About

Esteban O. Mazzoni is a professor in the Department of Cell Biology and the Department of Neuroscience at NYU Grossman School of Medicine. His research is centered on understanding how cells acquire their functions within a multicellular organism, with a focus on cell differentiation, neuronal physiology, and neurodegeneration. His work employs a blend of scientific approaches, including cutting-edge genomic and tissue culture technologies, to explore how DNA sequences can store temporary signals as permanent memories and how transcription factors influence cell differentiation. Mazzoni's research aims to answer fundamental questions about cell change and development, with particular interest in why some neurons are more susceptible to neurodegeneration than others. His laboratory uses innovative tools and techniques to study mammalian cell differentiation at a scale comparable to small invertebrate animals and yeast, enabling rapid and large-scale analysis while considering human genetic diversity. His contributions include elucidating mechanisms of chromatin organization, identifying regulatory factors in cell differentiation, and advancing understanding of neurodegenerative processes, all with the goal of translating basic scientific insights into future clinical applications.

Research topics

• Genetics
• Biology
• Computational biology
• Evolutionary biology
• Neuroscience
• Cell biology

Selected publications

• MASTR-seq enables multiplexed analysis of short tandem repeats with sequencing

  Cell Reports Methods · 2026-03-01

  articleOpen access

  More than 60 human disorders are caused by unstable expansion of short tandem repeat (STR) tracts. These can exhibit cell-type-specific mosaicism in several repeat expansion disorders and remain difficult to characterize due to technical challenges intrinsic to highly repetitive sequences. Long-read approaches can measure STR length and DNA methylation on the same single molecule but are low-throughput and cost-prohibitive across multiple experimental conditions or patient samples. Here, we present MASTR-seq, multiplexed analysis of short tandem repeats with sequencing, for cost-effective, high-throughput, accurate measurement of STR genotype and DNA methylation at single-allele resolution. MASTR-seq couples long-read sequencing, Cas9-mediated target enrichment, size selection, and PCR-free multiplexed barcoding to increase on-target read proportion for 8-12 pooled samples in a single MinION flow cell. MASTR-seq quantifies tract length and DNA methylation status for CGG, GGGGCC (G4C2), and CAG STR tracts in normal-length and mutation-length samples.

  PublisherDOI

• MASTR-Seq: Multiplexed Analysis of Short Tandem Repeats with Sequencing

  SSRN Electronic Journal · 2025-01-01

  preprintOpen access
  PublisherDOI

• CTCF-RNA interactions orchestrate cell-specific chromatin loop organization

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-03-19 · 1 citations

  preprintOpen access

  SUMMARY CCCTC-binding factor (CTCF) is essential for chromatin organization. CTCF interacts with endogenous RNAs, and deletion of its ZF1 RNA-binding region (ΔZF1) disrupts chromatin loops in mouse embryonic stem cells (ESCs). However, the functional significance of CTCF-ZF1 RNA interactions during cell differentiation is unknown. Using an ESC-to-neural progenitor cell (NPC) differentiation model, we show that CTCF-ZF1 is crucial for maintaining cell-type-specific chromatin loops. Expression of CTCF-ΔZF1 leads to disrupted loops and dysregulation of genes within these loops, particularly those involved in neuronal development and function. We identified NPC-specific, CTCF-ZF1 interacting RNAs. Truncation of two such coding RNAs, Podxl and Grb10 , disrupted chromatin loops in cis , similar to the disruption seen in CTCF-ΔZF1 expressing NPCs. These findings underscore the inherent importance of CTCF-ZF1 RNA interactions in preserving cell-specific genome structure and cellular identity. HIGHLIGHTS CTCF loop anchors induced after differentiation are disrupted in the ΔZF1 RNA-binding mutant. Loop loss in the ΔZF1 mutant is independent of its DNA binding and protein interactions. Chromatin loop loss is associated with gene dysregulation. Truncation of cell-specific, CTCF-ZF1-interacting RNAs disrupts chromatin loops in cis . GRAPHICAL ABSTRACT

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• CTCF-RNA interactions orchestrate cell-specific chromatin loop organization

