Genome-wide discovery and characterization of maize long non-coding RNAs

[1]  D. S. Gross,et al.  Chromatin , 2015, Current Biology.

[2]  C. Robin Buell,et al.  Maize Gene Atlas Developed by RNA Sequencing and Comparative Evaluation of Transcriptomes Based on RNA Sequencing and Microarrays , 2013, PloS one.

[3]  Zev N. Kronenberg,et al.  Transposable Elements Are Major Contributors to the Origin, Diversification, and Regulation of Vertebrate Long Noncoding RNAs , 2013, PLoS genetics.

[4]  Nathan M. Springer,et al.  Genomic Distribution of Maize Facultative Heterochromatin Marked by Trimethylation of H3K27[W] , 2013, Plant Cell.

[5]  Sanzhen Liu,et al.  Mendelian and Non-Mendelian Regulation of Gene Expression in Maize , 2013, PLoS genetics.

[6]  Nathan M. Springer,et al.  Spreading of Heterochromatin Is Limited to Specific Families of Maize Retrotransposons , 2012, PLoS genetics.

[7]  Steven P. Lund,et al.  Complementation contributes to transcriptome complexity in maize (Zea mays L.) hybrids relative to their inbred parents , 2012, Genome research.

[8]  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.

[9]  Zhe Wu,et al.  Flowering time control: another window to the connection between antisense RNA and chromatin. , 2012, Trends in genetics : TIG.

[10]  K. McGinnis,et al.  Computational Identification and Functional Predictions of Long Noncoding RNA in Zea mays , 2012, PloS one.

[11]  N. Bolduc,et al.  Unraveling the KNOTTED1 regulatory network in maize meristems. , 2012, Genes & development.

[12]  Wen-Hsiung Li,et al.  Characterizing Regulatory and Functional Differentiation between Maize Mesophyll and Bundle Sheath Cells by Transcriptomic Analysis1[W][OA] , 2012, Plant Physiology.

[13]  Howard Y. Chang,et al.  Genome regulation by long noncoding RNAs. , 2012, Annual review of biochemistry.

[14]  Qian-Hao Zhu,et al.  Molecular Functions of Long Non-Coding RNAs in Plants , 2012, Genes.

[15]  Patrick S. Schnable,et al.  Parent-of-Origin Effects on Gene Expression and DNA Methylation in the Maize Endosperm[W] , 2011, Plant Cell.

[16]  R. Sekhon,et al.  Utility of RNA Sequencing for Analysis of Maize Reproductive Transcriptomes , 2011 .

[17]  Cole Trapnell,et al.  Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. , 2011, Genes & development.

[18]  J. Doebley,et al.  Do Large Effect QTL Fractionate? A Case Study at the Maize Domestication QTL teosinte branched1 , 2011, Genetics.

[19]  Howard Y. Chang,et al.  Long noncoding RNAs and human disease. , 2011, Trends in cell biology.

[20]  C. Kanduri Kcnq1ot1: a chromatin regulatory RNA. , 2011, Seminars in cell & developmental biology.

[21]  Sibum Sung,et al.  Vernalization-Mediated Epigenetic Silencing by a Long Intronic Noncoding RNA , 2011, Science.

[22]  Hideaki Sugawara,et al.  The Sequence Read Archive , 2010, Nucleic Acids Res..

[23]  Robert Turgeon,et al.  The developmental dynamics of the maize leaf transcriptome , 2010, Nature Genetics.

[24]  J. Rinn,et al.  Large intergenic non-coding RNA-RoR modulates reprogramming of human induced pluripotent stem cells , 2010, Nature Genetics.

[25]  J. Rinn,et al.  A Large Intergenic Noncoding RNA Induced by p53 Mediates Global Gene Repression in the p53 Response , 2010, Cell.

[26]  Kan Nobuta,et al.  RNA-mediated trans-communication can establish paramutation at the b1 locus in maize , 2010, Proceedings of the National Academy of Sciences.

[27]  Cole Trapnell,et al.  Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. , 2010, Nature biotechnology.

[28]  P. Harrison,et al.  Mining Mammalian Transcript Data for Functional Long Non-Coding RNAs , 2010, PloS one.

[29]  Xiu-Jie Wang,et al.  Systematic identification and evolutionary features of rhesus monkey small nucleolar RNAs , 2010, BMC Genomics.

[30]  C. Dean,et al.  Cold-induced silencing by long antisense transcripts of an Arabidopsis Polycomb target , 2009, Nature.

[31]  Dawn H. Nagel,et al.  The B73 Maize Genome: Complexity, Diversity, and Dynamics , 2009, Science.

[32]  Paulo P. Amaral,et al.  Pervasive transcription of the eukaryotic genome: functional indices and conceptual implications. , 2009, Briefings in functional genomics & proteomics.

[33]  V. Chandler,et al.  A Dominant Mutation in mediator of paramutation2, One of Three Second-Largest Subunits of a Plant-Specific RNA Polymerase, Disrupts Multiple siRNA Silencing Processes , 2009, PLoS genetics.

[34]  Antonin Morillon,et al.  Pervasive transcription constitutes a new level of eukaryotic genome regulation , 2009, EMBO reports.

[35]  J. Rinn,et al.  Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression , 2009, Proceedings of the National Academy of Sciences.

