Discovery and functional analysis of lncRNAs: Methodologies to investigate an uncharacterized transcriptome.
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[1] H. Ueda,et al. Erratum to: Quartz-Seq: a highly reproducible and sensitive single-cell RNA sequencing method, reveals non-genetic gene-expression heterogeneity , 2017, Genome Biology.
[2] Spitale Robert,et al. Structural imprints in vivo decode RNA regulatory mechanisms , 2016 .
[3] J. Rinn,et al. Multiplexable, locus-specific targeting of long RNAs with CRISPR-Display , 2015, Nature Methods.
[4] K. Hua,et al. The long non-coding RNA HOTAIR promotes the proliferation of serous ovarian cancer cells through the regulation of cell cycle arrest and apoptosis. , 2015, Experimental cell research.
[5] Qiangfeng Cliff Zhang,et al. Systematic Discovery of Xist RNA Binding Proteins , 2015, Cell.
[6] Kun Zhang,et al. Fluorescent in situ sequencing (FISSEQ) of RNA for gene expression profiling in intact cells and tissues , 2015, Nature Protocols.
[7] John M. Shelton,et al. A Micropeptide Encoded by a Putative Long Noncoding RNA Regulates Muscle Performance , 2015, Cell.
[8] G. Shan,et al. Exon-intron circular RNAs regulate transcription in the nucleus , 2015, Nature Structural &Molecular Biology.
[9] James T. Elder,et al. Analysis of long non-coding RNAs highlights tissue-specific expression patterns and epigenetic profiles in normal and psoriatic skin , 2015, Genome Biology.
[10] F. Slack,et al. Junk DNA and the long non-coding RNA twist in cancer genetics , 2015, Oncogene.
[11] Zakary S. Singer,et al. Single-cell transcriptome analysis reveals dynamic changes in lncRNA expression during reprogramming. , 2015, Cell stem cell.
[12] Fangting Wu,et al. Targeting non-coding RNAs with the CRISPR/Cas9 system in human cell lines , 2014, Nucleic acids research.
[13] R. Parker,et al. Circular RNAs: diversity of form and function , 2014, RNA.
[14] Nicholas T Ingolia,et al. Ribosome profiling reveals pervasive translation outside of annotated protein-coding genes. , 2014, Cell reports.
[15] Sharon R Grossman,et al. RNA-RNA Interactions Enable Specific Targeting of Noncoding RNAs to Nascent Pre-mRNAs and Chromatin Sites , 2014, Cell.
[16] Keith W. Vance,et al. Transcriptional regulatory functions of nuclear long noncoding RNAs , 2014, Trends in genetics : TIG.
[17] Bian Hu,et al. Efficient in vivo deletion of a large imprinted lncRNA by CRISPR/Cas9 , 2014, RNA biology.
[18] R. Guigó,et al. The RIDL hypothesis: transposable elements as functional domains of long noncoding RNAs , 2014, RNA.
[19] A. Sandelin,et al. Deep transcriptome profiling of mammalian stem cells supports a regulatory role for retrotransposons in pluripotency maintenance , 2014, Nature Genetics.
[20] E. Lander,et al. Development and Applications of CRISPR-Cas9 for Genome Engineering , 2014, Cell.
[21] M. Albà,et al. Long non-coding RNAs as a source of new peptides , 2014, eLife.
[22] Nikolaus Rajewsky,et al. Identification of small ORFs in vertebrates using ribosome footprinting and evolutionary conservation , 2014, The EMBO journal.
[23] T. Gregory,et al. The Case for Junk DNA , 2014, PLoS genetics.
[24] Qiangfeng Cliff Zhang,et al. Landscape and variation of RNA secondary structure across the human transcriptome , 2014, Nature.
[25] C. Ponting,et al. Sequencing depth and coverage: key considerations in genomic analyses , 2014, Nature Reviews Genetics.
[26] Steven R. Head,et al. Technical Variations in Low-Input RNA-seq Methodologies , 2014, Scientific Reports.
