Evidence for Transcript Networks Composed of Chimeric RNAs in Human Cells

The classic organization of a gene structure has followed the Jacob and Monod bacterial gene model proposed more than 50 years ago. Since then, empirical determinations of the complexity of the transcriptomes found in yeast to human has blurred the definition and physical boundaries of genes. Using multiple analysis approaches we have characterized individual gene boundaries mapping on human chromosomes 21 and 22. Analyses of the locations of the 5′ and 3′ transcriptional termini of 492 protein coding genes revealed that for 85% of these genes the boundaries extend beyond the current annotated termini, most often connecting with exons of transcripts from other well annotated genes. The biological and evolutionary importance of these chimeric transcripts is underscored by (1) the non-random interconnections of genes involved, (2) the greater phylogenetic depth of the genes involved in many chimeric interactions, (3) the coordination of the expression of connected genes and (4) the close in vivo and three dimensional proximity of the genomic regions being transcribed and contributing to parts of the chimeric RNAs. The non-random nature of the connection of the genes involved suggest that chimeric transcripts should not be studied in isolation, but together, as an RNA network

Factors Associated with Revision Surgery after Internal Fixation of Hip Fractures

Background: Femoral neck fractures are associated with high rates of revision surgery after management with internal fixation. Using data from the Fixation using Alternative Implants for the Treatment of Hip fractures (FAITH) trial evaluating methods of internal fixation in patients with femoral neck fractures, we investigated associations between baseline and surgical factors and the need for revision surgery to promote healing, relieve pain, treat infection or improve function over 24 months postsurgery. Additionally, we investigated factors associated with (1) hardware removal and (2) implant exchange from cancellous screws (CS) or sliding hip screw (SHS) to total hip arthroplasty, hemiarthroplasty, or another internal fixation device. Methods: We identified 15 potential factors a priori that may be associated with revision surgery, 7 with hardware removal, and 14 with implant exchange. We used multivariable Cox proportional hazards analyses in our investigation. Results: Factors associated with increased risk of revision surgery included: female sex, [hazard ratio (HR) 1.79, 95% confidence interval (CI) 1.25-2.50; P = 0.001], higher body mass index (fo

Evidence for transcript networks composed of chimeric RNAs in human cells

The classic organization of a gene structure has followed the Jacob and Monod bacterial gene model proposed more than 50 years ago. Since then, empirical determinations of the complexity of the transcriptomes found in yeast to human has blurred the definition and physical boundaries of genes. Using multiple analysis approaches we have characterized individual gene boundaries mapping on human chromosomes 21 and 22. Analyses of the locations of the 5′ and 3′ transcriptional termini of 492 protein coding genes revealed that for 85% of these genes the boundaries extend beyond the current annotated termini, most often connecting with exons of transcripts from other well annotated genes. The biological and evolutionary importance of these chimeric transcripts is underscored by (1) the non-random interconnections of genes involved, (2) the greater phylogenetic depth of the genes involved in many chimeric interactions, (3) the coordination of the expression of connected genes and (4) the close in vivo and three dimensional proximity of the genomic regions being transcribed and contributing to parts of the chimeric RNAs. The non-random nature of the connection of the genes involved suggest that chimeric transcripts should not be studied in isolation, but together, as an RNA network

Evidence for transcript networks composed of chimeric RNAs in human cells

The classic organization of a gene structure has followed the Jacob and Monod bacterial gene model proposed more than 50 years ago. Since then, empirical determinations of the complexity of the transcriptomes found in yeast to human has blurred the definition and physical boundaries of genes. Using multiple analysis approaches we have characterized individual gene boundaries mapping on human chromosomes 21 and 22. Analyses of the locations of the 5′ and 3′ transcriptional termini of 492 protein coding genes revealed that for 85% of these genes the boundaries extend beyond the current annotated termini, most often connecting with exons of transcripts from other well annotated genes. The biological and evolutionary importance of these chimeric transcripts is underscored by (1) the non-random interconnections of genes involved, (2) the greater phylogenetic depth of the genes involved in many chimeric interactions, (3) the coordination of the expression of connected genes and (4) the close in vivo and three dimensional proximity of the genomic regions being transcribed and contributing to parts of the chimeric RNAs. The non-random nature of the connection of the genes involved suggest that chimeric transcripts should not be studied in isolation, but together, as an RNA network

Evidence for Transcript Networks Composed of Chimeric RNAs in Human Cells

International audienceThe classic organization of a gene structure has followed the Jacob and Monod bacterial gene model proposed more than 50 years ago. Since then, empirical determinations of the complexity of the transcriptomes found in yeast to human has blurred the definition and physical boundaries of genes. Using multiple analysis approaches we have characterized individual gene boundaries mapping on human chromosomes 21 and 22. Analyses of the locations of the 59 and 39 transcriptional termini of 492 protein coding genes revealed that for 85% of these genes the boundaries extend beyond the current annotated termini, most often connecting with exons of transcripts from other well annotated genes. The biological and evolutionary importance of these chimeric transcripts is underscored by (1) the non-random interconnections of genes involved, (2) the greater phylogenetic depth of the genes involved in many chimeric interactions, (3) the coordination of the expression of connected genes and (4) the close in vivo and three dimensional proximity of the genomic regions being transcribed and contributing to parts of the chimeric RNAs. The non-random nature of the connection of the genes involved suggest that chimeric transcripts should not be studied in isolation, but together, as an RNA network

Efficient targeted transcript discovery via array-based normalization of RACE libraries.

