Kathi Zarnack

This study identifies FMR1 as a translational enhancer of oskar in Drosophila oocytes and reveals how its RNA-binding domains regulate opposing translation functions through phase separation.

The paper introduces iCLIP3, a streamlined protocol for mapping RBP-RNA interactions at single-nucleotide resolution, with improvements in visualization, RNA isolation, and multiplexing.

This study identifies RS2Z36 as a splicing regulator that controls ovary patterning and fruit growth in tomato by affecting cell expansion and alternative splicing.

The paper shows that intron retention and alternative exon choice are coupled through multistep exon recognition by the spliceosome, which is disrupted in cancer.

The paper investigates the RNA binding roles of Rrm4's RRM domains in Ustilago maydis, revealing how different RRM interactions influence mRNA transport and stability.

RepliCNN predicts DNA replication timing and related features from strand-specific 3' DNA end sequencing data with high accuracy.

The paper investigates how RNA G-quadruplexes enable cooperative binding of HNRNPH and regulate splicing, showing clinical relevance in breast cancer.

The paper shows that CLB2 mRNA localization to the bud via the She2/She3 complex enhances translation, linking cell growth to cell cycle progression through a ZIP-code element in the coding sequence.

This study shows SRSF5 is critical for paraspeckle assembly and dynamics, with stress-induced changes and compensatory effects on TDP-43 and NEAT1.

This study identifies TRIM28's role in pre-mRNA splicing through phosphorylation and SUMOylation interactions with USP39, showing its impact on alternative splicing patterns.

The paper identifies RNA-dependent proteins in cell division using R-DeeP, revealing new interactions and phosphorylation events involving AURKA, KIFC1, and TPX2.

The paper uses kinetic modeling and statistical learning to quantify how mutations affect splicing outcomes, revealing context-dependent isoform changes and cryptic splice site activation.

This study develops a microbial iCLIP2 protocol to identify RNA-protein interactions in fungi, revealing Rrm4 binds mitochondrial mRNA stop codons.

This study identifies PUN motifs in yeast Loc1p that cooperate to catalyze RNA folding and drive phase separation, suggesting a role in RNA and DNA-related processes across species.

This study identifies RS2Z35 and RS2Z36 as plant-specific splicing factors that regulate HSFA2 intron splicing and thermotolerance in tomato under heat stress.

The paper evaluates how RNA-Seq library characteristics affect alternative splicing analysis using MAJIQ and recommends optimal parameters for improved sensitivity and precision.

This study defines Arid5a's DNA and RNA-binding preferences using biochemical and high-throughput methods, showing that disordered regions modulate its nucleic acid interactions and gene regulation.

The paper identifies a consensus motif for She2p/3p recognition sites in yeast RNA, showing that spatial arrangement of sequence features is more important than sequence order for function.

This study uses long-read transcriptome sequencing to analyze SF3B1 mutations in CLL and MDS patients, revealing common splicing alterations and their impact on disease prognosis.

racoon_clip processes iCLIP and eCLIP data to extract single-nucleotide RNA binding signals, providing automated analysis and visualization tools.

This study identifies circPLOD2 as a hypoxia-regulated circRNA that modulates pericyte function by regulating KLF4, affecting proliferation and vascular interactions.

This study shows that PURA depletion affects posttranscriptional regulation and P-body formation, linking PURA Syndrome to neurodevelopmental disorders.

The paper identifies mutations and RNA-binding proteins affecting CD19 splicing and CART-19 therapy resistance through high-throughput mutagenesis and mathematical modeling.

CHEUI predicts m6A and m5C modifications at single-molecule resolution, revealing co-occurrence of these modifications in mRNAs across cell lines and tissues.

The paper improves m6A RNA modification detection using miCLIP2 and m6Aboost, identifying thousands of high-confidence sites in human and mouse cells without requiring Mettl3 depletion.

The paper analyzes high-throughput mutagenesis data to show that exon definition is crucial for reliable alternative splicing in the RON proto-oncogene.

This study shows that Makorin1 promotes oskar translation by displacing Bruno from its 3' UTR, essential for embryonic patterning and germ cell formation in Drosophila.

This study identifies MKRN1 as a key player in ribosome-associated quality control by promoting ribosome stalling at poly(A) sequences to prevent erroneous protein production.

The paper introduces a workflow for identifying functional upstream open reading frames (uORFs) using ribosome profiling data and provides a human uORF annotation file.