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DTSTART;TZID=America/Los_Angeles:20260921T113000
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DTSTAMP:20260914T191617Z
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SUMMARY:Headrick\, C. (BMEB) - The Regulation of mRNA Cleavage in Nonsense-mediated mRNA Decay: From Inside (intra-pathway determinants) Out (extra-pathway regulation)
DESCRIPTION:Nonsense-mediated mRNA decay (NMD) is a translation-coupled quality control pathway that degrades mRNAs that harbor a premature termination codon (PTC) and 5-30% of normal cellular mRNAs. The NMD field sits at a pivotal moment with recent developments that endonucleolytic cleavage is the primary mechanism of mRNA decay conserved across metazoans. Discovery of a conserved NMD cleavage mechanism sets the stage for a dissection of mRNA cleavage determinants and regulators. \nTo better understand how mRNA cleavage during NMD is regulated\, I will use degradome-seq based approaches via 5’RACE-seq (Rapid Amplification of 5’ cDNA Ends) to isolate the cleavage products of the NMD pathway. I will first focus my analysis on core NMD factors and helicase UPF1\, the binding site of NMD decay effectors\, to examine how UPF1 enzymatic activity affects mRNA cleavage transcriptome-wide (Aim 1). In parallel\, to assess extra-pathway regulation of mRNA cleavage during NMD\, I will identify endogenous negative regulators of mRNA cleavage (Aim 2). Contemporary models of NMD are deprived of the functional impact of cellular NMD inhibitors. I will access this novel functional space with an innovative application of CRISPR screening and quantitative\, high-throughput NGS\, known as ReLiC (RNA-linked CRISPR) paired with degradome analysis. \n  \nEvent Host: Camille Headrick\, Ph.D. Student\, Biomolecular Engineering & Bioinformatics  \nAdvisor: Joshua Arribere \n 
URL:https://events.ucsc.edu/event/headrick-c-bmeb-the-regulation-of-mrna-cleavage-in-nonsense-mediated-mrna-decay-from-inside-intra-pathway-determinants-out-extra-pathway-regulation/
LOCATION:Biomedical Sciences Building\, 575 McLaughlin Drive
CATEGORIES:Ph.D. Presentations
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DTSTART;TZID=America/Los_Angeles:20260925T130000
DTEND;TZID=America/Los_Angeles:20260925T150000
DTSTAMP:20260911T151906Z
CREATED:20260911T151906Z
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SUMMARY:Mastoras\, M. (BMEB) - Polishing genome assemblies and leveraging their improved quality to study centromere variation
DESCRIPTION:A complete and accurate genome reconstruction serves as the foundation for studying an organism’s biology and the mechanisms underlying disease. It is particularly critical for reference genomes\, which provide a universal coordinate system for downstream genomic analysis. Errors or missing sequences in a reference genome create bias in all of the studies built on top of them. The Human Pangenome Reference Consortium (HPRC) seeks to address this bias by transitioning the field to a pangenome reference\, a graph based collection of many genome assemblies\, providing a better representation of variation in the human population. Removing errors in the HPRC assemblies is critical to ensure the pangenome serves as a robust standard for genomic variant discovery. In the first part of my thesis\, I improve the base level accuracy of the HPRC release 2 assemblies (HPRC2) with a machine learning model for assembly polishing called DeepPolisher. Next\, I make additional contributions to reference-based genomic analysis by polishing reference genomes of other model organisms\, and helping to develop a new method for de-novo assembly and variant calling from a single-flow cell nanopore sequencing protocol. Finally\, I take advantage of the highly accurate\, near complete assemblies from HPRC2 that I improved with DeepPolisher to study a region only recently made accessible to genomics analysis: the human centromere. I apply the tool Centrolign\, the first ever multiple-sequence-aligner for centromeres to the HPRC2 assemblies\, establishing precise estimates of mutation rates and spatial variation patterns across centromeric arrays. \nEvent Host: Mira Mastoras\, Ph.D. Candidate\, Biomolecular Engineering & Bioinformatics \nAdvisor: Benedict Paten \nZoom: https://ucsc.zoom.us/j/98960011053?pwd=mFKCwtSIhvT5FvEURbE85lRbbMvzuo.1 \nPasscode: 118488
URL:https://events.ucsc.edu/event/mastoras-m-bmeb-polishing-genome-assemblies-and-leveraging-their-improved-quality-to-study-centromere-variation/
LOCATION:Physical Sciences Building\, Physical Sciences Building\, Santa Cruz\, CA\, 95064
CATEGORIES:Ph.D. Presentations
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SUMMARY:Malekos\, E. (BMEB) - CRISPR screens of noncanonical ORFs uncover retroviral-derived immune regulators
DESCRIPTION:Ribosome profiling has revealed thousands of noncanonical translation events across mammalian genomes\, yet functional characterization has overwhelmingly focused on proliferative fitness in cancer cell lines. Here\, we present a comprehensive survey of noncanonical translation in the mouse immune system and its functional consequences in macrophages. By performing a unified Ribo-seq meta-analysis across 20 public mouse leukocyte datasets – spanning macrophages\, dendritic cells\, neutrophils\, B cells\, and T cells – we define a compendium of 22\,276 noncanonical coding sequences (CDSs)\, including upstream ORFs (uORFs)\, downstream ORFs\, and ORFs on noncoding RNAs and pseudogenes (ncORFs). Proteogenomic integration with reanalyzed mass spectrometry data prioritizes a high-confidence subset with detectable protein products\, including pseudogene-encoded and lncRNA-encoded zinc finger proteins. To move beyond cataloging\, we carried out two orthogonal CRISPR screens in immortalized bone marrow-derived macrophages: a fitness screen identifying noncanonical CDSs required for macrophage viability\, and a TLR1/TLR2-NFκB reporter screen uncovering CDSs that modulate innate immune signaling. These screens nominate uORFs\, several conserved between mouse and human\, that exert phenotypic effects on par with their cognate coding sequences. We unexpectedly discovered a family of endogenous retroviral envelope-derived proteins translated in adult myeloid cells. Among these\, SYNIR is a full-length syncytin-like membrane glycoprotein that positively regulates NFκB-responsive transcription\, while SEMR is a secreted protein with structural homology to the feline leukemia virus accessory protein FeLIX that drives broad transcriptional remodeling of macrophage gene programs upon knockout. Updated single-cell RNA-seq annotations and an interactive UCSC Genome Browser session integrating Ribo-seq\, proteomics\, and CRISPR screen data are provided as community resources. Together\, these findings expand the functional landscape of noncanonical translation in immunity and establish endogenous retroviral proteins as previously unrecognized regulators of macrophage biology. \nEvent Host: Eric Malekos\, Ph.D. Candidate\, Biomolecular Engineering & Bioinformatics  \nAdvisor: Susan Carpenter
URL:https://events.ucsc.edu/event/malekos-e-bmeb-crispr-screens-of-noncanonical-orfs-uncover-retroviral-derived-immune-regulators/
LOCATION:Biomedical Sciences\, Biomedical Sciences Building Red Hill Road\, Santa Cruz\, CA\, 95064
CATEGORIES:Ph.D. Presentations
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