The research team, led by Nana Matoba, Jessica McAfee, Hyejung Won and Jason Stein at the University of North Carolina at Chapel Hill, deployed a massively parallel reporter assay, or MPRA, to interrogate 9,092 genetic variants associated with human cortical structure. The logic of the assay is elegant. Each candidate variant is synthesized as a short 150-base-pair segment of DNA, cloned into a plasmid upstream of a minimal promoter that drives a luciferase reporter gene, and tagged with a random 20-base-pair barcode. When the pooled library is introduced into cells, the amount of barcode RNA produced by each construct reflects the regulatory power of the DNA segment attached to it. By sequencing both the RNA transcripts and the plasmid DNA, researchers can calculate a transcription rate for every element, and by testing both alleles of a variant side by side, they can detect whether one version of the sequence drives expression more strongly than the other.

The cellular context matters enormously here. The team performed the assay in primary human neural progenitor cells, the fetal-derived stem cells that generate the neurons of the developing cortex. Previous work had shown that variants associated with cortical structure are enriched in regulatory regions active in these progenitors and colocalize with genetic effects on chromatin accessibility and gene expression in the same cells. This supports a model in which noncoding variants act during prenatal development, altering transcription factor binding and gene expression in progenitor cells, and thereby influencing decisions about cell proliferation and fate that ultimately determine cortical size in adulthood. The researchers transfected the library into 16 biological replicates, and after 24 hours split the cultures: half received a vehicle control, while half were treated with CHIR99021, a potent inhibitor of GSK3β that activates the Wnt signaling pathway, a key developmental signal known to influence brain size.

The results were striking in their scale and reproducibility. Regulatory activity measurements correlated between replicates with a median Pearson’s coefficient of 0.99, and the positive control promoters behaved exactly as expected. Among 17,837 elements tested under baseline conditions, 988 showed regulatory activity significantly above the negative controls, representing 918 variants drawn from 150 of the 198 cortical-structure-associated loci examined—meaning that 76 percent of the loci contained at least one variant with detectable regulatory function. More than half of the active variants also showed allelic effects, meaning one DNA letter change measurably altered transcription. The team dubbed these expression-modulating variants, or emVars, and they represent the strongest candidates for the true causal variants hiding within blocks of correlated genetic variation that have long frustrated geneticists.

Perhaps the most surprising finding came when the researchers asked what sequence features distinguished the active elements. Active elements were dramatically enriched in short interspersed nuclear elements, or SINEs—a class of retrotransposons, the so-called jumping genes that copy and paste themselves throughout the genome. Within the SINE family, the enrichment was driven almost entirely by Alu elements, primate-specific repeats that have expanded in prevalence alongside increases in brain size over human evolution. A typical Alu element carries two conserved sequences in its left arm, the A box and the B box, which function as promoters for RNA polymerase III. The most active MPRA elements sat precisely in this left arm, and elements containing both boxes showed the highest activity of all. Variants with the strongest allelic effects clustered near these promoter boxes, and even a scrambled negative control that accidentally contained a B-box-like sequence showed strong activity—a striking confirmation of the mechanism.

Skeptics might worry that such activity is an artifact of the episomal plasmid system, in which DNA is not packaged into chromatin as it would be in the native genome. The team addressed this concern with multiple lines of endogenous evidence. Fetal brain tissue shows among the lowest levels of repressive chromatin marks, such as H3K9me3 and H3K27me3, deposited on Alu elements of any tissue in the body, and the MPRA-active Alu elements are rarely repressed in fetal brain specifically. The active elements were also enriched for enhancer RNAs and promoter upstream antisense RNAs, noncoding transcripts previously shown to mediate enhancer-promoter communication through Alu sequences. Finally, using CUT&RUN profiling, the researchers showed that MPRA-active Alu elements are significantly enriched within binding sites of TFIIIC, a transcription factor complex associated with polymerase III and Alu activity. Together, these data suggest that the reporter activity reflects genuine regulatory potential in the developing brain.

