About

Gregory E. Crawford is the Wilburt C. Davison Distinguished Professor of Pediatrics and a Professor in Pediatrics at Duke University School of Medicine. He also holds the position of Associate Professor in Molecular Genetics and Microbiology and is an affiliate of the Duke Regeneration Center. His contact information includes an email at greg.crawford@duke.edu and his office is located in Room 2111 CIEMAS, Durham, NC. The page indicates his involvement in the Third Year University Program in Genetics and Genomics, highlighting his focus on genetics and genomics within the context of pediatrics and molecular biology.

Research topics

• Biology
• Genetics
• Psychiatry
• Psychology
• Medicine
• Neuroscience
• Clinical psychology
• Computational biology
• Computer Science
• Demography
• Oncology
• Evolutionary biology
• Cell biology
• Internal medicine

Selected publications

• Mismatch tolerance of a gRNA for CRISPR-based gene activation confers broad activity critical for cell reprogramming

  bioRxiv (Cold Spring Harbor Laboratory) · 2026-02-03 · 1 citations

  articleOpen accessCorresponding

  CRISPR activation and interference systems (CRISPRa/i) are widely used for programmable transcriptional control. Although these technologies are capable of highly specific single-gene activity, some applications of transcriptional network reprogramming require broad, genome-wide effects. Here, we identify a CRISPRa gRNA that robustly reprograms astrocyte transcriptional state. Unexpectedly, this activity arises from extensive off-target binding that induces expression changes in thousands of genes, unlike neighboring gRNAs targeting the same intended on-target site. We leverage this promiscuous gRNA to dissect determinants of gRNA-driven off-target dCas9 binding in the context of transcriptional reprogramming. Using ChIP-seq, high-throughput protein-binding microarrays, and gRNA-variant library screening in cells, we demonstrate that PAM-proximal bases are primary determinants of genomic binding, mismatch tolerance is both gRNA- and base-specific, and targeted mutations within the PAM-proximal region can tune gRNA specificity. We further demonstrate that CRISPRa-driven phenotypes can reflect combined contributions from widespread off-target activity and dose-dependent on-target effects. These findings highlight the potentially widespread impacts of CRISPRa off-target activity, underscore the need to account for cryptic effects when selecting and evaluating gRNAs for programming cell phenotypes, and demonstrate that multi-site binding by CRISPRa systems can be exploited as a feature for network-level perturbations in cell reprogramming.

  PublisherOA PDFDOI

• Transcriptome-wide association study of schizophrenia and chromatin activity yields mechanistic disease insights

  UNC Libraries · 2026-02-10

  articleOpen access
  PublisherDOI

• Reprogramming of neuronal genome function and phenotype by astrocytes

  bioRxiv (Cold Spring Harbor Laboratory) · 2026-03-07

  articleOpen access

  Abstract Heterotypic cell-cell interactions are critical to governing cellular physiology, disease progression, and responses to the environment and pharmacologic interventions. For example, neurons and astrocytes engage in intricate interactions that are essential for brain development and function 1–3 . However, the transformation of these extracellular signals into epigenomic regulation that governs cell function is poorly understood. Here, we report that weeks of co-culture between human induced pluripotent stem cell (hiPSC)-derived neurons and mouse cortical astrocytes extensively reprograms gene expression and the chromatin accessibility landscape in neurons, affecting thousands of genes and putative gene regulatory elements (REs), including many transcription factors (TFs). These genes are enriched for functions implicated in neuronal differentiation and maturation, and tend to be impacted in schizophrenia, and autosomal dominant Alzheimer’s disease. Through complementary CRISPR interference and activation screens, we recapitulated hundreds of astrocyte-induced transcriptional and chromatin remodeling events in mono-cultured neurons at both promoters and distal regulatory elements (REs) of TF genes. We discovered functional REs for ∼50 astrocyte-responsive TF genes, providing a map of gene regulatory network control. Astrocyte-responsive TF genes fall into groups that exert independent or counter-balancing transcriptional effects, highlighting the complex coordination of the neuronal response to astrocytes. Functional effects of specific TFs, including POU3F2 and TFAP2E, on neurite morphology and neuronal electrophysiology are consistent with transcriptional effects, demonstrating the capacity of direct epigenetic control to mimic heterotypic cellular signals. This work illuminates the regulation of neurodevelopment-and disease-relevant gene modules by neuron-astrocyte interactions, and provides a blueprint for applying modern functional genomics to uncover the links between cell microenvironment and epigenomic programming. Highlights Neuronal gene expression and chromatin accessibility landscape are profoundly remodeled by astrocytes over weeks of co-culture Astrocyte-responsive neuronal gene modules and neuron-responsive astrocytic gene modules are enriched for genes associated with schizophrenia and familial Alzheimer’s Disease Single-cell CRISPR interference and activation screens of astrocyte-responsive gene regulatory elements identified dozens of functional regulatory elements of TF genes in neurons Single-cell CRISPR interference and activation screens of >200 astrocyte-responsive TF genes uncovered discrete functional clusters that promote neuronal maturity or stemness Astrocyte-responsive TF genes reprogram neuronal electrophysiology and neurite morphology