[27] R. Adams,et al. Evaluation of TRAP-sequencing technology with a versatile conditional mouse model , 2013, Nucleic acids research.
[28] M. Zavolan,et al. PAR-CLIP (Photoactivatable Ribonucleoside-Enhanced Crosslinking and Immunoprecipitation): a step-by-step protocol to the transcriptome-wide identification of binding sites of RNA-binding proteins. , 2014, Methods in enzymology.
[29] W. Sung,et al. Chromatin connectivity maps reveal dynamic promoter–enhancer long-range associations , 2013, Nature.
[30] Sarah K. Bowman,et al. High-resolution Xist binding maps reveal 2-step spreading during X-inactivation , 2013, Nature.
[31] D. Reinberg,et al. PRC2 binds to active promoters and contacts nascent RNAs in embryonic stem cells , 2013, Nature Structural &Molecular Biology.
[32] Karissa Y Sanbonmatsu,et al. 3S: shotgun secondary structure determination of long non-coding RNAs. , 2013, Methods.
[33] E. Lander,et al. The Xist lncRNA Exploits Three-Dimensional Genome Architecture to Spread Across the X Chromosome , 2013, Science.
[34] Nicholas T. Ingolia,et al. Ribosome Profiling Provides Evidence that Large Noncoding RNAs Do Not Encode Proteins , 2013, Cell.
[35] Erik Willems,et al. Quantitative Transcriptomics using Designed Primer-based Amplification , 2013, Scientific Reports.
[36] D. Tollervey,et al. Mapping the Human miRNA Interactome by CLASH Reveals Frequent Noncanonical Binding , 2013, Cell.
[37] L. Steinmetz,et al. Extensive transcriptional heterogeneity revealed by isoform profiling , 2013, Nature.
[38] M. Gill,et al. Development of Strategies for SNP Detection in RNA-Seq Data: Application to Lymphoblastoid Cell Lines and Evaluation Using 1000 Genomes Data , 2013, PloS one.
[39] Albert E. Almada,et al. Divergent transcription of long noncoding RNA/mRNA gene pairs in embryonic stem cells , 2013, Proceedings of the National Academy of Sciences.
[40] Manolis Kellis,et al. The tissue-specific lncRNA Fendrr is an essential regulator of heart and body wall development in the mouse. , 2013, Developmental cell.
[41] J. Kocher,et al. CPAT: Coding-Potential Assessment Tool using an alignment-free logistic regression model , 2013, Nucleic acids research.
[42] Carolyn J. Brown,et al. Targeting of >1.5 Mb of Human DNA into the Mouse X Chromosome Reveals Presence of cis-Acting Regulators of Epigenetic Silencing , 2012, Genetics.
[43] Piero Carninci,et al. Long non-coding antisense RNA controls Uchl1 translation through an embedded SINEB2 repeat , 2012, Nature.
[44] Toshiro K. Ohsumi,et al. Spreading of X chromosome inactivation via a hierarchy of defined Polycomb stations , 2012, Genome research.
[45] David G. Knowles,et al. The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression , 2012, Genome research.
[46] Nadav S. Bar,et al. Landscape of transcription in human cells , 2012, Nature.
[47] R. Sandberg,et al. Full-Length mRNA-Seq from single cell levels of RNA and individual circulating tumor cells , 2012, Nature Biotechnology.
[48] M. Esteller,et al. Intronic RNAs mediate EZH2 regulation of epigenetic targets , 2012, Nature Structural &Molecular Biology.
[49] A. Wakamatsu,et al. Genome-wide determination of RNA stability reveals hundreds of short-lived noncoding transcripts in mammals , 2012, Genome research.
[50] Jesse R. Dixon,et al. Topological Domains in Mammalian Genomes Identified by Analysis of Chromatin Interactions , 2012, Nature.
[51] Pawel Zajac,et al. Highly multiplexed and strand-specific single-cell RNA 5′ end sequencing , 2012, Nature Protocols.
[52] Alexander van Oudenaarden,et al. Single-cell analysis reveals that noncoding RNAs contribute to clonal heterogeneity by modulating transcription factor recruitment. , 2012, Molecular cell.
