynn RA, Bharadwaj M, Calabrese JM, Magnuson T, Heard E, Chang HY.
Systematic Discovery of Xist RNA Binding Proteins.
Cell. 2015 Apr 1. pii: S0092-8674(15)00312-8. doi: 10.1016/j.cell.2015.03.025.
Pubmed Cell   PDF

Spitale RC, Flynn RA, Zhang QC, Crisalli P, Lee B, Jung JW, Kuchelmeister HY, Batista PJ, Torre EA, Kool ET, Chang HY.
Structural imprints in vivo decode RNA regulatory mechanisms.
Nature. 2015 Mar 26;519(7544):486-90. doi: 10.1038/nature14263. Epub 2015 Mar 18.
Pubmed Nature.   PDF

Cho SW, Chang HY.
Genomics: CRISPR engineering turns on genes.
Nature. 2015 Jan 29;517(7536):560-2. doi: 10.1038/517560a.
Pubmed Nature.   PDF

Corley M, Solem A, Qu K, Chang HY, Laederach A.
Detecting riboSNitches with RNA folding algorithms: a genome-wide benchmark.
Nucleic Acids Res. 2015 Jan 23. pii: gkv010. [Epub ahead of print]
Pubmed Nucleic Acids Res.   PDF

Roost C, Lynch SR, Batista PJ, Qu K, Chang HY, Kool ET.
Structure and Thermodynamics of N6-Methyladenosine in RNA: A Spring-Loaded Base Modification.
J Am Chem Soc. 2015 Feb 2.
Pubmed J Am Chem Soc.   PDF

Chu C, Spitale RC, Chang HY.
Technologies to probe functions and mechanisms of long noncoding RNAs.
Nat Struct Mol Biol. 2015 Jan 7;22(1):29-35. doi: 10.1038/nsmb.2921.
Pubmed Nat Struct Mol Biol.   PDF

Buenrostro JD, Wu B, Chang HY, Greenleaf WJ.
ATAC-seq: A Method for Assaying Chromatin Accessibility Genome-Wide.
Curr Protoc Mol Biol. 2015 Jan 5;109:21.29.1-9. doi: 10.1002/0471142727.mb2129s109.
Pubmed Curr Protoc Mol Biol.   PDF

Quinn JJ, Chang HY.
In Situ Dissection of RNA Functional Subunits by Domain-Specific Chromatin Isolation by RNA Purification (dChIRP).
Methods Mol Biol. 2015;1262:199-213. doi: 10.1007/978-1-4939-2253-6_12.
Pubmed Methods Mol Biol.   PDF

2014

Calo E, Flynn RA, Martin L, Spitale RC, Chang HY, Wysocka J.
RNA helicase DDX21 coordinates transcription and ribosomal RNA processing.
Nature. 2014 Nov 24. doi: 10.1038/nature13923.
Pubmed Nature   PDF

Batista PJ, Molinie B, Wang J, Qu K, Zhang J, Li L, Bouley DM, Lujan E, Haddad B, Daneshvar K, Carter AC, Flynn RA, Zhou C, Lim KS, Dedon P, Wernig M, Mullen AC, Xing Y, Giallourakis CC, Chang HY.
m(6)A RNA Modification Controls Cell Fate Transition in Mammalian Embryonic Stem Cells.
Cell Stem Cell. 2014 Dec 4;15(6):707-19. doi: 10.1016/j.stem.2014.09.019. Epub 2014 Oct 16.
Pubmed Cell Stem Cell News PDF

Flynn RA, Martin L, Spitale RC, Do BT, Sagan SM, Zarnegar B, Qu K, Khavari PA, Quake SR, Sarnow P, Chang HY.
Dissecting noncoding and pathogen RNA-protein interactomes.
RNA. 2014 Nov 19.
Pubmed RNA   PDF