  PublisherDOI

• Does Childhood Trauma Moderate Polygenic Risk for Depression? A Meta-analysis of 5765 Subjects From the Psychiatric Genomics Consortium

  UNC Libraries · 2026-02-10

  articleOpen access
  PublisherDOI

• Enhancer hubs govern chromatin topology and Th17 cell identity

  bioRxiv (Cold Spring Harbor Laboratory) · 2026-04-04

  articleOpen access

  Abstract / Summary A wealth of noncoding regulatory elements has been described across mammalian cell types, yet determining their functional role remains a challenge. Regulatory control of gene expression is critical during active processes such as the adaptive immune response. Upon antigen presentation, a naive CD4+ T cell undergoes major transcriptional and structural reorganization necessary for establishment of subset identity and immune function. In this study, we systematically measure the regulatory potential of candidate regulatory elements associated with open chromatin across five mouse CD4+ T cell subsets. Using ATAC-STARR-seq, we found that approximately one quarter of open chromatin regions demonstrate regulatory activity. Most exhibit shared functional potential across subsets, though we identify enhancers with activity that is restricted to specific cellular contexts. To distinguish regulatory potential from endogenous function, we performed CRISPR-based epigenome editing screens at noncoding regions of Th17 cells and identified a set of core elements essential for subset polarization. Integrating Region Capture Micro-C, we resolved precise 3D chromatin topologies that explain functional regulatory networks via physical contacts. We characterize examples of active regulatory hubs formed through multiple CTCF-independent interactions organized in a hierarchical architecture. Furthermore, we discover a critical Batf enhancer that operates via these contacts. Using targeted perturbations, we disrupt local chromatin topology and gene expression with profound consequence to downstream Th17 cell phenotypes. We confirm the physiological necessity of these functional enhancers in vivo , demonstrating the importance of noncoding elements for Th17 cell identity. Together, this work reveals how DNA sequence and chromatin cooperate to shape the regulatory logic of Th17 cells, with implications for cis-regulatory principles beyond the immune system.

  PublisherDOI

• Unraveling the genetic complexity of Alzheimer's disease across diverse populations via integrative single‐cell multi‐omics

  Alzheimer s & Dementia · 2025-12-01

  articleOpen access

  BACKGROUND: The multifactorial and heterogenous nature of Late Onset Alzheimer's disease (LOAD) presents a challenge, particularly in capturing genetic complexity across diverse populations. Recent single-nucleus (sn)multi-omics analyses have advanced the LOAD genetics field. However, most studies were conducted in European ancestry subjects, while other populations remain largely understudied. Here, we aimed to explore the underpinning genetics of LOAD in diverse populations and to gain insights into the shared (pan-ethnic) and distinct (ancestry-specific) genetic drivers of LOAD between European and African ancestries. METHODS: We analyzed cortical tissues from European (EA) and African ancestry (AA) LOAD and control donors, and simultaneously characterized their transcriptomic (snRNA-seq) and chromatin accessibility (snATAC-seq) profiles at a single-cell level using 10x Genomics Multiome technology. We analyzed these datasets using our integrative genomic pipeline to catalogue differentially expressed genes (DEGs) in LOAD and to identify candidate cis-regulatory elements (cCREs) and their target DEGs at the cell-subtype level. Finally, we performed differential-expression analysis on the combined snRNA-seq datasets from both ancestries and modeled ancestry interactions for statistically robust inference of shared and divergent DEGs between ancestries. RESULTS: EA and AA nuclei were clustered into 32 cell-subtypes each, representing 8 major neuronal and glial cell types. The highest numbers of DEGs were found in GABAergic and interneuron subtypes in EA vs. GABAergic neuron and oligodendrocyte subtypes in AA. Analysis of cCRE-DEG pairs revealed differential chromatin interactions governing gene dysregulation across ancestries. For example, microglial APOE expression was predicted be regulated by six EA-specific and four AA-specific cCREs, and only one common cCRE. Differential expression analysis revealed the highest numbers of pan-ethnic DEGs in specific excitatory and inhibitory neuronal subtypes, with excitatory-neuron DEGs primarily associated with cellular growth and extracellular matrix assembly, and inhibitory-neuron DEGs largely associated with membrane trafficking. Ancestry-specific DEGs were more commonly identified in AA compared to EA. AA-specific DEGs were also primarily in excitatory-neurons, with roles in fatty acid metabolism and neuronal structure, and in inhibitory-neurons with roles in respiration and synaptic transmission. CONCLUSIONS: These results enhance our understanding of the shared and distinct cell-subtype gene dysregulation networks and biological processes underlying LOAD in African vs. European ancestries.

