About

J. Mauro Calabrese, Ph.D., is a Principal Investigator and Associate Professor as well as the Director of Graduate Studies in the Department of Pharmacology at the University of North Carolina at Chapel Hill. He received his B.S. from the University of Wisconsin in Madison in 2001 and earned his Ph.D. from the Massachusetts Institute of Technology in 2007, where he studied small RNA-mediated gene regulation under Dr. Phillip Sharp. In 2008, he joined UNC Chapel Hill as a post-doctoral fellow in Dr. Terry Magnuson’s laboratory, focusing on mechanisms of epigenetic regulation by long noncoding RNA. He began his independent faculty career as an Assistant Professor in the Department of Pharmacology at UNC in March 2014. His research centers on understanding the molecular mechanisms by which long noncoding RNAs regulate gene expression and epigenetic states, contributing to the broader knowledge of RNA-mediated gene regulation and epigenetic control.

Research topics

• Computational biology
• Biology
• Genetics
• Statistics

Selected publications

• Repeat expansions in <i>C9orf72</i> rewire the 3D chromatin landscape in ALS

  bioRxiv (Cold Spring Harbor Laboratory) · 2026-02-11

  articleOpen access

  Abstract Amyotrophic lateral sclerosis (ALS) is frequently driven by GGGGCC short tandem repeat (STR) expansions in C9orf72 , yet the mechanisms by which these expansions lead to neurodegeneration remain incompletely understood. Here, we propose a novel mechanism involving higher-order chromatin architecture where C9orf72 -STR expansions induce widespread, neuron-specific gains in chromatin loops that are closely linked to transcriptomic dysregulation in ALS. These ectopic loops colocalize with the genomic binding sites of C9orf72 -STR RNAs and the architectural protein CTCF, supporting a model in which RNA-DNA interactions promote aberrant loop formation. Together, our findings demonstrate how C9orf72 -STR expansions remodel the neuronal genome and disrupt gene expression, uncovering an RNA-driven mechanism of chromatin reorganization in C9-ALS that connects altered nuclear topology to gene dysregulation in neurodegeneration.

  PublisherOA PDFDOI

• Noncoding and coding mechanisms of aging heart failure with preserved ejection fraction with thyroid dysfunction.

  UNC Libraries · 2025-12-12

  articleOpen access

  Heart Failure with preserved Ejection Fraction (HFpEF) is a lethal, heterogeneous, geriatric syndrome. Long noncoding RNAs (lncRNAs) constitute the majority of the functional mammalian transcriptome and are key regulators in complex pathophysiology. However, the roles of lncRNAs in aging HFpEF associated with thyroid hormone (TH) dysfunction are unclear. We investigated the well-established ZSF1 model in early and severe, aged HFpEF (5-, 13-, and 20-months [mo]). Both serum THs significantly decreased in HFpEF in a temporal manner. Echocardiogram showed preserved cardiac function. Morphometric and histologic analyses showed significant cardiac hypertrophy in HFpEF. LncRNA microarray and RT-qPCR revealed that three lncRNAs were significantly increased predominantly in 13-mo HFpEF. LncRNA knockdown showed improvement in cell viability, which was further enhanced with T3 (active TH). Microarray analyses showed that two mRNAs were significantly altered in early HFpEF. We also identified previously unreported tissue and serum inflammatory cytokine markers in early and late HFpEF. Taken together, we have shown novel noncoding and coding markers in early and/or late-aged hypothyroid HFpEF. Further studies may develop translatable diagnostic and therapeutic targets for HFpEF.

  PublisherDOI

• <i>Xist</i> Repeat A coordinates an assembly of SR proteins to recruit SPEN and induce gene silencing

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-05-26 · 5 citations

  preprintOpen accessSenior author

  ABSTRACT The lncRNA Xist represents a paradigm to understand the mechanisms of RNA-mediated gene silencing in mammals, which remain largely unresolved. To induce silencing, Xist recruits the RNA-binding protein SPEN through its 5′-proximal Repeat A domain. Yet, how Repeat A recruits SPEN and how SPEN coordinates silencing remain unclear. We report that sequences in Repeat A critical for SPEN recruitment directly bind SR-rich splicing factors. SRSF1, one such factor, is required for optimal SPEN recruitment and its RS-domain recruits SPEN when tethered to Xist . SPEN and SR-protein-binding motifs promote Repeat A’s association with many proteins, including the m 6 A machinery and elongating RNA polymerase II. SPEN also represses autosomal genes where its recruitment coincides with SR-protein binding. Our results reveal an unexpectedly essential role for splicing factors in coordinating silencing by Xist and suggest that the sensing of SR-protein-rich assemblies is a general mechanism through which SPEN targets genes for repression.

