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Abstract: The global transcriptional profile during the first 4 weeks of treatment with pegylated interferon alfa (PEG-IFN-α) therapy for chronic hepatitis C (CHC) was evaluated. cDNA array technology was used to assess expression of 10,918 human genes in peripheral blood cells obtained from 17 CHC patients at days 0, 7, and 28 following treatment with PEG-IFN-α and ribavirin. Hierarchical average linkage clustering identified seven temporal profiles of differential expression comprising 148 genes. Gene expression profiles were comparable between the PEG-IFN-α-2a and PEG-IFN-α-2b therapy. Genes representing a broad range of molecular functions were differentially regulated with distinct temporal patterns of expression. The initial global response to interferon treatment appears to be a net up-regulation of genes, consistent with gene responses identified previously in vitro, though by 4 weeks an overall down-regulation of genes was observed. Novel transcription factors potentially involved in secondary gene regulation cascades, a potential dsRNA receptor and members of the ubiquitin signaling, including a novel predicted deubiquitinating peptidase were all identified as being up-regulated upon treatment with IFN. The overall findings provide new light on possible physiological effects of IFN-α and open new lines of investigations on the mode of action of PEG-IFN-α combination therapy. [Copyright &y& Elsevier]

We have determined the extent of the primary transcription unit for the two highly expressed genes nmt1 and nmt2 of Schizosaccharomyces pombe. Transcription run-on analysis in permeabilized yeast cells was employed to map polymerase density across the 3′-flanking region of these two genes. Surprisingly, polymerases were detected 4.3 kb beyond the nmt1 polyadenylation [poly(A)] site and 2.4 kb beyond the nmt2 poly(A) site, which in each case have transcribed through an entire convergent downstream transcription unit. However, the steady-state levels of both downstream genes were unaffected by the high level of nmt1 or nmt2 nascent transcription. Analysis of nmt1 and nmt2 RNA 3′ end formation signals indicates that efficient termination of transcription requires not only a poly(A) signal but also additional pause elements. The absence of such pause elements close to the poly(A) sites of these genes may account for their extended nascent transcripts. [ABSTRACT FROM AUTHOR]

Transcription ‘run-on’ (TRO) analysis using permeabilized yeast cells indicates that transcription terminates between 180 and 380 bp downstream of the poly(A) site of the Schizosaccharomyces pombe ura4 gene. Two signals direct RNA polymerase II (pol II) to stop transcription: the previously identified 3′ end formation signals located close to the poly(A) site and an additional downstream element (DSE) located at the region of termination. The downstream signal (135 bp) appears to act by pausing the elongating polymerase. TRO analysis indicates that elevated levels of transcribing polymerases accumulate over the DSE and that removal of this signal leads to transcription proceeding beyond the normal termination region. Furthermore, when inserted between two competing polyadenylation signals, this DSE increases the utilization of upstream poly(A) sites in vivo. We show that polymerase pausing over an extended region of template ensures termination of pol II transcription close to the poly(A) site. [ABSTRACT FROM AUTHOR]