The Sorghum bicolor reference genome: improved assembly, gene annotations, a transcriptome atlas, and signatures of genome organization.

Sorghum bicolor is a drought tolerant C4 grass used for the production of grain, forage, sugar, and lignocellulosic biomass and a genetic model for C4 grasses due to its relatively small genome (approximately 800 Mbp), diploid genetics, diverse germplasm, and colinearity with other C4 grass genomes. In this study, deep sequencing, genetic linkage analysis, and transcriptome data were used to produce and annotate a high-quality reference genome sequence. Reference genome sequence order was improved, 29.6 Mbp of additional sequence was incorporated, the number of genes annotated increased 24% to 34 211, average gene length and N50 increased, and error frequency was reduced 10-fold to 1 per 100 kbp. Subtelomeric repeats with characteristics of Tandem Repeats in Miniature (TRIM) elements were identified at the termini of most chromosomes. Nucleosome occupancy predictions identified nucleosomes positioned immediately downstream of transcription start sites and at different densities across chromosomes. Alignment of more than 50 resequenced genomes from diverse sorghum genotypes to the reference genome identified approximately 7.4 M single nucleotide polymorphisms (SNPs) and 1.9 M indels. Large-scale variant features in euchromatin were identified with periodicities of approximately 25 kbp. A transcriptome atlas of gene expression was constructed from 47 RNA-seq profiles of growing and developed tissues of the major plant organs (roots, leaves, stems, panicles, and seed) collected during the juvenile, vegetative and reproductive phases. Analysis of the transcriptome data indicated that tissue type and protein kinase expression had large influences on transcriptional profile clustering. The updated assembly, annotation, and transcriptome data represent a resource for C4 grass research and crop improvement

Advances in the Molecular Mechanisms of Abscisic Acid and Gibberellins Functions in Plants 2.0

Gibberellins (GA) and abscisic acid (ABA) are two phytohormones that regulate, in an antagonistic way, plant growth as well as several developmental processes from seed maturation and germination to flowering time, through hypocotyl elongation and root growth. In general, ABA and GA inhibit and promote, respectively, cell elongation and growth. Consequently, this mutual antagonism between GA and ABA governs many developmental decisions in plants.In addition to its role as a growth and development modulator, ABA is primarily known for being a major player in the response and adaptation of plants to diverse abiotic stress conditions, including cold, heat, drought, salinity or flooding. Remarkably, different works have also recently pointed to a function for GA in the control of some biological processes in response to stress.The selection of research and review papers of this book, mostly focused on ABA, covers a wide range of topics related to the most recent advances in the molecular mechanisms of ABA and GA functions in plants

The role of renal transporters and novel regulatory interactions in the TAL that control blood pressure

Hypertension (HTN), a major public health issue is currently the leading factor in the global burden of disease, where associated complications account for 9.4 million deaths worldwide every year (98). Excessive dietary salt intake is among the environmental factors that contribute to HTN, known as salt sensitivity. The heterogeneity of salt sensitivity and the multiple mechanisms that link high salt intake to increases in blood pressure are of upmost importance for therapeutic application. A continual increase in the kidney's reabsorption of sodium (Na+) relies on sequential actions at various segments along the nephron. When the distal segments of the nephron fail to regulate Na+, the effects on Na+ homeostasis are unfavourable. We propose that the specific nephron region where increased active uptake occurs as a result of variations in Na+ reabsorption is at the thick ascending limb of the loop of Henle (TAL). The purpose of this review is to urge the consideration of the TAL that contributes to the pathophysiology of salt sensitive HTN. Further research in this area will enable development of a therapeutic application for targeted treatment

Genome-Wide Identification, Evolution, and Co-expression Network Analysis of Mitogen-Activated Protein Kinase Kinase Kinases in Brachypodium distachyon

