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Briefings in Functional Genomics

Vaibhav Shukla, Vinay Koshy Varghese, Shama Prasada Kabekkodu, Sandeep Mallya, Kapaettu Satyamoorthy
Since the discovery of microRNAs (miRNAs), a class of noncoding RNAs that regulate the gene expression posttranscriptionally in sequence-specific manner, there has been a release of number of tools useful for both basic and advanced applications. This is because of the significance of miRNAs in many pathophysiological conditions including cancer. Numerous bioinformatics tools that have been developed for miRNA analysis have their utility for detection, expression, function, target prediction and many other related features...
February 25, 2017: Briefings in Functional Genomics
Georgi K Marinov
Throughout the past nearly a decade, the application of high-throughput sequencing to RNA molecules in the form of RNA sequencing (RNA-seq) and its many variations has revolutionized transcriptomic studies by enabling researchers to take a simultaneously deep and truly global look into the transcriptome. However, there is still considerable scope for improvement on RNA-seq data in its current form, primarily because of the short-read nature of the dominant sequencing technologies, which prevents the completely reliable reconstruction and quantification of full-length transcripts, and the sequencing library building protocols used, which introduce various distortions in the final data sets...
February 17, 2017: 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...
January 30, 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...
January 20, 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...
January 10, 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...
January 5, 2017: Briefings in Functional Genomics
Xiao-Jie Lu, Hong-Mei Sun, Yong Xu, Xi Yu, Biao Gu
No abstract text is available yet for this article.
January 2017: Briefings in Functional Genomics
Taeyoung Koo, Jin-Soo Kim
The rapid development of programmable nuclease-based genome editing technologies has enabled targeted gene disruption and correction both in vitro and in vivo This revolution opens up the possibility of precise genome editing at target genomic sites to modulate gene function in animals and plants. Among several programmable nucleases, the type II clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated nuclease 9 (Cas9) system has progressed remarkably in recent years, leading to its widespread use in research, medicine and biotechnology...
January 2017: Briefings in Functional Genomics
Tomoko Kato, Shuji Takada
In the past few years, extensive progress has been made in the development of genome-editing technology. Among several genome-editing tools, the clustered regularly interspaced short palindrome repeat-associated Cas9 nuclease (CRISPR/Cas9) system is particularly widely used owing to the ease of sequence-specific nuclease construction and the highly efficient introduction of mutations. The CRISPR/Cas9 system was originally constructed to induce small insertion and deletion mutations, but various methods have been developed to introduce point mutations, deletions, insertions, chromosomal translocations and so on...
January 2017: Briefings in Functional Genomics
Raul Torres-Ruiz, Sandra Rodriguez-Perales
Genome engineering is a powerful tool for a wide range of applications in biomedical research and medicine. The development of the clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 system has revolutionized the field of gene editing, thus facilitating efficient genome editing through the creation of targeted double-strand breaks of almost any organism and cell type. In addition, CRISPR-Cas9 technology has been used successfully for many other purposes, including regulation of endogenous gene expression, epigenome editing, live-cell labelling of chromosomal loci, edition of single-stranded RNA and high-throughput gene screening...
January 2017: Briefings in Functional Genomics
Xiaolong Qi, Jiwei Zhang, Yongzhao Zhao, Tao Chen, Yi Xiang, Jialiang Hui, Danxian Cai, Yanna Liu, Lei Xia, Tao Yu, Guoxin Li
CRISPR technology has rapidly changed the face of biological research, such that precise genome editing has now become routine for many labs within several years of its initial development. CRISPR/Cas9 (Clustered Regularly Interspace Short Palindromic Repeat/CRISPR-associated nuclease 9) gene editing system is a powerful and groundbreaking programmable genome editing technology developed based on an adaptive bacterial and archaea immune system resisting the invasion of exogenous nucleic acid. Compared with traditional genome editing technology, CRISPR/Cas9 system is easier, efficient and less cytotoxic...
