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En masse nascent transcription analysis to elucidate regulatory transcription factors.

ABSTRACT: Despite exhaustively informing about steady-state mRNA abundance, DNA microarrays have been used with limited success to identify regulatory transcription factors (TFs). The main limitation of this approach is that altered mRNA stability also strongly governs the patterns of expressed genes. Here, we used nuclear run-on assays and microarrays to systematically interrogate changes in nascent transcription in cells treated with the topoisomerase inhibitor camptothecin (CPT). Analysis of the promoters of coordinately transcribed genes after CPT treatment suggested the involvement of TFs c-Myb and Rfx1. The predicted CPT-dependent associations were subsequently confirmed by chromatin immunoprecipitation assays. Importantly, after RNAi-mediated knockdown of each TF, the CPT-elicited induction of c-Myb- and/or Rfx1-regulated mRNAs was diminished and the overall cellular response was impaired. The strategies described here permit the successful identification of the TFs responsible for implementing adaptive gene expression programs in response to cellular stimulation.

SUBMITTER: Fan J

PROVIDER: S-EPMC1408309 | biostudies-literature | 2006

REPOSITORIES: biostudies-literature

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En masse nascent transcription analysis to elucidate regulatory transcription factors.

Fan Jinshui J Zhan Ming M Shen Jikui J Martindale Jennifer L JL Yang Xiaoling X Kawai Tomoko T Gorospe Myriam M

Nucleic acids research 20060315 5

Despite exhaustively informing about steady-state mRNA abundance, DNA microarrays have been used with limited success to identify regulatory transcription factors (TFs). The main limitation of this approach is that altered mRNA stability also strongly governs the patterns of expressed genes. Here, we used nuclear run-on assays and microarrays to systematically interrogate changes in nascent transcription in cells treated with the topoisomerase inhibitor camptothecin (CPT). Analysis of the promot ...[more]

PMID: 16540593

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Project description:Background/aimRetraction of the upper incisors/canines requires maximum anchorage. The aim of the present study was to analyze the efficacy of mini implants in comparison to conventional devices in patients with need for en masse retraction of the front teeth in the upper jaw.Material and methodsAn electronic search of PubMed, Web of Science, and EMBASE and hand searching were performed. Relevant articles were assessed, and data were extracted for statistical analysis. A random effects model, weighted mean differences (WMD), and 95% confidence intervals (CI) were computed for horizontal and vertical anchorage loss at the first molars in the analyzed patient treatments.ResultsA total of seven RCTs employing direct anchorage through implants in the alveolar ridge were finally considered for qualitative and quantitative analysis, and further five publications were considered for the qualitative analysis only (three studies: indirect anchorage through implant in the mid-palate, two studies: direct/indirect anchorage in the alveolar ridge). In the control groups, anchorage was achieved through transpalatal arches, headgear, Nance buttons, intrusion arches, and differential moments. WMD [95% CI, p] in anchorage loss between test and control groups amounted to - 2.79 mm [- 3.56 to - 2.03 mm, p < 0.001] in the horizontal and - 1.76 mm [- 2.56 to - 0.97, p < 0.001] favoring skeletal anchorage over control measures. The qualitative analysis revealed that minor anchorage loss can be associated with indirect anchorage, whereas anchorage gain was commonly associated with direct anchorage. Implant failures were comparable for both anchorage modalities (direct 9.9%, indirect 8.6%).ConclusionWithin its limitations, the meta-analysis revealed that maximum anchorage en masse retraction can be achieved by orthodontic mini implants and direct anchorage; however, the ideal implant location (palate versus alveolar ridge) and the beneficial effect of direct over indirect anchorage needs to be further evaluated.

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En masse nascent transcription analysis to elucidate regulatory transcription factors.

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En masse nascent transcription analysis to elucidate regulatory transcription factors.

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