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1.  Annotating non-coding transcription using functional genomics strategies 
Non-coding RNA (ncRNA) transcripts are RNA molecules that do not code for proteins, but elicit function by other mechanisms. The vast majority of RNA produced in a cell is non-coding ribosomal RNA, produced from relatively few loci, however more recently complementary DNA (cDNA) cloning, tag sequencing, and genome tiling array studies suggest that ncRNAs also account for the majority of RNA species produced by a cell. ncRNA based regulation has been referred to as a ‘hidden layer’ of signals or ‘dark matter’ that control gene expression in cellular processes by poorly described mechanisms. These terms have appeared as ncRNAs until recently have been ignored by expression profiling and cDNA annotation projects and their mode of action is diverse (e.g. influencing chromatin structure and epigenetics, translational silencing, transcriptional silencing). Here, we highlight recent functional genomics strategies toward identifying and assigning function to ncRNA transcription.
doi:10.1093/bfgp/elp041
PMCID: PMC2762128  PMID: 19833699
non-coding RNA; Sequencing; transcription; annotation
2.  Cis-regulatory mutations in human disease 
Cis-acting regulatory sequences are required for the proper temporal and spatial control of gene expression. Variation in gene expression is highly heritable and a significant determinant of human disease susceptibility. The diversity of human genetic diseases attributed, in whole or in part, to mutations in non-coding regulatory sequences is on the rise. Improvements in genome-wide methods of associating genetic variation with human disease and predicting DNA with cis-regulatory potential are two of the major reasons for these recent advances. This review will highlight select examples from the literature that have successfully integrated genetic and genomic approaches to uncover the molecular basis by which cis-regulatory mutations alter gene expression and contribute to human disease. The fine mapping of disease-causing variants has led to the discovery of novel cis-acting regulatory elements that, in some instances, are located as far away as 1.5 Mb from the target gene. In other cases, the prior knowledge of the regulatory landscape surrounding the gene of interest aided in the selection of enhancers for mutation screening. The success of these studies should provide a framework for following up on the large number of genome-wide association studies that have identified common variants in non-coding regions of the genome that associate with increased risk of human diseases including, diabetes, autism, Crohn's, colorectal cancer, and asthma, to name a few.
doi:10.1093/bfgp/elp021
PMCID: PMC2742803  PMID: 19641089
cis regulation; transcription; gene expression; human disease
3.  Chromatin insulators: lessons from the fly 
Chromatin insulators are DNA–protein complexes with broad functions in nuclear biology. Drosophila has at least five different types of insulators; recent results suggest that these different insulators share some components that may allow them to function through common mechanisms. Data from genome-wide localization studies of insulator proteins indicate a possible functional specialization, with different insulators playing distinct roles in nuclear biology. Cells have developed mechanisms to control insulator activity by recruiting specialized proteins or by covalent modification of core components. Current results suggest that insulators set up cell-specific blueprints of nuclear organization that may contribute to the establishment of different patterns of gene expression during cell differentiation and development.
doi:10.1093/bfgp/elp032
PMCID: PMC2742804  PMID: 19752045
Drosophila; insulator; transcription; nucleus
4.  Identifying regulatory elements in eukaryotic genomes 
Proper development and functioning of an organism depends on precise spatial and temporal expression of all its genes. These coordinated expression-patterns are maintained primarily through the process of transcriptional regulation. Transcriptional regulation is mediated by proteins binding to regulatory elements on the DNA in a combinatorial manner, where particular combinations of transcription factor binding sites establish specific regulatory codes. In this review, we survey experimental and computational approaches geared towards the identification of proximal and distal gene regulatory elements in the genomes of complex eukaryotes. Available approaches that decipher the genetic structure and function of regulatory elements by exploiting various sources of information like gene expression data, chromatin structure, DNA-binding specificities of transcription factors, cooperativity of transcription factors, etc. are highlighted. We also discuss the relevance of regulatory elements in the context of human health through examples of mutations in some of these regions having serious implications in misregulation of genes and being strongly associated with human disorders.
