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The formation of R-loops is a natural consequence of the transcription process, caused by invasion of the DNA duplex by nascent transcripts. These structures have been considered rare transcriptional by-products with potentially harmful effects on genome integrity owing to the fragility of the displaced DNA coding strand. However, R-loops may also possess(More)
We demonstrate that distinct forms of the yeast chromatin-remodeling enzyme Isw1p sequentially regulate each stage of the transcription cycle. The Isw1a complex (Iswlp/Ioc3p) represses gene expression at initiation through specific positioning of a promoter proximal dinucleosome, whereas the Isw1b complex (Iswlp/Ioc2p/Ioc4p) acts within coding regions to(More)
Roles for long noncoding RNAs (lncRNAs) in gene expression are emerging, but regulation of the lncRNA itself is poorly understood. We have identified a homeodomain protein, AtNDX, that regulates COOLAIR, a set of antisense transcripts originating from the 3' end of Arabidopsis FLOWERING LOCUS C (FLC). AtNDX associates with single-stranded DNA rather than(More)
Transcriptional termination of mammalian RNA polymerase II (Pol II) is an essential but little-understood step in protein-coding gene expression. Mechanistically, termination by all DNA-dependent RNA polymerases can be reduced to two steps, namely release of the RNA transcript and release of the DNA template. Using a simple nuclear fractionation procedure,(More)
The finding that the metazoan hypoxic response is regulated by oxygen-dependent posttranslational hydroxylations, which regulate the activity and lifetime of hypoxia-inducible factor (HIF), has raised the question of whether other hydroxylases are involved in the regulation of gene expression. We reveal that the splicing factor U2 small nuclear(More)
Transcriptional termination of mammalian RNA polymerase II (Pol II) requires a poly(A) (pA) signal and, often, a downstream terminator sequence. Termination is triggered following recognition of the pA signal by Pol II and subsequent pre-mRNA cleavage, which occurs either at the pA site or in transcripts from terminator elements. Although this process has(More)
splicing. Instead it can effectively be considered a regulator of the poly(A) signal. The associated U1SnRNP may Sir William Dunn School of Pathology Chemical Pathology Unit in this context act as a poly(A) factor rather than splicing factor. Furthermore U1SnRNP has been shown to cross-University of Oxford South Parks Road link with poly(A) signals and may(More)
The elongation phase of transcription by RNA polymerase II (RNAPII) is highly regulated and tightly linked to pre-messenger RNA (pre-mRNA) processing. Recent studies have implicated an early elongation checkpoint that facilitates the link to pre-mRNA processing. Here we show that the yeast forkhead transcription factors, Fkh1p and Fkh2p, associate with the(More)
Given a matroid M represented by a linear subspace L ⊂ C n (equivalently by an arrangement of n hyperplanes in L), we define a graded ring R(L) which degenerates to the Stanley-Reisner ring of the broken circuit complex for any choice of ordering of the ground set. In particular, R(L) is Cohen-Macaulay, and may be used to compute the h-vector of the broken(More)