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Briefings in Functional Genomics

A Saleembhasha, Seema Mishra
Powerful next-generation sequencing (NGS) technologies, more specifically RNA sequencing (RNA-seq), have been pivotal toward the detection and analysis and hypotheses generation of novel biomolecules, long noncoding RNAs (lncRNAs), tRNA-derived fragments (tRFs) and circular RNAs (circRNAs). Experimental validation of the occurrence of these biomolecules inside the cell has been reported. Their differential expression and functionally important role in several cancers types as well as other diseases such as Alzheimer's and cardiovascular diseases have garnered interest toward further studies in this research arena...
June 20, 2017: Briefings in Functional Genomics
Miao Cui, Che-Yi Lin, Yi-Hsien Su
Studies on the gene regulatory networks (GRNs) of sea urchin embryos have provided a basic understanding of the molecular mechanisms controlling animal development. The causal links in GRNs have been verified experimentally through perturbation of gene functions. Microinjection of antisense morpholino oligonucleotides (MOs) into the egg is the most widely used approach for gene knockdown in sea urchin embryos. The modification of MOs into a membrane-permeable form (vivo-MOs) has allowed gene knockdown at later developmental stages...
June 12, 2017: Briefings in Functional Genomics
Mark Viney
Nematodes are highly abundant animals, and many species have a parasitic lifestyle. Nematode parasites are important pathogens of humans and other animals, and there is considerable interest in understanding their molecular and genomic adaptations to nematode parasitism. This has been approached in three main ways: comparing the genomes of closely related parasitic and free-living taxa, comparing the gene expression of parasitic and free-living life cycle stages of parasitic nematode species, and analysing the molecules that parasitic nematodes excrete and secrete...
May 3, 2017: Briefings in Functional Genomics
Yaron Orenstein, Ron Shamir
Protein-DNA binding plays a central role in gene regulation and by that in all processes in the living cell. Novel experimental and computational approaches facilitate better understanding of protein-DNA binding preferences via high-throughput measurement of protein binding to a large number of DNA sequences and inference of binding models from them. Here we review the state of the art in measuring protein-DNA binding in vitro, emphasizing the advantages and limitations of different technologies. In addition, we describe models for representing protein-DNA binding preferences and key computational approaches to learn those from high-throughput data...
May 1, 2017: Briefings in Functional Genomics
Xiangqun Zheng-Bradley, Paul Flicek
The 1000 Genomes Project created a valuable, worldwide reference for human genetic variation. Common uses of the 1000 Genomes dataset include genotype imputation supporting Genome-wide Association Studies, mapping expression Quantitative Trait Loci, filtering non-pathogenic variants from exome, whole genome and cancer genome sequencing projects, and genetic analysis of population structure and molecular evolution. In this article, we will highlight some of the multiple ways that the 1000 Genomes data can be and has been utilized for genetic studies...
May 1, 2017: Briefings in Functional Genomics
David Roy Smith
Next-generation sequencing technologies have revolutionized genomics and altered the scientific publication landscape. Life-science journals abound with genome papers-peer-reviewed descriptions of newly sequenced chromosomes. Although they once filled the pages of Nature and Science, genome papers are now mostly relegated to journals with low-impact factors. Some have forecast the death of the genome paper and argued that they are using up valuable resources and not advancing science. However, the publication rate of genome papers is on the rise...
May 1, 2017: Briefings in Functional Genomics
Luis María Vaschetto
Recently, the conjunction of disciplines such as developmental biology and proteomics enabled the dissection of diverse cellular processes, by analysis of their transcriptional regulatory pathways. In particular, it has been shown that transcription factor interactions play critical roles in the development of many complex traits and control cellular phenotypic plasticity, whereas protein phosphorylation modifications regulate protein activity at the posttranslational level. The present work posits that protein-protein interactions by functional motifs, as well as the phosphorylation state in these sites, are fundamental plant biological phenotype determinants, whose elucidation and understanding will allow manipulation of complex traits, thereby contributing to the design of novel methodologies for molecular breeders and plant physiologists...