  Science Advances · 2025-11-26 · 1 citations

  articleOpen access

  CCCTC-binding factor (CTCF) is essential for chromatin organization. CTCF interacts with endogenous RNAs, and deletion of its ZF1 RNA binding region (∆ZF1) disrupts chromatin loops in mouse embryonic stem cells (ESCs). However, the functional significance of CTCF-ZF1 RNA interactions during cell differentiation is unknown. Using an ESC–to–neural progenitor cell (NPC) differentiation model, we show that CTCF-ZF1 is crucial for maintaining cell type–specific chromatin loops. Expression of CTCF-∆ZF1 leads to disrupted loops and dysregulation of genes within these loops, particularly those involved in neuronal development and function. We identified NPC-specific, CTCF-ZF1 interacting RNAs. Truncation of two such coding RNAs, Podxl and Grb10 , disrupted chromatin loops in cis, similar to the disruption seen in CTCF-∆ZF1–expressing NPCs. These findings underscore the inherent importance of CTCF-ZF1 RNA interactions in preserving cell-specific genome structure and cellular identity.

  PublisherDOI

• AAV-based delivery of RNAi targeting ataxin-2 improves survival and pathology in TDP-43 mice

  Nature Communications · 2025-06-25 · 7 citations

  articleOpen access

  Amyotrophic lateral sclerosis (ALS) involves motor neuron death due to mislocalized TDP-43. Pathologic TDP-43 associates with stress granules (SGs), and lowering the SG-associated protein ataxin-2 (ATXN2) using Atxn2-targeting antisense oligonucleotides prolongs survival in TAR4/4 sporadic ALS mice but failed in clinical trials likely due to poor target engagement. Here we show that an AAV with potent motor neuron transduction delivering Atxn2-targeting miRNAs reduces Atxn2 throughout the central nervous system at doses 40x lower than published work. In TAR4/4 mice, miAtxn2 increased survival (50%) and strength, and reduced motor neuron death, inflammation, and phosphorylated TDP-43. TAR4/4 transcriptomic dysregulation recapitulated ALS gene signatures that were rescued by miAtxn2, identifying potential therapeutic mechanisms and biomarkers. In slow progressing hemizygous mice, miAtxn2 slowed disease progression, and in ALS patient-derived lower motor neurons, our AAV vector transduced >95% of cells and potently reduced ATXN2 at MOI 4 logs lower than previously reported. These data support AAV-RNAi targeting ATXN2 as a translatable therapy for sporadic ALS. Amado et al. develop a gene therapy for sporadic ALS using motor neuron-targeting AAVs to deliver RNAi targeting ataxin-2. In a mouse model, survival, strength, and disease-related pathology are improved; and human motor neurons are strongly transduced.

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• Author Correction: AAV-based delivery of RNAi targeting ataxin-2 improves survival and pathology in TDP-43 mice

  Nature Communications · 2025-10-23 · 1 citations

  articleOpen access

  In the version of the article initially published, a reference citation was missing in the first sentence of the Results "Translatability to human targets" section, which now reads "To determine the ability of miAtxn2 to target human ATXN2, we used the 127Q transgenic mouse model of spinocerebellar ataxia type 2, in which mice overexpress mutant human ATXN2 in cerebellar Purkinje cells [Hansen, S.

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• Stem cell-based approach to identify regulatory TFs during mammalian cell differentiation

  Stem Cell Reports · 2025-11-20

  articleOpen accessSenior author

  Cell differentiation is regulated by transcription factors (TFs), but specific TFs needed for mammalian differentiation pathways are not fully understood. For example, during spinal motor neuron (MN) differentiation, 1,370 TFs are transcribed, yet only 55 have reported functional relevance. We developed a method combining pluripotent stem cell differentiation, single-cell transcriptomics, and a CRISPR-based TF loss-of-function screen and applied it to MN differentiation. The CRISPR screen identified 245 genes important for mouse MN differentiation, including 116 TFs. This screen uncovered important genes not showing differential transcription and identified a regulatory hub at the MN progenitor (pMN) stage. A secondary human screen of 69 selected candidates revealed a conservation between mouse pMN and human pMN and ventral pMN (vpMN) regulations. The validation of three hits required for efficient human MN differentiation supported the effectiveness of our approach. Collectively, our strategy offers a framework for identifying important TFs in various differentiation pathways.

