Motif models proposing independent and interdependent impacts of nucleotides are related to high and low affinity transcription factor binding sites in Arabidopsis

Position weight matrix (PWM) is the traditional motif model representing the transcription factor (TF) binding sites. It proposes that the positions contribute independently to TFs binding affinity, although this hypothesis does not fit the data perfectly. This explains why PWM hits are missing in a substantial fraction of ChIP-seq peaks. To study various modes of the direct binding of plant TFs, we compiled the benchmark collection of 111 ChIP-seq datasets for Arabidopsis thaliana, and applied the traditional PWM, and two alternative motif models BaMM and SiteGA, proposing the dependencies of the positions. The variation in the stringency of the recognition thresholds for the models proposed that the hits of PWM, BaMM, and SiteGA models are associated with the sites of high/medium, any, and low affinity, respectively. At the medium recognition threshold, about 60% of ChIP-seq peaks contain PWM hits consisting of conserved core consensuses, while BaMM and SiteGA provide hits for an additional 15% of peaks in which a weaker core consensus is compensated through intra-motif dependencies. The presence/absence of these dependencies in the motifs of alternative/traditional models was confirmed by the dependency logo DepLogo visualizing the position-wise partitioning of the alignments of predicted sites. We exemplify the detailed analysis of ChIP-seq profiles for plant TFs CCA1, MYC2, and SEP3. Gene ontology (GO) enrichment analysis revealed that among the three motif models, the SiteGA had the highest portions of genes with the significantly enriched GO terms among all predicted genes. We showed that both alternative motif models provide for traditional PWM greater extensions in predicted sites for TFs MYC2/SEP3 with condition/tissue specific functions, compared to those for TF CCA1 with housekeeping functions. Overall, the combined application of standard and alternative motif models is beneficial to detect various modes of the direct TF-DNA interactions in the maximal portion of ChIP-seq loci

A plausible mechanism for auxin patterning along the developing root

<p>Abstract</p> <p>Background</p> <p>In plant roots, auxin is critical for patterning and morphogenesis. It regulates cell elongation and division, the development and maintenance of root apical meristems, and other processes. In <it>Arabidopsis</it>, auxin distribution along the central root axis has several maxima: in the root tip, in the basal meristem and at the shoot/root junction. The distal maximum in the root tip maintains the stem cell niche. Proximal maxima may trigger lateral or adventitious root initiation.</p> <p>Results</p> <p>We propose a <it>reflected flow </it>mechanism for the formation of the auxin maximum in the root apical meristem. The mechanism is based on auxin's known activation and inhibition of expressed PIN family auxin carriers at low and high auxin levels, respectively. Simulations showed that these regulatory interactions are sufficient for self-organization of the auxin distribution pattern along the central root axis under varying conditions. The mathematical model was extended with rules for discontinuous cell dynamics so that cell divisions were also governed by auxin, and by another morphogen <it>Division Factor </it>which combines the actions of cytokinin and ethylene on cell division in the root. The positional information specified by the gradients of these two morphogens is able to explain root patterning along the central root axis.</p> <p>Conclusion</p> <p>We present here a plausible mechanism for auxin patterning along the developing root, that may provide for self-organization of the distal auxin maximum when the <it>reverse fountain </it>has not yet been formed or has been disrupted. In addition, the proximal maxima are formed under the <it>reflected flow </it>mechanism in response to periods of increasing auxin flow from the growing shoot. These events may predetermine lateral root initiation in a rhyzotactic pattern. Another outcome of the <it>reflected flow </it>mechanism - the predominance of lateral or adventitious roots in different plant species - may be based on the different efficiencies with which auxin inhibits its own transport in different species, thereby distinguishing two main types of plant root architecture: taproot vs. fibrous.</p

Доміно-реакції 3-метил-5-амінопіразолу з 1-феніл-3-(4-алкоксифеніл)піразол-4-карбальдегідами та 2,2-диметил-1,3-діоксан-4,6-діоном

