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1.  Heart genetics in a small package, exploiting the condensed genome of Ciona intestinalis 
Defects in the initial establishment of cardiogenic cell fate are likely to contribute to pervasive human congenital cardiac abnormalities. However, the molecular underpinnings of nascent cardiac fate induction have proven difficult to decipher. In this review we explore the participation of extracellular, cellular and nuclear factors in comprehensive specification networks. At each level, we elaborate on insights gained through the study of cardiogenesis in the invertebrate chordate Ciona intestinalis and propose productive lines of future research. In-depth discussion of pre-cardiac induction is intended to serve as a paradigm, illustrating the potential use of Ciona to elucidate comprehensive networks underlying additional aspects of chordate cardiogenesis, including directed migration and subspecification of cardiac and pharyngeal lineages.
doi:10.1093/bfgp/elt034
PMCID: PMC3896895  PMID: 24005910
Mesp; FGF; gene regulatory networks; extracellular matrix; cardiac induction; chordate evolution
2.  Epigenetic mechanisms and developmental choice hierarchies in T-lymphocyte development 
Briefings in Functional Genomics  2013;12(6):512-524.
Three interlocking problems in gene regulation are: how to explain genome-wide targeting of transcription factors in different cell types, how prior transcription factor action can establish an ‘epigenetic state’ that changes the options for future transcription factor action, and how directly a sequence of developmental decisions can be memorialized in a hierarchy of repression structures applied to key genes of the ‘paths not taken’. This review uses the finely staged process of T-cell lineage commitment as a test case in which to examine how changes in developmental status are reflected in changes in transcription factor expression, transcription factor binding distribution across genomic sites, and chromatin modification. These are evaluated in a framework of reciprocal effects of previous chromatin structure features on transcription factor access and of transcription factor binding on other factors and on future chromatin structure.
doi:10.1093/bfgp/elt027
PMCID: PMC3838197  PMID: 23922132
DNA binding; histone methylation; DNA methylation; lineage commitment; repression; hematopoiesis
3.  Fungal cellulose degradation by oxidative enzymes: from dysfunctional GH61 family to powerful lytic polysaccharide monooxygenase family 
Briefings in Functional Genomics  2014;13(6):471-481.
Our understanding of fungal cellulose degradation has shifted dramatically in the past few years with the characterization of a new class of secreted enzymes, the lytic polysaccharide monooxygenases (LPMO). After a period of intense research covering structural, biochemical, theoretical and evolutionary aspects, we have a picture of them as wedge-like copper-dependent metalloenzymes that on reduction generate a radical copper-oxyl species, which cleaves mainly crystalline cellulose. The main biological function lies in the synergism of fungal LPMOs with canonical hydrolytic cellulases in achieving efficient cellulose degradation. Their important role in cellulose degradation is highlighted by the wide distribution and often numerous occurrences in the genomes of almost all plant cell-wall degrading fungi. In this review, we provide an overview of the latest achievements in LPMO research and consider the open questions and challenges that undoubtedly will continue to stimulate interest in this new and exciting group of enzymes.
doi:10.1093/bfgp/elu032
PMCID: PMC4239789  PMID: 25217478
AA9; GH61; cellobiose dehydrogenase; oxidative cellulose degradation
4.  Genomic approaches in breast cancer research 
Briefings in Functional Genomics  2013;12(5):391-396.
Microarray technologies provide high-throughput analysis of genes that are differentially expressed in humans and other species, and thereby provide a means to measure how biological systems are altered during development or disease states. Within, we review how high-throughput genomic technologies have increased our understanding about the molecular complexity of breast cancer, identified distinct molecular phenotypes and how they can be used to increase the accuracy of predicted clinical outcome.
doi:10.1093/bfgp/elt019
PMCID: PMC3776566  PMID: 23788797
breast cancer; microarray; genomics; tumor; histology
5.  Structural variations in plant genomes 
Briefings in Functional Genomics  2014;13(4):296-307.
