Transcriptional Maps of 10 Human Chromosomes at 5-Nucleotide Resolution

  title={Transcriptional Maps of 10 Human Chromosomes at 5-Nucleotide Resolution},
  author={Jill Cheng and Philipp Kapranov and Jorg Drenkow and Sujit Dike and Shane A. Brubaker and Sandeep Patel and Jeffrey C. Long and David Stern and Hari Tammana and Gregg A. Helt and Victor I. Sementchenko and Antonio Piccolboni and Stefan Bekiranov and Dione K. Bailey and Madhavan Ganesh and Srinka Ghosh and Ian Bell and Daniela S. Gerhard and Thomas R. Gingeras},
  pages={1149 - 1154}
Sites of transcription of polyadenylated and nonpolyadenylated RNAs for 10 human chromosomes were mapped at 5–base pair resolution in eight cell lines. Unannotated, nonpolyadenylated transcripts comprise the major proportion of the transcriptional output of the human genome. Of all transcribed sequences, 19.4, 43.7, and 36.9% were observed to be polyadenylated, nonpolyadenylated, and bimorphic, respectively. Half of all transcribed sequences are found only in the nucleus and for the most part… 

A high-resolution map of transcription in the yeast genome.

By quantifying RNA expression on both strands of the complete genome of Saccharomyces cerevisiae using a high-density oligonucleotide tiling array, this study identifies the boundary, structure, and level of coding and noncoding transcripts.

Organization and transcriptional output of a novel mRNA-like piRNA gene (mpiR) located on mouse chromosome 10.

Overall, this work provides a picture of a novel, lineage-specific, noncoding RNA gene and describes its processing into both mRNA-like and piRNA products.

The Biology of Long Non-Coding RNA

The biology, conservation, function and roles in disease as well as various approaches to their characterisation of long non-coding RNAs are examined.

RNA Maps Reveal New RNA Classes and a Possible Function for Pervasive Transcription

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.

Transcriptional and post-transcriptional profile of human chromosome 21.

It is demonstrated that the combination of RNA fractionation and tiling arrays is a powerful method to assess the transcriptional and post-transcriptional properties of genomic regions.

Transcriptional landscape of the human and fly genomes: nonlinear and multifunctional modular model of transcriptomes.

An interlaced model of the genome in which many regions serve multifunctional purposes and are highly modular in their utilization is illustrated, illustrating the underappreciated organizational complexity ofThe genome and one of the functional roles of transcription from unannotated portions of the genomes.

The Transcriptional Landscape of the Mammalian Genome

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.

Biological function of unannotated transcription during the early development of Drosophila melanogaster

Identification of P element mutations within or near newly identified 5′ exons provides a strategy for mapping previously uncharacterized mutations to their respective genes and indicates that at least 85% of the fly genome is transcribed and processed into mature transcripts representing at least 30% ofThe fly genome.

Regulation of gene expression by non-protein-coding RNAs

It is found that there are widespread occurrences of NATs in mammalian genomes and that many of these regulatory elements are indeed functionally relevant in controlling conventional (sense) gene expression.

chromatin architecture related to 3 ' end RNA polyadenylation A Genomics Analysis of RNA polymerase II modification and

The results suggest that transcription termination may involve the separable events of loss of histone3 lysine 36 methylation and later release of RNA polymerase, which is often associated with polymerase pausing before release.



Large-Scale Transcriptional Activity in Chromosomes 21 and 22

Empirically derived maps identifying active areas of RNA transcription on these chromosomes have been constructed with the use of cytosolic polyadenylated RNA obtained from 11 human cell lines with results that indicate there are approximately 770 well-characterized and predicted genes.

Novel RNAs identified from an in-depth analysis of the transcriptome of human chromosomes 21 and 22.

The argument for a re-evaluation of the total number of human genes and an alternative term for "gene" to encompass these growing, novel classes of RNA transcripts in the human genome is strongly supported.

Global Identification of Human Transcribed Sequences with Genome Tiling Arrays

This work constructed a series of high-density oligonucleotide tiling arrays representing sense and antisense strands of the entire nonrepetitive sequence of the human genome and found 10,595 transcribed sequences not detected by other methods.

The transcriptional activity of human Chromosome 22.

A DNA microarray representing nearly all of the unique sequences of human Chromosome 22 was constructed and used to measure global-transcriptional activity in placental poly(A)(+) RNA and revealed twice as many transcribed bases as have been reported previously.

Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs

The present work, completely supported by physical clones, provides the most comprehensive survey of a mammalian transcriptome so far, and is a valuable resource for functional genomics.

A Gene Expression Map for the Euchromatic Genome of Drosophila melanogaster

A maskless photolithography method is used to produce DNA oligonucleotide microarrays with unique probe sequences tiled throughout the genome of Drosophila melanogaster and across predicted splice junctions to provide a draft expression map for the entire nonrepetitive genome, which reveals a much more extensive and diverse set of expressed sequences than was previously predicted.

The Sequence of the Human Genome

Comparative genomic analysis indicates vertebrate expansions of genes associated with neuronal function, with tissue-specific developmental regulation, and with the hemostasis and immune systems are indicated.

Experimental annotation of the human genome using microarray technology

Using ‘exon’ and ‘tiling’ arrays fabricated by ink-jet oligonucleotide synthesis, an experimental approach is devised to validate and refine computational gene predictions and define full-length transcripts on the basis of co-regulated expression of their exons.

Distribution of NF-κB-binding sites across human chromosome 22

The results suggest that binding is not restricted to promoter regions and that NF-κB binding occurs at a significant number of genes whose expression is not altered, thereby suggesting that binding alone is not sufficient for gene activation.