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 representation among organisms. Their biosynthesis occurs by oxidative cleavage of carotenoids, a high-value reaction, mediated by carotenoid cleavage oxygenases or carotenoid cleavage dioxygenases (CCDs)-a family of non-heme iron enzymes. Structurally, this protein family displays wide diversity but is limited in its distribution among plants. Functionally, this protein family has been recognized to offer a role in phytohormones, volatiles and signal production. Further, their wide presence and clade-specific functional disparity demands a comprehensive account. This review focuses on the critical assessment of CCDs of higher plants, describing recent progress in their functional aspects and regulatory mechanisms, domain architecture, classification and localization. The work also highlights the relevant discussion for further exploration of this multi-prospective protein family for the betterment of its functional understanding and improvement of crops.
journal_name
Brief Funct Genomicsjournal_title
Briefings in functional genomicsauthors
Dhar MK,Mishra S,Bhat A,Chib S,Kaul Sdoi
10.1093/bfgp/elz037subject
Has Abstractpub_date
2020-01-22 00:00:00pages
1-9issue
1eissn
2041-2649issn
2041-2657pii
5686226journal_volume
19pub_type
杂志文章,评审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
pub_type: 杂志文章,评审
doi:10.1093/bfgp/elu022
更新日期:2014-09-01 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
pub_type: 杂志文章,评审
doi:10.1093/bfgp/els065
更新日期:2013-05-01 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
pub_type: 杂志文章,评审
doi:10.1093/bfgp/elx042
更新日期:2018-11-26 00:00:00
abstract::The advent of high-throughput genomics techniques, along with the completion of genome sequencing projects, identification of protein-protein interactions and reconstruction of genome-scale pathways, has accelerated the development of systems biology research in the yeast organism Saccharomyces cerevisiae In particula...
journal_title:Briefings in functional genomics
pub_type: 杂志文章,评审
doi:10.1093/bfgp/elv040
更新日期:2016-03-01 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
pub_type: 杂志文章
doi:10.1093/bfgp/elaa026
更新日期:2021-01-25 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
pub_type: 杂志文章,评审
doi:10.1093/bfgp/elq014
更新日期:2010-07-01 00:00:00
abstract::RNA-seq is a methodology for RNA profiling based on next-generation sequencing that enables to measure and compare gene expression patterns at unprecedented resolution. Although the appealing features of this technique have promoted its application to a wide panel of transcriptomics studies, the fast-evolving nature o...
journal_title:Briefings in functional genomics
pub_type: 杂志文章,评审
doi:10.1093/bfgp/elu035
更新日期:2015-03-01 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
pub_type: 杂志文章
doi:10.1093/bfgp/elaa016
更新日期:2020-12-04 00:00:00
abstract::Chronic infection of hepatitis C virus (HCV) leads to severe life-threatening liver diseases such as cirrhosis of liver, fibrosis and hepatocellular carcinoma (HCC). Severity of the disease infects >180 million people worldwide. In recent years, many computational approaches have been proposed to study and analyze the...
journal_title:Briefings in functional genomics
pub_type: 杂志文章,评审
doi:10.1093/bfgp/elx040
更新日期:2018-11-26 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
pub_type: 杂志文章
doi:10.1093/bfgp/elz043
更新日期:2020-07-29 00:00:00
abstract::Aberrant DNA methylation is considered to be one of the most common hallmarks of cancer. Several recent advances in assessing the DNA methylome provide great promise for deciphering the cancer-specific DNA methylation patterns. Herein, we present the current key technologies used to detect high-throughput genome-wide ...
journal_title:Briefings in functional genomics
pub_type: 杂志文章,评审
doi:10.1093/bfgp/elw010
更新日期:2016-11-01 00:00:00
abstract::Next generation Sequencing (NGS) provides a powerful tool for discovery of domestication genes in crop plants and their wild relatives. The accelerated domestication of new plant species as crops may be facilitated by this knowledge. Re-sequencing of domesticated genotypes can identify regions of low diversity associa...