May 1, 2017: Briefings in Functional Genomics
Yingying Wang, Yunpeng Cai
The relationships between microRNAs (miRNAs) and diseases are garnering greater interest in the biological research fields. Recently, miRNA-disease databases have emerged as powerful tools for bioinformatics studies of these relationships. However, guidelines for comparing the features of this type of database have not yet been established. In this article, the details of popular miRNA-disease databases are analyzed, and their features are compared from several different aspects, including database scale, disease classification, miRNA targets, miRNA detection technique, miRNA regulation, quantitative scores, study design and tissue/cell lines...
May 1, 2017: Briefings in Functional Genomics
Mojdeh Nasrollahzadeh-Khakiani, Modjtaba Emadi-Baygi, Wolfgang Arthur Schulz, Parvaneh Nikpour
Recent studies of the human transcriptome, most prominently by the ENCyclopedia Of DNA Elements project, have revealed an unexpected number of noncoding RNAs (ncRNAs). Long noncoding RNAs (lncRNAs) are typically referred to a heterogeneous group of polyadenylated long ncRNAs, with a length of > 200 nt. LncRNAs constitute an integral part of tumor biology, with many lncRNAs discovered to be aberrantly expressed in various cancer types. They are involved in many aspects of cancer pathogenesis from its initiation to progression, metastasis and treatment response...
May 1, 2017: Briefings in Functional Genomics
Min Zhao, Di Liu, Hong Qu
High-throughput next-generation sequencing (NGS) technologies have rapidly generated a large volume of genomic data. To aid the development and evaluation of new statistical models and computational methods, NGS-based simulators have been proposed to construct better experimental workflows. However, the comparative performance of these NGS simulators remains unclear. In this review, we conducted a comprehensive investigation of NGS simulators for various sequencing techniques, including DNA sequencing, metagenomic sequencing, RNA-seq, ChIP-seq and bisulfite sequencing for methylation...
May 1, 2017: Briefings in Functional Genomics
Tomas Klingstrom, Erik Bongcam-Rudloff, Jane Reichel
When obtaining samples from biobanks, resolving ethical and legal concerns is a time-consuming task where researchers need to balance the needs of privacy, trust and scientific progress. The Biobanking and Biomolecular Resources Research Infrastructure-Large Prospective Cohorts project has resolved numerous such issues through intense communication between involved researchers and experts in its mission to unite large prospective study sets in Europe. To facilitate efficient communication, it is useful for nonexperts to have an at least basic understanding of the regulatory system for managing biological samples...
April 27, 2017: Briefings in Functional Genomics
Modjtaba Emadi-Baygi, Rina Sedighi, Nooshin Nourbakhsh, Parvaneh Nikpour
Cancer burden rises globally at an alarming pace. According to GLOBOCAN 2012, gastric cancer (GC) is regarded as the fifth most common malignancy in the world. Being twice as high in men as in women, GC is the third leading cause of cancer mortality in both sexes globally. Being labeled as 'junk DNA', pseudogenes were considered as nonfunctional 'trash', which contribute nothing to survival of the organism; therefore, a number of strategies have been developed to circumvent their accidental detection. Recent progresses have confirmed that pseudogenes can have broad and multifaceted spectrum of activities in human cancers in general and GC in particular...
April 27, 2017: Briefings in Functional Genomics
Qingfeng Chen, Chaowang Lan, Liang Zhao, Jianxin Wang, Baoshan Chen, Yi-Ping Phoebe Chen
The application of advanced sequencing technologies and the rapid growth of various sequence data have led to increasing interest in DNA sequence assembly. However, repeats and polymorphism occur frequently in genomes, and each of these has different impacts on assembly. Further, many new applications for sequencing, such as metagenomics regarding multiple species, have emerged in recent years. These not only give rise to higher complexity but also prevent short-read assembly in an efficient way. This article reviews the theoretical foundations that underlie current mapping-based assembly and de novo-based assembly, and highlights the key issues and feasible solutions that need to be considered...
April 26, 2017: Briefings in Functional Genomics
Samuel Corless, Nick Gilbert
Supercoiling is a fundamental property of DNA, generated by polymerases and other DNA-binding proteins as a consequence of separating/bending the DNA double helix. DNA supercoiling plays a key role in gene expression and genome organization, but has proved difficult to study in eukaryotes because of the large, complex and chromatinized genomes. Key approaches to study DNA supercoiling in eukaryotes are (1) centrifugation-based or electrophoresis-based techniques in which supercoiled plasmids extracted from eukaryotic cells form a compacted writhed structure that migrates at a rate proportional to the level of DNA supercoiling; (2) in vivo approaches based on the preferential intercalation of psoralen molecules into under-wound DNA...