The evolutionary implications are tantalizing. Alu elements can be dated by their accumulated mutations, measured as sequence divergence from the ancestral consensus. The younger Alu elements—those with fewer than 100 mismatches per thousand bases—showed significantly higher regulatory activity than older ones, particularly when located in the left arm of the element. Because Alu insertions have proliferated in the primate lineage in step with brain size expansion, the findings suggest that relatively recent retrotransposon insertions created new regulatory elements that influenced neurodevelopmental genes and may have contributed to the expansion of the human cortex. The authors caution that a neutral decay of regulatory potential in older elements over evolutionary time could also explain the pattern, but the convergence with known primate-specific biology makes the adaptive interpretation compelling.

The study also connected individual variants to specific transcription factors and, remarkably, to specific brain regions. Active elements were enriched for binding motifs of three transcription factor clusters—ZNF135/ZNF460, MEF2A-D and Zfx—and the magnitude of a variant’s allelic effect correlated strongly with how severely it disrupted a predicted motif. Disruption of RARA, RARG, ZNF135 and NR2F1 motifs produced the largest impacts. Intriguingly, the consensus sequences of recently evolved Alu subfamilies contain retinoic acid receptor binding sites, linking the transposon story to developmental signaling. Even more strikingly, when the team compared the regional pattern of a variant’s effect on cortical structure with the expression of the disrupted transcription factor across prenatal brain regions from the BrainSpan Atlas, they found significant correlations for seven variants. A variant that disrupts the RARG binding motif, for example, reduced surface area most strongly in regions where RARG expression was highest—suggesting that the regional specificity of genetic effects is governed by where the relevant transcription factors are actually present.

Wnt stimulation added another layer of complexity. Under CHIR treatment, the team detected a similar number of active elements, but 32 elements gained activity specifically under stimulation while seven lost it, and 12 variants showed allelic effects that differed significantly between conditions. One example, rs4670759, associated with the surface area of the inferior temporal cortex, showed enhanced activity and increased chromatin accessibility under Wnt stimulation; it sits in the promoter of CDC42EP3, a gene involved in actin cytoskeleton formation whose expression rises with Wnt activation, and the risk allele is predicted to disrupt a PLAGL2 motif that is itself upregulated by the pathway. Another variant, rs2802295 within an intron of FOXO3, showed an allelic effect only under stimulation near a Wnt-responsive element. The team then used CRISPR interference to silence that element in progenitor cells and confirmed that FOXO3 expression dropped—experimentally tying a cortical-structure-associated variant to its target gene in a condition-specific manner.

The study is not without limitations. The MPRA measures regulatory potential on episomal plasmids, and the overlap with endogenous chromatin accessibility quantitative trait loci was limited, indicating that native chromatin context modifies some effects. The analysis also focused on variants tested primarily in populations of European ancestry and did not address sex-dependent effects. Nevertheless, by experimentally separating correlated variants, identifying the transcription factors they disrupt, and demonstrating condition-dependent function, the work delivers a genome-scale functional framework for one of the most complex traits in human neuroimaging genetics. It transforms a catalog of statistical associations into a mechanistic hypothesis space—one in which ancient jumping genes, developmental signaling pathways and spatially patterned transcription factors jointly sculpt the most distinctive feature of the human brain.

Subject of Research: Functional characterization of noncoding genetic variants associated with human cortical structure using massively parallel reporter assays in neural progenitor cells

Article Title: Massively parallel assessment of gene regulatory activity at human cortical-structure-associated variants

Article References: Matoba, N., McAfee, J. C., Krupa, O., Beltran, A. A., Bell, J. L., Le, B. D., Valone, J. M., Min, H., Crawford, G. E., Raab, J. R., Won, H., & Stein, J. L. (2026). Massively parallel assessment of gene regulatory activity at human cortical-structure-associated variants. Nature Neuroscience. https://doi.org/10.1038/s41593-026-02454-2