Benitez CM, Qu K, Sugiyama T, Pauerstein PT, Liu Y, Tsai J, Gu X, Ghodasara A, Arda HE, Zhang J, Dekker JD, Tucker HO, Chang HY, Kim SK.
An integrated cell purification and genomics strategy reveals multiple regulators of pancreas development.
PLoS Genet. 2014 Oct 16;10(10):e1004645. doi: 10.1371/journal.pgen.1004645. eCollection 2014.
Pubmed PLoS Genet.   PDF

Quinn JJ, Chang HY.
RNA switch at enhancers.
Nat Genet. 2014 Aug 27;46(9):929-31. doi: 10.1038/ng.3074.
Pubmed Nat Genet.   PDF

Spitale RC1, Flynn RA, Torre EA, Kool ET, Chang HY.
RNA structural analysis by evolving SHAPE chemistry.
Wiley Interdiscip Rev RNA. 2014 Aug 15. doi: 10.1002/wrna.1253.
Pubmed Wiley Interdiscip Rev RNA.   PDF

Li L, Chang HY.
Physiological roles of long noncoding RNAs: insight from knockout mice.
Trends Cell Biol. 2014 Jul 9. pii: S0962-8924(14)00100-7. doi: 10.1016/j.tcb.2014.06.003.
Pubmed Trends Cell Biol.   PDF

Quinn JJ, Ilik IA, Qu K, Georgiev P, Chu C, Akhtar A, Chang HY.
Revealing long noncoding RNA architecture and functions using domain-specific chromatin isolation by RNA purification.
Nat Biotechnol. 2014 Jul 6. doi: 10.1038/nbt.2943
Pubmed Nat Biotechnol. News PDF

Flynn RA, Chang HY.
Long Noncoding RNAs in Cell-Fate Programming and Reprogramming.
Cell Stem Cell. 2014 Jun 5;14(6):752-761. doi: 10.1016/j.stem.2014.05.014.
Pubmed Cell Stem Cell. Cover PDF

Zheng GX, Do BT, Webster DE, Khavari PA, Chang HY.
Dicer-microRNA-Myc circuit promotes transcription of hundreds of long noncoding RNAs.
Nat Struct Mol Biol. 2014 Jun 15. doi: 10.1038/nsmb.2842
Pubmed Nat Struct Mol Biol.   PDF

Buenrostro JD, Araya CL, Chircus LM, Layton CJ, Chang HY, Snyder MP, Greenleaf WJ.
Quantitative analysis of RNA-protein interactions on a massively parallel array reveals biophysical and evolutionary landscapes.
Nat Biotechnol. 2014 Apr 13. doi: 10.1038/nbt.2880
Pubmed Nat Biotechnol. Cover PDF

Yang YW, Flynn RA, Chen Y, Qu K, Wan B, Wang KC, Lei M, Chang HY.
Essential role of lncRNA binding for WDR5 maintenance of active chromatin and embryonic stem cell pluripotency.
Elife. 2014 Feb 12;3:e02046. doi: 10.7554/eLife.02046.
Pubmed Elife   PDF

Wan Y, Qu K, Zhang QC, Flynn RA, Manor O, Ouyang Z, Zhang J, Spitale RC, Snyder MP, Segal E, Chang HY.
Landscape and variation of RNA secondary structure across the human transcriptome.
Nature. 2014 Jan 30;505(7485):706-9. doi: 10.1038/nature12946.
Pubmed Nature News and Views PDF

2013

Harcourt EM, Ehrenschwender T, Batista PJ, Chang HY, Kool ET.
Identification of a selective polymerase enables detection of n(6)-methyladenosine in RNA.
J Am Chem Soc. 2013 Dec 26;135(51):19079-82. doi: 10.1021/ja4105792. Epub 2013 Dec 11.
Pubmed J Am Chem Soc   PDF

