About

Jef D. Boeke is a Professor of Biochemistry and Molecular Pharmacology and a Professor of Biomedical Engineering at NYU Tandon School of Engineering. He is also the Director of the Institute for Systems Genetics and a member of the National Academy of Sciences (NAS) and the American Academy of Arts and Sciences (AAA&S). His laboratory is well known for foundational work on mechanistic and genomic aspects of retro-transposition in yeast and mammalian systems. The Boeke lab is heavily involved in developing novel technologies in genetics, genomics, and synthetic biology, using yeast as a platform for exploring the construction of fully synthetic chromosomes for practical and theoretical studies. His team has assembled an international consortium called SC2.0 to rewrite and synthesize the first eukaryotic organism, Saccharomyces cerevisiae, with a projected complete synthesis and debugging of the entire genome by the end of 2020. His research interests include cancer, computational biology, genome integrity, genomics, microbiology, pharmacology, stem cell biology, systems biology, yeast, and retrotransposons. Boeke holds a Ph.D. from Rockefeller University and has experience at NYU Langone Health and the Institute for Systems Genetics.

Research topics

• Biology
• Genetics
• Evolutionary biology
• Cell biology
• Internal medicine
• Biochemistry
• Computational biology
• Urology
• Medicine
• Andrology

Selected publications

• Improved vector toolkit for genome writing in mammalian cells

  bioRxiv (Cold Spring Harbor Laboratory) · 2026-03-16

  articleOpen access

  Efficient genome writing in mammalian cells requires robust methods for integrating large DNA payloads. The previously described method mammalian Switching Antibiotic resistance markers Progressively for Integration (mSwAP-In) enables iterative, biallelic genome rewriting in mammalian stem cells with DNA payloads exceeding 100 kb. However, the lack of standardized vectors and certain technical constraints have limited its broader adoption. Here we present an improved plasmid toolkit designed to streamline the implementation of mSwAP-In. The toolkit includes two core vectors. pLP-TK (pCTC174) is a landing-pad plasmid compatible with Golden Gate assembly of genomic homology arms and supports both mSwAP-In and the recombinase-mediated cassette exchange method Big-IN. mSwAP-In MC2v2 (pKBA135) is a versatile Big DNA assembly and delivery vector that supports Gibson-based assembly and incorporates positive, negative, and fluorescent selection markers, as well as a backbone counterselection cassette to minimize unwanted plasmid integration. The vector architecture also enables propagation in yeast and bacterial hosts, inducible plasmid copy-number amplification in standard E. coli strains, and CRISPR/Cas9-mediated payload release through preinstalled guide RNA target sites. We further characterize the FCU1/5-FC counterselection system in mouse embryonic stem cells and define conditions that minimize its bystander toxicity. Finally, we provide a set of Cas9-gRNA expression plasmids optimized for common mSwAP-In applications. Together, these reagents constitute a standardized and experimentally validated toolkit that simplifies large-scale genome writing using mSwAP-In.

  PublisherOA PDFDOI

• Intrahepatic reporter assay reveals leaky somatic blockade of L1 retrotransposition in mice

  bioRxiv (Cold Spring Harbor Laboratory) · 2026-02-12

  articleOpen access

  Abstract Long interspersed element-1 (LINE-1, L1) retrotransposition has long been proposed to occur in somatic tissues, yet direct experimental evidence distinguishing adult somatic events from early embryonic insertions has remained limited. Here we establish an intrahepatic L1 reporter assay that enables immunohistochemical detection and quantitative analysis of L1 retrotransposition in vivo . Using autonomous and non-autonomous L1 reporter variants, we demonstrate clearly detectable somatic L1 activity in the mouse liver. Comparative analysis of L1 activity in liver tissue and tumor-derived cell culture reveals that tumor cells preferentially restrict L1 at early regulatory stages, consistent with epigenetic control, whereas downstream defence mechanisms are comparatively permissive. In contrast, normal liver tissue shows stronger restriction at later stages of the L1 life cycle. Together, our results provide direct experimental evidence for somatic L1 retrotransposition in vivo in adult liver and reveal distinct regulatory strategies that shape L1 activity in tumor versus normal somatic cells. Teaser Genome destabilizing L1 retrotransposon activity is present in somatic tissues, where it likely contributes to cancer development.

