Protein Interaction Verification and Functional Annotation by Integrated Analysis of Genome-scale Data

Molecular Cell. May, 2002  |  Pubmed ID: 12049748

Assays capable of determining the properties of thousands of genes in parallel present challenges with regard to accurate data processing and functional annotation. Collections of microarray expression data are applied here to assess the quality of different high-throughput protein interaction data sets. Significant differences are found. Confidence in 973 out of 5342 putative two-hybrid interactions from S. cerevisiae is increased. Besides verification, integration of expression and interaction data is employed to provide functional annotation for over 300 previously uncharacterized genes. The robustness of these approaches is demonstrated by experiments that test the in silico predictions made. This study shows how integration improves the utility of different types of functional genomic data and how well this contributes to functional annotation.

A High Resolution Protein Interaction Map of the Yeast Mediator Complex

Nucleic Acids Research. 2004  |  Pubmed ID: 15477388

Mediator is a large, modular protein complex remotely conserved from yeast to man that conveys regulatory signals from DNA-binding transcription factors to RNA polymerase II. In Saccharomyces cerevisiae, Mediator is thought to be composed of 24 subunits organized in four sub-complexes, termed the head, middle, tail and Cdk8 (Srb8-11) modules. In this work, we have used screening and pair-wise two-hybrid approaches to investigate protein-protein contacts between budding yeast Mediator subunits. The derived interaction map includes the delineation of numerous interaction domains between Mediator subunits, frequently corresponding to segments that have been conserved in evolution, as well as novel connections between the Cdk8 (Srb8-11) and head modules, the head and middle modules, and the middle and tail modules. The two-hybrid analysis, together with co-immunoprecipitation studies and gel filtration experiments revealed that Med31 (Soh1) is associated with the yeast Mediator that therefore comprises 25 subunits. Finally, analysis of the protein interaction network within the Drosophila Mediator middle module indicated that the structural organization of the Mediator complex is conserved from yeast to metazoans. The resulting interaction map provides a framework for delineating Mediator structure-function and investigating how Mediator function is regulated.

Genome-wide Analyses Reveal RNA Polymerase II Located Upstream of Genes Poised for Rapid Response Upon S. Cerevisiae Stationary Phase Exit

Molecular Cell. Apr, 2005  |  Pubmed ID: 15837421

The resting state of eukaryotic cells (G0) is relatively uncharacterized. We have applied DNA microarray expression profiling of S. cerevisiae to reveal multiple transitions during a complete 9-day growth cycle between stationary phase (SP) exit and entry. The findings include distinct waves of transcription after the diauxic shift (DS), identification of genes active in SP, and upregulation of over 2500 genes during the first minutes of lag phase. This provides a framework for analyzing large-scale reprogramming of gene expression. Despite global repression, the general transcription machinery is found to be present in quiescent cells but is largely inactive. Genome-wide location analysis by chromatin immunoprecipitation (ChIP on chip) reveals that RNA polymerase II is more predominantly bound at intergenic regions in SP, upstream of hundreds of genes immediately induced upon exit. In contrast to current models of activation-coupled recruitment, the results show that RNA polymerase II is located and maintained upstream of many inactive genes in quiescence.

Determining Spatial Chromatin Organization of Large Genomic Regions Using 5C Technology