Wapinski OL, Vierbuchen T, Qu K, Lee QY, Chanda S, Fuentes DR, Giresi PG, Ng YH, Marro S, Neff NF, Drechsel D, Martynoga B, Castro DS, Webb AE, Südhof TC, Brunet A, Guillemot F, Chang HY, Wernig M.
Hierarchical mechanisms for direct reprogramming of fibroblasts to neurons.
Cell. 2013 Oct 24;155(3):621-35. doi: 10.1016/j.cell.2013.09.028. Epub 2013 Oct 24.
Pubmed Cell   PDF

Buenrostro JD, Giresi PG, Zaba LC, Chang HY, Greenleaf WJ.
Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position.
Nat Methods 2013 Oct 6. doi: 10.1038/nmeth.2688.
Pubmed Nat Methods   PDF

Li L, Liu B, Wapinski OL, Tsai MC, Qu K, Zhang J, Carlson JC, Lin M, Fang F, Gupta RA, Helms JA, Chang HY.
Targeted Disruption of Hotair Leads to Homeotic Transformation and Gene Derepression.
Cell Rep 2013 Sep 25. pii: S2211-1247(13)00501-9. doi: 10.1016/j.celrep.2013.09.003
Pubmed Cell Rep   PDF

Chang AL, Atzmon G, Bergman A, Brugmann S, Atwood SX, Chang HY, Barzilai N.
Identification of Genes Promoting Skin Youthfulness by Genome-Wide Association Study.
J Invest Dermatol 2013 Sep 13. doi: 10.1038/jid.2013.381
Pubmed J Invest Dermatol   PDF

Schmitt AM, Chang HY.
Gene regulation: Long RNAs wire up cancer growth
Nature 2013 Aug 29;500(7464):536-7. doi: 10.1038/nature12548. Epub 2013 Aug 14.
Pubmed Nature   PDF

Rapicavoli NA, Qu K, Zhang J, Mikhail M, Laberge RM, Chang HY.
A mammalian pseudogene lncRNA at the interface of inflammation and anti-inflammatory therapeutics.
eLIFE 2013 Jul 23;2:e00762. doi: 10.7554/eLife.00762. Print 2013.
Pubmed eLIFE News PDF

Ilik IA, Quinn JJ, Georgiev P, Tavares-Cadete F, Maticzka D, Toscano S, Wan Y, Spitale RC, Luscombe N, Backofen R, Chang HY, Akhtar A.
Tandem Stem-Loops in roX RNAs Act Together to Mediate X Chromosome Dosage Compensation in Drosophila.
Mol Cell 2013 Jul 25;51(2):156-73. doi: 10.1016/j.molcel.2013.07.001.
Pubmed Mol Cell Cover PDF

Shah N, Jin K, Cruz LA, Park S, Sadik H, Cho S, Goswami CP, Nakshatri H, Gupta R, Chang HY, Zhang Z, Cimino-Mathews A, Cope L, Umbricht C, Sukumar S.
HOXB13 mediates tamoxifen resistance and invasiveness in human breast cancer by suppressing ERα and inducing IL-6 expression.
Cancer Res. 2013 Jul 5.
Pubmed Cancer Res.   PDF

Wan Y, Qu K, Ouyang Z, Chang HY.
Genome-wide mapping of RNA structure using nuclease digestion and high-throughput sequencing.
Nat Protoc. 2013 May;8(5):849-69. doi: 10.1038/nprot.2013.045. Epub 2013 Apr 4.
Pubmed Nat Protoc.   PDF

Batista PJ, Chang HY.
Long Noncoding RNAs: Cellular Address Codes in Development and Disease.
Cell 2013 Mar 14;152(6):1298-307. doi: 10.1016/j.cell.2013.02.012.
Pubmed Cell   PDF

Gomez JA, Wapinski OL, Yang YW, Bureau JF, Gopinath S, Monack DM, Chang HY, Brahic M, Kirkegaard K.
The NeST Long ncRNA Controls Microbial Susceptibility and Epigenetic Activation of Interferon-gamma Locus.
Cell 2013 Feb 14;152(4):743-54. doi: 10.1016/j.cell.2013.01.015.
Pubmed Cell   PDF

