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1.  The era of epigenetics 
Briefings in Functional Genomics  2010;9(5-6):425-428.
PMCID: PMC3080744  PMID: 21266345
2.  Nuclear processes associated with plant immunity and pathogen susceptibility 
Briefings in Functional Genomics  2015;14(4):243-252.
Plants are sessile organisms that have evolved exquisite and sophisticated mechanisms to adapt to their biotic and abiotic environment. Plants deploy receptors and vast signalling networks to detect, transmit and respond to a given biotic threat by inducing properly dosed defence responses. Genetic analyses and, more recently, next-generation -omics approaches have allowed unprecedented insights into the mechanisms that drive immunity. Similarly, functional genomics and the emergence of pathogen genomes have allowed reciprocal studies on the mechanisms governing pathogen virulence and host susceptibility, collectively allowing more comprehensive views on the processes that govern disease and resistance. Among others, the identification of secreted pathogen molecules (effectors) that modify immunity-associated processes has changed the plant–microbe interactions conceptual landscape. Effectors are now considered both important factors facilitating disease and novel probes, suited to study immunity in plants. In this review, we will describe the various mechanisms and processes that take place in the nucleus and help regulate immune responses in plants. Based on the premise that any process required for immunity could be targeted by pathogen effectors, we highlight and describe a number of functional assays that should help determine effector functions and their impact on immune-related processes. The identification of new effector functions that modify nuclear processes will help dissect nuclear signalling further and assist us in our bid to bolster immunity in crop plants.
PMCID: PMC4513213  PMID: 25846755
nucleus; immunity; pathogen; effector; susceptibility; next-generation sequencing (NGS)
3.  Mutagenesis and phenotyping resources in zebrafish for studying development and human disease 
The zebrafish (Danio rerio) is an important model organism for studying development and human disease. The zebrafish has an excellent reference genome and the functions of hundreds of genes have been tested using both forward and reverse genetic approaches. Recent years have seen an increasing number of large-scale mutagenesis projects and the number of mutants or gene knockouts in zebrafish has increased rapidly, including for the first time conditional knockout technologies. In addition, targeted mutagenesis techniques such as zinc finger nucleases, transcription activator-like effector nucleases and clustered regularly interspaced short sequences (CRISPR) or CRISPR-associated (Cas), have all been shown to effectively target zebrafish genes as well as the first reported germline homologous recombination, further expanding the utility and power of zebrafish genetics. Given this explosion of mutagenesis resources, it is now possible to perform systematic, high-throughput phenotype analysis of all zebrafish gene knockouts.
PMCID: PMC3954039  PMID: 24162064
zebrafish; mutagenesis; phenotyping; resources; knockouts
4.  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.
PMCID: PMC3896895  PMID: 24005910
Mesp; FGF; gene regulatory networks; extracellular matrix; cardiac induction; chordate evolution
5.  High-throughput characterization of protein–RNA interactions 
RNA-binding proteins (RBPs) are important regulators of eukaryotic gene expression. Genomes typically encode dozens to hundreds of proteins containing RNA-binding domains, which collectively recognize diverse RNA sequences and structures. Recent advances in high-throughput methods for assaying the targets of RBPs in vitro and in vivo allow large-scale derivation of RNA-binding motifs as well as determination of RNA–protein interactions in living cells. In parallel, many computational methods have been developed to analyze and interpret these data. The interplay between RNA secondary structure and RBP binding has also been a growing theme. Integrating RNA–protein interaction data with observations of post-transcriptional regulation will enhance our understanding of the roles of these important proteins.
PMCID: PMC4303715  PMID: 25504152
RNA-binding proteins; RBP target identification; high-throughput sequencing; RNA secondary structure
6.  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.
