About

Our research bridges computational and experimental sciences to discover new regulatory aspects in the human genome - specifically how long noncoding RNA (lncRNA) genes regulate numerous biological processes.

Research topics

• Biology
• Genetics
• Computational biology
• Cell biology
• Computer Science
• Statistics
• Evolutionary biology
• Biochemistry
• Mathematics

Selected publications

• Widespread specific intron retention events in nuclear RNA complexes identified by sedimentation analysis of pluripotent cellular extracts

  Genome Research · 2025-08-26 · 3 citations

  articleOpen accessSenior author

  Many essential cellular processes require RNA to interact with protein(s) to form ribonucleic protein complexes (RNPs). For example, all cellular proteins are produced by the ribosome, a large and stable RNP. Gene splicing requires a choreography of numerous small and large RNPs; even the replication of telomeric DNA requires an RNP. All these examples are stable RNPs that exhibit specific sedimentation rates (e.g., in a sucrose gradient) based on the composition of RNA and protein. In this study, we aimed to identify RNA components of discrete RNPs on a transcriptome-wide scale. Using sucrose gradient sedimentation followed by sequencing, we identified 1057 RNA transcripts, both coding and noncoding, that are likely to be components of cellular RNPs. We named these transcripts gradient-enriched transcripts (GETs). GETs were predominantly nuclear, metabolically stable, and they were not the major splice isoforms, but instead they were mostly retained-intron isoforms, each containing a specific retained intron, and this intron retention phenomenon is conserved in humans and mice. Collectively, our study reveals a widespread phenomenon of a specific intron being retained in a stable nuclear RNPs.

  PublisherOA PDFDOI

• <i>Rroid2</i> regulates effector-to-memory CD8 ⁺ T cell differentiation during infection in vivo

  Proceedings of the National Academy of Sciences · 2025-11-24 · 1 citations

  articleOpen access

  CD8 + T cell differentiation has been associated with changes in the expression of long noncoding RNAs (lncRNAs). Yet, which and how lncRNAs regulate CD8 + T cell responses following infection in vivo remains incompletely understood. We performed deep RNA-seq to map the lncRNA expression landscape of CD8 + T cell subsets during infection and generated lncRNA knockout mouse models to evaluate the in vivo relevance of six lncRNAs. We identified Rroid2 to regulate effector CD8 + T cell function and effector-to-memory differentiation. Rroid2 -deficient mice displayed increased CD44 dim Foxp3 + regulatory T cells while the development of other immune cells, such as natural killer cells, was not affected. In CD8 + T cells, Rroid2 deficiency resulted in a fine-tuned downregulation of transcription factors Id2 and T-bet and impaired KLRG1 + and KLRG1 − effector CD8 + T cell proliferation and cytotoxicity as well as effector-to-memory CD8 + T cell differentiation. The human orthologue of Rroid2 , LINC01814 , is also upstream of the transcriptional regulator ID2 and is highly expressed in human memory CD8 + T cells. Taken together, Rroid2 represents a key regulatory layer that controls CD8 + T cell differentiation.

  PublisherDOI

• Biophysical characterization of high-confidence, small human proteins

  bioRxiv (Cold Spring Harbor Laboratory) · 2024-04-15 · 2 citations

  preprintOpen access

  Significant efforts have been made to characterize the biophysical properties of proteins. Small proteins have received less attention because their annotation has historically been less reliable. However, recent improvements in sequencing, proteomics, and bioinformatics techniques have led to the high-confidence annotation of small open reading frames (smORFs) that encode for functional proteins, producing smORF-encoded proteins (SEPs). SEPs have been found to perform critical functions in several species, including humans. While significant efforts have been made to annotate SEPs, less attention has been given to the biophysical properties of these proteins. We characterized the distributions of predicted and curated biophysical properties, including sequence composition, structure, localization, function, and disease association of a conservative list of previously identified human SEPs. We found significant differences between SEPs and both larger proteins and control sets. Additionally, we provide an example of how our characterization of biophysical properties can contribute to distinguishing protein-coding smORFs from non-coding ones in otherwise ambiguous cases.