Methods in Molecular Biology (Clifton, N.J.). 2009  |  Pubmed ID: 19588094

Spatial organization of chromatin plays an important role at multiple levels of genome regulation. On a global scale, its function is evident in processes like metaphase and chromosome segregation. On a detailed level, long-range interactions between regulatory elements and promoters are essential for proper gene regulation. Microscopic techniques like FISH can detect chromatin contacts, although the resolution is generally low making detection of enhancer-promoter interaction difficult. The 3C methodology allows for high-resolution analysis of chromatin interactions. 3C is now widely used and has revealed that long-range looping interactions between genomic elements are widespread. However, studying chromatin interactions in large genomic regions by 3C is very labor intensive. This limitation is overcome by the 5C technology. 5C is an adaptation of 3C, in which the concurrent use of thousands of primers permits the simultaneous detection of millions of chromatin contacts. The design of the 5C primers is critical because this will determine which and how many chromatin interactions will be examined in the assay. Starting material for 5C is a 3C template. To make a 3C template, chromatin interactions in living cells are cross-linked using formaldehyde. Next, chromatin is digested and subsequently ligated under conditions favoring ligation events between cross-linked fragments. This yields a genome-wide 3C library of ligation products representing all chromatin interactions in vivo. 5C then employs multiplex ligation-mediated amplification to detect, in a single assay, up to millions of unique ligation products present in the 3C library. The resulting 5C library can be analyzed by microarray analysis or deep sequencing. The observed abundance of a 5C product is a measure of the interaction frequency between the two corresponding chromatin fragments. The power of the 5C technique described in this chapter is the high-throughput, high-resolution, and quantitative way in which the spatial organization of chromatin can be examined.

My5C: Web Tools for Chromosome Conformation Capture Studies

Nature Methods. Oct, 2009  |  Pubmed ID: 19789528

Comprehensive Mapping of Long-range Interactions Reveals Folding Principles of the Human Genome

Science (New York, N.Y.). Oct, 2009  |  Pubmed ID: 19815776

We describe Hi-C, a method that probes the three-dimensional architecture of whole genomes by coupling proximity-based ligation with massively parallel sequencing. We constructed spatial proximity maps of the human genome with Hi-C at a resolution of 1 megabase. These maps confirm the presence of chromosome territories and the spatial proximity of small, gene-rich chromosomes. We identified an additional level of genome organization that is characterized by the spatial segregation of open and closed chromatin to form two genome-wide compartments. At the megabase scale, the chromatin conformation is consistent with a fractal globule, a knot-free, polymer conformation that enables maximally dense packing while preserving the ability to easily fold and unfold any genomic locus. The fractal globule is distinct from the more commonly used globular equilibrium model. Our results demonstrate the power of Hi-C to map the dynamic conformations of whole genomes.

A Consensus of Core Protein Complex Compositions for Saccharomyces Cerevisiae

Molecular Cell. Jun, 2010  |  Pubmed ID: 20620961

Analyses of biological processes would benefit from accurate definitions of protein complexes. High-throughput mass spectrometry data offer the possibility of systematically defining protein complexes; however, the predicted compositions vary substantially depending on the algorithm applied. We determine consensus compositions for 409 core protein complexes from Saccharomyces cerevisiae by merging previous predictions with a new approach. Various analyses indicate that the consensus is comprehensive and of high quality. For 85 out of 259 complexes not recorded in GO, literature search revealed strong support in the form of coprecipitation. New complexes were verified by an independent interaction assay and by gene expression profiling of strains with deleted subunits, often revealing which cellular processes are affected. The consensus complexes are available in various formats, including a merge with GO, resulting in 518 protein complex compositions. The utility is further demonstrated by comparison with binary interaction data to reveal interactions between core complexes.

Mediator and Cohesin Connect Gene Expression and Chromatin Architecture

Nature. Sep, 2010  |  Pubmed ID: 20720539

Transcription factors control cell-specific gene expression programs through interactions with diverse coactivators and the transcription apparatus. Gene activation may involve DNA loop formation between enhancer-bound transcription factors and the transcription apparatus at the core promoter, but this process is not well understood. Here we report that mediator and cohesin physically and functionally connect the enhancers and core promoters of active genes in murine embryonic stem cells. Mediator, a transcriptional coactivator, forms a complex with cohesin, which can form rings that connect two DNA segments. The cohesin-loading factor Nipbl is associated with mediator-cohesin complexes, providing a means to load cohesin at promoters. DNA looping is observed between the enhancers and promoters occupied by mediator and cohesin. Mediator and cohesin co-occupy different promoters in different cells, thus generating cell-type-specific DNA loops linked to the gene expression program of each cell.

Evidence for Transcript Networks Composed of Chimeric RNAs in Human Cells

PloS One. 2012  |  Pubmed ID: 22238572

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.