Batista PJ, Chang HY.
Cytotopic localization by long noncoding RNAs.
Curr Opin Cell Biol 2012 Dec 29. pii: S0955-0674(12)00191-3. doi: 10.1016/j.ceb.2012.12.001.
Pubmed Curr Opin Cell Biol   PDF

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. doi: 10.1038/nature11661. Epub 2012 Dec 2.
Pubmed Nature Web Supplement PDF

Spitale RC, Crisalli P, Flynn RA, Torre EA, Kool ET, Chang HY
RNA SHAPE analysis in living cells.
Nat Chem Biol. 2013 Jan;9(1):18-20. doi: 10.1038/nchembio.1131. Epub 2012 Nov 25.
Pubmed Nat Chem Biol. Web Supplement PDF

2012

Martin L, Meier M, Lyons SM, Sit RV, Marzluff WF, Quake SR, Chang HY.
Systematic reconstruction of RNA functional motifs with high-throughput microfluidics.
Nat Methods. 2012 Nov 11. doi: 10.1038/nmeth.2225.
Pubmed Nat Methods.   PDF

Ouyang Z, Snyder MP, Chang HY.
SeqFold: Genome-scale reconstruction of RNA secondary structure integrating high-throughput sequencing data.
Genome Res. 2012 Oct 11.
Pubmed Genome Res. Web Supplement PDF

Wan Y, Qu K, Ouyang Z, Kertesz M, Li J, Tibshirani R, Makino DL, Nutter RC, Segal E, Chang HY.
Genome-wide Measurement of RNA Folding Energies.
Mol Cell. 2012 Sep 12. pii: S1097-2765(12)00695-8. doi: 10.1016/j.molcel.2012.08.008.
Pubmed Mol Cell   PDF

Lee CS, Ungewickell A, Bhaduri A, Qu K, Webster DE, Armstrong R, Weng WK, Aros CJ, Mah A, Chen RO, Lin M, Sundram U, Chang HY, Kretz M, Kim YH, Khavari PA.
Transcriptome sequencing in Sezary syndrome identifies Sezary cell and mycosis fungoides-associated LncRNAs and novel transcripts.
Blood. 2012 Aug 30.
Pubmed Blood   PDF

Chang AL, Bitter PH Jr, Qu K, Lin M, Rapicavoli NA, Chang HY.
Rejuvenation of Gene Expression Pattern of Aged Human Skin by Broadband Light Treatment: A Pilot Study.
J Invest Dermatol. 2012 Aug 30. doi: 10.1038/jid.2012.287.
Pubmed J Invest Dermatol.   PDF

Brunner AL, Beck AH, Edris B, Sweeney RT, Zhu SX, Li R, Montgomery K, Varma S, Gilks T, Guo X, Foley JW, Witten DM, Giacomini CP, Flynn RA, Pollack JR, Tibshirani R, Chang HY, van de Rijn M, West RB.
Transcriptional profiling of lncRNAs and novel transcribed regions across a diverse panel of archived human cancers.
Genome Biol. 2012 Aug 28;13(8):R75.
Pubmed Genome Biol.   PDF

Rinn JL, Chang HY.
Genome Regulation by Long Noncoding RNAs.
Annu Rev Biochem. 2012 Jul 7;81:145-66.
Pubmed Annual Reviews   PDF

Wu AR, Kawahara TL, Rapicavoli NA, Riggelen JV, Shroff EH, Xu L, Felsher DW, Chang HY, Quake SR.
High throughput automated chromatin immunoprecipitation as a platform for drug screening and antibody validation.
Lab Chip. 2012 May 8. [Epub ahead of print]
Pubmed Lab Chip.   PDF