Aim. To synthesize 1-phenyl-3-(4-alkoxyphenyl)pyrazole-4-carbaldehydes and determine the direction of their interaction in the three-component condensation with 3-methyl-5-aminopyrazole and 2,2-dimethyl-1,3-dioxane-4,6-dione.Results and discussion. A series of 1-phenyl-3-(4-alkoxyphenyl)pyrazole-4-carbaldehydes was synthesized from arylhydrazone by the Vilsmeier–Haak reaction. The domino-reactions of these aldehydes with 3-methyl-5-aminopyrazole and 2,2-dimethyl-1,3-dioxane-4,6-dione lead to pyrazolo[3,4-b]pyridone systems.Experimental part. The synthesis of 1-phenyl-3-(4-alkoxyphenyl)pyrazole-4-carbaldehyde was carried out by formylation of arylhydrazones under the conditions of the Vilsmeier–Haack reaction with the yield of 55 – 88 %. Refluxing in 2-propanol equimolar amounts of these aldehydes, 3-methyl-5-aminopyrazole and 2,2-dimethyl-1,3-dioxane-4,6-dione gave 3-methyl-4-(1',3'-diarylpyrazol-4'-yl)tetrahydropyrazolo[3,4-b]pyridin-6-ones with the yield of 48 – 75 %. The structure and composition of all substances synthesized were proven by 1H NMR, IR-spectra and elemental analysis.Conclusions. It has been found that the reactions of 1,3-diaryl substituted pyrazole-4-carbaldehydes with 3-methyl-5-aminopyrazole and 2,2-dimethyl-1,3-dioxane-4,6-dione are regioselective and lead to the formation of pyrazolo[3,4-b]pyridone systems. This orientation of the process corresponds to the interaction of the β-carbon atom of the probable intermediate, which is formed at the first stage of the reaction from dioxandione and aldehyde, with the carbon nucleophilic center in the aminoazole molecule, and then the exocyclic amino group in the heterylamine attacks the C=O group in the dioxane-4,6-dione fragment.Цель. Синтезировать 1-фенил-3-(4-алкоксифенил)пиразол-4-карбальдегиды и установить направленность их взаимодействия в трехкомпонентной конденсации с 3-метил-5-аминопиразолом и 2,2-диметил-1,3-диоксан-4,6-дионом.Результаты и их обсуждение. Формилированием арилгидразонов по Вильсмейеру–Хааку синтезирован ряд 1-фенил-3-(4-алкоксифенил)пиразол-4-карбальдегидов. Домино-реакции этих альдегидов с 3-метил-5-амино­пиразолом и 2,2-диметил-1,3-диоксан-4,6-дионом завершаются образованием пиразоло[3,4-b]-пиридоновых систем.Экспериментальная часть. Синтез 1-фенил-3-(4-алкоксифенил)­пира­зол-4-карбальдегидов осуществлен  формилированием арилгидразонов в условиях реакции Вильсмейера–Хаака с выходом 55 – 88 %. Кипячением в 2-пропаноле эквимолярных количеств этих альдегидов, 3-метил-5-аминопиразола и 2,2-диметил-1,3-диоксан-4,6-диона получены 3-метил-4-(1′,3′-диарилпиразол-4′-ил)тетрагидропиразоло[3,4-b]пиридин-6-оны. Выход целевых соединений – 48 – 75 %. Строение и состав всех синтезированных веществ доказаны данными 1Н ЯМР-, ИК-спектров и элементным анализом.Выводы. Установлено, что реакции 1,3-диарилзамещенных пиразол-4-карбальдегидов с 3-метил- 5-аминопиразолом и 2,2‑диметил-1,3-диоксан-4,6-дионом региоселективны и завершаются образованием 3,4-пиразоло[3,4-b]пиридоновых систем. Такая направленность процесса отвечает взаимодействию β-углеродного атома возможного интермедиата, образующегося на первой стадии из диоксандиона и альдегида, с углеродным нуклеофильным центром в молекуле аминоазола, а атома углерода С=О группы диоксан-4,6-диона – с экзоциклической аминогруппой гетериламина. Received: 13.01.2019Revised: 31.01.2020Accepted: 27.02.2020Мета. Синтезувати 1-феніл-3-(4-алкоксифеніл)піразол-4-карбальдегіди і встановити направленість їх взаємодії у трикомпонентній конденсації з 3-метил-5-амінопіразолом та 2,2-диметил-1,3-діоксан-4,6-діоном.Результати та їх обговорення. Синтезовано ряд 1-феніл-3-(4-алкоксифеніл)піразол-4-карбальдегідів формілюванням арилгідразонів за Вільсмейером–Хааком. Доміно-реакції цих альдегідів з 3-метил-5-амінопіразолом та 2,2-диметил-1,3-діоксан-4,6-діоном завершуються утворенням піразоло[3,4-b]піридонових систем.Експериментальна частина. Синтез 1-феніл-3-(4-алкоксифеніл)піразол-4-карбальдегідів здійснено формілюванням арилгідразонів в умовах реакції Вільсмейера–Хаака з виходом 55 – 88 %. Кип’ятінням у 2-пропанолі суміші еквімольних кількостей цих альдегідів, 3-метил-5-амінопіразолу та 2,2-диметил-1,3-діоксан-4,6-діону одержано 3-метил-4-(1',3'-діарилпіразол-4'-іл)тетрагідропіразоло[3,4-b]піридин-6-они. Вихід цільових сполук – 48 – 75 %. Структуру і склад усіх синтезованих речовин доведено даними 1Н ЯМР-, ІЧ-спектрів та елементним аналізом.Висновки. Встановлено, що реакції 1,3-діарилзаміщених піразол-4-карбальдегідів з 3-метил-5-амінопіразолом та 2,2‑диметил-1,3-діоксан-4,6-діоном є регіоселективними і завершуються утворенням виключно 3,4-піразоло[3,4-b]-піридин-6-онових систем. Така направленість процесу відповідає взаємодії β-вуглецевого атома ймовірного інтермедіату, який утворюється на першій стадії з діоксандіону та альдегіду, з вуглецевим нуклеофільним центром у молекулі аміноазолу, а атома вуглецю С=О групи діоксан-4,6-діону – з екзоциклічною аміногрупою гетериламіну. Received: 13.01.2019Revised: 31.01.2020Accepted: 27.02.202

