Epigenetic regulation of gene expression in cancer: techniques, resources and analysis.

abstract：:A plant communicates within itself and with the outside world by deploying an array of agents that include several attractants by virtue of their color and smell. In this category, the contribution of 'carotenoids and apocarotenoids' is very significant. Apocarotenoids, the carotenoid-derived compounds, show wide repr...

journal_title：Briefings in functional genomics

authors： Dhar MK,Mishra S,Bhat A,Chib S,Kaul S

更新日期：2020-01-22 00:00:00

abstract：:In the current era of epigenetics research, we have observed many examples of epigenetic modifications, like histone modification and DNA methylation, in various fatal diseases. These include solid tumors, hematological malignancies and viral infections with DNA or RNA viruses. The purpose of this review is to summari...

journal_title：Briefings in functional genomics

authors： Sen S,Maulik U

更新日期：2018-11-26 00:00:00

abstract：:The Notch signalling pathway plays crucial roles in cardiac development and postnatal cardiac homoeostasis. Gain- and loss-of-function approaches indicate that Notch promotes or inhibits cardiogenesis in a stage-dependent manner. However, the molecular mechanisms are poorly defined because many downstream effectors re...

journal_title：Briefings in functional genomics

authors： MacGrogan D,Luxán G,de la Pompa JL

更新日期：2014-01-01 00:00:00

abstract：: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 raise...

journal_title：Briefings in functional genomics

authors： Ishii T

更新日期：2017-01-01 00:00:00

abstract：:Research on plant three-dimensional (3D) genome architecture made rapid progress over the past 5 years. Numerous Hi-C interaction data sets were generated in a wide range of plant species, allowing for a comprehensive overview on 3D chromosome folding principles in the plant kingdom. Plants lack important genes report...

journal_title：Briefings in functional genomics

authors： Grob S

更新日期：2020-03-23 00:00:00

abstract：:Patterns of evolution in immune defense genes help to understand the evolutionary dynamics between hosts and pathogens. Multiple insect genomes have been sequenced, with many of them having annotated immune genes, which paves the way for a comparative genomic analysis of insect immunity. In this review, I summarize th...

journal_title：Briefings in functional genomics

authors： Viljakainen L

更新日期：2015-11-01 00:00:00

abstract：: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 develope...

journal_title：Briefings in functional genomics

authors： Liu H,Li S,Wang X,Zhu J,Wei Y,Wang Y,Wen Y,Wang L,Huang Y,Zhang B,Shang S,Zhang Y

更新日期：2016-11-01 00:00:00

abstract：:Hemagglutinin (HA) is a transmembrane protein of the influenza A virus and a key component in its life cycle. The protein allows the virus to enter a host cell by recognizing specific glycans attached to transmembrane proteins of the host, which leads to viral endocytosis. In recent years, significant progress has bee...

journal_title：Briefings in functional genomics

authors： Lazniewski M,Dawson WK,Szczepinska T,Plewczynski D

更新日期：2018-11-26 00:00:00

abstract：:Epigenetic memory represents a natural mechanism whereby the identity of a cell is maintained through successive cell cycles, allowing the specification and maintenance of differentiation during development and in adult cells. Cancer is a loss or reversal of the stable differentiated state of adult cells and may be me...

journal_title：Briefings in functional genomics

authors： Halley-Stott RP,Gurdon JB

更新日期：2013-05-01 00:00:00

abstract：:The involvement of epigenetic processes in the origin and progression of cancer is now widely appreciated. Consequently, targeting the enzymatic machinery that controls the epigenetic regulation of the genome has emerged as an attractive new strategy for therapeutic intervention. The development of epigenetic drugs re...

journal_title：Briefings in functional genomics

authors： Bartke T,Borgel J,DiMaggio PA

更新日期：2013-05-01 00:00:00

abstract：:Gastric cancer remains the second most common cause of cancer-related death worldwide. Because of the poor prognosis of late-stage gastric cancer patients, it is imperative to develop new strategies to improve the survival rate of this disease. Currently, immunotherapy is considered as an innovative approach for cance...

