Genome-wide analysis of ABA-responsive elements ABRE and CE3 reveals divergent patterns in Arabidopsis and rice

Gomez-Porras J, Riano-Pachon DM, Dreyer I, Mayer JE, Mueller-Roeber B. Genome-wide analysis of ABA-responsive elements ABRE and CE3 reveals divergent patterns in Arabidopsis and rice. BMC GENOMICS. 2007;8(1): 260.Background: In plants, complex regulatory mechanisms are at the core of physiological and developmental processes. The phytohormone abscisic acid ( ABA) is involved in the regulation of various such processes, including stomatal closure, seed and bud dormancy, and physiological responses to cold, drought and salinity stress. The underlying tissue or plant-wide control circuits often include combinatorial gene regulatory mechanisms and networks that we are only beginning to unravel with the help of new molecular tools. The increasing availability of genomic sequences and gene expression data enables us to dissect ABA regulatory mechanisms at the individual gene expression level. In this paper we used an insilico-based approach directed towards genome-wide prediction and identification of specific features of ABA-responsive elements. In particular we analysed the genome-wide occurrence and positional arrangements of two well-described ABA-responsive cis-regulatory elements ( CREs), ABRE and CE3, in thale cress ( Arabidopsis thaliana) and rice ( Oryza sativa). Results: Our results show that Arabidopsis and rice use the ABA-responsive elements ABRE and CE3 distinctively. Earlier reports for various monocots have identified CE3 as a coupling element ( CE) associated with ABRE. Surprisingly, we found that while ABRE is equally abundant in both species, CE3 is practically absent in Arabidopsis. ABRE-ABRE pairs are common in both genomes, suggesting that these can form functional ABA-responsive complexes ( ABRCs) in Arabidopsis and rice. Furthermore, we detected distinct combinations, orientation patterns and DNA strand preferences of ABRE and CE3 motifs in rice gene promoters. Conclusion: Our computational analyses revealed distinct recruitment patterns of ABA-responsive CREs in upstream sequences of Arabidopsis and rice. The apparent absence of CE3s in Arabidopsis suggests that another CE pairs with ABRE to establish a functional ABRC capable of interacting with transcription factors. Further studies will be needed to test whether the observed differences are extrapolatable to monocots and dicots in general, and to understand how they contribute to the fine-tuning of the hormonal response. The outcome of our investigation can now be used to direct future experimentation designed to further dissect the ABA-dependent regulatory networks

Traumatic brain injury: integrated approaches to improve prevention, clinical care, and research

No abstract available

Repositioning of the global epicentre of non-optimal cholesterol

High blood cholesterol is typically considered a feature of wealthy western countries(1,2). However, dietary and behavioural determinants of blood cholesterol are changing rapidly throughout the world(3) and countries are using lipid-lowering medications at varying rates. These changes can have distinct effects on the levels of high-density lipoprotein (HDL) cholesterol and non-HDL cholesterol, which have different effects on human health(4,5). However, the trends of HDL and non-HDL cholesterol levels over time have not been previously reported in a global analysis. Here we pooled 1,127 population-based studies that measured blood lipids in 102.6 million individuals aged 18 years and older to estimate trends from 1980 to 2018 in mean total, non-HDL and HDL cholesterol levels for 200 countries. Globally, there was little change in total or non-HDL cholesterol from 1980 to 2018. This was a net effect of increases in low- and middle-income countries, especially in east and southeast Asia, and decreases in high-income western countries, especially those in northwestern Europe, and in central and eastern Europe. As a result, countries with the highest level of non-HDL cholesterol-which is a marker of cardiovascular riskchanged from those in western Europe such as Belgium, Finland, Greenland, Iceland, Norway, Sweden, Switzerland and Malta in 1980 to those in Asia and the Pacific, such as Tokelau, Malaysia, The Philippines and Thailand. In 2017, high non-HDL cholesterol was responsible for an estimated 3.9 million (95% credible interval 3.7 million-4.2 million) worldwide deaths, half of which occurred in east, southeast and south Asia. The global repositioning of lipid-related risk, with non-optimal cholesterol shifting from a distinct feature of high-income countries in northwestern Europe, north America and Australasia to one that affects countries in east and southeast Asia and Oceania should motivate the use of population-based policies and personal interventions to improve nutrition and enhance access to treatment throughout the world.Peer reviewe

Heterogeneous contributions of change in population distribution of body mass index to change in obesity and underweight NCD Risk Factor Collaboration (NCD-RisC)

