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The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression.
TLDR
The most complete human lncRNA annotation to date is presented, produced by the GENCODE consortium within the framework of the ENCODE project and comprising 9277 manually annotated genes producing 14,880 transcripts, and expression correlation analysis indicates that lncRNAs show particularly striking positive correlation with the expression of antisense coding genes.
Landscape of transcription in human cells
TLDR
Evidence that three-quarters of the human genome is capable of being transcribed is reported, as well as observations about the range and levels of expression, localization, processing fates, regulatory regions and modifications of almost all currently annotated and thousands of previously unannotated RNAs that prompt a redefinition of the concept of a gene.
Initial sequencing and comparative analysis of the mouse genome.
TLDR
The results of an international collaboration to produce a high-quality draft sequence of the mouse genome are reported and an initial comparative analysis of the Mouse and human genomes is presented, describing some of the insights that can be gleaned from the two sequences.
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
TLDR
Functional data from multiple, diverse experiments performed on a targeted 1% of the human genome as part of the pilot phase of the ENCODE Project are reported, providing convincing evidence that the genome is pervasively transcribed, such that the majority of its bases can be found in primary transcripts.
Monitoring the expression profiles of 7000 Arabidopsis genes under drought, cold and high-salinity stresses using a full-length cDNA microarray.
TLDR
A full-length cDNA microarray containing approximately 7000 independent, full- length cDNA groups is prepared to analyse the expression profiles of genes under drought, cold (low temperature) and high-salinity stress conditions over time, suggesting that various transcriptional regulatory mechanisms function in the drought,cold or high- salinity stress signal transduction pathways.
An atlas of active enhancers across human cell types and tissues
TLDR
It is shown that enhancers share properties with CpG-poor messenger RNA promoters but produce bidirectional, exosome-sensitive, relatively short unspliced RNAs, the generation of which is strongly related to enhancer activity.
Genome-wide analysis of mammalian promoter architecture and evolution
TLDR
These tagging methods allow quantitative analysis of promoter usage in different tissues and show that differentially regulated alternative TSSs are a common feature in protein-coding genes and commonly generate alternative N termini.
Comprehensive analysis of NAC family genes in Oryza sativa and Arabidopsis thaliana.
TLDR
A comprehensive analysis of NAC family genes in Oryza sativa and Arabidopsis thaliana found 13 common sequence motifs from transcriptional activation regions in the C-terminal regions of predicted NAC proteins that probably diverged having correlations with NAC domain structures.
The Transcriptional Landscape of the Mammalian Genome
TLDR
Detailed polling of transcription start and termination sites and analysis of previously unidentified full-length complementary DNAs derived from the mouse genome provide a comprehensive platform for the comparative analysis of mammalian transcriptional regulation in differentiation and development.
Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences
The National Institutes of Health Mammalian Gene Collection (MGC) Program is a multiinstitutional effort to identify and sequence a cDNA clone containing a complete ORF for each human and mouse gene.
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