January 2017: Briefings in Functional Genomics
Marc Zuckermann, Daisuke Kawauchi, Jan Gronych
Advanced biological technologies allowing for genetic manipulation of the genome are increasingly being used to unravel the molecular pathogenesis of human diseases. The clustered regulatory interspaced short palindromic repeat/CRISPR-associated protein (CRISPR/Cas) technology started a revolution of this field owing to its flexibility and relative ease of use. Recently, application of the CRISPR/Cas9 system has been extended to in vivo approaches, leveraging its potential for human disease modeling. Particularly in oncological research, where genetic defects in somatic cells are tightly linked to etiology and pathological phenotypes, the CRISPR/Cas technology is being used to recapitulate various types of genetic aberrations...
January 2017: Briefings in Functional Genomics
Tetsuya Ishii
Genome editing allows for the versatile genetic modification of somatic cells, germ cells and embryos. In particular, CRISPR/Cas9 is worldwide used in biomedical research. Although the first report on Cas9-mediated gene modification in human embryos focused on the prevention of a genetic disease in offspring, it raised profound ethical and social concerns over the safety of subsequent generations and the potential misuse of genome editing for human enhancement. The present article considers germ line genome editing approaches from various clinical and ethical viewpoints and explores its objectives...
January 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...
November 29, 2016: Briefings in Functional Genomics
Hongbo Liu
No abstract text is available yet for this article.
November 2016: Briefings in Functional Genomics
Hongbo Liu, Song Li, Xinyu Wang, Jiang Zhu, Yanjun Wei, Yihan Wang, Yanhua Wen, Libo Wang, Yan Huang, Bin Zhang, Shipeng Shang, Yan Zhang
DNA methylation is an epigenetic modification of cytosines that undergoes dynamic changes in a temporal, spatial and cell-type-specific manner. Recent advances in technology have permitted the profiling of high-throughput methylomes in large numbers of biological samples. Various computational tools have been developed to identify and analyze DNA methylation dynamics in a variety of critical biological processes. As DNA methylation is becoming increasingly viewed as a dynamic process, the mechanisms governing DNA methylation dynamics and its roles in the transcriptional regulatory network are of great interest...
November 2016: Briefings in Functional Genomics
Mònica Suelves, Elvira Carrió, Yaiza Núñez-Álvarez, Miguel A Peinado
DNA methylation is an essential epigenetic modification for mammalian development and is crucial for the establishment and maintenance of cellular identity. Traditionally, DNA methylation has been considered as a permanent repressive epigenetic mark. However, the application of genome-wide approaches has allowed the analysis of DNA methylation in different genomic contexts, revealing a more dynamic regulation than originally thought, as active DNA methylation and demethylation occur during cell fate commitment and terminal differentiation...
November 2016: Briefings in Functional Genomics
Dao-Peng Chen, Ying-Chao Lin, Cathy S J Fann
DNA methylation is one of the most important epigenetic mechanisms, and participates in the pathogenic processes of many diseases. Differentially methylated regions (DMRs) in the genome have been reported and implicated in a number of different diseases, tissues and cell types, and are associated with gene expression levels. Therefore, identification of DMRs is one of the most critical and fundamental issues in dissecting the disease etiologies. Based on bisulfite conversion, advances in sequence- and array-based technologies have helped investigators study genome-wide DNA methylation...
November 2016: Briefings in Functional Genomics
Floriana Della Ragione, Marcella Vacca, Salvatore Fioriniello, Giuseppe Pepe, Maurizio D'Esposito
It has been a long trip from 1992, the year of the discovery of MECP2, to the present day. What is surprising is that some of the pivotal roles of MeCP2 were already postulated at that time, such as repression of inappropriate expression from repetitive elements and the regulation of pericentric heterochromatin condensation. However, MeCP2 performs many more functions. MeCP2 is a reader of epigenetic information contained in methylated (and hydroxymethylated) DNA, moving from the 'classical' CpG doublet to the more complex view addressed by the non-CpG methylation, which is a feature of the postnatal brain...
November 2016: Briefings in Functional Genomics
Veronique G LeBlanc, Marco A Marra
Adult diffuse gliomas account for the majority of primary malignant brain tumours, and are in most cases lethal. Current therapies are often only marginally effective, and improved options will almost certainly benefit from further insight into the various processes contributing to gliomagenesis and pathology. While molecular characterization of these tumours classifies them on the basis of genetic alterations and chromosomal abnormalities, DNA methylation patterns are increasingly understood to play a role in glioma pathogenesis...
November 2016: Briefings in Functional Genomics
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