Differences between plant genomes range from single nucleotide polymorphisms to large-scale duplications, deletions and rearrangements. The large polymorphisms are termed structural variants (SVs). SVs have received significant attention in human genetics and were found to be responsible for various chronic diseases. However, little effort has been directed towards understanding the role of SVs in plants. Many recent advances in plant genetics have resulted from improvements in high-resolution technologies for measuring SVs, including microarray-based techniques, and more recently, high-throughput DNA sequencing. In this review we describe recent reports of SV in plants and describe the genomic technologies currently used to measure these SVs.
doi:10.1093/bfgp/elu016
PMCID: PMC4110416  PMID: 24907366
structural variations (SVs); next-generation sequencing (NGS); copy number variations (CNVs); presence and absence variations (PAVs); inversions; translocations
6.  The impact of linked selection on plant genomic variation 
Briefings in Functional Genomics  2014;13(4):268-275.
Understanding the forces that shape patterns of genetic variation across the genome is a major aim in evolutionary genetics. An emerging insight from analyses of genome-wide polymorphism and divergence data is that selection on linked sites can have an important impact on neutral genetic variation. However, in contrast to Drosophila, which exhibits a signature of recurrent hitchhiking, many plant genomes studied so far seem to mainly be affected by background selection. Moreover, many plants do not exhibit classic signatures of linked selection, such as a correlation between recombination rate and neutral diversity. In this review, I discuss the impact of genome architecture and mating system on the expected signature of linked selection in plants and review empirical evidence for linked selection, with a focus on plant model systems. Finally, I discuss the implications of linked selection for inference of demographic history in plants.
doi:10.1093/bfgp/elu009
PMCID: PMC4110415  PMID: 24759704
hitchhiking; genetic draft; recombination rate; genome size; FST; demographic inference
7.  Turning single cells into microarrays by super-resolution barcoding 
In this review, we discuss a strategy to bring genomics and proteomics into single cells by super-resolution microscopy. The basis for this new approach are the following: given the 10 nm resolution of a super-resolution microscope and a typical cell with a size of (10 µm)3, individual cells contain effectively 109 super-resolution pixels or bits of information. Most eukaryotic cells have 104 genes and cellular abundances of 10–100 copies per transcript. Thus, under a super-resolution microscope, an individual cell has 1000 times more pixel volume or information capacities than is needed to encode all transcripts within that cell. Individual species of mRNA can be uniquely identified by labeling them each with a distinct combination of fluorophores by fluorescence in situ hybridization. With at least 15 fluorophores available in super-resolution, hundreds of genes in can be barcoded with a three-color barcode (3C15 = 455). These calculations suggest that by combining super-resolution microscopy and barcode labeling, single cells can be turned into informatics platforms denser than microarrays and that molecular species in individual cells can be profiled in a massively parallel fashion.
doi:10.1093/bfgp/els054
PMCID: PMC3609437  PMID: 23178478
super-resolution microscopy; systems biology; single cells; single-molecule FISH
8.  Dynamics of the DNA damage response: insights from live-cell imaging 
Briefings in Functional Genomics  2013;12(2):109-117.
All organisms have to safeguard the integrity of their genome to prevent malfunctioning and oncogenic transformation. Sophisticated DNA damage response mechanisms have evolved to detect and repair genomic lesions. With the emergence of live-cell microscopy of individual cells, we now begin to appreciate the complex spatiotemporal kinetics of the DNA damage response and can address the causes and consequences of the heterogeneity in the responses of genetically identical cells. Here, we highlight key discoveries where live-cell imaging has provided unprecedented insights into how cells respond to DNA double-strand breaks and discuss the main challenges and promises in using this technique.
doi:10.1093/bfgp/els059
PMCID: PMC3609438  PMID: 23292635
live-cell imaging; single cell; DNA damage; fluorescence microscopy; dynamics
9.  Restoring totipotency through epigenetic reprogramming 
Briefings in Functional Genomics  2012;12(2):118-128.