  PublisherOA PDFDOI

• Early Host-Virus RNA Interactions Reveal SPEN-Driven m ⁶ A Regulation as a Major Determinant of Henipavirus Infection

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-11-23

  preprintOpen access

  SUMMARY Early interactions between viral RNA and host-encoded RNA-binding proteins are pivotal in shaping the trajectory of RNA virus infection. Henipaviruses are emerging, highly lethal BSL-4 pathogens whose mechanisms of pathogenesis remain largely elusive. To illuminate the earliest moments of host-virus interplay, we employed Viral Cross-linking and Solid-phase Purification (VIR-CLASP) to capture host proteins bound to the incoming henipavirus genome within the first hour of infection. This approach establishes the first henipavirus RNA-host protein interactome, revealing 146 human proteins directly associated with the primary viral RNA. Among these, SPEN, RBM15, and RBM15B - canonical regulators of lncRNA Xist – emerged as key host factors that actively promote viral infection. Direct RNA sequencing further uncovered that SPEN depletion induces widespread hypomethylation, affecting ~98% of differentially modified m 6 A sites, ~87% of which localize to the L mRNA transcript encoding the viral RNA-dependent RNA polymerase. Collectively, these findings expose a critical layer of host dependency at the very onset of infection and reveal a previously unappreciated role for SPEN family proteins in facilitating henipavirus infection.

  PublisherOA PDFDOI

• A monoclonal antibody raised against human EZH2 cross-reacts with the RNA-binding protein SAFB

  UNC Libraries · 2025-12-02

  articleOpen access1st authorCorresponding

  The Polycomb Repressive Complex 2 (PRC2) is a conserved enzyme that tri-methylates Lysine 27 on Histone 3 (H3K27me3) to promote gene silencing. PRC2 is remarkably responsive to the expression of certain long noncoding RNAs (lncRNAs). In the most notable example, PRC2 is recruited to the X-chromosome shortly after expression of the lncRNA Xist begins during X-chromosome inactivation. However, the mechanisms by which lncRNAs recruit PRC2 to chromatin are not yet clear. We report that a broadly used rabbit monoclonal antibody raised against human EZH2, a catalytic subunit of PRC2, cross-reacts with an RNA-binding protein called Scaffold Attachment Factor B (SAFB) in mouse embryonic stem cells (ESCs) under buffer conditions that are commonly used for chromatin immunoprecipitation (ChIP). Knockout of EZH2 in ESCs demonstrated that the antibody is specific for EZH2 by western blot (no cross-reactivity). Likewise, comparison to previously published datasets confirmed that the antibody recovers PRC2-bound sites by ChIP-Seq. However, RNA-IP from formaldehyde-crosslinked ESCs using ChIP wash conditions recovers distinct peaks of RNA association that co-localize with peaks of SAFB and whose enrichment disappears upon knockout of SAFB but not EZH2. IP and mass spectrometry-based proteomics in wild-type and EZH2 knockout ESCs confirm that the EZH2 antibody recovers SAFB in an EZH2-independent manner. Our data highlight the importance of orthogonal assays when studying interactions between chromatin-modifying enzymes and RNA.

  PublisherDOI

• Protocol for evaluating RNA-protein associations in mammalian cells with RIP-seq and RIP-qPCR

  STAR Protocols · 2025-12-26

  articleOpen accessSenior author

  .