Mitogen-activated protein kinase (MAPK) cascades are the conserved and universal signal transduction modules in all eukaryotes, which play the vital roles in plant growth, development and in response to multiple stresses. In this study, we used bioinformatics methods to identify 86 MAPKKK protein encoded by 73 MAPKKK genes in Brachypodium. Phylogenetic analysis of MAPKKK family from Arabidopsis, rice and Brachypodium has classified them into three subfamilies, of which 28 belonged to MEKK, 52 to Raf and 6 to ZIK subfamily respectively. Conserved protein motif, exon-intron organization and splicing intron phase in kinase domains supported the evolutionary relationships inferred from the phylogenetic analysis. And gene duplication analysis suggested the chromosomal segment duplication happened before the divergence of the rice and Brachypodium, while all of three tandem duplicated gene pairs happened after their divergence. We further demonstrated that the MAPKKKs have evolved under strong purifying selection, implying the conservation of them. The splicing transcripts expression analysis showed that the splicesome translating longest protein tended to be adopted. Furthermore, the expression analysis of BdMAPKKKs in different organs and development stages as well as heat, virus and drought stresses revealed that the MAPKKK genes were involved in various signaling pathways. And the circadian analysis suggested there were 41 MAPKKK genes in Brachypodium showing cycled expression in at least one condition, of which seven MAPKKK genes expressed in all conditions and the promoter analysis indicated these genes possessed many cis-acting regulatory elements involved in circadian and light response. Finally, the co-expression network of MAPK, MAPKK and MAPKKK in Brachypodium was constructed using 144 microarray and RNA-seq datasets, and ten potential MAPK cascades pathway were predicted. To conclude, our study provided the important information for evolutionary and functional characterization of MAPKKK family in Brachypodium, which will facilitate the functional analysis of BdMAPKKK genes, and also will facilitate better understanding the MAPK signal pathway in Brachypodium and beyond

Novel polymorphic AluYb8 insertion in the WNK1 gene is associated with blood pressure variation in Europeans

Mutations in WNK1 and WNK4 cause familial hypertension, the Gordon syndrome. WNK1 and WNK4 conserved noncoding regions were targeted to polymorphism screening using DHPLC and DGGE. The scan identified an undescribed polymorphic AluYb8 insertion in WNK1 intron 10. Screening in primates revealed that this Alu-insertion has probably occurred in human lineage. Genotyping in 18 populations from Europe, Asia, and Africa (n = 854) indicated an expansion of the WNK1 AluYb8 bearing chromosomes out of Africa. The allele frequency in Sub-Saharan Africa was ∼3.3 times lower than in other populations (4.8 vs. 15.8%; P = 9.7 × 10−9). Meta-analysis across three European sample sets (n = 3,494; HYPEST, Estonians; BRIGHT, the British; CADCZ, Czech) detected significant association of the WNK1 AluYb8 insertion with blood pressure (BP; systolic BP, P = 4.03 × 10−3, effect 1.12; diastolic BP, P = 1.21 × 10−2, effect 0.67). Gender-stratified analysis revealed that this effect might be female-specific (n = 2,088; SBP, P = 1.99 × 10−3, effect 1.59; DBP P = 3.64 × 10−4, effect 1.23; resistant to Bonferroni correction), whereas no statistical support was identified for the association with male BP (n = 1,406). In leucocytes, the expressional proportions of the full-length WNK1 transcript and the splice-form skipping exon 11 were significantly shifted in AluYb8 carriers compared to noncarriers. The WNK1 AluYb8 insertion might affect human BP via altering the profile of alternatively spliced transcripts. Hum Mutat 32:1–9, 2011. © 2011 Wiley-Liss, Inc

Signal transduction pathways involving the hypertension-related WNK1 and WNK4 protein kinases

