Journal ArticleDOI
Mapping and quantifying mammalian transcriptomes by RNA-Seq.
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TLDR
Although >90% of uniquely mapped reads fell within known exons, the remaining data suggest new and revised gene models, including changed or additional promoters, exons and 3′ untranscribed regions, as well as new candidate microRNA precursors.Abstract:
We have mapped and quantified mouse transcriptomes by deeply sequencing them and recording how frequently each gene is represented in the sequence sample (RNA-Seq). This provides a digital measure of the presence and prevalence of transcripts from known and previously unknown genes. We report reference measurements composed of 41–52 million mapped 25-base-pair reads for poly(A)-selected RNA from adult mouse brain, liver and skeletal muscle tissues. We used RNA standards to quantify transcript prevalence and to test the linear range of transcript detection, which spanned five orders of magnitude. Although >90% of uniquely mapped reads fell within known exons, the remaining data suggest new and revised gene models, including changed or additional promoters, exons and 3′ untranscribed regions, as well as new candidate microRNA precursors. RNA splice events, which are not readily measured by standard gene expression microarray or serial analysis of gene expression methods, were detected directly by mapping splice-crossing sequence reads. We observed 1.45 × 10 5 distinct splices, and alternative splices were prominent, with 3,500 different genes expressing one or more alternate internal splices. The mRNA population specifies a cell’s identity and helps to govern its present and future activities. This has made transcriptome analysis a general phenotyping method, with expression microarrays of many kinds in routine use. Here we explore the possibility that transcriptome analysis, transcript discovery and transcript refinement can be done effectively in large and complex mammalian genomes by ultra-high-throughput sequencing. Expression microarrays are currently the most widely used methodology for transcriptome analysis, although some limitations persist. These include hybridization and cross-hybridization artifacts 1–3 , dye-based detection issues and design constraints that preclude or seriously limit the detection of RNA splice patterns and previously unmapped genes. These issues have made it difficult for standard array designs to provide full sequence comprehensiveness (coverage of all possible genes, including unknown ones, in large genomes) or transcriptome comprehensiveness (reliable detection of all RNAs of all prevalence classes, including the least abundant ones that are physiologically relevant). Otherread more
Citations
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A long noncoding RNA mediates both activation and repression of immune response genes.
Susan Carpenter,Daniel Aiello,Maninjay K. Atianand,Emiliano P. Ricci,Pallavi Gandhi,Lisa L. Hall,Meg Byron,Brian G. Monks,Meabh Henry-Bezy,Jeanne B. Lawrence,Luke A. J. O'Neill,Melissa J. Moore,Daniel R. Caffrey,Katherine A. Fitzgerald +13 more
TL;DR: A central role is identified of lincRNA-Cox2 as a broad-acting regulatory component of the circuit that controls the inflammatory response in mice, which is central to antimicrobial defenses.
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Braveheart, a Long Noncoding RNA Required for Cardiovascular Lineage Commitment
Carla Andrea Klattenhoff,Johanna C. Scheuermann,Lauren E. Surface,Robert K. Bradley,Paul A. Fields,Matthew L. Steinhauser,Huiming Ding,Vincent L. Butty,Lillian Torrey,Simon Haas,Ryan Abo,Mohammadsharif Tabebordbar,Mohammadsharif Tabebordbar,Richard T. Lee,Richard T. Lee,Christopher B. Burge,Laurie A. Boyer +16 more
TL;DR: Braveheart (Bvht), a heart-associated lncRNA in mouse is identified and it is found that Bvht is necessary for activation of a core cardiovascular gene network and functions upstream of mesoderm posterior 1 (MesP1), a master regulator of a common multipotent cardiovascular progenitor.
Journal ArticleDOI
Under pressure: Investigating the biology of plant infection by Magnaporthe oryzae
TL;DR: This work shows how functional genomics approaches are providing new insight into the genetic control of plant infection by M. oryzae, and looks ahead to the key questions that need to be addressed to provide a better understanding of the molecular processes that lead to plant disease and the prospects for sustainable control of rice blast.
Journal ArticleDOI
The draft genome of sweet orange (Citrus sinensis).
Qiang Xu,Ling-Ling Chen,Xiaoan Ruan,Dijun Chen,Andan Zhu,Chunli Chen,Denis Bertrand,Wen-Biao Jiao,Bao Hai Hao,Matthew P. Lyon,Jiongjiong Chen,Song Gao,Feng Xing,Hong Lan,Ji Wei Chang,Xianhong Ge,Yang Lei,Qun Hu,Yin Miao,Lun Wang,Shi-Xin Xiao,Manosh Kumar Biswas,Wenfang Zeng,Fei Guo,Hongbo Cao,Xiaoming Yang,Xi Wen Xu,Yun Jiang Cheng,Juan Xu,Ji-Hong Liu,Oscar Junhong Luo,Zhonghui Tang,Wen-Wu Guo,Hanhui Kuang,Hong-Yu Zhang,Mikeal L. Roose,Niranjan Nagarajan,Xiuxin Deng,Yijun Ruan,Yijun Ruan +39 more
TL;DR: Focused analysis on genes involved in vitamin C metabolism showed that GalUR, encoding the rate-limiting enzyme of the galacturonate pathway, is significantly upregulated in orange fruit, and the recent expansion of this gene family may provide a genomic basis.
Journal ArticleDOI
Activation of proto-oncogenes by disruption of chromosome neighborhoods
Denes Hnisz,Abraham S. Weintraub,Daniel S. Day,Anne-Laure Valton,Rasmus O. Bak,Charles H. Li,Johanna Goldmann,Bryan R. Lajoie,Zi Peng Fan,Alla A. Sigova,Jessica Reddy,Diego Borges-Rivera,Tong Ihn Lee,Rudolf Jaenisch,Matthew H. Porteus,Job Dekker,Job Dekker,Richard A. Young +17 more
TL;DR: Insulated neighborhoods in T cell acute lymphoblastic leukemia (T-ALL) are mapped and it is found that tumor cell genomes contain recurrent microdeletions that eliminate the boundary sites of insulated neighborhoods containing prominent T-ALL proto-oncogenes.
References
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Journal ArticleDOI
Highly Integrated Single-Base Resolution Maps of the Epigenome in Arabidopsis
Ryan Lister,Ronan C. O'Malley,Julian Tonti-Filippini,Brian D. Gregory,Charles C. Berry,A. Harvey Millar,Joseph R. Ecker +6 more
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Journal ArticleDOI
RNA Maps Reveal New RNA Classes and a Possible Function for Pervasive Transcription
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TL;DR: Three potentially functional classes of RNAs have been identified, two of which are syntenically conserved and correlate with the expression state of protein-coding genes and support a highly interleaved organization of the human transcriptome.
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