journal_title：Briefings in functional genomics

authors： Zhao Q,Cao L,Guan L,Bie L,Wang S,Xie B,Chen X,Shen X,Cao F

更新日期：2019-03-22 00:00:00

abstract：:Omics, such as genomics, transcriptome and proteomics, has been affected by the era of big data. A huge amount of high dimensional and complex structured data has made it no longer applicable for conventional machine learning algorithms. Fortunately, deep learning technology can contribute toward resolving these chall...

journal_title：Briefings in functional genomics

authors： Zhang Z,Zhao Y,Liao X,Shi W,Li K,Zou Q,Peng S

更新日期：2019-02-14 00:00:00

abstract：:A central environment and interface for microRNA (miRNA) registry and repository and a general standardized framework for their systematic annotation was established over a decade ago. However, the numbers of experimentally and computationally identified miRNAs are swiftly accumulating, and new aspects of miRNA-mediat...

journal_title：Briefings in functional genomics

authors： Budak H,Bulut R,Kantar M,Alptekin B

更新日期：2016-01-01 00:00:00

abstract：:Neisseria meningitidis is a strictly human pathogen and is one of the major causes of septicemia and meningitis worldwide. Functional genomics approaches have been extensively applied to study how N. meningitidis adapts to grow and survive in different human niches encountered during the infection. DNA microarrays per...

journal_title：Briefings in functional genomics

authors： Del Tordello E,Serruto D

更新日期：2013-07-01 00:00:00

abstract：:Acquisition of evolutionary novelties is a fundamental process for adapting to the external environment and invading new niches and results in the diversification of life, which we can see in the world today. How such novel phenotypic traits are acquired in the course of evolution and are built up in developing embryo...

journal_title：Briefings in functional genomics

authors： Moriyama Y,Koshiba-Takeuchi K

更新日期：2018-09-27 00:00:00

abstract：:Submitting sequences to the National Center for Biotechnology Information (NCBI) is an integral part of research and the publication process for many disciplines within the life sciences, and it will only become more important as sequencing technologies continue to improve. Here, I argue that the available infrastruct...

journal_title：Briefings in functional genomics

authors： Smith DR

更新日期：2020-12-04 00:00:00

abstract：:Molecular network data are increasingly becoming available, necessitating the development of well performing computational tools for their analyses. Such tools enabled conceptually different approaches for exploring human diseases to be undertaken, in particular, those that study the relationship between a multitude o...

journal_title：Briefings in functional genomics

authors： Janjić V,Pržulj N

更新日期：2012-11-01 00:00:00

abstract：:Differential gene expression plays a critical role in the development and physiology of multicellular organisms. At a 'systems level' (e.g. at the level of a tissue, organ or whole organism), this process can be studied using gene regulatory network (GRN) models that capture physical and regulatory interactions betwee...

journal_title：Briefings in functional genomics

authors： Arda HE,Walhout AJ

更新日期：2010-01-01 00:00:00

abstract：:Pluripotent embryonic stem (ES) cells are specialized cells with a dynamic chromatin structure, which is intimately connected with their pluripotency and physiology. In recent years somatic cells have been reprogrammed to a pluripotent state through over-expression of a defined set of transcription factors. These cell...

journal_title：Briefings in functional genomics

authors： Delgado-Olguín P,Recillas-Targa F

更新日期：2011-01-01 00:00:00

abstract：:Piwi-interacting RNAs (piRNAs) and CRISPR RNAs (crRNAs) are two recently discovered classes of small noncoding RNA that are found in animals and prokaryotes, respectively. Both of these novel RNA species function as components of adaptive immune systems that protect their hosts from foreign nucleic acids-piRNAs repres...