PMCID: PMC3838197  PMID: 23922132
DNA binding; histone methylation; DNA methylation; lineage commitment; repression; hematopoiesis
7.  Evolving insights on how cytosine methylation affects protein–DNA binding 
Many anecdotal observations exist of a regulatory effect of DNA methylation on gene expression. However, in general, the underlying mechanisms of this effect are poorly understood. In this review, we summarize what is currently known about how this important, but mysterious, epigenetic mark impacts cellular functions. Cytosine methylation can abrogate or enhance interactions with DNA-binding proteins, or it may have no effect, depending on the context. Despite being only a small chemical change, the addition of a methyl group to cytosine can affect base readout via hydrophobic contacts in the major groove and shape readout via electrostatic contacts in the minor groove. We discuss the recent discovery that CpG methylation increases DNase I cleavage at adjacent positions by an order of magnitude through altering the local 3D DNA shape and the possible implications of this structural insight for understanding the methylation sensitivity of transcription factors (TFs). Additionally, 5-methylcytosines change the stability of nucleosomes and, thus, affect the local chromatin structure and access of TFs to genomic DNA. Given these complexities, it seems unlikely that the influence of DNA methylation on protein–DNA binding can be captured in a small set of general rules. Hence, data-driven approaches may be essential to gain a better understanding of these mechanisms.
PMCID: PMC4303714  PMID: 25319759
epigenetics; DNA methylation; 5-methylcytosine; protein–DNA interactions; DNase I endonuclease; transcription factors
8.  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.
PMCID: PMC4239789  PMID: 25217478
AA9; GH61; cellobiose dehydrogenase; oxidative cellulose degradation
9.  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.
PMCID: PMC3776566  PMID: 23788797
breast cancer; microarray; genomics; tumor; histology
10.  Elucidation of primary metabolic pathways in Aspergillus species: Orphaned research in characterizing orphan genes 
Briefings in Functional Genomics  2014;13(6):451-455.
Primary metabolism affects all phenotypical traits of filamentous fungi. Particular examples include reacting to extracellular stimuli, producing precursor molecules required for cell division and morphological changes as well as providing monomer building blocks for production of secondary metabolites and extracellular enzymes. In this review, all annotated genes from four Aspergillus species have been examined. In this process, it becomes evident that 80–96% of the genes (depending on the species) are still without verified function. A significant proportion of the genes with verified metabolic functions are assigned to secondary or extracellular metabolism, leaving only 2–4% of the annotated genes within primary metabolism. It is clear that primary metabolism has not received the same attention in the post-genomic area as many other research areas—despite its role at the very centre of cellular function. However, several methods can be employed to use the metabolic networks in tandem with comparative genomics to accelerate functional assignment of genes in primary metabolism. In particular, gaps in metabolic pathways can be used to assign functions to orphan genes. In this review, applications of this from the Aspergillus genes will be examined, and it is proposed that, where feasible, this should be a standard part of functional annotation of fungal genomes.
PMCID: PMC4239788  PMID: 25114096
Aspergillus; primary metabolism; functional genomics; metabolic networks
11.  Using population isolates in genetic association studies 
Briefings in Functional Genomics  2014;13(5):371-377.
The use of genetically isolated populations can empower next-generation association studies. In this review, we discuss the advantages of this approach and review study design and analytical considerations of genetic association studies focusing on isolates. We cite successful examples of using population isolates in association studies and outline potential ways forward.
PMCID: PMC4168662  PMID: 25009120
isolated populations; rare variants; complex disease; genetic association studies
12.  Biochemical and bioinformatic methods for elucidating the role of RNA–protein interactions in posttranscriptional regulation 
Briefings in Functional Genomics  2014;14(2):102-114.
Our understanding of transcriptional gene regulation has dramatically increased over the past decades, and many regulators of gene expression, such as transcription factors, have been analyzed extensively. Additionally, in recent years, deeper insights into the physiological roles of RNA have been obtained. More precisely, splicing, polyadenylation, various modifications, localization and the translation of messenger RNAs (mRNAs) are regulated by their interaction with RNA-binding proteins (RBPs). New technologies now enable the analysis of this regulation at different levels. A technique known as ultraviolet (UV) cross-linking and immunoprecipitation (CLIP) allows us to determine physical protein–RNA interactions on a genome-wide scale. UV cross-linking introduces covalent bonds between interacting RBPs and RNAs. In combination with immunoprecipitation and deep sequencing techniques, tens of millions of short reads (representing bound RNAs by an RBP of interest) are generated and are used to characterize the regulatory network mediated by an RBP. Other methods, such as mass spectrometry, can also be used for characterization of cross-linked RBPs and RNAs instead of CLIP methods. In this review, we discuss experimental and computational methods for the generation and analysis of CLIP data. The computational methods include short-read alignment, annotation and RNA-binding motif discovery. We describe the challenges of analyzing CLIP data and indicate areas where improvements are needed.