Image Credits: AI Generated

DOI: 10.1038/s41593-026-02454-2

Keywords: cortical structure, massively parallel reporter assay, noncoding variants, Alu elements, neural progenitor cells, Wnt signaling, transcription factors, ENIGMA, gene regulation, brain development, retrotransposons, CRISPRi

UBAP2L first attracted attention from geneticists through the patients themselves. Rare variants in the UBAP2L gene have been repeatedly identified in individuals diagnosed with neurodevelopmental disorders, including autism spectrum disorder, a condition that affects communication, social interaction, and learning in millions of families worldwide. What those human genetic findings could not establish, however, was mechanism. Correlation between a mutated gene and a disorder does not reveal whether the protein acts during embryonic brain construction, in mature neurons, or in both. The new study was designed to answer precisely that question by removing the gene selectively from the developing nervous system of laboratory mice and watching what breaks.

The team used a well-established genetic engineering strategy known as the Nestin-Cre conditional knockout system. Nestin is a marker gene active in neural stem and progenitor cells, so pairing it with the Cre recombinase enzyme allows researchers to delete Ubap2l specifically and efficiently in the embryonic nervous system while leaving the gene intact everywhere else in the body. The researchers generated two groups of animals: heterozygous mutants, called cHET, carrying one functional copy of the gene, and homozygous conditional knockouts, called cKO, in which both copies were deleted from neural tissue. This design also mirrors the human genetic situation, where many patients carry a single damaged copy.

The anatomical consequences were unambiguous. Adult cKO mice weighed significantly less than their normal littermates, and histological examination of their brains revealed a marked reduction in the number of mature cortical neurons. The cortex, the folded outer layer of the brain responsible for perception, cognition, and voluntary movement, is built in an inside-out sequence: the earliest-born neurons settle in the deepest layers while successive waves of newborn neurons migrate past them to form the outer layers. At embryonic day 18.5, near the end of gestation, the knockout mice showed abnormal cortical lamination, meaning this precisely choreographed layering had gone wrong. The blueprint of the cortex had been corrupted at its source.

Tracing the defect further back in time, the researchers examined embryos at embryonic day 14.5, the height of the cortical neurogenic period when neural progenitor cells are dividing furiously to produce the neurons that will populate the cortex. At this stage, the abundance of cortical neural progenitor cells was already reduced, and the proliferation of the remaining progenitors was impaired. In other words, the root cause of the later cortical disorganization was not a failure of neurons to migrate or survive, but a failure of the stem cell pool to expand and deliver its full quota of neurons on schedule. Fewer progenitors dividing less efficiently means fewer neurons, and fewer neurons means a thinner, mislayered cortex.

Behavioral testing translated the cellular damage into functional terms. The cKO mice exhibited impaired social interaction and deficits in learning and memory, phenotypes that resonate strongly with the diagnostic features of autism spectrum disorder and related neurodevelopmental conditions. Importantly, the cHET mice, with only one copy of the gene deleted, showed milder behavioral and cognitive impairments. This dose-sensitive pattern, where gene copy number tracks with symptom severity, is a hallmark of many neurodevelopmental disorders and strengthens the argument that the mouse model faithfully recapitulates the human condition associated with UBAP2L variants.

To understand what was happening inside the cells, the researchers performed transcriptomic profiling, sequencing the RNA of the embryonic day 14.5 cortex to measure the activity of every gene. The differentially expressed genes clustered around three biological themes: transcriptional regulation, neuronal differentiation, and cell proliferation, with proliferation-related genes predominantly downregulated. Pathway analysis sharpened the picture further, revealing dysregulation of three major signaling cascades known to steer brain development: the PI3K-AKT pathway, which controls cell growth and survival; the MAPK pathway, which transmits proliferative signals; and the Wnt pathway, a master regulator of embryonic patterning and progenitor behavior. The convergence of these three pathways on a single deleted gene suggests that UBAP2L sits at or near a hub coordinating the proliferative program of neural progenitors.