  PublisherDOI

• Noncoding and coding mechanisms of aging-related heart failure with preserved ejection fraction associated with thyroid dysfunction

  Disease Models & Mechanisms · 2025-09-29

  articleOpen access

  Heart failure with preserved ejection fraction (HFpEF) is a lethal, heterogeneous, geriatric syndrome. Long noncoding RNAs (lncRNAs) constitute the majority of the functional mammalian transcriptome and are key regulators in complex pathophysiological processes. However, the roles of lncRNAs in aging HFpEF associated with thyroid hormone (TH) dysfunction are unclear. We used the well-established ZSF1 rat model to investigate early and severe age-related HFpEF in 5-, 13- or 20-months-old (mo) animals. Both serum THs significantly decreased in HFpEF in a temporal manner. Echocardiograms showed preserved cardiac function. Gravimetric and histologic analyses showed significant cardiac hypertrophy in HFpEF. Microarrays and RT-qPCR revealed that three lncRNAs were significantly increased predominantly in 13-mo HFpEF. Knockdown of lncRNA showed improvement in cell viability, which was further enhanced with T3 (active TH). Microarray analyses showed that two mRNAs were significantly altered in early HFpEF. We also identified previously unreported tissue and serum inflammatory cytokine markers in early and late HFpEF. Taken together, we have shown novel noncoding and coding markers in early- and/or late-aging-related hypothyroid HFpEF. Further studies may develop translatable diagnostic and therapeutic targets for HFpEF.

  PublisherOA PDFDOI

• Isogenic comparison of Airn and Xist reveals core principles of Polycomb recruitment by lncRNAs

  Molecular Cell · 2025-03-01 · 6 citations

  articleOpen accessSenior author
  PublisherOA PDFDOI

• Improved functions for non-linear sequence comparison using SEEKR

  bioRxiv (Cold Spring Harbor Laboratory) · 2024-03-10 · 1 citations

  preprintOpen accessSenior authorCorresponding

  Abstract SEquence Evaluation through k -mer Representation (SEEKR) is a method of sequence comparison that utilizes sequence substrings called k -mers to quantify non-linear similarity between nucleic acid species. We describe the development of new functions within SEEKR that enable end-users to estimate p-values that ascribe statistical significance to SEEKR-derived similarities as well as visualize different aspects of k -mer similarity. We apply the new functions to identify chromatin-enriched long noncoding RNAs (lncRNAs) that harbor XIST -like sequence fragments and show that several of these fragments are bound by XIST -associated proteins. We also highlight the best practice of using RNA-Seq data to evaluate support for lncRNA annotations prior to their in-depth study in cell types of interest.

  PublisherOA PDFDOI

• Improved functions for nonlinear sequence comparison using SEEKR

  RNA · 2024-08-26 · 4 citations

  articleOpen accessSenior author

  SEquence Evaluation through k -mer Representation (SEEKR) is a method of sequence comparison that uses sequence substrings called k -mers to quantify the nonlinear similarity between nucleic acid species. We describe the development of new functions within SEEKR that enable end-users to estimate P- values that ascribe statistical significance to SEEKR-derived similarities, as well as visualize different aspects of k -mer similarity. We apply the new functions to identify chromatin-enriched lncRNAs that contain XIST -like sequence features, and we demonstrate the utility of applying SEEKR on lncRNA fragments to identify potential RNA-protein interaction domains. We also highlight ways in which SEEKR can be applied to augment studies of lncRNA conservation, and we outline the best practice of visualizing RNA-seq read density to evaluate support for lncRNA annotations before their in-depth study in cell types of interest.

  PublisherOA PDFDOI

Recent grants

• A computational approach to identify non-linear sequence similarity between lncRNAs

  NSF · $663k · 2023–2027

• Mechanisms of gene silencing induced by long noncoding RNAs

  NIH · $2.3M · 2017–2026

• Mechanisms of gene regulation by long noncoding RNAs

  NIH · $1.9M · 2024–2029

• Cooperative control of Polycomb Repressive Complexes by long noncoding RNAs, CpG island DNA, and RNA-binding proteins

  NIH · $1.5M · 2020–2025

Frequent coauthors

• Terry Magnuson

  UNC Lineberger Comprehensive Cancer Center

  46 shared

• Phillip A. Sharp

  Massachusetts Institute of Technology

  35 shared

• Megan D. Schertzer

  Columbia University

  29 shared

• Jackson B. Trotman

  University of North Carolina at Chapel Hill

  24 shared

• David M. Lee

  Oregon Health & Science University

  21 shared

• Rachel E. Cherney

  Segeberger Kliniken

  21 shared

• Aki K. Braceros

  University of North Carolina at Chapel Hill

  18 shared

• Kaoru Inoue

  Doshisha University

  17 shared

Labs

• Calabrese LabPI

Education

• Bachelors of Arts, Chemistry, Biochemistry, and Molecular Biology

  University of Wisconsin–Madison

  2001