Elongation and premature termination of transcripts initiated from c-fos and c-myc promoters show dissimilar patterns

RNA polymerase II seems to be prone to stop at intrinsic pause sites, thus introducing a further potential level of regulation. It was recently shown that RNA polymerase II was held at the P2 promoter of c-myc gene. We confirmed the presence of engaged polymerases in the murine fibroblastic Ltk- and pre-B lymphoid 70Z3 cell lines. High resolution run-on analysis and in vivo permanganate-dependent footprinting showed that this holds true for the c-fos gene in unstimulated cells where a strong block to transcription elongation was evidenced. In contrast to what was observed in the c-myc gene, an even more intense signal was observed in run-on experiments downstream to the promoter, on a c-fos oligonucleotide including position +385 where an in vitro transcription arrest site was previously mapped. Genomic footprinting of DNA from intact cells and isolated nuclei confirmed the involvement of several thymidines belonging to a T-rich stretch in a melted region which was not detected upon polymerase release. In order to observe a short abortive c-fos transcript accumulating in vivo we resorted to microinjection of c-fos templates in Xenopus oocytes where transcripts were stable

Root calcretes and uranium-bearing silcretes at sedimentary discontinuities in the miocene of the Madrid Basin (Toledo, Spain)

This paper reports a detailed study of the calcrete and silcrete profiles in the Miocene detrital deposits in the western area of Madrid, at the boundary of two main sedimentary units. The aims of this work were to better understand the pedogenic and diagenetic environments in which these profiles formed and to determine the cause(s) of their enrichment in uranium. Calcrete and silcrete duricrusts are characteristic features of closed continental basins in semiarid climates; this paper discusses the significance of duricrusts as indicators of important change in such basins.The detailed macromorphological, micromorphological, and geochemical study of three duricrust profiles revealed the sequence of pedogenic, vadose, and groundwater processes responsible for their formation. During the first stage of their development, carbonate laminae formed a white “grill-like” structure within the detrital parent materials. The microstructure and macrostructure of the carbonate, which includes alveolar septal structures and needle-fiber calcite, indicates the important role of roots and their associated microorganisms in calcrete formation. Early silicification occurred in the pedogenic-vadose environment affecting the detrital parent material, roots, and calcretes, forming an early silcrete defined by opaline glaebules and silica rhizoliths. The detailed preservation of the cells in the silicified roots denotes the early replacement of root organic matter.The green or green-yellowish fluorescence of the silicified root structures under short-wavelength UV shows their preferential enrichment in uranium. Calcitization and silicification coexisted in the pedogenic vadose environment, leading to several reversible replacements of calcite and silica. Later, the rise of the water table promoted silicification under phreatic conditions, as indicated by the good preservation of the texture of the detrital host rocks and calcretes. Other silcrete textures, such as ovoidal opaline accumulations, intraclasts produced by autobrecchification, and vadose silica cements, indicate later vadose environments, and consequently variations in the water table.The geochemical features of the calcretes and silcretes (major, minor, and rare earth elements) were inherited from their parent materials. The rare-earth-element patterns of some silcretes show them to have a positive Ce anomaly, suggesting that oxidizing conditions reigned during their formation. The good correlation between silica and uranium suggests that the silica phases acquired uranium through the direct silicification of roots that had fixed uranium from organic matter.This study shows that calcrete–silcrete duricrusts provide detailed information regarding the processes occurring in semiarid continental basins. In the studied basin, roots played a key role in both the development of the duricrust profiles and their enrichment in uranium. These duricrusts provide important information for understanding the overall stratigraphy of the studied basin and its large-scale sequential evolution

Hydromorphological response and fluvial management influence during a Mediterranean flood event (Aude Watershed, France)

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Cyclin A expression is under negative transcriptional control during the cell cycle

International audienceTranscription of the gene coding for cyclin A, a protein required for S-phase transit, is cell cycle regulated and is restricted to proliferating cells. To further explore transcriptional regulation linked to cell division cycle control, a genomic clone containing 5' flanking sequences of the murine cyclin A gene was isolated. When it was fused to a luciferase reporter gene, it was shown to function as a proliferation-regulated promoter in NIH 3T3 cells. Transcription of the mouse cyclin A gene is negatively regulated by arrest of cell proliferation. A mutation of a GC-rich sequence conserved between mice and humans is sufficient to relieve transcriptional repression, resulting in a promoter with constitutively high activity. In agreement with this result, in vivo footprinting reveals a protection of the cell cycle-responsive element in G0/early G1 cells which is not observed at later stages of the cell cycle. Moreover, the footprint is present in dimethyl sulfoxide-induced differentiating and not in proliferating Friend erythroleukemia cells. Conversely, two other sites, which in vitro bind ATF-1 and NF-Y, respectively, are constitutively occupied throughout cell cycle progression

In vivo footprints between the murine c-myc P1 and P2 promoters.

International audienceAssuming that when transcription starts at the P2 promoter of the c-myc gene sites located immediately upstream from P2 are occupied whereas in the absence of initiation they are not, the polymerase chain reaction (PCR)-based method of Mueller & Wold [(1989). Science, 246, 780-786] was used to map in vivo footprints upstream from the P2 promoter in various mouse cell lines. In cultured Friend erythroleukemic cells induced to differentiate with dimethysulfoxide (DMSO), a clear protection corresponding to ME1a2 and E2F sites was observed, consistent with in vitro band-shift and footprint data. However, in cell lines in which the gene was either silent or truncated the footprints were no longer visible. Friend c-myc transcripts decreased to a barely detectable level after 3 h of DMSO treatment. Transcription, as measured by in vitro run-on, was turned off at the level of RNA polymerase elongation rather than initiation [Mechti N., Piechaczyk, M. Blanchard, J.-M., Marty, L., Bonnieu, A., Jeanteur, Ph. & Lebler, B. (1986). Nucleic Acids Res., 24, 9653-9666]. The state of occupancy of the sites did not vary from the first hours up to 9 days of DMSO treatment, suggesting that DNA occupancy per se cannot explain premature termination, which rather would involve a more complex phenomenon

In vivo footprints between the murine c-myc P1 and P2 promoters

International audienc

In vivo footprints between the murine c-myc P1 and P2 promoters.

International audienceAssuming that when transcription starts at the P2 promoter of the c-myc gene sites located immediately upstream from P2 are occupied whereas in the absence of initiation they are not, the polymerase chain reaction (PCR)-based method of Mueller & Wold [(1989). Science, 246, 780-786] was used to map in vivo footprints upstream from the P2 promoter in various mouse cell lines. In cultured Friend erythroleukemic cells induced to differentiate with dimethysulfoxide (DMSO), a clear protection corresponding to ME1a2 and E2F sites was observed, consistent with in vitro band-shift and footprint data. However, in cell lines in which the gene was either silent or truncated the footprints were no longer visible. Friend c-myc transcripts decreased to a barely detectable level after 3 h of DMSO treatment. Transcription, as measured by in vitro run-on, was turned off at the level of RNA polymerase elongation rather than initiation [Mechti N., Piechaczyk, M. Blanchard, J.-M., Marty, L., Bonnieu, A., Jeanteur, Ph. & Lebler, B. (1986). Nucleic Acids Res., 24, 9653-9666]. The state of occupancy of the sites did not vary from the first hours up to 9 days of DMSO treatment, suggesting that DNA occupancy per se cannot explain premature termination, which rather would involve a more complex phenomenon