Martin L, Chang HY.
Uncovering the role of genomic "dark matter" in human disease.
J Clin Invest. 2012 May 1;122(5):1589-95. doi: 10.1172/JCI60020. Epub 2012 May 1.
Pubmed J Clin Invest.   PDF

Chu C, Quinn J, Chang HY.
Chromatin Isolation by RNA Purification (ChIRP).
J Vis Exp. 2012 Mar 25;(61). pii: 3912. doi: 10.3791/3912.
Pubmed J Vis Exp.   PDF

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. Epub 2012 Feb 2.
Pubmed Genes Dev. Cover PDF

Rando TA, Chang HY.
Aging, rejuvenation, and epigenetic reprogramming: resetting the aging clock.
Cell 2012 Jan 20;148(1-2):46-57.
Pubmed Cell   PDF

Wang P, McKnight KD, Wong DJ, Rodriguez RT, Sugiyama T, Gu X, Ghodasara A, Qu K, Chang HY, Kim S.
A molecular signature for purified definitive endoderm guides differentiation and isolation of endoderm from mouse and human embryonic stem cells.
Stem Cells Dev. 2012 Jan 11.
Pubmed Stem Cells Dev.   PDF

2011

Flynn RA, Chang HY.
Active chromatin and noncoding RNAs: an intimate relationship.
Curr Opin Genet Dev 2011 Dec 7.
Pubmed Curr Opin Genet Dev   PDF

Chu C, Qu K, Zhong FL, Artandi SE, Chang HY.
Genomic Maps of Long Noncoding RNA Occupancy Reveal Principles of RNA-Chromatin Interactions
Mol Cell 2011 Sep 29.
Pubmed Mol Cell Cover PDF

Marro S, Pang ZP, Yang N, Tsai MC, Qu K, Chang HY, Südhof TC, Wernig M.
Direct Lineage Conversion of Terminally Differentiated Hepatocytes to Functional Neurons
Cell Stem Cell 2011 Sep 29.
Pubmed Cell Stem Cell Cover PDF

Wang KC, Chang HY.
Molecular Mechanisms of Long Noncoding RNAs.
Mol Cell 2011 Sep 16;43(6):904-14.
Pubmed Mol Cell   PDF

Alastalo TP, Li M, de Jesus Perez V, Pham D, Sawada H, Wang JK, Koskenvuo M, Wang L, Freeman BA, Chang HY, Rabinovitch M.
Disruption of PPAR?/ß-catenin-mediated regulation of apelin impairs BMP-induced mouse and human pulmonary arterial EC survival.
J Clin Invest 2011 Sep 1;121(9):3735-46. doi: 10.1172/JCI43382. Epub 2011 Aug 8.
Pubmed J Clin Invest   PDF

Wan Y, Kertesz M, Spitale RC, Segal E, Chang HY.
Understanding the transcriptome through RNA structure.
Nat Rev Genet. 2011 Aug 18;12(9):641-55. doi: 10.1038/nrg3049.
Pubmed Nat Rev Genet.   PDF

Kawahara TL, Rapicavoli NA, Wu AR, Qu K, Quake SR, Chang HY.
Dynamic chromatin localization of sirt6 shapes stress- and aging-related transcriptional networks.
PLoS Genet. 2011 Jun;7(6):e1002153. Epub 2011 Jun 30.
Pubmed PLoS Genet.   PDF

Wapinski O, Chang HY.
Long noncoding RNAs and human disease.
Trends Cell Biol. 2011 Jun;21(6):354-61. Epub 2011 May 6.
Pubmed Trends Cell Biol   PDF

Chen Y, Wan B, Wang KC, Cao F, Yang Y, Protacio A, Dou Y, Chang HY, Lei M.
Crystal structure of the N-terminal region of human Ash2L shows a winged-helix motif involved in DNA binding.
EMBO Rep. 2011 Jun 10. doi: 10.1038/embor.2011.101. [Epub ahead of print]
Pubmed EMBO Rep   PDF