Dissertação apresentada para obtenção do Grau de Doutor em Biologia, na especialidade de Genética Molecular, pela Universidade Nova de Lisboa, Faculdade de Ciências e TecnologiaThe genes WNK1 and WNK4 belong to the subfamily of WNK protein kinases and their mutation causes pseudohypoaldosteronism type II, a rare familial form of hypertension with hyperkalemia and hypercalciuria. The molecular mechanisms underlying this condition involve the regulation of renal electrolyte homeostasis and the modulation of diverse ion channels and transporters via WNK kinases. Additionally, WNKs have also been reported to participate in signal transduction pathways related to cell survival and proliferation. The objective of the present thesis was to identify novel WNK1 and WNK4 interacting proteins and the underlying signal transduction pathways. First, it was found that WNK1 forms a protein complex with the Rab-GAP TBC1D4 and phosphorylates it in vitro. It was shown that the expression levels of WNK1 regulate surface expression of the constitutive glucose transporter GLUT1 in HEK293 cells. WNK1 is shown to increase the binding of TBC1D4 to regulatory 14-3-3 proteins while reducing its interaction with the exocytic small GTPase Rab8A. Moreover, these effects were kinase activity-dependent. Together, the data describe a pathway regulating constitutive glucose uptake via GLUT1, the expression level of which is related to several human diseases. Second, WNK4 was found to promote the cell surface expression of the CFTR chloride channel in mammalian cells. The mechanism by which WNK4 acts on CFTR involves interaction with the tyrosine kinase Syk, which we found to phosphorylate tyrosine 512 (Tyr512) in the first nucleotide-binding domain of CFTR. The presence of WNK4 prevents this in vitro phosphorylation in a kinase-independent manner. In BHK21 cells stably expressing CFTR, Syk reduces, while WNK4 promotes, the cell surface expression of CFTR. Mutation of Tyr512 revealed that its phosphorylation is a novel signal regulating the prevalence of CFTR at the cell surface and that WNK4 and Syk play an antagonistic role in this process. Finally, ten WNK4 variants were detected in a cohort of Portuguese patients and control individuals, which subsequently were tested for association to hypertension and/or osteoporosis. Despite none of the variants yield any significant association to hypertension, a rare missense alteration (rs56116165) in a highly conserved arginine residue showed a nominal association to osteoporosis. This finding advocates that this polymorphism is a rare allelic variant, in a candidate gene with a biological function in renal calcium homeostasis, that may contribute to a genetic predisposition to osteoporosis.Fundação para a Ciência e Tecnologia - 2006 a 2009 (SFRH/BD/23001/2005),Programa de Financiamento Plurianual do Centro de Investigação em Genética Molecular Humana e do projecto POCI/SAU-MMO/56439/200

Preparation for hypertension specialists : genomics reveals the pathogenesis of hypertension

Genomics is a discipline in genetics that applies recombinant DNA, DNA sequencing methods, and bioinformatics to sequence, assemble, and analyze the function and structure of genomes, the complete set of DNA within a single cell of an organism. Research into the genetics of hypertension has now expanded to genomics. Two approaches have dominated this field. One relies on large populations in which the phenotype, hypertension versus no hypertension, or hypertension-relevant phenotypes are compared. Genome-wide association (GWAS) analyses of (>1 million) common variants identify relevant loci and possible genes exerting small effects. Detailed studies on APOL1 and SH2B3 are opening entire new fields of research. Family-based Mendelian studies have identified rare variants that exert very large effects on blood pressure. Mechanistically these studies have been a bonanza of new information. The approaches are complementary

Genetic Programming of Hypertension

The heritability of hypertension (HTN) is widely recognized and as a result, extensive studies ranging from genetic linkage analyses to genome-wide association studies are actively ongoing to elucidate the etiology of both monogenic and polygenic forms of HTN. Due to the complex nature of essential HTN, however, single genes affecting blood pressure (BP) variability remain difficult to isolate and identify and have rendered the development of single-gene targeted therapies challenging. The roles of other causative factors in modulating BP, such as gene–environment interactions and epigenetic factors, are increasingly being brought to the forefront. In this review, we discuss the various monogenic HTN syndromes and corresponding pathophysiologic mechanisms, the different methodologies employed in genetic studies of essential HTN, the mechanisms for epigenetic modulation of essential HTN, pharmacogenomics and HTN, and finally, recent advances in genetic studies of essential HTN in the pediatric population