From 1985 to 2016, the prevalence of underweight decreased, and that of obesity and severe obesity increased, in most regions, with significant variation in the magnitude of these changes across regions. We investigated how much change in mean body mass index (BMI) explains changes in the prevalence of underweight, obesity, and severe obesity in different regions using data from 2896 population-based studies with 187 million participants. Changes in the prevalence of underweight and total obesity, and to a lesser extent severe obesity, are largely driven by shifts in the distribution of BMI, with smaller contributions from changes in the shape of the distribution. In East and Southeast Asia and sub-Saharan Africa, the underweight tail of the BMI distribution was left behind as the distribution shifted. There is a need for policies that address all forms of malnutrition by making healthy foods accessible and affordable, while restricting unhealthy foods through fiscal and regulatory restrictions

Genome-wide analysis of ABA-responsive elements ABRE and CE3 reveals divergent patterns in Arabidopsis and rice-7

<p><b>Copyright information:</b></p><p>Taken from "Genome-wide analysis of ABA-responsive elements ABRE and CE3 reveals divergent patterns in Arabidopsis and rice"</p><p>http://www.biomedcentral.com/1471-2164/8/260</p><p>BMC Genomics 2007;8():260-260.</p><p>Published online 1 Aug 2007</p><p>PMCID:PMC2000901.</p><p></p>atrix; (c) CE3 sequence logo; (d) CE3 frequency matrix

Genome-wide analysis of ABA-responsive elements ABRE and CE3 reveals divergent patterns in Arabidopsis and rice-1

<p><b>Copyright information:</b></p><p>Taken from "Genome-wide analysis of ABA-responsive elements ABRE and CE3 reveals divergent patterns in Arabidopsis and rice"</p><p>http://www.biomedcentral.com/1471-2164/8/260</p><p>BMC Genomics 2007;8():260-260.</p><p>Published online 1 Aug 2007</p><p>PMCID:PMC2000901.</p><p></p>atrix; (c) CE3 sequence logo; (d) CE3 frequency matrix

Genome-wide analysis of ABA-responsive elements ABRE and CE3 reveals divergent patterns in Arabidopsis and rice-3

<p><b>Copyright information:</b></p><p>Taken from "Genome-wide analysis of ABA-responsive elements ABRE and CE3 reveals divergent patterns in Arabidopsis and rice"</p><p>http://www.biomedcentral.com/1471-2164/8/260</p><p>BMC Genomics 2007;8():260-260.</p><p>Published online 1 Aug 2007</p><p>PMCID:PMC2000901.</p><p></p

Genome-wide analysis of ABA-responsive elements ABRE and CE3 reveals divergent patterns in Arabidopsis and rice-0

<p><b>Copyright information:</b></p><p>Taken from "Genome-wide analysis of ABA-responsive elements ABRE and CE3 reveals divergent patterns in Arabidopsis and rice"</p><p>http://www.biomedcentral.com/1471-2164/8/260</p><p>BMC Genomics 2007;8():260-260.</p><p>Published online 1 Aug 2007</p><p>PMCID:PMC2000901.</p><p></p>oding gene the translation initiation codon (ATG) was located and a 1-kb upstream sequence was extracted. The genomic data set thus obtained contained 26,140 entries for and 49,472 entries for . For each species 100 independent randomised data sets were generated by reshuffling the nucleotide sequence of each entry. (b) screening using a CRE-specific frequency matrix. A positive hit was recorded if the matrix score reached a 95% cut-off threshold. (c) Determination of the distance of an element to the ATG. In the illustrated example d1 and d3 are the distances to the ATG for the elements localized on the [+] strand; d2 is the distance to the ATG for the element localized on the [-] strand. (d) Gap length between elements. In the example above Δ1 is the gap between two -oriented CREs (in this case [+/+]), and Δ2 and Δ3 are gaps between two -oriented CREs [-/+] and [+/-], respectively

Genome-wide analysis of ABA-responsive elements ABRE and CE3 reveals divergent patterns in Arabidopsis and rice-5

<p><b>Copyright information:</b></p><p>Taken from "Genome-wide analysis of ABA-responsive elements ABRE and CE3 reveals divergent patterns in Arabidopsis and rice"</p><p>http://www.biomedcentral.com/1471-2164/8/260</p><p>BMC Genomics 2007;8():260-260.</p><p>Published online 1 Aug 2007</p><p>PMCID:PMC2000901.</p><p></p>ndent gap length distribution for ABRE-CE3 pairs (c) [+/+]; (d) [+/-]; (e) [-/+]; (f) and [-/-]. Data are presented as in Figure 3

Genome-wide analysis of ABA-responsive elements ABRE and CE3 reveals divergent patterns in Arabidopsis and rice-4

<p><b>Copyright information:</b></p><p>Taken from "Genome-wide analysis of ABA-responsive elements ABRE and CE3 reveals divergent patterns in Arabidopsis and rice"</p><p>http://www.biomedcentral.com/1471-2164/8/260</p><p>BMC Genomics 2007;8():260-260.</p><p>Published online 1 Aug 2007</p><p>PMCID:PMC2000901.</p><p></p>; and (c) for -oriented pairs. Data are presented as in Figure 3