Current Genomics (v.14, #3)

Compatible Solute Engineering in Plants for Abiotic Stress Tolerance - Role of Glycine Betaine by Shabir Hussain Wani, Naorem Brajendra Singh, Athokpam Haribhushan, Javed Iqbal Mir (157-165).
Abiotic stresses collectively are responsible for crop losses worldwide. Among these, drought and salinity arethe most destructive. Different strategies have been proposed for management of these stresses. Being a complex trait,conventional breeding approaches have resulted in less success. Biotechnology has emerged as an additional and noveltool for deciphering the mechanism behind these stresses. The role of compatible solutes in abiotic stress tolerance hasbeen studied extensively. Osmotic adjustment, at the physiological level, is an adaptive mechanism involved in drought orsalinity tolerance, which permits the maintenance of turgor under conditions of water deficit, as it can counteract the effectsof a rapid decline in leaf water potential. Increasing evidence from a series of in vivo and in vitro studies of thephysiology, biochemistry, genetics, and molecular biology of plants suggest strongly that Glycine Betaine (GB) performsan important function in plants subjected to environmental stresses. It plays an adaptive role in mediating osmotic adjustmentand protecting the sub-cellular structures in stressed plants, protection of the transcriptional and translational machineriesand intervention as a molecular chaperone in the refolding of enzymes. Many important crops like rice do notaccumulate glycinebetaine under stress conditions. Both the exogenous application of GB and the genetically engineeredbiosynthesis of GB in such crops is a promising strategy to increase stress tolerance. In this review we will discuss theimportance of GB for abiotic stress tolerance in plants. Further, strategies like exogenic application and transgenic developmentof plants accumulating GB will be also be discussed. Work done on exogenic application and genetically engineeredbiosynthesis of GB will be listed and its advantages and limitations will be described.

Epigenetics in Ocular Diseases by Melissa M. Liu, Chi-Chao Chan, Jingsheng Tuo (166-172).
Epigenetics pertains to heritable alterations in gene expression that do not involve modification of the underlyinggenomic DNA sequence. Historically, the study of epigenetic mechanisms has focused on DNA methylation and histonemodifications, but the concept of epigenetics has been more recently extended to include microRNAs as well. Epigeneticpatterning is modified by environmental exposures and may be a mechanistic link between environmental risk factorsand the development of disease. Epigenetic dysregulation has been associated with a variety of human diseases, includingcancer, neurological disorders, and autoimmune diseases. In this review, we consider the role of epigenetics incommon ocular diseases, with a particular focus on DNA methylation and microRNAs. DNA methylation is a criticalregulator of gene expression in the eye and is necessary for the proper development and postmitotic survival of retinalneurons. Aberrant methylation patterns have been associated with age-related macular degeneration, susceptibility to oxidativestress, cataract, pterygium, and retinoblastoma. Changes in histone modifications have also been observed in experimentalmodels of diabetic retinopathy and glaucoma. The expression levels of specific microRNAs have also beenfound to be altered in the context of ocular inflammation, retinal degeneration, pathological angiogenesis, diabetic retinopathy,and ocular neoplasms. Although the complete spectrum of epigenetic modifications remains to be more fully explored,it is clear that epigenetic dysregulation is an important contributor to common ocular diseases and may be a relevanttherapeutic target.

Strand-Specific RNA-Seq Provides Greater Resolution of Transcriptome Profiling by James Dominic Mills, Yoshihiro Kawahara, Michael Janitz (173-181).
RNA-Seq is a recently developed sequencing technology, that through the analysis of cDNA allows for uniqueinsights into the transcriptome of a cell. The data generated by RNA-Seq provides information on gene expression, alternativesplicing events and the presence of non-coding RNAs. It has been realised non-coding RNAs are more then just artefactsof erroneous transcription and play vital regulatory roles at the genomic, transcriptional and translational level.Transcription of the DNA sense strand produces antisense transcripts. This is known as antisense transcription and oftenresults in the production of non-coding RNAs that are complementary to their associated sense transcripts. Antisense transcriptionhas been identified in bacteria, fungi, protozoa, plants, invertebrates and mammals. It seems that antisense transcriptional'hot spots' are located around nucleosome-free regions such as those associated with promoters, indicating thatit is likely that antisense transcripts carry out important regulatory functions. This underlines the importance of identifyingthe presence and understanding the function of these antisense non-coding RNAs. The information concerning strand originis often lost during conventional RNA-Seq; capturing this information would substantially increase the worth of anyRNA-Seq experiment. By manipulating the input cDNA during the template preparation stage it is possible to retain thisvital information. This forms the basis of strand-specific RNA-Seq. With an ability to unlock immense portions of new informationsurrounding the transcriptome, this cutting edge technology may hold the key to developing a greater understandingof the transcriptome.