[53] Karissa Y. Sanbonmatsu,et al. Structural architecture of the human long non-coding RNA, steroid receptor RNA activator , 2012, Nucleic acids research.
[54] Cole Trapnell,et al. Targeted RNA sequencing reveals the deep complexity of the human transcriptome , 2011, Nature Biotechnology.
[55] H. Ueda,et al. Quartz-Seq : a highly reproducible and sensitive single-cell RNA-Seq reveals non-genetic gene expression heterogeneity , 2012 .
[56] P. Sorensen,et al. The majority of total nuclear-encoded non-ribosomal RNA in a human cell is 'dark matter' un-annotated RNA , 2011, BMC Biology.
[57] Brad A Chapman,et al. The genomic binding sites of a noncoding RNA , 2011, Proceedings of the National Academy of Sciences.
[58] Howard Y. Chang,et al. Genomic maps of long noncoding RNA occupancy reveal principles of RNA-chromatin interactions. , 2011, Molecular cell.
[59] M. Esteller. Non-coding RNAs in human disease , 2011, Nature Reviews Genetics.
[60] Nicholas T. Ingolia,et al. Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity and Dynamics of Mammalian Proteomes , 2011, Cell.
[61] Emily A. Vucic,et al. Human Cancer Long Non-Coding RNA Transcriptomes , 2011, PloS one.
[62] Cole Trapnell,et al. Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. , 2011, Genes & development.
[63] Howard Y. Chang,et al. Understanding the transcriptome through RNA structure , 2011, Nature Reviews Genetics.
[64] John T. Wei,et al. Transcriptome sequencing across a prostate cancer cohort identifies PCAT-1, an unannotated lincRNA implicated in disease progression , 2011, Nature Biotechnology.
[65] Jeannie T. Lee,et al. YY1 Tethers Xist RNA to the Inactive X Nucleation Center , 2011, Cell.
[66] Albert E. Almada,et al. Antisense RNA polymerase II divergent transcripts are P-TEFb dependent and substrates for the RNA exosome , 2011, Proceedings of the National Academy of Sciences.
[67] Elphège P. Nora,et al. Regulation of X-chromosome inactivation by the X-inactivation centre , 2011, Nature Reviews Genetics.
[68] Howard Y. Chang,et al. Extensive and coordinated transcription of noncoding RNAs within cell cycle promoters , 2011, Nature Genetics.
[69] David Tollervey,et al. Cross-linking, ligation, and sequencing of hybrids reveals RNA–RNA interactions in yeast , 2011, Proceedings of the National Academy of Sciences.
[70] Blaz Zupan,et al. iCLIP - Transcriptome-wide Mapping of Protein-RNA Interactions with Individual Nucleotide Resolution , 2011, Journal of visualized experiments : JoVE.
[71] J. Ule,et al. Characterizing the RNA targets and position-dependent splicing regulation by TDP-43. , 2011, Nature neuroscience.
[72] Leighton J. Core,et al. Regulating RNA polymerase pausing and transcription elongation in embryonic stem cells. , 2011, Genes & development.
[73] Tim R. Mercer,et al. Global analysis of the mammalian RNA degradome reveals widespread miRNA-dependent and miRNA-independent endonucleolytic cleavage , 2011, Nucleic acids research.
[74] J. Ule,et al. Characterising the RNA targets and position-dependent splicing regulation by TDP-43; implications for neurodegenerative diseases , 2011, Nature Neuroscience.
[75] Li Yang,et al. Genomewide characterization of non-polyadenylated RNAs , 2011, Genome Biology.
[76] A. Børresen-Dale,et al. Identification of fusion genes in breast cancer by paired-end RNA-sequencing , 2011, Genome Biology.
[77] D. Haussler,et al. FragSeq: transcriptome-wide RNA structure probing using high-throughput sequencing , 2010, Nature Methods.
[78] K. Weeks,et al. Toward global RNA structure analysis , 2010, Nature Biotechnology.