  PublisherOA PDFDOI

• Genome writing and Targeted Delivery of the <i>NKX6-3/ANK1</i> gene cluster and its Type 2 Diabetes GWAS Variants to Human iPSCs

  bioRxiv (Cold Spring Harbor Laboratory) · 2026-01-05

  articleOpen accessSenior authorCorresponding

  Abstract Genome-wide association studies (GWAS) identified over 600 loci containing single-nucleotide polymorphisms (SNPs) associated with type 2 diabetes (T2D), most of which reside in non-coding regions. Among the set of T2D SNPs, linking causal genome variants to disease risk experimentally has remained a challenge; however, advances in synthetic mammalian genome writing techniques now enable the delivery of multiple haplotypes to human induced pluripotent stem cells (hiPSCs) to create a series of isogenic cell lines that can be differentiated and phenotyped in vitro . Here, to begin efforts in dissecting a T2D GWAS locus, we engineered an NKX6-3/ANK1 gene cluster knockout hiPSC line and introduced a landing pad facilitating the delivery of synthetic haplotype payloads. We built four haplotypes, including several that are not observed in nature, containing risk SNPs spanning the NKX6-3/ANK1 gene cluster using a method called “variant Switching Auxotrophic markers for Integration” (vSwAP-In), and integrated them precisely into hiPSCs. NKX6-3/ANK1 deletion blocked pancreatic progenitor and skeletal muscle differentiation, suggesting that NKX6-3 and ANK1 are required for early pancreatic and skeletal muscle development, and perhaps related to the existence of two nonoverlapping sets of SNPs in linkage disequilibrium that associate with the expression of the two adjacent genes. When NKX6-3 / ANK1 T2D “Risk” haplotypes were reintroduced, skeletal muscle and pancreatic progenitor differentiation capabilities were restored. ANK1 expression was elevated in the ANK1 Risk and All-Risk haplotypes compared to the NKX6-3 Risk and Non-Risk haplotypes, establishing a functional experimental platform to examine risk SNP clusters in their native contexts. Overall, this work establishes a platform for the dissection of GWAS loci using synthetic haplotype genomics in hiPSCs. Significance Statement Genome-wide association studies have been used to identify disease-associated SNPs; however, most SNPs lie in non-coding regions, making functional experimentation difficult to perform. Using vSwAP-In, a yeast-based DNA variant-building method, and mSwAP-In, a mammalian genome engineering approach, we establish a platform for functional GWAS dissection in hiPSCs. This platform allows us to build DNA harboring virtually any combination of disease-risk SNPs, allowing for functional characterization of SNPs without the limitations of linkage disequilibrium. We demonstrate this approach using a Type 2 diabetes GWAS gene cluster, NKX6-3/ANK1 .

  PublisherOA PDFDOI

• To make biology programmable, we must master its generative grammar

  Molecular Therapy · 2026-02-24

  articleOpen accessSenior author
  PublisherOA PDFDOI

• Ancient co-option of LTR retrotransposons as yeast centromeres

  Nature · 2026-02-18 · 2 citations

  articleOpen accessSenior author

  Abstract Centromeres ensure accurate chromosome segregation, yet their DNA evolves rapidly across eukaryotes leaving the origins of new centromere architectures unclear 1–4 . The brewer’s yeast Saccharomyces cerevisiae exemplifies this long-standing puzzle. Its centromeres shifted ancestrally from large, repeat-rich, epigenetically specified forms to the compact, genetically defined ‘point’ centromeres 1,5 . How this transition occurred has remained unresolved 6 . Here we identify evolutionarily related ‘proto-point’ centromeres that provide a resolution to the evolutionary origins of point centromeres. Proto-point centromeres contain a single centromeric nucleosome positioned over an AT-rich core, accompanied by relaxed organization and sequence variability of flanking cis -elements. In two species, these proto-point centromeres lie within retrotransposon-derived repeat clusters, linking ancestral repeat-rich centromeres to genetically encoded ones. Comparative and phylogenetic analyses indicate that proto-point and point centromeres evolved in an ancestor with retrotransposon-rich centromeres. These results identify long-terminal-repeat retrotransposons, specifically Ty5 sequences, as the genetic substrate for point-centromere evolution and provide a mechanistic route by which an epigenetic centromere can become genetically specified. More broadly, they show how selfish elements can be co-opted to perform essential chromosomal functions.

  PublisherDOI

• Physiology and immunology of a pig-to-human decedent kidney xenotransplant

  Nature · 2025-11-13 · 16 citations

  article
  PublisherDOI

• Multi-omics analysis of a pig-to-human decedent kidney xenotransplant

  Nature · 2025-11-13 · 13 citations

  articleOpen access
  PublisherOA PDFDOI

• Retrotransposon Activation in the Aged and Alzheimer’s Disease Brain Examined by Nanopore Long-read DNA Sequencing

