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Briefings in Functional Genomics

Mazahar Moin, Achala Bakshi, Anusree Saha, Mouboni Dutta, P B Kirti
The epitome of any genome research is to identify all the existing genes in a genome and investigate their roles. Various techniques have been applied to unveil the functions either by silencing or over-expressing the genes by targeted expression or random mutagenesis. Rice is the most appropriate model crop for generating a mutant resource for functional genomic studies because of the availability of high-quality genome sequence and relatively smaller genome size. Rice has syntenic relationships with members of other cereals...
July 1, 2017: Briefings in Functional Genomics
Claire E Duff, Matthew J Simmonds
Kidney and pancreas transplantation have helped transform the lives of people with end-stage renal failure and individuals with type 1 diabetes who have poor glycaemic control/severe secondary complications, respectively. Despite an improvement in immunosuppressive regimes, operative techniques and decreased initial rejection rates, there has been little improvement in long-term graft survival rates over the past decade. Whilst limited progress has been made in establishing clinical markers of graft function, several genetic markers of long-term graft function have been identified...
July 1, 2017: Briefings in Functional Genomics
Vivek Dhar Dwivedi, Indra Prasad Tripathi, Ramesh Chandra Tripathi, Shiv Bharadwaj, Sarad Kumar Mishra
The genome of a pathogenic organism possesses a specific order of nucleotides that contains not only information about the synthesis and expression of proteomes, which are required for its growth and survival, but also about its evolution. Inhibition of any particular protein, which is required for the survival of that pathogenic organism, can be used as a potential therapeutic target for the development of effective drugs to treat its infections. In this review, the genomics, proteomics and evolution of dengue virus have been discussed, which will be helpful in better understanding of its origin, growth, survival and evolution, and may contribute toward development of new efficient anti-dengue drugs...
July 1, 2017: Briefings in Functional Genomics
Ylenia D'Agostino, Salvatore D'Aniello
The clustered regularly interspaced short palindromic repeats (CRISPR/Cas9) system is a recently discovered tool for genome editing that has quickly revolutionized the ability to generate site-specific mutations in a wide range of animal models, including nonhuman primates. Indeed, a significant number of scientific reports describing single or multiplex guide RNA microinjection, double-nicking strategies, site-specific knock-in and conditional knock-out have been published in less than three years. However, despite the great potential of this new technology, there are some limitations because of the presence of off-target genomic sites, which must be taken into consideration...
July 1, 2017: Briefings in Functional Genomics
Fernando de Castro, Ruth Seal, Roberto Maggi
It is accepted that confusion regarding the description of genetic variants occurs when researchers do not use standard nomenclature. The Human Genome Organization Gene Nomenclature Committee contacted a panel of consultants, all working on the KAL1 gene, to propose an update of the nomenclature of the gene, as there was a convention in the literature of using the 'KAL1' symbol, when referring to the gene, but using the name 'anosmin-1' when referring to the protein. The new name, ANOS1, reflects protein name and is more transferrable across species...
July 1, 2017: Briefings in Functional Genomics
Quanhu Sheng, Kasey Vickers, Shilin Zhao, Jing Wang, David C Samuels, Olivia Koues, Yu Shyr, Yan Guo
Quality control (QC) is a critical step in RNA sequencing (RNA-seq). Yet, it is often ignored or conducted on a limited basis. Here, we present a multi-perspective strategy for QC of RNA-seq experiments. The QC of RNA-seq can be divided into four related stages: (1) RNA quality, (2) raw read data (FASTQ), (3) alignment and (4) gene expression. We illustrate the importance of conducting QC at each stage of an RNA-seq experiment and demonstrate our recommended RNA-seq QC strategy. Furthermore, we discuss the major and often neglected quality issues associated with the three major types of RNA-seq: mRNA, total RNA and small RNA...
July 1, 2017: Briefings in Functional Genomics
Syed Shujaat Ali Zaidi, Xuegong Zhang
Microbial diversity in unique environmental settings enables abrupt responses catalysed by altering the gene regulation and formation of gene clusters called operons. Operons increases bacterial adaptability, which in turn increases their survival. This review article presents the emergence of computational operon prediction methods for whole microbial genomes and metagenomes, and discusses their strengths and limitations. Most of the whole-genome operon prediction methods struggle to generalize on unrelated genomes...
July 1, 2017: 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
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