Spt6 directly interacts with Cdc73 and is required for Paf1 complex occupancy at active genes in Saccharomyces cerevisiae.

The Paf1 complex (Paf1C) is a conserved transcription elongation factor that regulates transcription elongation efficiency, facilitates co-transcriptional histone modifications, and impacts molecular processes linked to RNA synthesis, such as polyA site selection. Coupling of the activities of Paf1C to transcription elongation requires its association with RNA polymerase II (Pol II). Mutational studies in yeast identified Paf1C subunits Cdc73 and Rtf1 as important mediators of Paf1C association with Pol II on active genes.

Immunologic risk stratification of pediatric heart transplant patients by combining HLAMatchmaker and PIRCHE-II.

Background: Molecular-level human leukocyte antigen (HLA) mismatch is a powerful biomarker of rejection; however, few studies have explored its use in heart transplant recipients, and none have attempted to use the results of separate algorithms synergistically. Here we tested the hypothesis that a combination of HLAMatchmaker and Predicted Indirectly Recognizable HLA Epitopes (PIRCHE-II) can be used to identify more patients at low risk of rejection.

Methods: We studied 274 recipient/donor pairs enrolled in the Clinical Trials in Organ Transplantation in Children (CTOTC) performing class I and II HLA genotyping by next-generation sequencing to determine eplet mismatch (epMM) load and PIRCHE-II score.

Opposing functions of the Hda1 complex and histone H2B mono-ubiquitylation in regulating cryptic transcription in Saccharomyces cerevisiae.

Maintenance of chromatin structure under the disruptive force of transcription requires cooperation among numerous regulatory factors. Histone post-translational modifications can regulate nucleosome stability and influence the disassembly and reassembly of nucleosomes during transcription elongation. The Paf1 transcription elongation complex, Paf1C, is required for several transcription-coupled histone modifications, including the mono-ubiquitylation of H2B.

The nucleosome DNA entry-exit site is important for transcription termination and prevention of pervasive transcription.

Compared to other stages in the RNA polymerase II transcription cycle, the role of chromatin in transcription termination is poorly understood. We performed a genetic screen in to identify histone mutants that exhibit transcriptional readthrough of terminators. Amino acid substitutions identified by the screen map to the nucleosome DNA entry-exit site.

Complex Genetics in Pancreatitis: Insights Gained From a New Candidate Locus Panel.

Objectives: Chronic pancreatitis is the end stage of a pathologic inflammatory syndrome with multiple etiological factors, including genetic. We hypothesized that some pancreatitis etiology originates in pancreatic acinar or duct cells and requires both injury and compensatory mechanism failure.

Methods: One hundred pancreatitis patients were assessed using a DNA sequencing panel for pancreatitis.

MutantHuntWGS: A Pipeline for Identifying Mutations.

MutantHuntWGS is a user-friendly pipeline for analyzing whole-genome sequencing data. It uses available open-source programs to: (1) perform sequence alignments for paired and single-end reads, (2) call variants, and (3) predict variant effect and severity. MutantHuntWGS outputs a shortlist of variants while also enabling access to all intermediate files.

The Paf1 Complex Broadly Impacts the Transcriptome of .

The Polymerase Associated Factor 1 complex (Paf1C) is a multifunctional regulator of eukaryotic gene expression important for the coordination of transcription with chromatin modification and post-transcriptional processes. In this study, we investigated the extent to which the functions of Paf1C combine to regulate the transcriptome. While previous studies focused on the roles of Paf1C in controlling mRNA levels, here, we took advantage of a genetic background that enriches for unstable transcripts, and demonstrate that deletion of affects all classes of Pol II transcripts including multiple classes of noncoding RNAs (ncRNAs).

Salinity stress results in differential Hsp70 expression in the Exaiptasia pallida and Symbiodinium symbiosis.

Abiotic factors affect cnidarian-algal symbiosis and, if severe enough, can result in bleaching. Increased temperature and light are well characterized causes of bleaching, but other factors like salinity can also stress the holobiont. In cnidarian-dinoflagellate systems, the expression of host genes, including heat shock protein 70 (Hsp70), changes due to thermal and light stress.

In situ hybridization for the detection of rust fungi in paraffin embedded plant tissue sections.

Background: Rust fungi are obligate pathogens with multiple life stages often including different spore types and multiple plant hosts. While individual rust pathogens are often associated with specific plants, a wide range of plant species are infected with rust fungi. To study the interactions between these important pathogenic fungi and their host plants, one must be able to differentiate fungal tissue from plant tissue.