The most mechanistically revealing experiments came from direct cell-cycle analysis. By examining cell-cycle phases in the embryonic cortex and running flow cytometric analysis on UBAP2L-deficient cells in culture, the team demonstrated that loss of Ubap2l produces two distinct cell-cycle defects: the S phase, during which DNA is replicated, became abnormally shortened, and cells accumulated in the G2/M checkpoint, indicating arrest before or during mitosis. A shortened S phase raises the specter of incomplete or error-prone DNA replication, while G2/M arrest halts division altogether. Together, these defects would throttle the output of the progenitor pool exactly when the cortex can least afford it. The cell cycle, it turns out, is where UBAP2L exerts its essential function.

The rescue experiments delivered the study’s most compelling verdict. When the researchers re-introduced wild-type UBAP2L into the deficient cells, the cell-cycle defects were reversed, confirming that the phenotype was specifically caused by the absence of this protein rather than by collateral damage from the engineering process. Critically, however, UBAP2L variants associated with neurodevelopmental disorders in patients failed to rescue cell-cycle progression. This is the functional smoking gun: the very mutations found in affected individuals abolish the protein’s ability to support normal cell division, directly linking patient genetics to a concrete cellular failure mode.

The broader implications reach well beyond a single gene. UBAP2L is known to participate in RNA processing and the assembly of membraneless cellular compartments called stress granules, and this study now positions it as a bridge between the cell’s gene-expression machinery and the proliferative demands of embryonic neurogenesis. For the growing number of families carrying UBAP2L variants, the work offers a biological explanation for their children’s conditions and a defined cellular process, progenitor cell-cycle control, as a potential point of therapeutic intervention. More generally, the study adds to a compelling emerging theme in neuroscience: many autism-related genes converge not on synapses or neurotransmitters, as once assumed, but on the fundamental mechanics of how the embryonic brain builds itself, one dividing progenitor at a time.

Subject of Research: The role of the UBAP2L protein in neural progenitor proliferation, cortical development, and autism-related neurodevelopmental disorders

Article Title: Neural-specific UBAP2L deficiency causes developmental delay and cortical abnormalities in mice

Article References: Neural-specific UBAP2L deficiency causes developmental delay and cortical abnormalities in mice. (n.d.). https://doi.org/10.1007/s00018-026-06416-6

Image Credits: AI Generated

DOI: 10.1007/s00018-026-06416-6

Keywords: UBAP2L, autism spectrum disorder, neurodevelopmental disorder, cerebral cortex, neural progenitor cells, cell cycle, conditional knockout mice, PI3K-AKT pathway, MAPK pathway, Wnt signaling, cortical lamination, developmental delay

One of the most striking exceptions is the common marmoset (Callithrix jacchus), a small South American monkey that has become an increasingly important model organism in biomedical research. Despite being a genuine primate, the marmoset carries a brain that is smooth and virtually unfolded, a feature that sets it apart from the majority of its relatives. For developmental neuroscientists, this raises an obvious and compelling question: if marmosets and humans descend from a shared primate lineage, what cellular changes during embryonic development cause the marmoset brain to grow less, remain smaller, and never acquire the pronounced folds seen in other species?

A team at the German Primate Center (DPZ) — the Leibniz Institute for Primate Research in Göttingen — set out to answer exactly that question. In a study published in Science Advances, the researchers traced the developmental divergence between smooth and folded primate brains back to specific differences in neural progenitor cells, the self-renewing precursors from which all neurons arise. Their central finding is that the marmoset brain does not start out different. In early embryogenesis it displays the typical structure and composition of a large, folded primate brain, and only later do particular processes intervene to slow the production of nerve cells.

“We wanted to understand which changes at the cellular level cause the marmoset brain to grow less and form fewer folds,” explains Lidiia Tynianskaia, one of the study’s two first authors and a PhD student in the Junior Research Group Brain Development and Evolution at the DPZ. “At the beginning of development, the common marmoset brain exhibits the typical structure and composition of a large, folded primate brain. As development progresses, processes must therefore occur that effectively slow down the production of nerve cells.” That framing matters, because it reframes the smooth marmoset brain not as a primitive starting point but as the outcome of active developmental regulation imposed partway through embryogenesis.