Epigenetic modifications are implicated in the maintenance and regulation of transcriptional memory by marking genes that were previously transcribed to facilitate transmission of these expression patterns through cell division. During germline specification and maintenance, extensive epigenetic modifications are acquired. Yet somehow at fertilization, the fusion of the highly differentiated sperm and egg results in formation of the totipotent zygote. This massive change in cell fate implies that the selective erasure and maintenance of epigenetic modifications at fertilization may be critical for the re-establishment of totipotency. In this review, we discuss recent studies that provide insight into the extensive epigenetic reprogramming that occurs around fertilization and the mechanisms that may be involved in the re-establishment of totipotency in the embryo.
doi:10.1093/bfgp/els042
PMCID: PMC4023274  PMID: 23117862
10.  Epigenomics and the concept of degeneracy in biological systems 
Briefings in Functional Genomics  2013;13(3):191-202.
Researchers in the field of epigenomics are developing more nuanced understandings of biological complexity, and exploring the multiple pathways that lead to phenotypic expression. The concept of degeneracy—referring to the multiple pathways that a system recruits to achieve functional plasticity—is an important conceptual accompaniment to the growing body of knowledge in epigenomics. Distinct from degradation, redundancy and dilapidation; degeneracy refers to the plasticity of traits whose function overlaps in some environments, but diverges in others. While a redundant system is composed of repeated identical elements performing the same function, a degenerate system is composed of different elements performing similar or overlapping functions. Here, we describe the degenerate structure of gene regulatory systems from the basic genetic code to flexible epigenomic modifications, and discuss how these structural features have contributed to organism complexity, robustness, plasticity and evolvability.
doi:10.1093/bfgp/elt050
PMCID: PMC4031454  PMID: 24335757
epigenetic code; pluripotentiality; robustness; redundancy; DNA methylation; histone modifications; social insect; honey bee
11.  C. elegans epigenetic regulation in development and aging 
Briefings in Functional Genomics  2013;13(3):223-234.
The precise developmental map of the Caenorhabditis elegans cell lineage, as well as a complete genome sequence and feasibility of genetic manipulation make this nematode species highly attractive to study the role of epigenetics during development. Genetic dissection of phenotypical traits, such as formation of egg-laying organs or starvation-resistant dauer larvae, has illustrated how chromatin modifiers may regulate specific cell-fate decisions and behavioral programs. Moreover, the transparent body of C. elegans facilitates non-invasive microscopy to study tissue-specific accumulation of heterochromatin at the nuclear periphery. We also review here recent findings on how small RNA molecules contribute to epigenetic control of gene expression that can be propagated for several generations and eventually determine longevity.
doi:10.1093/bfgp/elt048
PMCID: PMC4031453  PMID: 24326118
Caenorhabditis elegans; chromatin organization; longevity; organogenesis; small RNA; transcriptional silencing
12.  Zebrafish sex: a complicated affair 
Briefings in Functional Genomics  2013;13(2):172-187.
In this review, we provide a detailed overview of studies on the elusive sex determination (SD) and gonad differentiation mechanisms of zebrafish (Danio rerio). We show that the data obtained from most studies are compatible with polygenic sex determination (PSD), where the decision is made by the allelic combinations of several loci. These loci are typically dispersed throughout the genome, but in some teleost species a few of them might be located on a preferential pair of (sex) chromosomes. The PSD system has a much higher level of variation of SD genotypes both at the level of gametes and the sexual genotype of individuals, than that of the chromosomal sex determination systems. The early sexual development of zebrafish males is a complicated process, as they first develop a ‘juvenile ovary’, that later undergoes a transformation to give way to a testis. To date, three major developmental pathways were shown to be involved with gonad differentiation through the modulation of programmed cell death. In our opinion, there are more pathways participating in the regulation of zebrafish gonad differentiation/transformation. Introduction of additional powerful large-scale genomic approaches into the analysis of zebrafish reproduction will result in further deepening of our knowledge as well as identification of additional pathways and genes associated with these processes in the near future.
doi:10.1093/bfgp/elt041
PMCID: PMC3954038  PMID: 24148942
polygenic sex determination; sex chromosome; gonad differentiation; teleost; fish; Danio rerio
13.  Interpreting the regulatory genome: the genomics of transcription factor function in Drosophila melanogaster 
Briefings in Functional Genomics  2012;11(5):336-346.