doi:10.1093/bfgp/elp014
PMCID: PMC2764519  PMID: 19498043
transcriptional regulation; enhancers; silencers; tissue-specific regulatory elements; population variation; non-coding diseases; computational analysis of regulatory element sequence composition
5.  Current affairs in quantitative targeted proteomics: multiple reaction monitoring–mass spectrometry 
Quantitative targeted proteomics has recently taken front stage in the proteomics community. Centered on multiple reaction monitoring–mass spectrometry (MRM–MS) methodologies, quantitative targeted proteomics is being used in the verification of global proteomics data, the discovery of lower abundance proteins, protein post-translational modifications, discrimination of select highly homologous protein isoforms and as the final step in biomarker discovery. An older methodology utilized with small molecule analysis, the proteomics community is making great technological strides to develop MRM–MS as the next method to address previously challenging issues in global proteomics experimentation, namely dynamic range, identification of post-translational modifications, sensitivity and selectivity of measurement which will undoubtedly further biomedical knowledge. This brief review will provide a general introduction of MRM–MS and highlight its novel application for targeted quantitative proteomic experimentations.
doi:10.1093/bfgp/eln056
PMCID: PMC2722263  PMID: 19279071
absolute quantification; quantitative proteomics; mass spectrometry; multiple reaction monitoring; stable isotope dilution; targeted proteomics
6.  18O Stable Isotope Labeling in MS-based Proteomics 
A variety of stable isotope labeling techniques have been developed and used in mass spectrometry (MS)-based proteomics, primarily for relative quantitation of changes in protein abundances between two compared samples, but also for qualitative characterization of differentially labeled proteomes. Differential 16O/18O coding relies on the 18O exchange that takes place at the C-terminal carboxyl group of proteolytic fragments, where two 16O atoms are typically replaced by two 18O atoms by enzyme-catalyzed oxygen-exchange in the presence of H218O. The resulting mass shift between differentially labeled peptide ions permits identification, characterization and quantitation of proteins from which the peptides are proteolytically generated. This review focuses on the utility of 16O/18O labeling within the context of mass spectrometry-based proteome research. Different strategies employing 16O/18O are examined in the context of global comparative proteome profiling, targeted subcellular proteomics, analysis of post-translational modifications and biomarker discovery. Also discussed are analytical issues related to this technique, including variable 18O exchange along with advantages and disadvantages of 16O/18O labeling in comparison with other isotope-coding techniques.
doi:10.1093/bfgp/eln055
PMCID: PMC2722262  PMID: 19151093
18O labeling; enzyme-mediated isotope incorporation; stable isotope labeling; MS-based proteomics; relative protein quantitation; LC/MS/MS
7.  Quantitative strategies to fuel the merger of discovery and hypothesis-driven shotgun proteomics 
The ultimate goal of most shotgun proteomic pipelines is the discovery of novel biomarkers to direct the development of quantitative diagnostics for the detection and treatment of disease. Differential comparisons of biological samples identify candidate peptides that can serve as proxys of candidate proteins. While these discovery approaches are robust and fairly comprehensive, they have relatively low throughput. When merged with targeted mass spectrometry, this pipeline can fuel hypothesis-driven studies and the development of novel diagnostics and therapeutics.
doi:10.1093/bfgp/elp008
PMCID: PMC3105289  PMID: 19398505
quantitative shotgun proteomics; biomarker discovery; targeted mass spectrometry; human tissue
8.  Finding common susceptibility variants for complex disease: past, present and future 
The identification of complex disease susceptibility loci has been accelerated considerably by advances in high-throughput genotyping technologies, improved insight into correlation patterns of common variants and the availability of large-scale sample sets. Linkage scans and small-scale candidate gene studies have now given way to genome-wide association scans. In this review, we summarize insights gained from the past, highlight practical issues relating to the design and analysis of current state-of-the-art GWA studies and look into future trends in the field of human complex trait genetics.
doi:10.1093/bfgp/elp020
PMCID: PMC2758134  PMID: 19571035
association study; complex disease; single nucleotide polymorphism; genome-wide association scan; meta-analysis; sequencing

Results 1-8 (8)