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-12-15

  articleOpen access

  Background: Cellular defenses against retrotransposable elements (RTEs) weaken with age and RTEs have been reported to contribute to Alzheimer's disease (AD) pathogenesis by promoting neuroinflammation. The mechanisms implicated include DNA damage promoted by retrotransposition and interferon system activation by RTE-derived cDNA intermediates. LINE-1 (L1) retrotransposons are of particular interest because they are the only autonomously active RTEs in the human genome. Results: To investigate L1 activation and retrotransposition in AD, we performed Nanopore long-read DNA sequencing on six late-onset AD (LOAD) and six age-matched control human prefrontal cortex (PFC) samples. We developed and validated a stringent RTE insertion calling pipeline and identified two high-confidence somatic insertions, one AluY and one L1HS. We estimate that ∼1% of cells in the aged PFC have a somatic RTE insertion. AD samples were hypomethylated, and genome-wide analysis of differentially methylated regions (DMRs) supports a process of epigenetic drift in AD. DMR-associated gene sets primarily related to brain function and inflammation. To investigate L1 activation we used CpG methylation as a proxy for L1 expression. We observed decreased methylation at young L1 elements. While most reads overlapping the L1HS promoter were highly methylated (>80% methylated), 7% were <50% methylated, 1% were <25%, and the highly demethylated read fraction increased in AD. L1HS 5' UTR methylation was strongly correlated with RNA expression. Conclusions: CpG methylation-mediated repression of young RTEs is compromised in old age - our findings indicate that this is further exacerbated in AD. Amid these failing defenses, we report somatic retrotransposition events in the aging and demented brain.

  PublisherOA PDFDOI

• Myelin pathology is a key feature of X-linked Dystonia Parkinsonism

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-10-08

  preprintOpen access

  X-linked Dystonia-Parkinsonism (XDP) is a progressive, adult-onset neurodegenerative movement disorder that predominantly affects males of Filipino descent 1-3 . The disease is caused by the insertion of a SINE-VNTR-Alu subfamily F (SVA_F) retrotransposon within an intron of the TATA-box binding protein-associated factor 1 ( TAF1 ) gene 4 . A major barrier to understanding the pathophysiology of XDP has been the lack of relevant animal models. Here, we introduce a novel conditional humanized XDP mouse model harboring a hybrid mouse-human Taf1 / TAF1 gene (hy TAF1 ) containing the pathogenic SVA_F insertion. We activated the hy TAF1 in Nestin+ neural progenitor cells and found that the resulting XDP male mice recapitulate features of the human disease including severe motor impairment, striatal atrophy, and reactive gliosis. Transcriptomic, histological, and electron microscopy analysis revealed a dramatic reduction in oligodendrocyte lineage cells and widespread myelin disruption. Consistent with these findings, postmortem brain tissue from XDP patients revealed similar myelin pathology, including near-complete loss of myelin in parts of the medial prefrontal cortex. Together, these results identify oligodendrocyte dysfunction and myelin loss as previously unrecognized contributors to XDP pathogenesis, providing new mechanistic insight into this debilitating disorder.

  PublisherOA PDFDOI

• Figure 6 from Selective Depletion of Cancer Cells with Extrachromosomal DNA via Lentiviral Infection

  2025-08-28

  preprintOpen access

  &lt;p&gt;Integrase-deficient lentivirus does not rescue the effect of integrase-intact lentivirus on ecDNA depletion. &lt;b&gt;A,&lt;/b&gt; PC3-NCI and (&lt;b&gt;B&lt;/b&gt;) HeLa-MTX-Res cells were either untreated or transduced with Cas9-expressing lentivirus (genome size = 8 kb) generated either using wild-type integrase (Cas9 WT integrase) or point mutant integrase (Cas9 D64V integrase) that does not integrate into the genome. After 48 hours of transduction, cells were cultured for 2 weeks. FISH analysis with oncogene probes was performed to quantify subpopulations (ANOVA; *, &lt;i&gt;P&lt;/i&gt; &lt; 0.01; **, &lt;i&gt;P&lt;/i&gt; &lt; 0.05; #, &lt;i&gt;P&lt;/i&gt; &lt; 0.05; ##, &lt;i&gt;P&lt;/i&gt; &lt; 0.01; ns = 2).&lt;/p&gt;

  PublisherDOI

Recent grants

• Synthesis and Restructuring of a Yeast Chromosome

  NSF · $707k · 2007–2011

• Brca1-Mediated Suppression Of Retrotransposon Activity - Resubmission - 1

  NIH · $436k · 2020–2023

• Synthesis And Restructuring of a Yeast Chromosome

  NSF · $599k · 2014–2016

• NIH Grant R01GM036481

  NIH · $9.1M · 2014

• NIH Grant P50GM10763206

  NIH · $4.1M · 2019

Frequent coauthors

• Joel S. Bader

  206 shared

• Leslie A. Mitchell

  Institute for Systems Biology

  125 shared

• Junbiao Dai

  Chinese Academy of Agricultural Sciences

  117 shared

• Kathleen H. Burns

  115 shared

• Yizhi Cai

  University of Manchester

  97 shared

• Giovanni Stracquadanio

  University of Edinburgh

  88 shared

• Xuewen Pan

  Tango Therapeutics (United States)

  86 shared

• David Fenyö

  78 shared

Labs

• Health Tech HubPI

Education

• Ph.D., Molecular and Cell Biology

  University of California, San Francisco

  1985

• M.S., Molecular and Cell Biology

  University of California, San Francisco

  1981

• B.S., Biology

  University of California, San Diego

  1977

Awards & honors

• Fellow of the National Academy of Inventors