Hung T, Wang Y, Lin MF, Koegel AK, Kotake Y, Grant GD, Horlings HM, Shah N, Umbricht C, Wang P, Wang Y, Kong B, LangerOd A, BOrresen-Dale AL, Kim SK, van de Vijver M, Sukumar S, Whitfield ML, Kellis M, Xiong Y, Wong DJ, Chang HY.
Extensive and coordinated transcription of noncoding RNAs within cell-cycle promoters.
Nat Genet. 2011 Jun 5. [Epub ahead of print]
Pubmed Nat Genet   PDF

Wang KC, Yang YW, Liu B, Sanyal A, Corces-Zimmerman R, Chen Y, Lajoie BR, Protacio A, Flynn RA, Gupta RA, Wysocka J, Lei M, Dekker J, Helms JA, Chang HY.
A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression.
Nature. 2011 Mar 20. [Epub ahead of print]
Pubmed Nature   PDF

Spitale RC, Tsai MC, Chang HY.
RNA templating the epigenome: Long noncoding RNAs as molecular scaffolds.
Epigenetics. 2011 May 1;6(5). [Epub ahead of print]
Pubmed Epigenetics    

Tsai MC, Spitale RC, Chang HY.
Long intergenic noncoding RNAs: new links in cancer progression.
Cancer Res. 2011 Jan 1;71(1):3-7.
Pubmed Cancer Res   PDF

2010

Ouyang Z, Zheng GX, Chang HY.
Noncoding RNA landmarks of pluripotency and reprogramming.
Cell Stem Cell. 2010 Dec 3;7(6):649-50.
Pubmed Cell Stem Cell   PDF

Wirt SE, Adler AS, Gebala V, Weimann JM, Schaffer BE, Saddic LA, Viatour P, Vogel H, Chang HY, Meissner A, Sage J.
G1 arrest and differentiation can occur independently of Rb family function.
J Cell Biol. 2010 Nov 15;191(4):809-25. Epub 2010 Nov 8.
Pubmed J Cell Biol   PDF

Hung T, Chang HY.
Long noncoding RNA in genome regulation: Prospects and mechanisms.
RNA Biol. 2010 Sep 2;7(5).
Pubmed RNA Biol    

Wan Y, Chang HY.
HOTAIR: Flight of noncoding RNAs in cancer metastasis.
Cell Cycle 2010 Sep;9(17):3391-2. Epub 2010 Sep 21.
Pubmed Cell Cycle   PDF

Tsai MC, Wang JK, Chang HY.
Tumor suppression by the histone demethylase UTX
Cell Cycle 2010 Jun 18;9(11).
Pubmed Cell Cycle   PDF

Kertesz M, Wan Y, Mazor E, Rinn JL, Nutter RC, Chang HY, Segal E.
Genome-wide measurement of RNA secondary structure in yeast.
Nature 2010 Sep 2;467(7311):103-7.
Pubmed Nature Web Supplement PDF
iPARS      

Tsai MC, Manor O, Wan Y, Mosammaparast N, Wang JK, Lan F, Shi Y, Segal E, Chang HY.
Long Noncoding RNA as Modular Scaffold of Histone Modification Complexes.
Science 2010 Jul 8. [Epub ahead of print]
Pubmed Science   PDF

Gupta RA, Shah N, Wang KC, Kim J, Horlings HM, Wong DJ, Tsai MC, Hung T, Argani P, Rinn JL, Wang Y, Brzoska P, Kong B, Li R, West RB, van de Vijver MJ, Sukumar S, Chang HY.
Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis.
Nature 2010 Apr 15;464(7291):1071-6.
Pubmed Nature Web Supplement PDF

Wang JK, Tsai MC, Poulin G, Adler AS, Chen S, Liu H, Shi Y, Chang HY.
The histone demethylase UTX enables RB-dependent cell fate control.
Genes & Development. 2010 Feb 1.
Pubmed Genes Dev   PDF

2009-2007 | Before 2007
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