April 24, 2017: Briefings in Functional Genomics
Isabelle S Peter
A growing body of evidence shows that gene expression in multicellular organisms is controlled by the combinatorial function of multiple transcription factors. This indicates that not the individual transcription factors or signaling molecules, but the combination of expressed regulatory molecules, the regulatory state, should be viewed as the functional unit in gene regulation. Here, I discuss the concept of the regulatory state and its proposed role in the genome-wide control of gene expression. Recent analyses of regulatory gene expression in sea urchin embryos have been instrumental for solving the genomic control of cell fate specification in this system...
April 24, 2017: Briefings in Functional Genomics
Dean C Semmens, Maurice R Elphick
Neuropeptides are evolutionarily ancient mediators of neuronal signalling that regulate a wide range of physiological processes and behaviours in animals. Neuropeptide signalling has been investigated extensively in vertebrates and protostomian invertebrates, which include the ecdysozoans Drosophila melanogaster (Phylum Arthropoda) and Caenorhabditis elegans (Phylum Nematoda). However, until recently, an understanding of evolutionary relationships between neuropeptide signalling systems in vertebrates and protostomes has been impaired by a lack of genome/transcriptome sequence data from non-ecdysozoan invertebrates...
April 21, 2017: Briefings in Functional Genomics
Manoj K Dhar, Munish Sharma, Archana Bhat, Nikhil K Chrungoo, Sanjana Kaul
Saffron is considered to be the costliest spice of the world. It has been regarded as highly valued medicinal plant in Ayurveda to treat various ailments. Over the past few years, considerable interest has developed in saffron because of its anticancer, antimutagenic, antioxidant and immunomodulatory properties. Saffron's colour, bitter taste and aroma are its three main and peculiar characteristics, which are conferred by three chemicals namely: crocin, picrocrocin and safranal, respectively. The present review focuses on recent research/progress made in saffron in the area of functional genomics and highlights the potential of several genes and transcription factors involved in carotenoid/apocarotenoid pathway and responsible for flavour and aroma of saffron...
March 28, 2017: Briefings in Functional Genomics
Fabian V Filipp
Histone methylation is an epigenetic modification of chromatin undergoing dynamic changes and balancing tissue-specific demands of proliferation and differentiation. In cancer, aberrant histone methylation can facilitate oncogenic and tumor suppression programs by modulating gene expression. Histone remodelers such as lysine methyltransferases and lysine demethylases are seemingly opposite or contrary forces but may be part of an interconnected network complementing each other. We identify several layers of molecular communication where epigenetic master regulators engage in crosstalk between tumor metabolism and histone remodeling...
March 24, 2017: Briefings in Functional Genomics
Vineetha Mandlik, Ritika Kabra, Shailza Singh
The new era in systems pharmacology has revolutionized the human biology. Its applicability, precise treatment, adequate response and safety measures fit into all the paradigm of medical/clinical practice. The importance of mathematical models in understanding the disease pathology and epideomology is now being realized. The advent of high-throughput technologies and the emergence of systems biology have resulted in the creation of systems pharmacogenomics and the focus is now on personalized medicine. However, there are some regulatory issues that need to be addresssed; are we ready for this universal adoption? This article details some of the infectious disease pharmacogenomics to the developments in this area...
March 21, 2017: Briefings in Functional Genomics
Swadha Singh, Raghvendra Singh
Riboswitches, the small structured RNA elements, were discovered about a decade ago. It has been the subject of intense interest to identify riboswitches, understand their mechanisms of action and use them in genetic engineering. The accumulation of genome and transcriptome sequence data and comparative genomics provide unprecedented opportunities to identify riboswitches in the genome. In the present study, we have evaluated the following six machine learning algorithms for their efficiency to classify riboswitches: J48, BayesNet, Naïve Bayes, Multilayer Perceptron, sequential minimal optimization, hidden Markov model (HMM)...
March 1, 2017: Briefings in Functional Genomics
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