Researchers have now had access to the fully sequenced Drosophila melanogaster genome for over a decade, and the sequenced genomes of 11 additional Drosophila species have been available for almost 5 years, with more species’ genomes becoming available every year [Adams MD, Celniker SE, Holt RA, et al. The genome sequence of Drosophila melanogaster. Science 2000;287:2185–95; Clark AG, Eisen MB, Smith DR, et al. Evolution of genes and genomes on the Drosophila phylogeny. Nature 2007;450:203–18]. Although the best studied of the D. melanogaster transcription factors (TFs) were cloned before sequencing of the genome, the availability of sequence data promised to transform our understanding of TFs and gene regulatory networks. Sequenced genomes have allowed researchers to generate tools for high-throughput characterization of gene expression levels, genome-wide TF localization and analyses of evolutionary constraints on DNA elements across multiple species. With an estimated 700 DNA-binding proteins in the Drosophila genome, it will be many years before each potential sequence-specific TF is studied in detail, yet the last decade of functional genomics research has already impacted our view of gene regulatory networks and TF DNA recognition.
doi:10.1093/bfgp/els034
PMCID: PMC3459015  PMID: 23023663
Drosophila; transcription factor; genomics; enhancer; Zelda
14.  The IL-10/STAT3-mediated anti-inflammatory response: recent developments and future challenges 
Briefings in Functional Genomics  2013;12(6):489-498.
Inflammation is a fundamental response of the immune system whose successful termination involves the elimination of the invading pathogens, the resolution of inflammation and the repair of the local damaged tissue. In this context, the interleukin 10 (IL-10)-mediated anti-inflammatory response (AIR) represents an essential homeostatic mechanism that controls the degree and duration of inflammation. Here, we review recent work on the mechanistic characterization of the IL-10-mediated AIR on multiple levels: from the cataloguing of the in vivo genomic targets of STAT3 (the transcription factor downstream of IL-10) to the identification of specific co-factors that endow STAT3 with genomic-binding specificity, and how genomic and computational methods are being used to elucidate the regulatory mechanisms of this essential physiological response in macrophages.
doi:10.1093/bfgp/elt028
PMCID: PMC3838198  PMID: 23943603
IL-10; JAK1; STAT3; anti-inflammatory response; macrophages; transcriptional regulatory modules; bioinformatics
15.  WRAD: enabler of the SET1-family of H3K4 methyltransferases 
Briefings in Functional Genomics  2012;11(3):217-226.
Methylation of histone H3 at lysine 4 (H3K4) is a conserved feature of active chromatin catalyzed by methyltransferases of the SET1-family (SET1A, SET1B, MLL1, MLL2, MLL3 and MLL4 in humans). These enzymes participate in diverse gene regulatory networks with a multitude of known biological functions, including direct involvement in several human disease states. Unlike most lysine methyltransferases, SET1-family enzymes are only fully active in the context of a multi-subunit complex, which includes a protein module comprised of WDR5, RbBP5, ASH2L and DPY-30 (WRAD). These proteins bind in close proximity to the catalytic SET domain of SET1-family enzymes and stimulate H3K4 methyltransferase activity. The mechanism by which WRAD promotes catalysis involves elements of allosteric control and possibly the utilization of a second H3K4 methyltransferase active site present within WRAD itself. WRAD components also engage in physical interactions that recruit SET1-family proteins to target sites on chromatin. Here, the known molecular mechanisms through which WRAD enables the function of SET1-related enzymes will be reviewed.
doi:10.1093/bfgp/els017
PMCID: PMC3388306  PMID: 22652693
SET1; MLL; WDR5; RbBP5; ASH2L; DPY-30
16.  TET proteins: on the frenetic hunt for new cytosine modifications 
Briefings in Functional Genomics  2013;12(3):191-204.