Combination of searches for heavy spin-1 resonances using 139 fb−1 of proton-proton collision data at s = 13 TeV with the ATLAS detector

A combination of searches for new heavy spin-1 resonances decaying into different pairings of W, Z, or Higgs bosons, as well as directly into leptons or quarks, is presented. The data sample used corresponds to 139 fb−1 of proton-proton collisions at = 13 TeV collected during 2015–2018 with the ATLAS detector at the CERN Large Hadron Collider. Analyses selecting quark pairs (qq, bb, , and tb) or third-generation leptons (τν and ττ) are included in this kind of combination for the first time. A simplified model predicting a spin-1 heavy vector-boson triplet is used. Cross-section limits are set at the 95% confidence level and are compared with predictions for the benchmark model. These limits are also expressed in terms of constraints on couplings of the heavy vector-boson triplet to quarks, leptons, and the Higgs boson. The complementarity of the various analyses increases the sensitivity to new physics, and the resulting constraints are stronger than those from any individual analysis considered. The data exclude a heavy vector-boson triplet with mass below 5.8 TeV in a weakly coupled scenario, below 4.4 TeV in a strongly coupled scenario, and up to 1.5 TeV in the case of production via vector-boson fusion

Combination of searches for heavy spin-1 resonances using 139 fb−1 of proton-proton collision data at √s = 13 TeV with the ATLAS detector

