Project description:Genome-wide probing of nascent RNA structure in eukaryotes reveals dynamics of cotranscriptional folding and its anticorrelation with spontaneous mutation rate of DNA
Project description:RPA12 is a subunit of RNA polymerase I. We used microarrays to know the effect RPA12 deltion in lipid metabolism and identified distinct classes of up-regulated genes during this process.
Project description:In eukaryotes, three of the four ribosomal RNAs (rRNAs), the 5.8S, 18S and 25S/28S rRNAs, are processed from a single pre-rRNA transcript and assembled into ribosomes. The fourth rRNA, the 5S rRNA, is transcribed by RNA polymerase III and is assembled into the 5S ribonucleoprotein particle (5S RNP), containing ribosomal proteins Rpl5/uL18 and Rpl11/uL5, prior to its incorporation into pre-ribosomes. In mammals the 5S RNP is also central regulator of the homeostasis of the tumour suppressor p53. The nucleolar localisation of the 5S RNP and its assembly into pre-ribosomes is performed by a specialised complex composed of Rpf2 and Rrs1 in yeast or Bxdc1 and hRrs1 in humans. Here we report the structural and functional characterisation of the Rpf2-Rrs1 complex alone, in complex with the 5S RNA and within pre-60S ribosomes. We show that the Rpf2-Rrs1 complex contains a specialised 5S RNA E loop binding module, contacts the Rpl5 protein and also contacts the ribosome assembly factor Rsa4 and the 25S RNA. We propose that the Rpf2-Rrs1 complex establishes a network of interactions that guide the incorporation of the 5S RNP in pre-ribosomes in the initial conformation prior to its rotation to form the central protuberance found in the mature large ribosomal subunit.
Project description:Native elongating transcript sequencing (NET-seq), nascnet RNA-seq, and total RNA-seq of wild type and RNA polymerase II C-terminal domain mutants and ChIP-nexus of RNA polymerase II C-terminal domains phosphoisoforms and splicing factors in S. cerevisiae