To investigate those processes, the researchers turned to brain organoids — small, three-dimensional cell cultures grown from stem cells that recapitulate key aspects of early brain development. Comparative organoid experiments using marmoset and human cells allowed the team to focus on the brain’s progenitor cells, the population whose behavior largely determines how many neurons the cortex will ultimately contain. Since neuron number is one of the decisive factors governing both the size of a brain and the degree to which its surface folds, differences in progenitor behavior are a natural place to look for the roots of anatomical divergence.

The comparisons revealed that several distinct mechanisms, operating at different levels and in different progenitor cell types, converge to reduce the size and folding of the marmoset cerebral cortex. “Our investigations have shown that certain progenitor cells in the common marmoset divide significantly more slowly than in humans,” says César Mateo Bastidas Betancourt, the study’s other first author and also a PhD student in the Junior Research Group. “Other progenitor cells have a simpler structure than their human counterparts, with fewer processes, and are therefore less proliferative. Both of these factors ultimately result in fewer nerve cells, which contributes to a smaller size and less folding of the cerebral cortex in marmosets.”

These two mechanisms are complementary rather than redundant. Slower cell division directly limits how quickly the progenitor pool expands, while a simpler morphology — fewer of the cellular processes that in more proliferative progenitors help sustain repeated rounds of division — appears to constrain the cells’ proliferative capacity itself. In folded primate brains, progenitor cells in the developing neocortex typically undergo many rounds of division, amplifying the pool of neurons that will populate the expanding cortical sheet. When that amplification is dialed down, as it is in marmosets, the downstream consequence is a thinner, smaller cortex with less surface area to fold.

Timing emerged as a third, crucial dimension of the story. The scientists showed that certain characteristics and behaviors of marmoset progenitor cells appear at altered time points compared with their human counterparts, with the net effect that marmoset progenitors have a shorter overall window during which they can proliferate rapidly. In developmental biology, such shifts in timing are a well-known engine of evolutionary change: modest adjustments to when developmental programs switch on or off can produce large differences in final organ size without requiring wholesale redesign of the underlying machinery. The marmoset data suggest that a compressed proliferative window is one such adjustment, quietly capping the neuron output of the developing cortex.

Because most of the experiments relied on organoids, establishing that the cultures faithfully mirrored real development was essential. “The study combines the advantages of in vivo and in vitro methods,” says Michael Heide, head of the Junior Research Group Brain Development and Evolution. “Organoids are well-suited for obtaining statistically robust results because such sample sizes are not feasible in primates. We subsequently repeated some key experiments in fetal brain tissue to confirm the results from the organoids.” The team found that 50-day-old marmoset organoids closely resemble natural brain development at day 90, a correspondence that allowed them to align the developmental clock of the organoids with that of the actual marmoset embryo and interpret their results with confidence. That validation step is what elevates the findings from an interesting culture phenomenon to a credible account of what happens inside a developing primate.

The broader significance of the work runs in two directions. Evolutionarily, it offers a concrete, mechanistic scenario for how the striking diversity of primate brain sizes and shapes could have arisen: not through the appearance of entirely new cell types, but through coordinated changes in how existing progenitor cells divide, mature, and keep to their developmental schedule. Medically, the same cellular programs that scale a brain up or down are the ones that can go awry in developmental disorders, and the study provides an important framework for understanding both the processes themselves and the consequences of their disruption in the human brain. For a small monkey with a smooth brain, the common marmoset is now teaching scientists a great deal about what it took to build a folded one.

Subject of Research: Cellular mechanisms of neural progenitor development underlying smooth versus folded primate brains

Article Title: Smooth instead of folded—brain development in primates

Article References: Smooth instead of folded—brain development in primates. (n.d.). Original publication

Image Credits: AI Generated

DOI: Not provided

Keywords: marmoset, brain development, neural progenitor cells, brain organoids, cortical folding, primate evolution, cerebral cortex, neurogenesis, German Primate Center, Science Advances, developmental neuroscience, brain size