Epigenetic genome marking and chromatin regulation are central to establishing tissue-specific gene expression programs, and hence to several biological processes. Until recently, the only known epigenetic mark on DNA in mammals was 5-methylcytosine, established and propagated by DNA methyltransferases and generally associated with gene repression. All of a sudden, a host of new actors—novel cytosine modifications and the ten eleven translocation (TET) enzymes—has appeared on the scene, sparking great interest. The challenge is now to uncover the roles they play and how they relate to DNA demethylation. Knowledge is accumulating at a frantic pace, linking these new players to essential biological processes (e.g. cell pluripotency and development) and also to cancerogenesis. Here, we review the recent progress in this exciting field, highlighting the TET enzymes as epigenetic DNA modifiers, their physiological roles, and their functions in health and disease. We also discuss the need to find relevant TET interactants and the newly discovered TET–O-linked N-acetylglucosamine transferase (OGT) pathway.
doi:10.1093/bfgp/elt010
PMCID: PMC3662890  PMID: 23625996
epigenetics; DNA methylation; hydroxymethylation; TET proteins; OGT
17.  The amphioxus genome provides unique insight into the evolution of immunity 
Briefings in Functional Genomics  2012;11(2):167-176.
Immune systems evolve as essential strategies to maintain homeostasis with the environment, prevent microbial assault and recycle damaged host tissues. The immune system is composed of two components, innate and adaptive immunity. The former is common to all animals while the latter consists of a vertebrate-specific system that relies on somatically derived lymphocytes and is associated with near limitless genetic diversity as well as long-term memory. Deuterostome invertebrates provide a view of immune repertoires in phyla that immediately predate the origins of vertebrates. Genomic studies in amphioxus, a cephalochordate, have revealed homologs of genes encoding most innate immune receptors found in vertebrates; however, many of the gene families have undergone dramatic expansions, greatly increasing the innate immune repertoire. In addition, domain-swapping accounts for the innovation of new predicted pathways of receptor function. In both amphioxus and Ciona, a urochordate, the VCBPs (variable region containing chitin-binding proteins), which consist of immunoglobulin V (variable) and chitin binding domains, mediate recognition through the V domains. The V domains of VCBPs in amphioxus exhibit high levels of allelic complexity that presumably relate to functional specificity. Various features of the amphioxus immune repertoire reflect novel selective pressures, which likely have resulted in innovative strategies. Functional genomic studies underscore the value of amphioxus as a model for studying innate immunity and may help reveal how unique relationships between innate immune receptors and both pathogens and symbionts factored in the evolution of adaptive immune systems.
doi:10.1093/bfgp/els007
PMCID: PMC3310213  PMID: 22402506
innate immunity; Toll-like receptors; expanded immune repertoire; allelic complexity; gut immunity
18.  Translational control by 3′-UTR-binding proteins 
The regulation of mRNA translation is a major checkpoint in the flux of information from the transcriptome to the proteome. Critical for translational control are the trans-acting factors, RNA-binding proteins (RBPs) and small RNAs that bind to the mRNA and modify its translatability. This review summarizes the mechanisms by which RBPs regulate mRNA translation, with special focus on those binding to the 3′-untranslated region. It also discusses how recent high-throughput technologies are revealing exquisite layers of complexity and are helping to untangle translational regulation at a genome-wide scale.
doi:10.1093/bfgp/els056
PMCID: PMC3548161  PMID: 23196851
RNA-binding protein; translation; UTR; RNP; CLIP; ribosome profiling
19.  Tumor biobanks in translational medicine 
The concept of tissue banking as a “bio-repository” aimed to collection, storing and distribution of human biological material and clinical information, is emerging as a successful strategy to support clinical and translational research. In particular, Tumor Biobanks represent a key resource for diagnosis, research and experimental therapies, especially for those correlated to clinical application of a new type of medicine known as “intelligent drugs”.
Biobanks are not “spontaneous” collections, but they needs an institutional organization, basically a research unit, whose effectiveness and quality can be guaranteed only if it is carefully organized according to precise and shared rules.
doi:10.1186/1479-5876-10-204
PMCID: PMC3548748  PMID: 23031272
21.  Application of spectroscopy in herbal metabolomics 
doi:10.1186/2008-2231-20-91
PMCID: PMC3584975  PMID: 23351723
23.  An integrative functional genomics approach for discovering biomarkers in schizophrenia 
Briefings in Functional Genomics  2011;10(6):387-399.