journal_title：Briefings in functional genomics

authors： Kumar MS,Chen KC

更新日期：2012-07-01 00:00:00

abstract：:A recent highlight of genomics research has been the discovery of many families of transcripts which have function but do not code for proteins. An important group is long noncoding RNAs (lncRNAs), which are typically longer than 200 nt, and whose members originate from thousands of loci across genomes. We review prog...

journal_title：Briefings in functional genomics

authors： Bai Y,Dai X,Harrison AP,Chen M

更新日期：2015-03-01 00:00:00

abstract：:Recent data have revealed that the paradigmatic tumour suppressor gene RB1 on chromosome 13 is preferentially expressed from the maternal allele. Imprinted expression of RB1 is linked to a differentially methylated CpG island in intron 2 of this gene (CpG 85). On the paternal chromosome, CpG 85 is unmethylated and act...

journal_title：Briefings in functional genomics

authors： Buiting K,Kanber D,Horsthemke B,Lohmann D

更新日期：2010-07-01 00:00:00

abstract：:Less than 2% of the human genome DNA is composed of protein-coding genes, although the majority of the human genome is transcribed, indicating the transcripts mostly are noncoding RNAs. Those noncoding RNAs with length between 200 nt and 200 kb are categorized as long noncoding RNA (lncRNA). Around 30 000 lncRNAs have...

journal_title：Briefings in functional genomics

authors： Wang G,Liu C,Deng S,Zhao Q,Li T,Qiao S,Shen L,Zhang Y,Lü J,Meng L,Liang C,Yu Z

更新日期：2016-05-01 00:00:00

abstract：:The presence of microchimeric cells is known for >100 years and well documented since decades. Earlier, microchimeric cells were mainly used for cell-based non-invasive prenatal diagnostics during early pregnancy. Microchimeric cells are also present beyond delivery and are associated to various autoimmune diseases, t...

journal_title：Briefings in functional genomics

authors： Ståhlberg A,El-Heliebi A,Sedlmayr P,Kroneis T

更新日期：2018-07-01 00:00:00

abstract：:Lysine N-ε-acetylation is a post-translational modification that regulates the function of histone and non-histone proteins. In several malignancies, histone acetyltransferase (HAT) activities are disturbed as a consequence of various genetic or epigenetic alterations. In particular, HATs can function as tumor suppres...

journal_title：Briefings in functional genomics

authors： Di Cerbo V,Schneider R

更新日期：2013-05-01 00:00:00

abstract：: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 gener...

journal_title：Briefings in functional genomics

authors： Moin M,Bakshi A,Saha A,Dutta M,Kirti PB

更新日期：2017-07-01 00:00:00

abstract：:The human genome has an almost equal distribution of unique and transposable genetic elements. Although at the transcriptome level, a relatively higher contribution from transposable elements derived RNA has been reported. This is further highlighted with evidence from pervasive transcription. Of the total RNA, noncod...

journal_title：Briefings in functional genomics

authors： Chattopadhyay P,Srinivasa Vasudevan J,Pandey R

更新日期：2021-01-25 00:00:00

abstract：:Coronary artery disease (CAD) and ischemic stroke are the two most predominant forms of cardiovascular diseases (CVDs) caused by genetic, epigenetic and environmental risk factors. Although studies on the impact of 'epigenetics' in CVDs is not new, its effects are increasingly being realized as a key regulatory determ...

journal_title：Briefings in functional genomics

authors： Sharma AR,Shashikiran U,Uk AR,Shetty R,Satyamoorthy K,Rai PS

更新日期：2020-07-29 00:00:00

abstract：:The growing appreciation of the importance of long noncoding RNAs (lncRNAs), together with the awareness that some of these RNAs are associated with chromatin, has inspired the development of methods to detect their sites of interaction on a genome-wide scale at high resolution. Hybridization capture methods combine a...

journal_title：Briefings in functional genomics

authors： Machyna M,Simon MD

更新日期：2018-03-01 00:00:00

abstract：: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 ...

journal_title：Briefings in functional genomics

authors： Hatzikotoulas K,Gilly A,Zeggini E

更新日期：2014-09-01 00:00:00