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The human and mouse genomes share a number of long, perfectly conserved nucleotide sequences, termed ultraconserved elements. Whereas these regions can act as transcriptional enhancers when upstream of genes, those within genes are less well understood. In particular, the function of ultraconserved elements that overlap alternatively spliced exons of genes(More)
La is a conserved eukaryotic RNA-binding protein best known for its role in the biogenesis of noncoding RNAs transcribed by RNA polymerase III. To broaden our understanding of the function of the La homologous protein (Lhp1) in Saccharomyces cerevisiae, we have taken a genomics approach. Lhp1 ribonucleoprotein complexes were immunoprecipitated and bound(More)
I. Supplementary methods and results ........................................................................S1 II. Supplementary figures (5) .......................................................................................S7 III. Supplementary tables (5)........................................................................................S12 IV.(More)
Pre-mRNA processing is an essential control-point in the gene expression pathway of eukaryotic organisms. The budding yeast Saccharomyces cerevisiae offers a powerful opportunity to examine the regulation of this pathway. In this chapter, we will describe methods that have been developed in our lab and others to examine pre-mRNA splicing from a genome-wide(More)
The characterization of DNA replication origins in yeast has shed much light on the mechanisms of initiation of DNA replication. However, very little is known about the evolution of origins or the evolution of mechanisms through which origins are recognized by the initiation machinery. This lack of understanding is largely due to the vast evolutionary(More)
SR proteins play critical roles in the regulation of pre-mRNA splicing. We show that most human SR protein genes are themselves alternatively spliced, and their alternative splice forms are often targets of a degradation pathway known as nonsense-mediated mRNA decay (NMD). By mining EST databases for sequences corresponding to the 11 human SR protein genes,(More)
J proteins are structurally diverse, obligatory cochaperones of Hsp70s, each with a highly conserved J domain that plays a critical role in the stimulation of Hsp70's ATPase activity. The essential protein, Cwc23, is one of 13 J proteins found in the cytosol and/or nucleus of Saccharomyces cerevisiae. We report that a partial loss-of-function CWC23 mutant(More)
Eukaryotic gene expression requires that RNA Polymerase II (RNAP II) gain access to DNA in the context of chromatin. The C-terminal domain (CTD) of RNAP II recruits chromatin modifying enzymes to promoters, allowing for transcription initiation or repression. Specific CTD phosphorylation marks facilitate recruitment of chromatin modifiers, transcriptional(More)
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