[79] I. Grummt,et al. Interaction of noncoding RNA with the rDNA promoter mediates recruitment of DNMT3b and silencing of rRNA genes. , 2010, Genes & development.
[80] B. Blencowe,et al. The nuclear-retained noncoding RNA MALAT1 regulates alternative splicing by modulating SR splicing factor phosphorylation. , 2010, Molecular cell.
[81] Howard Y. Chang,et al. Genome-wide measurement of RNA secondary structure in yeast , 2010, Nature.
[82] M. Teitell,et al. PNPASE Regulates RNA Import into Mitochondria , 2010, Cell.
[83] Howard Y. Chang,et al. Long Noncoding RNA as Modular Scaffold of Histone Modification Complexes , 2010, Science.
[84] J. Rinn,et al. A Large Intergenic Noncoding RNA Induced by p53 Mediates Global Gene Repression in the p53 Response , 2010, Cell.
[85] Carsten O. Daub,et al. Linking promoters to functional transcripts in small samples with nanoCAGE and CAGEscan , 2010, Nature Methods.
[86] J. Rinn,et al. Ab initio reconstruction of transcriptomes of pluripotent and lineage committed cells reveals gene structures of thousands of lincRNAs , 2010, Nature Biotechnology.
[87] J. Ragoussis,et al. A Large Fraction of Extragenic RNA Pol II Transcription Sites Overlap Enhancers , 2010, PLoS biology.
[88] J. Rinn,et al. Ab initio reconstruction of transcriptomes of pluripotent and lineage committed cells reveals gene structures of thousands of lincRNAs , 2010, Nature biotechnology.
[89] P. Robson,et al. Conserved long noncoding RNAs transcriptionally regulated by Oct4 and Nanog modulate pluripotency in mouse embryonic stem cells. , 2010, RNA.
[90] J. Mattick,et al. Non‐coding RNAs: regulators of disease , 2010, The Journal of pathology.
[91] P. Avner,et al. 2-D Structure of the A Region of Xist RNA and Its Implication for PRC2 Association , 2010, PLoS biology.
[92] L. Holm,et al. The Pfam protein families database , 2005, Nucleic Acids Res..
[93] A. Jacquier. The complex eukaryotic transcriptome: unexpected pervasive transcription and novel small RNAs , 2009, Nature Reviews Genetics.
[94] I. Amit,et al. Comprehensive mapping of long range interactions reveals folding principles of the human genome , 2011 .
[95] Kristen K. Dang,et al. Architecture and Secondary Structure of an Entire HIV-1 RNA Genome , 2009, Nature.
[96] Leo J. Lee,et al. Current-generation high-throughput sequencing: deepening insights into mammalian transcriptomes. , 2009, Genes & development.
[97] J. Kawai,et al. The regulated retrotransposon transcriptome of mammalian cells , 2009, Nature Genetics.
[98] Nicholas T. Ingolia,et al. Genome-Wide Analysis in Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling , 2009, Science.
[99] J. Mattick. The Genetic Signatures of Noncoding RNAs , 2009, PLoS genetics.
[100] Lior Pachter,et al. Sequence Analysis , 2020, Definitions.
[101] W. Reik,et al. The long noncoding RNA Kcnq1ot1 organises a lineage-specific nuclear domain for epigenetic gene silencing , 2009, Development.
[102] Michael F. Lin,et al. Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals , 2009, Nature.
[103] Gene W. Yeo,et al. Divergent Transcription from Active Promoters , 2008, Science.
[104] P. Greengard,et al. A Translational Profiling Approach for the Molecular Characterization of CNS Cell Types , 2008, Cell.
[105] Jeannie T. Lee,et al. Polycomb Proteins Targeted by a Short Repeat RNA to the Mouse X Chromosome , 2008, Science.
[106] Marcel H. Schulz,et al. A Global View of Gene Activity and Alternative Splicing by Deep Sequencing of the Human Transcriptome , 2008, Science.
[107] R. Lister,et al. A link between RNA metabolism and silencing affecting Arabidopsis development. , 2008, Developmental cell.
