J. Mauro Calabrese

This paper introduces a three-factor mathematical model to explain symmetry breaking and the n-1 rule in X-chromosome inactivation by integrating Xist, an X-linked activator, and SPEN.

The paper introduces hmSEEKR, a k-mer-based hidden Markov model that identifies non-linear sequence similarities in transcriptomes, revealing functional RNA domains with biological relevance.

This study shows that C9orf72 repeat expansions alter chromatin loops in neurons, linking RNA-DNA interactions to gene dysregulation in ALS.

The paper identifies SPEN-driven m6A regulation as a key factor in henipavirus infection by analyzing host-virus RNA interactions using VIR-CLASP.

This study investigates the role of lncRNAs and thyroid dysfunction in aging HFpEF, identifying novel lncRNA and inflammatory markers in early and late stages.

The paper compares RNA-protein associations across lncRNAs Airn, Kcnq1ot1, and Xist, identifying HNRNPU's role in long-range Polycomb recruitment by Airn and Kcnq1ot1.

The paper identifies how Xist Repeat A recruits SPEN via SR proteins to induce gene silencing, revealing a role for splicing factors in this process.

The paper introduces new functions in SEEKR to calculate p-values and visualize k-mer similarity, applying them to identify chromatin-enriched lncRNAs with XIST-like fragments.

The paper shows a monoclonal antibody against EZH2 cross-reacts with SAFB, highlighting the need for orthogonal assays in studying RNA-chromatin interactions.

The paper shows that Airn lncRNA can deposit Polycomb with potency comparable to Xist when expressed at similar levels, but Xist is more potent when promoter activation is equal.

The paper shows that the lncRNA Airn recruits Polycomb Repressive Complexes to silence genes during mouse embryogenesis through chromatin contacts and regulatory elements.

This study identifies SAFB-associated RNAs in mouse embryonic stem cells and shows SAFB promotes gene expression by binding purine-rich regions in nascent transcripts.

The paper introduces MiniMUGA, a genotyping array for mouse genetic QC, showing it effectively discriminates strains, detects genetic constructs, and identifies sex chromosome abnormalities.

The paper identifies SPEN-independent transcriptional antiterminator activity in the 5' end of Xist that promotes full-length RNA production and resists silencing.

The paper introduces CRISPR-Bac, a piggyBac-based system for inducible CRISPR-Cas9 genome editing in mammalian cells, enabling efficient gene knockdown, deletion, and transcriptional activation/repression.

The paper shows non-linear sequence similarity between Xist and Rsx repeat domains, suggesting shared functional roles through similar protein-binding motif enrichments.