PMCID: PMC4471435  PMID: 24951655
Next-generation sequencing; cross-linking and immunoprecipitation; posttranscriptional gene regulation; RNA-binding motif discovery
13.  Methodology for the analysis of rare genetic variation in genome-wide association and re-sequencing studies of complex human traits 
Briefings in Functional Genomics  2014;13(5):362-370.
Genome-wide association studies have been successful in identifying common variants that impact complex human traits and diseases. However, despite this success, the joint effects of these variants explain only a small proportion of the genetic variance in these phenotypes, leading to speculation that rare genetic variation might account for much of the ‘missing heritability’. Consequently, there has been an exciting period of research and development into the methodology for the analysis of rare genetic variants, typically by considering their joint effects on complex traits within the same functional unit or genomic region. In this review, we describe a general framework for modelling the joint effects of rare genetic variants on complex traits in association studies of unrelated individuals. We summarise a range of widely used association tests that have been developed from this model and provide an overview of the relative performance of these approaches from published simulation studies.
PMCID: PMC4168660  PMID: 24916163
rare variant; burden test; dispersion test; statistical methodology; genome-wide association; whole-genome and whole-exome re-sequencing
14.  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.
PMCID: PMC4110416  PMID: 24907366
structural variations (SVs); next-generation sequencing (NGS); copy number variations (CNVs); presence and absence variations (PAVs); inversions; translocations
15.  TAL effectors: tools for DNA Targeting 
Briefings in Functional Genomics  2014;13(5):409-419.
Xanthomonas phytopathogenic bacteria produce unique transcription activator-like effector (TALE) proteins that recognize and activate specific plant promoters through a set of tandem repeats. A unique TALE-DNA-binding code uses two polymorphic amino acids in each repeat to mediate recognition of specific nucleotides. The order of repeats determines effector’s specificity toward the cognate nucleotide sequence of the sense DNA strand. Artificially designed TALE-DNA-binding domains fused to nuclease or activation and repressor domains provide an outstanding toolbox for targeted gene editing and gene regulation in research, biotechnology and gene therapy. Gene editing with custom-designed TALE nucleases (TALENs) extends the repertoire of targeted genome modifications across a broad spectrum of organisms ranging from plants and insect to mammals.
PMCID: PMC4168661  PMID: 24907364
TALE; TALEN; ZFN; FokI; DNA editing
16.  Event-based text mining for biology and functional genomics 
Briefings in Functional Genomics  2014;14(3):213-230.
The assessment of genome function requires a mapping between genome-derived entities and biochemical reactions, and the biomedical literature represents a rich source of information about reactions between biological components. However, the increasingly rapid growth in the volume of literature provides both a challenge and an opportunity for researchers to isolate information about reactions of interest in a timely and efficient manner. In response, recent text mining research in the biology domain has been largely focused on the identification and extraction of ‘events’, i.e. categorised, structured representations of relationships between biochemical entities, from the literature. Functional genomics analyses necessarily encompass events as so defined. Automatic event extraction systems facilitate the development of sophisticated semantic search applications, allowing researchers to formulate structured queries over extracted events, so as to specify the exact types of reactions to be retrieved. This article provides an overview of recent research into event extraction. We cover annotated corpora on which systems are trained, systems that achieve state-of-the-art performance and details of the community shared tasks that have been instrumental in increasing the quality, coverage and scalability of recent systems. Finally, several concrete applications of event extraction are covered, together with emerging directions of research.
PMCID: PMC4499874  PMID: 24907365
text mining; event extraction; semantic annotation; semantic search
17.  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.