[108] S. Luo,et al. Global identification of microRNA–target RNA pairs by parallel analysis of RNA ends , 2008, Nature Biotechnology.
[109] D. Bartel,et al. Endogenous siRNA and miRNA Targets Identified by Sequencing of the Arabidopsis Degradome , 2008, Current Biology.
[110] Changning Liu,et al. MicroRNA-encoding long non-coding RNAs , 2008, BMC Genomics.
[111] Joseph R Ecker,et al. Mapping the genome landscape using tiling array technology. , 2007, Current opinion in plant biology.
[112] M. Takeichi,et al. The mRNA-like noncoding RNA Gomafu constitutes a novel nuclear domain in a subset of neurons , 2007, Journal of Cell Science.
[113] Howard Y. Chang,et al. Functional Demarcation of Active and Silent Chromatin Domains in Human HOX Loci by Noncoding RNAs , 2007, Cell.
[114] P. Stadler,et al. RNA Maps Reveal New RNA Classes and a Possible Function for Pervasive Transcription , 2007, Science.
[115] C. Brenner,et al. p53 Activation by Knockdown Technologies , 2007, PLoS genetics.
[116] Ana Serra Barros,et al. Repression of the human dihydrofolate reductase gene by a non-coding interfering transcript , 2007, Nature.
[117] G. Lang. [Cross linking]. , 2007, Klinische Monatsblatter fur Augenheilkunde.
[118] David Bryder,et al. Transcription factor profiling in individual hematopoietic progenitors by digital RT-PCR , 2006, Proceedings of the National Academy of Sciences.
[119] Jun Kawai,et al. Clusters of Internally Primed Transcripts Reveal Novel Long Noncoding RNAs , 2006, PLoS genetics.
[120] S. Batalov,et al. Antisense Transcription in the Mammalian Transcriptome , 2005, Science.
[121] S. Salzberg,et al. The Transcriptional Landscape of the Mammalian Genome , 2005, Science.
[122] B. Séraphin,et al. Cryptic Pol II Transcripts Are Degraded by a Nuclear Quality Control Pathway Involving a New Poly(A) Polymerase , 2005, Cell.
[123] G. Helt,et al. Transcriptional Maps of 10 Human Chromosomes at 5-Nucleotide Resolution , 2005, Science.
[124] J. Ecker,et al. Applications of DNA tiling arrays for whole-genome analysis. , 2005, Genomics.
[125] J. Goodrich,et al. The SINE-encoded mouse B2 RNA represses mRNA transcription in response to heat shock , 2004, Nature Structural &Molecular Biology.
[126] J. Mattick. RNA regulation: a new genetics? , 2004, Nature Reviews Genetics.
[127] Tyra G. Wolfsberg,et al. Short interfering RNAs can induce unexpected and divergent changes in the levels of untargeted proteins in mammalian cells , 2004, Proceedings of the National Academy of Sciences of the United States of America.
[128] Robert D. Finn,et al. The Pfam protein families database , 2004, Nucleic Acids Res..
[129] J. Kawai,et al. Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usage , 2003, Proceedings of the National Academy of Sciences of the United States of America.
[130] E. Birney,et al. Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs , 2002, Nature.
[131] Ji Huang,et al. [Serial analysis of gene expression]. , 2002, Yi chuan = Hereditas.
[132] S. Eddy. Non–coding RNA genes and the modern RNA world , 2001, Nature Reviews Genetics.
[133] J. Mcneil,et al. XIST RNA paints the inactive X chromosome at interphase: evidence for a novel RNA involved in nuclear/chromosome structure , 1996, The Journal of cell biology.
[134] K. Maruyama,et al. Oligo-capping: a simple method to replace the cap structure of eukaryotic mRNAs with oligoribonucleotides. , 1994, Gene.
[135] C. Waldron,et al. Effect of growth rate on the amounts of ribosomal and transfer ribonucleic acids in yeast , 1975, Journal of bacteriology.
[136] D. Comings. The structure and function of chromatin. , 1972, Advances in human genetics.