journal_title:Briefings in functional genomics
pub_type: 杂志文章,评审
doi:10.1093/bfgp/elr032
更新日期:2012-01-01 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
pub_type: 杂志文章
doi:10.1093/bfgp/elz024
更新日期:2020-03-23 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
pub_type: 杂志文章,评审
doi:10.1093/bfgp/elv049
更新日期:2016-05-01 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
pub_type: 杂志文章,评审
doi:10.1093/bfgp/elx038
更新日期:2018-03-01 00:00:00
abstract::Gene Set Enrichment (GSE) is a computational technique which determines whether a priori defined set of genes show statistically significant differential expression between two phenotypes. Currently, the gene sets used for GSE are derived from annotation or pathway databases, which often contain computationally based ...
journal_title:Briefings in functional genomics
pub_type: 杂志文章
doi:10.1093/bfgp/elq021
更新日期:2010-12-01 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
pub_type: 杂志文章,评审
doi:10.1093/bfgp/elt011
更新日期:2013-05-01 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
pub_type: 杂志文章,评审
doi:10.1093/bfgp/elp049
更新日期:2010-01-01 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
pub_type: 杂志文章,评审
doi:10.1093/bfgp/elw029
更新日期:2016-11-01 00:00:00
abstract::In order to better understand several cellular processes, it is helpful to study how various components make up the system. This systems perspective is supported by several modelling tools including network analysis. Networks of protein-protein interactions (PPI networks) offer a way to depict, visualize and quantify ...
journal_title:Briefings in functional genomics
pub_type: 杂志文章,评审
doi:10.1093/bfgp/els035
更新日期:2012-11-01 00:00:00
abstract::Premature termination of transcription, or attenuation, is an efficient RNA-based regulatory strategy that is commonly used in bacterial organisms. Attenuators are generally located in the 50 untranslated regions of genes or operons and combine a Rho-independent terminator, controlling transcription, with an RNA eleme...
journal_title:Briefings in functional genomics
pub_type: 更正并重新发布的文章,杂志文章,评审
doi:10.1093/bfgp/elq008
更新日期:2010-03-01 00:00:00
abstract::The specificity of protein-DNA interactions can be determined directly by sequencing the bound and unbound fractions in a standard binding reaction. The procedure is easy and inexpensive, and the accuracy can be high for thousands of sequences assayed in parallel. From the measurements, simple models of specificity, s...
journal_title:Briefings in functional genomics
pub_type: 杂志文章,评审
doi:10.1093/bfgp/elu043
更新日期:2015-01-01 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
pub_type: 杂志文章,评审
doi:10.1093/bfgp/elt002
更新日期:2013-05-01 00:00:00
abstract::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 pe...
journal_title:Briefings in functional genomics
pub_type: 杂志文章,评审
doi:10.1093/bfgp/elw012
更新日期:2017-05-01 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
pub_type: 杂志文章,评审
doi:10.1093/bfgp/ely019
更新日期:2019-03-22 00:00:00
abstract::The evolution of next-generation sequencing technologies has facilitated the detection of causal genetic variants in diseases previously undiagnosed at a molecular level. However, in genome sequencing studies, the identification of disease genes among a candidate gene list is often difficult because of the large numbe...
journal_title:Briefings in functional genomics
pub_type: 杂志文章
doi:10.1093/bfgp/ely033
更新日期:2019-02-14 00:00:00
abstract::Genetic variation is crucial for successful barley improvement. Genomic technologies are improving dramatically and are providing access to the genetic diversity within this important crop species. Diverse collections of barley germplasm are being assembled and mined via genome-wide association studies and the identif...
journal_title:Briefings in functional genomics
pub_type: 杂志文章
doi:10.1093/bfgp/elu006
更新日期:2014-07-01 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
pub_type: 杂志文章,评审
doi:10.1093/bfgp/elv026
更新日期:2016-01-01 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
pub_type: 杂志文章,评审
doi:10.1093/bfgp/elt036
更新日期:2014-01-01 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
pub_type: 杂志文章
doi:10.1093/bfgp/elw041
更新日期:2017-07-01 00:00:00