01445nas a2200145   4500008004100000020004600041245009100087210006900178300001200247490000900259520092600268100002201194700001501216856006801231       2017                        eng d  a1940-6029 (Electronic)1064-3745 (Linking)00aDNase I SIM: A Simplified In-Nucleus Method for DNase I Hypersensitive Site Sequencing0 aDNase I SIM A Simplified InNucleus Method for DNase I Hypersensi  a141-1540 v16293 a<p>Identifying cis-regulatory elements is critical in understanding the direct and indirect interactions that occur within gene regulatory networks. Current approaches include DNase-seq, a technique that combines sensitivity to the nonspecific endonuclease DNase I with high-throughput sequencing to identify regions of regulatory DNA on a genome-wide scale. Yet, challenges still remain in processing recalcitrant tissues that have low DNA content. Here, we describe DNase I SIM (for Simplified In-nucleus Method), a protocol that simplifies and facilitates generation of DNase-seq libraries from plant tissues for high-resolution mapping of DNase I hypersensitive sites. By removing steps requiring the use of gel agarose plugs in DNase-seq, DNase I SIM reduces the time required to perform the protocol by at least 2 days, while also making possible the processing of difficult plant tissues including plant roots.</p>1 aFilichkin, S., A.1 aMegraw, M.  uhttps://link.springer.com/protocol/10.1007/978-1-4939-7125-1_1002614nas a2200517   4500008004100000020004600041245014500087210006900232260001200301300001200313490000700325520091000332653004701242653005901289653002401348653003801372653002901410653001701439653002001456653002101476653002001497653003601517653003301553653003001586653004301616653004101659653004801700653003301748100001901781700001501800700001801815700001101833700001801844700001301862700002001875700001401895700001401909700002101923700001401944700002201958700001501980700001501995700001802010700001902028856004902047       2016                        eng d  a1878-1551 (Electronic)1534-5807 (Linking)00aEstablishment of Expression in the SHORTROOT-SCARECROW Transcriptional Cascade through Opposing Activities of Both Activators and Repressors0 aEstablishment of Expression in the SHORTROOTSCARECROW Transcript  c12/2016  a585-5960 v393 a<p>Tissue-specific gene expression is often thought to arise from spatially restricted transcriptional cascades. However, it is unclear how expression is established at the top of these cascades in the absence of pre-existing specificity. We generated a transcriptional network to explore how transcription factor expression is established in the Arabidopsis thaliana root ground tissue. Regulators of the SHORTROOT-SCARECROW transcriptional cascade were validated in planta. At the top of this cascade, we identified both activators and repressors of SHORTROOT. The aggregate spatial expression of these regulators is not sufficient to predict transcriptional specificity. Instead, modeling, transcriptional reporters, and synthetic promoters support a mechanism whereby expression at the top of the SHORTROOT-SCARECROW cascade is established through opposing activities of activators and repressors.</p>10aArabidopsis Proteins/ genetics/ metabolism10aArabidopsis/ genetics/growth & development/ metabolism10aComputer Simulation10aGene Expression Regulation, Plant10aGene Regulatory Networks10aGenes, Plant10aGenes, Reporter10aGenes, Synthetic10aModels, Genetic10aPlant Roots/cytology/metabolism10aPlants, Genetically Modified10aPromoter Regions, Genetic10aRepressor Proteins/genetics/metabolism10aTrans-Activators/genetics/metabolism10aTranscription Factors/ genetics/ metabolism10aTwo-Hybrid System Techniques1 aSparks, E., E.1 aDrapek, C.1 aGaudinier, A.1 aLi, S.1 aAnsariola, M.1 aShen, N.1 aHennacy, J., H.1 aZhang, J.1 aTurco, G.1 aPetricka, J., J.1 aForet, J.1 aHartemink, A., J.1 aGordan, R.1 aMegraw, M.1 aBrady, S., M.1 aBenfey, P., N.  uhttps://doi.org/10.1016/j.devcel.2016.09.031