  PublisherOA PDFDOI

• Cross-tissue molecular responses in the liver and blood after toxicant exposures

  Research Square · 2025-10-10 · 1 citations

  preprintOpen access
  PublisherOA PDFDOI

• Cell Modeling and Rescue of a Novel Non-coding Genetic Cause of Glycogen Storage Disease IX

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-05-17

  preprintOpen access

  Abstract Delayed diagnosis of Mendelian disease substantially prevents early therapeutic intervention that could improve symptoms and prognosis. One major contributing challenge is the functional interpretation of non-coding variants that cause disease by altering splicing and/or gene expression. We identified two siblings with glycogen storage disease (GSD) type IX γ2, both of whom had a classic clinical presentation, enzyme deficiency, and a known pathogenic splice acceptor variant on one allele of PHKG2 . Despite the autosomal recessive nature of the disease, no variant on the second allele was identified by gene panel sequencing. To identify a potential missing second pathogenic variant, we completed whole genome sequencing (WGS) and detected putative deep intronic splicing variant in PHKG2 in both siblings. We confirmed the functional splicing effects of this variant using short-read and long-read RNA-seq on patient blood and a HEK293T cell model in which we installed the variant using CRISPR editing. Using the cell model, we demonstrated multiple biochemical and cellular impacts that are consistent with GSD IX γ2, and a reversal of aberrant splicing using antisense splice-switching oligonucleotides. In doing so, we demonstrate a novel and robust pathway for detecting, validating, and reversing the impacts of novel non-coding causes of rare disease.

  PublisherOA PDFDOI

• Toxicogenomic Insights into Environmental Toxicant Exposures: The TaRGET II Resource

  Research Square · 2025-08-20

  preprintOpen access
  PublisherOA PDFDOI

• Promoter Deletion Leading to Allele Specific Expression in a Genetically Unsolved Case of Primary Ciliary Dyskinesia

  UNC Libraries · 2025-10-05

  articleOpen access

  Variation in the non-coding genome represents an understudied mechanism of disease and it remains challenging to predict if single nucleotide variants, small insertions and deletions, or structural variants in non-coding genomic regions will be detrimental. Our approach using complementary RNA-seq and targeted long-read DNA sequencing can prioritize identification of non-coding variants that lead to disease via alteration of gene splicing or expression. We have identified a patient with primary ciliary dyskinesia with a pathogenic coding variant on one allele of the SPAG1 gene, while the second allele appears normal by whole exome sequencing despite an autosomal recessive inheritance pattern. RNA sequencing revealed reduced SPAG1 transcript levels and exclusive allele specific expression of the known pathogenic allele, suggesting the presence of a non-coding variant on the second allele that impacts transcription. Targeted long-read DNA sequencing identified a heterozygous 3 kilobase deletion of the 5' untranslated region of SPAG1, overlapping the promoter and first non-coding exon. This non-coding deletion was missed by whole exome sequencing and gene-specific deletion/duplication analysis, highlighting the importance of investigating the non-coding genome in patients with "missing" disease-causing variation. This paradigm demonstrates the utility of both RNA and long-read DNA sequencing in identifying pathogenic non-coding variants in patients with unexplained genetic disease.

  PublisherDOI

Recent grants

• NIH Grant R41GM119914

  NIH · $225k · 2017

• NIH Grant R21NS084336

  NIH · $422k · 2015

• NIH Grant R01ES023195

  NIH · $2.2M · 2018

• Engineering Targeted Epigenetic Modifiers for Precise Control of Gene Regulation

  NIH · $2.6M · 2013–2018

• NIH Grant U54HG004563

  NIH · $9.7M · 2013

Frequent coauthors

• Lingyun Song

  212 shared

• Alexias Safi

  Duke Medical Center

  134 shared

• Thomas G. Schulze

  National Institute of Mental Health

  94 shared

• Timothy E. Reddy

  Duke University

  92 shared

• Fabian Streit

  Central Institute of Mental Health

  71 shared

• Terrence S. Furey

  University of North Carolina at Chapel Hill

  66 shared

• Stephan Ripke

  Charité - Universitätsmedizin Berlin

  66 shared

• Josef Frank

  Heidelberg University

  62 shared