A combination of searches for new heavy spin-1 resonances decaying into different pairings of W, Z, or Higgs bosons, as well as directly into leptons or quarks, is presented. The data sample used corresponds to 139 fb−1 of proton-proton collisions at √s = 13 TeV collected during 2015–2018 with the ATLAS detector at the CERN Large Hadron Collider. Analyses selecting quark pairs (qq, bb, tt¯, and tb) or third-generation leptons (τν and ττ) are included in this kind of combination for the first time. A simplified model predicting a spin-1 heavy vector-boson triplet is used. Cross-section limits are set at the 95% confidence level and are compared with predictions for the benchmark model. These limits are also expressed in terms of constraints on couplings of the heavy vector-boson triplet to quarks, leptons, and the Higgs boson. The complementarity of the various analyses increases the sensitivity to new physics, and the resulting constraints are stronger than those from any individual analysis considered. The data exclude a heavy vector-boson triplet with mass below 5.8 TeV in a weakly coupled scenario, below 4.4 TeV in a strongly coupled scenario, and up to 1.5 TeV in the case of production via vector-boson fusion

Combination of searches for heavy spin-1 resonances using 139 fb−1 of proton-proton collision data at √s = 13 TeV with the ATLAS detector

A combination of searches for new heavy spin-1 resonances decaying into diferent pairings of W, Z, or Higgs bosons, as well as directly into leptons or quarks, is presented. The data sample used corresponds to 139 fb−1 of proton-proton collisions at √s = 13 TeV collected during 2015–2018 with the ATLAS detector at the CERN Large Hadron Collider. Analyses selecting quark pairs (qq, bb, tt¯, and tb) or third-generation leptons (τν and τ τ ) are included in this kind of combination for the frst time. A simplifed model predicting a spin-1 heavy vector-boson triplet is used. Cross-section limits are set at the 95% confdence level and are compared with predictions for the benchmark model. These limits are also expressed in terms of constraints on couplings of the heavy vector-boson triplet to quarks, leptons, and the Higgs boson. The complementarity of the various analyses increases the sensitivity to new physics, and the resulting constraints are stronger than those from any individual analysis considered. The data exclude a heavy vector-boson triplet with mass below 5.8 TeV in a weakly coupled scenario, below 4.4 TeV in a strongly coupled scenario, and up to 1.5 TeV in the case of production via vector-boson fusion

Deciphering Auxin-Ethylene Crosstalk at a Systems Level

The auxin and ethylene pathways cooperatively regulate a variety of developmental processes in plants. Growth responses to ethylene are largely dependent on auxin, the key regulator of plant morphogenesis. Auxin, in turn, is capable of inducing ethylene biosynthesis and signaling, making the interaction of these hormones reciprocal. Recent studies discovered a number of molecular events underlying auxin-ethylene crosstalk. In this review, we summarize the results of fine-scale and large-scale experiments on the interactions between the auxin and ethylene pathways in Arabidopsis. We integrate knowledge on molecular crosstalk events, their tissue specificity, and associated phenotypic responses to decipher the crosstalk mechanisms at a systems level. We also discuss the prospects of applying systems biology approaches to study the mechanisms of crosstalk between plant hormones

metaRE R Package for Meta-Analysis of Transcriptome Data to Identify the cis-Regulatory Code behind the Transcriptional Reprogramming

At the molecular level, response to an external factor or an internal condition causes reprogramming of temporal and spatial transcription. When an organism undergoes physiological and/or morphological changes, several signaling pathways are activated simultaneously. Examples of such complex reactions are the response to temperature changes, dehydration, various biologically active substances, and others. A significant part of the regulatory ensemble in such complex reactions remains unidentified. We developed metaRE, an R package for the systematic search for cis-regulatory elements enriched in the promoters of the genes significantly changed their transcription in a complex reaction. metaRE mines multiple expression profiling datasets generated to test the same organism&rsquo;s response and identifies simple and composite cis-regulatory elements systematically associated with differential expression of genes. Here, we showed metaRE performance for the identification of low-temperature-responsive cis-regulatory code in Arabidopsis thaliana and Danio rerio. MetaRE identified potential binding sites for known as well as unknown cold response regulators. A notable part of cis-elements was found in both searches discovering great conservation in low-temperature responses between plants and animals