[36]  D. Kliebenstein Quantitative genomics: analyzing intraspecific variation using global gene expression polymorphisms or eQTLs. , 2009, Annual review of plant biology.

[37]  X. Liu,et al.  Genome-Wide and Organ-Specific Landscapes of Epigenetic Modifications and Their Relationships to mRNA and Small RNA Transcriptomes in Maize[W] , 2009, The Plant Cell Online.

[38]  Lior Pachter,et al.  Sequence Analysis , 2020, Definitions.

[39]  Michael F. Lin,et al.  Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals , 2009, Nature.

[40]  P. Zamore,et al.  Small silencing RNAs: an expanding universe , 2009, Nature Reviews Genetics.

[41]  Tao Jiang,et al.  Computational prediction of novel non-coding RNAs in Arabidopsis thaliana , 2009, BMC Bioinformatics.

[42]  M. Crespi,et al.  Novel long non-protein coding RNAs involved in Arabidopsis differentiation and stress responses. , 2008, Genome research.

[43]  Kan Nobuta,et al.  Distinct size distribution of endogenous siRNAs in maize: Evidence from deep sequencing in the mop1-1 mutant , 2008, Proceedings of the National Academy of Sciences.

[44]  Masakazu Satou,et al.  Arabidopsis transcriptome analysis under drought, cold, high-salinity and ABA treatment conditions using a tiling array. , 2008, Plant & cell physiology.

[45]  Pamela J Green,et al.  Diamonds in the rough: mRNA-like non-coding RNAs. , 2008, Trends in plant science.

[46]  B. Williams,et al.  Mapping and quantifying mammalian transcriptomes by RNA-Seq , 2008, Nature Methods.

[47]  M. Todesco,et al.  Target mimicry provides a new mechanism for regulation of microRNA activity , 2007, Nature Genetics.

[48]  Roberto Tuberosa,et al.  Conserved noncoding genomic sequences associated with a flowering-time quantitative trait locus in maize , 2007, Proceedings of the National Academy of Sciences.

[49]  Yong Zhang,et al.  CPC: assess the protein-coding potential of transcripts using sequence features and support vector machine , 2007, Nucleic Acids Res..

[50]  Howard Y. Chang,et al.  Functional Demarcation of Active and Silent Chromatin Domains in Human HOX Loci by Noncoding RNAs , 2007, Cell.

[51]  Alexander P. Gultyaev,et al.  Identification of conserved secondary structures and expansion segments in enod40 RNAs reveals new enod40 homologues in plants , 2007, Nucleic acids research.

[52]  B. Meyers,et al.  An expression atlas of rice mRNAs and small RNAs , 2007, Nature Biotechnology.

[53]  Brian J. Parker,et al.  In Silico Identification and Characterization of mRNA-Like Noncoding Transcripts in Medicago truncatula , 2007, Silico Biol..

[54]  S. Henikoff,et al.  Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription , 2007, Nature Genetics.

[55]  Joshua P. White,et al.  An RNA-dependent RNA polymerase is required for paramutation in maize , 2006, Nature.

[56]  Laurent Duret,et al.  The Xist RNA Gene Evolved in Eutherians by Pseudogenization of a Protein-Coding Gene , 2006, Science.

[57]  Richard M. Clark,et al.  A distant upstream enhancer at the maize domestication gene tb1 has pleiotropic effects on plant and inflorescent architecture , 2006, Nature Genetics.

[58]  C. Bult,et al.  Transcript Annotation in FANTOM3: Mouse Gene Catalog Based on Physical cDNAs , 2006, PLoS genetics.

[59]  Jun Kawai,et al.  The Abundance of Short Proteins in the Mammalian Proteome , 2006, PLoS genetics.

[60]  Vincent Lefort,et al.  Characterization of 43 Non-Protein-Coding mRNA Genes in Arabidopsis, Including the MIR162a-Derived Transcripts1[W] , 2006, Plant Physiology.

[61]  Jun Wang,et al.  Genome-wide transcription analyses in rice using tiling microarrays , 2006, Nature Genetics.

[62]  M. Bucan,et al.  Promoter features related to tissue specificity as measured by Shannon entropy , 2005, Genome Biology.

[63]  M. Crespi,et al.  Enod40, a Short Open Reading Frame–Containing mRNA, Induces Cytoplasmic Localization of a Nuclear RNA Binding Protein in Medicago truncatula , 2004, The Plant Cell Online.

[64]  D. Grant,et al.  Expanding the genetic map of maize with the intermated B73 × Mo17 (IBM) population , 2002, Plant Molecular Biology.

[65]  J. Fletcher,et al.  Shoot apical meristem maintenance: the art of a dynamic balance. , 2003, Trends in plant science.

[66]  Jürgen Brosius,et al.  Experimental RNomics Identification of 140 Candidates for Small Non-Messenger RNAs in the Plant Arabidopsis thaliana , 2002, Current Biology.

[67]  J. Bennetzen,et al.  The regulatory regions required for B' paramutation and expression are located far upstream of the maize b1 transcribed sequences. , 2002, Genetics.

[68]  P J Green,et al.  Identification and analysis of Arabidopsis expressed sequence tags characteristic of non-coding RNAs. , 2001, Plant physiology.

[69]  J. Doebley,et al.  teosinte branched1 and the origin of maize: evidence for epistasis and the evolution of dominance. , 1995, Genetics.