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• Genome-wide screening identifies Trim33 as an essential regulator of dendritic cell differentiation

  Science Immunology · 2024-04-12 · 14 citations

  articleOpen access

  The development of dendritic cells (DCs), including antigen-presenting conventional DCs (cDCs) and cytokine-producing plasmacytoid DCs (pDCs), is controlled by the growth factor Flt3 ligand (Flt3L) and its receptor Flt3. We genetically dissected Flt3L-driven DC differentiation using CRISPR-Cas9–based screening. Genome-wide screening identified multiple regulators of DC differentiation including subunits of TSC and GATOR1 complexes, which restricted progenitor growth but enabled DC differentiation by inhibiting mTOR signaling. An orthogonal screen identified the transcriptional repressor Trim33 (TIF-1γ) as a regulator of DC differentiation. Conditional targeting in vivo revealed an essential role of Trim33 in the development of all DCs, but not of monocytes or granulocytes. In particular, deletion of Trim33 caused rapid loss of DC progenitors, pDCs, and the cross-presenting cDC1 subset. Trim33-deficient Flt3 + progenitors up-regulated pro-inflammatory and macrophage-specific genes but failed to induce the DC differentiation program. Collectively, these data elucidate mechanisms that control Flt3L-driven differentiation of the entire DC lineage and identify Trim33 as its essential regulator.

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• Members of an array of zinc-finger proteins specify distinct Hox chromatin boundaries

  Molecular Cell · 2024-08-23 · 21 citations

  articleOpen access

  Partitioning of repressive from actively transcribed chromatin in mammalian cells fosters cell-type-specific gene expression patterns. While this partitioning is reconstructed during differentiation, the chromatin occupancy of the key insulator, CCCTC-binding factor (CTCF), is unchanged at the developmentally important Hox clusters. Thus, dynamic changes in chromatin boundaries must entail other activities. Given its requirement for chromatin loop formation, we examined cohesin-based chromatin occupancy without known insulators, CTCF and Myc-associated zinc-finger protein (MAZ), and identified a family of zinc-finger proteins (ZNFs), some of which exhibit tissue-specific expression. Two such ZNFs foster chromatin boundaries at the Hox clusters that are distinct from each other and from MAZ. PATZ1 was critical to the thoracolumbar boundary in differentiating motor neurons and mouse skeleton, while ZNF263 contributed to cervicothoracic boundaries. We propose that these insulating activities act with cohesin, alone or combinatorially, with or without CTCF, to implement precise positional identity and cell fate during development.

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• Identification of molecular signatures defines the differential proteostasis response in induced spinal and cranial motor neurons

  Cell Reports · 2024-03-01 · 4 citations

  articleOpen access

  Amyotrophic lateral sclerosis damages proteostasis, affecting spinal and upper motor neurons earlier than a subset of cranial motor neurons. To aid disease understanding, we exposed induced cranial and spinal motor neurons (iCrMNs and iSpMNs) to proteotoxic stress, under which iCrMNs showed superior survival, quantifying the transcriptome and proteome for >8,200 genes at 0, 12, and 36 h. Two-thirds of the proteome showed cell-type differences. iSpMN-enriched proteins related to DNA/RNA metabolism, and iCrMN-enriched proteins acted in the endoplasmic reticulum (ER)/ER chaperone complex, tRNA aminoacylation, mitochondria, and the plasma/synaptic membrane, suggesting that iCrMNs expressed higher levels of proteins supporting proteostasis and neuronal function. When investigating the increased proteasome levels in iCrMNs, we showed that the activity of the 26S proteasome, but not of the 20S proteasome, was higher in iCrMNs than in iSpMNs, even after a stress-induced decrease. We identified Ublcp1 as an iCrMN-specific regulator of the nuclear 26S activity.

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Recent grants

• Understanding CTCF Boundaries Controlling Hox Gene Expression

  NIH · $3.6M · 2018–2029

• NIH Grant R01HD079682

  NIH · $1.5M · 2020

Frequent coauthors

• Shaun Mahony

  32 shared

• Hynek Wichterle

  Columbia University

  30 shared

• Elizabeth C. Engle

  Howard Hughes Medical Institute

  19 shared

• David K. Gifford

  Massachusetts Institute of Technology

  18 shared

• Matthew F. Rose

  Boston Children's Hospital

  18 shared

• Ryosuke Fujiki

  Kokura Memorial Hospital

  15 shared

• Begüm Aydın

  Rockefeller University

  14 shared

• Disi An

  13 shared