PMCID: PMC4110415  PMID: 24759704
hitchhiking; genetic draft; recombination rate; genome size; FST; demographic inference
18.  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.
PMCID: PMC4023274  PMID: 23117862
19.  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.
PMCID: PMC3609437  PMID: 23178478
super-resolution microscopy; systems biology; single cells; single-molecule FISH
20.  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.
PMCID: PMC3609438  PMID: 23292635
live-cell imaging; single cell; DNA damage; fluorescence microscopy; dynamics
21.  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.
PMCID: PMC4031454  PMID: 24335757
epigenetic code; pluripotentiality; robustness; redundancy; DNA methylation; histone modifications; social insect; honey bee
22.  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.
PMCID: PMC4031453  PMID: 24326118
Caenorhabditis elegans; chromatin organization; longevity; organogenesis; small RNA; transcriptional silencing
23.  Advances in genomics of bony fish 
Briefings in Functional Genomics  2013;13(2):144-156.
In this review, we present an overview of the recent advances of genomic technologies applied to studies of fish species belonging to the superclass of Osteichthyes (bony fish) with a major emphasis on the infraclass of Teleostei, also called teleosts. This superclass that represents more than 50% of all known vertebrate species has gained considerable attention from genome researchers in the last decade. We discuss many examples that demonstrate that this highly deserved attention is currently leading to new opportunities for answering important biological questions on gene function and evolutionary processes. In addition to giving an overview of the technologies that have been applied for studying various fish species we put the recent advances in genome research on the model species zebrafish and medaka in the context of its impact for studies of all fish of the superclass of Osteichthyes. We thereby want to illustrate how the combined value of research on model species together with a broad angle perspective on all bony fish species will have a huge impact on research in all fields of fundamental science and will speed up applications in many societally important areas such as the development of new medicines, toxicology test systems, environmental sensing systems and sustainable aquaculture strategies.
PMCID: PMC3954040  PMID: 24291769
fish models; teleosts; genomics; aquaculture; next-generation sequencing; zebrafish; medaka
24.  Applications of the site-specific recombinase Cre to the study of genomic imprinting 
Briefings in functional genomics  2010;9(4):10.1093/bfgp/elq017.
The development of gene targeting approaches has had a tremendous impact on the functional analysis of the mouse genome. A specific application of this technique has been the adaptation of the bacteriophage P1 Cre/loxP site-specific recombinase system which allows for the precise recombination between two loxP sites, resulting in deletion or inversion of the intervening sequences. Because of the efficiency of this system, it can be applied to conditional deletions of relatively short coding sequences or regulatory elements but also to more extensive chromosomal rearrangement strategies. Both mechanistic and functional studies of genomic imprinting have benefited from the development of the Cre/loxP technology. Since imprinted genes within large chromosomal regions are regulated by the action of cis-acting sequences known as imprinting centres, chromosomal engineering approaches are particularly well suited to the elucidation of long-range mechanisms controlling the imprinting of autosomal genes. Here we review the applications of the Cre/loxP technology to the study of genomic imprinting, highlight important insights gained from these studies and discuss future directions in the field.
PMCID: PMC3815648  PMID: 20601421 CAMSID: cams3612
genomic imprinting; Cre-loxP system; chromosome engineering
25.  Retrotransposition and genomic imprinting 
Briefings in functional genomics  2010;9(4):10.1093/bfgp/elq015.
Studies of large imprinted clusters, such as the Gnas locus, have revealed much about the significance of DNA methylation, transcription and other factors in the establishment and maintenance of imprinted gene expression. However, the complexity of such loci can make manipulating them and interpreting the results challenging. We review here a distinct class of imprinted genes, which have arisen by retrotransposition, and which have the potential to be used as models for the dissection of the fundamental features and mechanisms required for imprinting. They are also of interest in their own right, generating diversity in the transcriptome and providing raw material upon which selection can act.
PMCID: PMC3814061  PMID: 20591835
retrotransposition; retrogenes; genomic imprinting; epigenetics

Results 1-25 (98)