Rapid amplification of cDNA ends (RACE) is a widely used approach for transcript identification. Random clone selection from the RACE mixture, however, is an ineffective sampling strategy if the dynamic range of transcript abundances is large. To improve sampling efficiency of human transcripts, we hybridized the products of the RACE reaction onto tiling arrays and used the detected exons to delineate a series of reverse-transcriptase (RT)-PCRs, through which the original RACE transcript population was segregated into simpler transcript populations. We independently cloned the products and sequenced randomly selected clones. This approach, RACEarray, is superior to direct cloning and sequencing of RACE products because it specifically targets new transcripts and often results in overall normalization of transcript abundance. We show theoretically and experimentally that this strategy leads indeed to efficient sampling of new transcripts, and we investigated multiplexing the strategy by pooling RACE reactions from multiple interrogated loci before hybridization

Landscape of transcription in human cells

Eukaryotic cells make many types of primary and processed RNAs that are found either in specific subcellular compartments or throughout the cells. A complete catalogue of these RNAs is not yet available and their characteristic subcellular localizations are also poorly understood. Because RNA represents the direct output of the genetic information encoded by genomes and a significant proportion of a cell's regulatory capabilities are focused on its synthesis, processing, transport, modification and translation, the generation of such a catalogue is crucial for understanding genome function. Here we report evidence that three-quarters of the human genome is capable of being transcribed, 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. These observations, taken together, prompt a redefinition of the concept of a gene.This work was supported by the National Human Genome Research Institute (NHGRI) production grants U54HG004557, U54HG004555, U54HG004576 and U54HG004558, and by the NHGRI pilot grant R01HG003700. It was also supported by the NHGRI ARRA stimulus grant 1RC2HG005591, the National Science Foundation (SNF) grant 127375, the European Research Council (ERC) grant/n249968, a research grant for the RIKEN Omics Science Center from the Japanese Ministry of Education, Culture, Sports, Science and Technology, and grants BIO2011-26205, CSD2007-00050 and INB GNV-1 from the Spanish Ministry of Scienc

RACEfrag transcription map statistics.

<p><b>A- Distribution of RACEfrags among annotated genomic domains.</b> The proportion of RACEfrags overlapping different annotated genic features is represented in this histogram. Blue: intronic RACEfrags; Light orange: exonic RACEfrags; Light grey: intergenic RACEfrags. The three categories on the X axis are, from left to right: (1) - external genic RACEfrags (i.e. RACEfrags falling within the boundaries of a gene not interrogated by RACE, (2) - intergenic RACEfrags, (3) - internal RACEfrags (i.e., RACEfrags detected within the RACE-primed gene). <b>B- RACEfrag descriptive analysis.</b> The top bar plot represents proportions of genomic domains covered by RACEfrags, and the bottom bar plot represents proportions of RACEfrags in different genomic domains (refinement of part A). As RACE is carried out in the two possible directions, 5′ and 3′, each bar plot is thus sub-divided into two sub-bar plots: proportions relative to 5′ RACEfrags in gray, and proportions relative to 3′ RACEfrags in blue. As expected: (1) RACEfrag coming from a given gene covers this gene more than any other gene; (2) for a given RACE-interrogated gene, internal exons and introns are equally covered by 5′ and 3′ RACEfrags, whereas 5′ most exons are more covered by 5′ RACEfrags and 3′ most exons by 3′ RACEfrags. The bottom bar plot also shows that most RACEfrags are exonic, then intronic and finally intergenic, and that exonic RACEfrags are first found in internal exons, then in most 3′ exons and finally in most 5′ exons.</p

Characteristics of hub genes. A- Expression of hub genes.

<p>The distribution of expression of the 74 hubs and of the 362 non hubs is plotted in blue and orange respectively. The expression of a gene is computed based on tiling array experiments performed on the same 16 cell lines and tissues as the RACE experiments (see details in the text). As we can see hubs tend to have higher expression values than non hubs. <b>B- </b><b>Phylogenetic conservation of hub genes.</b> In each of the three gene network categories (<i>i.e.</i>, hubs, non-hubs, and all RACEd genes), the proportion of genes having a detected ortholog in each eukaryotic species represented on the X axis (ordered by decreasing phylogenetic distance from human) is reported on the Y axis. Instances where the proportion of orthologs found in the <i>hub</i> category is significantly higher than for <i>non-hubs</i> (<i>p</i><0.01, Fisher test) are marked with an asterisk.</p

Reciprocal gene/gene connections.

<p><b>A - General definition of reciprocal gene/gene connections</b>. Top panel: graphical illustration of reciprocity. Exons are symbolized by light blue boxes, introns by solid black lines. Dashed arrows, directed from the index exon to the RACEfrag, correspond to chimeric connections in distinct cell types, which are rendered in different colors. Two reciprocal gene/gene connections can be observed in this example, between genes A and B, and B and C. The (A–B) reciprocal pair is said to be (i), <i>unique to cell type 2</i>, and (ii), <i>pure</i> (<i>i.e.</i>, its reciprocity is observed at least once in the same condition, cell type <i>2</i> in this example), whereas (B–C) is <i>composite</i> (<i>i.e.</i>, its reciprocity can only be deduced from connections observed in different cell types). The counts of each connection type in this example are summarized in the tables in the bottom panel. <b>B - Observed numbers of reciprocal gene/gene connections across 10 different cell types</b>. This table is based on the template used in part A.</p