  PublisherOA PDFDOI

• Biophysical characterization of high-confidence, small human proteins

  Biophysical Reports · 2024-06-22 · 3 citations

  articleOpen access

  Significant efforts have been made to characterize the biophysical properties of proteins. Small proteins have received less attention because their annotation has historically been less reliable. However, recent improvements in sequencing, proteomics, and bioinformatics techniques have led to the high-confidence annotation of small open reading frames (smORFs) that encode for functional proteins, producing smORF-encoded proteins (SEPs). SEPs have been found to perform critical functions in several species, including humans. While significant efforts have been made to annotate SEPs, less attention has been given to the biophysical properties of these proteins. We characterized the distributions of predicted and curated biophysical properties, including sequence composition, structure, localization, function, and disease association of a conservative list of previously identified human SEPs. We found significant differences between SEPs and both larger proteins and control sets. In addition, we provide an example of how our characterization of biophysical properties can contribute to distinguishing protein-coding smORFs from noncoding ones in otherwise ambiguous cases.

  PublisherDOI

• The temporal dynamics of lncRNA Firre-mediated epigenetic and transcriptional regulation

  Nature Communications · 2024-08-09 · 22 citations

  articleOpen accessSenior authorCorresponding

  Numerous studies have now demonstrated that lncRNAs can influence gene expression programs leading to cell and organismal phenotypes. Typically, lncRNA perturbations and concomitant changes in gene expression are measured on the timescale of many hours to days. Thus, we currently lack a temporally grounded understanding of the primary, secondary, and tertiary relationships of lncRNA-mediated transcriptional and epigenetic regulation—a prerequisite to elucidating lncRNA mechanisms. To begin to address when and where a lncRNA regulates gene expression, we genetically engineer cell lines to temporally induce the lncRNA Firre. Using this approach, we are able to monitor lncRNA transcriptional regulatory events from 15 min to four days. We observe that upon induction, Firre RNA regulates epigenetic and transcriptional states in trans within 30 min. These early regulatory events result in much larger transcriptional changes after 12 h, well before current studies monitor lncRNA regulation. Moreover, Firre-mediated gene expression changes are epigenetically remembered for days. Overall, this study suggests that lncRNAs can rapidly regulate gene expression by establishing persistent epigenetic and transcriptional states. Typically, lncRNA perturbations are measured on the timescale of many hours to days. Here, the authors investigate when and where the lncRNA Firre influences epigenetic and transcriptional states, suggesting that lncRNA-mediated gene regulation occurs within minutes and is retained for days.

  PublisherOA PDFDOI

• X-linked deletion of Crossfirre, Firre, and Dxz4 in vivo uncovers diverse phenotypes and combinatorial effects on autosomes

  Nature Communications · 2024-12-05 · 4 citations

  articleOpen accessCorresponding

  The lncRNA Crossfirre was identified as an imprinted X-linked gene, and is transcribed antisense to the trans-acting lncRNA Firre. The Firre locus forms an inactive-X-specific interaction with Dxz4, both loci providing the platform for the largest conserved chromatin structures. Here, we characterize the epigenetic profile of these loci, revealing them as the most female-specific accessible regions genome-wide. To address their in vivo role, we perform one of the largest X-linked knockout studies by deleting Crossfirre, Firre, and Dxz4 individually and in combination. Despite their distinct epigenetic features observed on the X chromosome, our allele-specific analysis uncovers these loci as dispensable for imprinted and random X chromosome inactivation. However, we provide evidence that Crossfirre affects autosomal gene regulation but only in combination with Firre. To shed light on the functional role of these sex-specific loci, we perform an extensive standardized phenotyping pipeline and uncover diverse knockout and sex-specific phenotypes. Collectively, our study provides the foundation for exploring the intricate interplay of conserved X-linked loci in vivo.

  PublisherOA PDFDOI

• Massively parallel dissection of RNA in RNA–protein interactions in vivo

  Nucleic Acids Research · 2024-05-10 · 4 citations

  articleOpen access

  Many of the biological functions performed by RNA are mediated by RNA-binding proteins (RBPs), and understanding the molecular basis of these interactions is fundamental to biology. Here, we present massively parallel RNA assay combined with immunoprecipitation (MPRNA-IP) for in vivo high-throughput dissection of RNA-protein interactions and describe statistical models for identifying RNA domains and parsing the structural contributions of RNA. By using custom pools of tens of thousands of RNA sequences containing systematically designed truncations and mutations, MPRNA-IP is able to identify RNA domains, sequences, and secondary structures necessary and sufficient for protein binding in a single experiment. We show that this approach is successful for multiple RNAs of interest, including the long noncoding RNA NORAD, bacteriophage MS2 RNA, and human telomerase RNA, and we use it to interrogate the hitherto unknown sequence or structural RNA-binding preferences of the DNA-looping factor CTCF. By integrating systematic mutation analysis with crosslinking immunoprecipitation, MPRNA-IP provides a novel high-throughput way to elucidate RNA-based mechanisms behind RNA-protein interactions in vivo.