Schizophrenia (SZ) is a complex disorder resulting from both genetic and environmental causes with a lifetime prevalence world-wide of 1%; however, there are no specific, sensitive and validated biomarkers for SZ. A general unifying hypothesis has been put forward that disease-associated single nucleotide polymorphisms (SNPs) from genome-wide association study (GWAS) are more likely to be associated with gene expression quantitative trait loci (eQTL). We will describe this hypothesis and review primary methodology with refinements for testing this paradigmatic approach in SZ. We will describe biomarker studies of SZ and testing enrichment of SNPs that are associated both with eQTLs and existing GWAS of SZ. SZ-associated SNPs that overlap with eQTLs can be placed into gene–gene expression, protein–protein and protein–DNA interaction networks. Further, those networks can be tested by reducing/silencing the gene expression levels of critical nodes. We present pilot data to support these methods of investigation such as the use of eQTLs to annotate GWASs of SZ, which could be applied to the field of biomarker discovery. Those networks that have association with SNP markers, especially cis-regulated expression, might lead to a more clear understanding of important candidate genes that predispose to disease and alter expression. This method has general application to many complex disorders.
doi:10.1093/bfgp/elr036
PMCID: PMC3277082  PMID: 22155586
expression quantitative trait loci; cis-regulatory SNPs; GWAS; gene expression; lymphoblastoid cell lines
24.  New approaches to the representation and analysis of phenotype knowledge in human diseases and their animal models 
Briefings in Functional Genomics  2011;10(5):258-265.
The systematic investigation of the phenotypes associated with genotypes in model organisms holds the promise of revealing genotype–phenotype relations directly and without additional, intermediate inferences. Large-scale projects are now underway to catalog the complete phenome of a species, notably the mouse. With the increasing amount of phenotype information becoming available, a major challenge that biology faces today is the systematic analysis of this information and the translation of research results across species and into an improved understanding of human disease. The challenge is to integrate and combine phenotype descriptions within a species and to systematically relate them to phenotype descriptions in other species, in order to form a comprehensive understanding of the relations between those phenotypes and the genotypes involved in human disease. We distinguish between two major approaches for comparative phenotype analyses: the first relies on evolutionary relations to bridge the species gap, while the other approach compares phenotypes directly. In particular, the direct comparison of phenotypes relies heavily on the quality and coherence of phenotype and disease databases. We discuss major achievements and future challenges for these databases in light of their potential to contribute to the understanding of the molecular mechanisms underlying human disease. In particular, we discuss how the use of ontologies and automated reasoning can significantly contribute to the analysis of phenotypes and demonstrate their potential for enabling translational research.
doi:10.1093/bfgp/elr031
PMCID: PMC3189694  PMID: 21987712
phenotype; animal model; disease; database; comparative phenomics; ontology
25.  A growing molecular toolbox for the functional analysis of microRNAs in Caenorhabditis elegans 
Briefings in Functional Genomics  2011;10(4):175-180.
With the growing number of microRNAs (miRNAs) being identified each year, more innovative molecular tools are required to efficiently characterize these small RNAs in living animal systems. Caenorhabditis elegans is a powerful model to study how miRNAs regulate gene expression and control diverse biological processes during development and in the adult. Genetic strategies such as large-scale miRNA deletion studies in nematodes have been used with limited success since the majority of miRNA genes do not exhibit phenotypes when individually mutated. Recent work has indicated that miRNAs function in complex regulatory networks with other small RNAs and protein-coding genes, and therefore the challenge will be to uncover these functional redundancies. The use of miRNA inhibitors such as synthetic antisense 2′-O-methyl oligoribonucleotides is emerging as a promising in vivo approach to dissect out the intricacies of miRNA regulation.
doi:10.1093/bfgp/elr012
PMCID: PMC3144738  PMID: 21624898
microRNA; Caenorhabditis elegans; miRNA inhibitors; antisense 2′-O-methyl oligoribonucleotides

Results 1-25 (69)