Review: Alternative Splicing (AS) of Genes As An Approach for Generating Protein Complexity by Bishakha Roy, Larisa M. Haupt, Lyn R. Griffiths (182-194).
Prior to the completion of the human genome project, the human genome was thought to have a greater numberof genes as it seemed structurally and functionally more complex than other simpler organisms. This along with the beliefof "one gene, one protein", were demonstrated to be incorrect. The inequality in the ratio of gene to protein formationgave rise to the theory of alternative splicing (AS). AS is a mechanism by which one gene gives rise to multiple proteinproducts. Numerous databases and online bioinformatic tools are available for the detection and analysis of AS. Bioinformaticsprovides an important approach to study mRNA and protein diversity by various tools such as expressed sequencetag (EST) sequences obtained from completely processed mRNA. Microarrays and deep sequencing approachesalso aid in the detection of splicing events. Initially it was postulated that AS occurred only in about 5% of all genes butwas later found to be more abundant. Using bioinformatic approaches, the level of AS in human genes was found to befairly high with 35-59% of genes having at least one AS form. Our ability to determine and predict AS is important asdisorders in splicing patterns may lead to abnormal splice variants resulting in genetic diseases. In addition, the diversityof proteins produced by AS poses a challenge for successful drug discovery and therefore a greater understanding of ASwould be beneficial.

Mitochondria and Familial Predisposition to Breast Cancer by Stefania Weigl, Angelo Paradiso, Stefania Tommasi (195-203).
Mitochondrial genome and functional alterations are related to various diseases including cancer. In all cases,the role of these organelles is associated with defects in oxidative energy metabolism and control of tumor-induced oxidativestress. The present study examines the involvement of mitochondrial DNA in cancer and in particular in breast cancer.Furthermore, since mitochondrial DNA is maternally inherited, hereditary breast cancer has been focused on.

Genomics of Chronic Obstructive Pulmonary Disease (COPD); Exploring the SNPs of Protease-Antiprotease Pathway by Manish Kumar, Neetu Phougat, Sonam Ruhil, Sandeep Dhankhar, Meenakshi Balhara, Anil Kumar Chhillar (204-213).
The COPD has been an important respiratory condition that affects people worldwide and its incidence hasbeen alarming. The increasing incidence of this disorder has been attributed to global industrialization and environmentalpollution. Although the exposures to environmental pollutants and smoking have been important triggers, the geneticcomponent of individuals has been shown to be important for development and progression of COPD. Recent literaturereported that protease-antiprotease imbalance to be important in etiopathogenesis of COPD. The enzymes namely neutrophilelastase and matrix metalloprotienases are considered to be foremost proteolytic molecules released by neutrophils andmacrophages during inflammatory events in COPD. Normally, the lungs remain protected from the destructive effect of thesetwo antiproteases by α1-antitrypsin (α1AT) and tissue inhibitors of metalloproteinases (TIMPs) respectively. In this review, weare trying to highlight the work by various research groups in exploring the SNPs of various genes of inflammatory pathwaysand the protease-antiprotease pathway, which may have some degree of association with COPD.

Phylogenetic Analysis of Brassica rapa MATH-Domain Proteins by Liming Zhao, Yong Huang, Yan Hu, Xiaoli He, Wenhui Shen, Chunlin Liu, Ying Ruan (214-223).
The MATH (meprin and TRAF-C homology) domain is a fold of seven anti-parallel β-helices involved in protein-protein interaction. Here, we report the identification and characterization of 90 MATH-domain proteins from theBrassica rapa genome. By sequence analysis together with MATH-domain proteins from other species, the B. rapaMATH-domain proteins can be grouped into 6 classes. Class-I protein has one or several MATH domains without anyother recognizable domain; Class-II protein contains a MATH domain together with a conserved BTB (Broad Complex,Tramtrack, and Bric-a-Brac ) domain; Class-III protein belongs to the MATH/Filament domain family; Class-Iv proteincontains a MATH domain frequently combined with some other domains; Class-V protein has a relative long sequencebut contains only one MATH domain; Class-VI protein is characterized by the presence of Peptidase and UBQ (Ubiquitinylation)domains together with one MATH domain. As part of our study regarding seed development of B. rapa, sixgenes are screened by SSH (Suppression Subtractive Hybridization) and their expression levels are analyzed in combinationwith seed developmental stages, and expression patterns suggested that Bra001786, Bra03578 and Bra036572 may beseed development specific genes, while Bra001787, Bra020541 and Bra040904 may be involved in seed and flower organdevelopment. This study provides the first characterization of the MATH domain proteins in B. rapa.