  PublisherOA PDFDOI

• Single-cell profiling of lncRNA expression during Ebola virus infection in rhesus macaques

  Zenodo (CERN European Organization for Nuclear Research) · 2023-05-03

  articleOpen access

  Raw count matrices for the three datasets used in the study: - Multitissue short-read bulk RNA-sequencing data from Ebola virus-infected and not infected Rhesus Macaque (GSE192447, GSE115785 ) - Sigle-cell RNA-sequencing data from Rhesus Macaque PBMCs infected with Ebola virus <em>in vivo </em>(GSE158390) - Sigle-cell RNA-sequencing data from Rhesus Macaque PBMCs infected with Ebola virus ex<em> vivo </em>(GSE158390)

  PublisherDOI

• Natural history of Ebola virus disease in rhesus monkeys shows viral variant emergence dynamics and tissue-specific host responses

  Cell Genomics · 2023-11-21 · 4 citations

  articleOpen access

  Ebola virus (EBOV) causes Ebola virus disease (EVD), marked by severe hemorrhagic fever; however, the mechanisms underlying the disease remain unclear. To assess the molecular basis of EVD across time, we performed RNA sequencing on 17 tissues from a natural history study of 21 rhesus monkeys, developing new methods to characterize host-pathogen dynamics. We identified alterations in host gene expression with previously unknown tissue-specific changes, including downregulation of genes related to tissue connectivity. EBOV was widely disseminated throughout the body; using a new, broadly applicable deconvolution method, we found that viral load correlated with increased monocyte presence. Patterns of viral variation between tissues differentiated primary infections from compartmentalized infections, and several variants impacted viral fitness in a EBOV/Kikwit minigenome system, suggesting that functionally significant variants can emerge during early infection. This comprehensive portrait of host-pathogen dynamics in EVD illuminates new features of pathogenesis and establishes resources to study other emerging pathogens.

  PublisherOA PDFDOI

• T-REX17 is a transiently expressed non-coding RNA essential for human endoderm formation

  eLife · 2023-01-16 · 4 citations

  articleOpen access

  Long non-coding RNAs (lncRNAs) have emerged as fundamental regulators in various biological processes, including embryonic development and cellular differentiation. Despite much progress over the past decade, the genome-wide annotation of lncRNAs remains incomplete and many known non-coding loci are still poorly characterized. Here, we report the discovery of a previously unannotated lncRNA that is transcribed 230 kb upstream of the SOX17 gene and located within the same topologically associating domain. We termed it T-REX17 ( T ranscript R egulating E ndoderm and activated by so X17 ) and show that it is induced following SOX17 activation but its expression is more tightly restricted to early definitive endoderm. Loss of T-REX17 affects crucial functions independent of SOX17 and leads to an aberrant endodermal transcriptome, signaling pathway deregulation and epithelial to mesenchymal transition defects. Consequently, cells lacking the lncRNA cannot further differentiate into more mature endodermal cell types. Taken together, our study identified and characterized T-REX17 as a transiently expressed and essential non-coding regulator in early human endoderm differentiation.

  PublisherDOI

Recent grants

• NIH Grant R01ES020260

  NIH · $2.1M · 2017

• Dissecting the establishment and regulation of human pluripotency

  NIH · $42.5M · 2011–2023

• Deciphering the function and mechanisms of lncRNA-mediated organization of nuclear compartments

  NIH · $750k · 2015–2020

• NIH Grant DP2OD006670

  NIH · $2.5M · 2014

• Functional Roles of Long Noncoding RNAs During Neuronal Development

  NIH · $2.1M · 2014–2020

Frequent coauthors

• Chiara Gerhardinger

  Broad Institute

  126 shared

• Loyal A. Goff

  Johns Hopkins University

  125 shared

• Eric S. Lander

  Broad Institute

  115 shared

• Marta Melé

  Barcelona Supercomputing Center

  106 shared

• William Mallard

  Broad Institute

  94 shared

• Moran N. Cabili

  Foundation Medicine (United States)

  90 shared

• Abigail F. Groff

  Whitehead Institute for Biomedical Research

  87 shared

• Alexander Meissner

  Max Planck Institute for Molecular Genetics

  74 shared

Education

• Ph.D., Molecular and Cellular Biology

  Harvard University

  1996

• B.S., Biology

  University of California, San Diego

  1991

Awards & honors

• HHMI Faculty Scholars (2016)
• Thompson Reuters Most Influential Scientist (2014)
• National Academy of Science Distinctive Voices (2014)
• National Academy of Science Sackler Colloquium (2014)
• Alvin and Esta Starr Associate Professorship (2013)