Sequence and epigenetic landscapes of active and silent nucleolus organizer regions in .

has two ribosomal RNA (rRNA) gene loci, nucleolus organizer regions and , whose complete sequences are missing in current genome assemblies. Ultralong DNA sequences assembled using an unconventional approach yielded ~5.5- and 3.

Reaching for the off switch in nucleolar dominance.

Nucleolus organizer regions (NORs) are eukaryotic chromosomal loci where ribosomal RNA (rRNA) genes are clustered, typically in hundreds to thousands of copies. Transcription of these rRNA genes by RNA polymerase I and processing of their transcripts results in the formation of the nucleolus, the sub-nuclear domain in which ribosomes are assembled. Approximately 90 years ago, cytogenetic observations revealed that NORs inherited from the different parents of an interspecific hybrid sometimes differ in morphology at metaphase.

Complete Genome Sequence of Rhodopseudomonas palustris CGA0092 and Corrections to the R. palustris CGA009 Genome Sequence.

Rhodopseudomonas palustris CGA009 is a versatile model purple nonsulfur bacterium used for both fundamental and applied research. Here, we present a new genome sequence for the derivative strain CGA0092. We further present an improved CGA009 genome assembly that differs from the original CGA009 sequence at three positions.

Targeted Enrichment of rRNA Gene Tandem Arrays for Ultra-Long Sequencing by Selective Restriction Endonuclease Digestion.

Large regions of nearly identical repeats, such as the 45S ribosomal RNA (rRNA) genes of Nucleolus Organizer Regions (NORs), can account for major gaps in sequenced genomes. To assemble these regions, ultra-long sequencing reads that span multiple repeats have the potential to reveal sets of repeats that collectively have sufficient sequence variation to unambiguously define that interval and recognize overlapping reads. Because individual repetitive loci typically represent a small proportion of the genome, methods to enrich for the regions of interest are desirable.

Functional Dissection of the Pol V Largest Subunit CTD in RNA-Directed DNA Methylation.

Plant multisubunit RNA polymerase V (Pol V) transcription recruits Argonaute-small interfering RNA (siRNA) complexes that specify sites of RNA-directed DNA methylation (RdDM) for gene silencing. Pol V's largest subunit, NRPE1, evolved from the largest subunit of Pol II but has a distinctive C-terminal domain (CTD). We show that the Pol V CTD is dispensable for catalytic activity in vitro yet essential in vivo.

Genome-Wide Analysis of Nascent Transcription in Saccharomyces cerevisiae.

The assessment of transcriptional regulation requires a genome-wide survey of active RNA polymerases. Thus, we combined the nuclear run-on assay, which labels and captures nascent transcripts, with high-throughput DNA sequencing to examine transcriptional activity in exponentially growing Saccharomyces cerevisiae. Sequence read data from these nuclear run-on libraries revealed that transcriptional regulation in yeast occurs not only at the level of RNA polymerase recruitment to promoters but also at postrecruitment steps.

Global analysis of RNA oxidation in Saccharomyces cerevisiae.

Oxidative RNA damage has been linked to loss of RNA function and to the development of many human age-related diseases. Consequently, a need exists for methods to identify and quantify the extent of RNA oxidation on a genome-wide basis. We developed such a method by combining affinity selection of mRNA containing 8-hydroxyguanine with high throughput DNA sequencing.

A genomic perspective on the potential of Actinobacillus succinogenes for industrial succinate production.

Background: Succinate is produced petrochemically from maleic anhydride to satisfy a small specialty chemical market. If succinate could be produced fermentatively at a price competitive with that of maleic anhydride, though, it could replace maleic anhydride as the precursor of many bulk chemicals, transforming a multi-billion dollar petrochemical market into one based on renewable resources. Actinobacillus succinogenes naturally converts sugars and CO2 into high concentrations of succinic acid as part of a mixed-acid fermentation.

Interaction of an atypical Plasmodium falciparum ETRAMP with human apolipoproteins.

Background: In order to establish a successful infection in the human host, the malaria parasite Plasmodium falciparum must establish interactions with a variety of human proteins on the surface of different cell types, as well as with proteins inside the host cells. To better understand this aspect of malaria pathogenesis, a study was conducted with the goal of identifying interactions between proteins of the parasite and those of its human host.

Methods: A modified yeast two-hybrid methodology that preferentially selects protein fragments that can be expressed in yeast was used to conduct high-throughput screens with P.