Control of human neurodevelopment by a group of hominoid-specific transposons

Human brain development requires the timely activation of developmental genes. As cells differentiate, gene activation is modulated primarily by non-coding DNA elements, called enhancers, usually located far away from their target genes. Following the input of DNA-binding proteins (transcription factors), the enhancers interact with the target genes, eliciting their activation.

Transposable Elements (TEs) are parasitic genomic elements that take advantage of the host genomes to propagate across generations. Nonetheless, some TEs present specific characteristics that are useful to the host genome. For instance, the DNA sequence of the TEs may include particular sequence motifs that are recognized by specific transcription factors.

When this is the case, the TEs may be "co-opted" by the genome to become functional enhancers. This host-parasite mutualism is usually cell type specific, in that the TEs may be co-opted as enhancers in some cell-types and repressed in others.

In this context, a young family of TEs, called SINE-VNTR-Alu (SVA), may play an important role during human neurodevelopment. SVAs are exclusive of the great apes (orangutan, gorilla, chimpanzee, humans), and nearly half of the ~2,700 copies present in the human genome are exclusive of our species.

There is strong preliminary evidence suggesting that the human-specific SVAs control human neurodevelopment by acting as enhancers.

Here, we will investigate the mechanisms by which SVAs control human neurodevelopment. There are several questions we would like to address: 1) which stages of human neurodevelopment are controlled by the SVAs? 2) Do SVAs function as developmental enhancers only in specific brain cell types, or is this phenomenon universal in the brain? 3) Have the SVA-derived brain enhancers accumulated genetic variation in their sequence across human populations? And is this variation associated with specific neurodevelopmental human traits?

To answer these questions, we will model human neurodevelopment in vitro using cerebral organoid generation from induced pluripotent stem cells (iPSCs). The iPSCs are stem cells derived from human somatic cells that have been engineered in vitro to become stem-like cells. The iPSCs can be treated with specific reagents to trigger the rapid development of brain-like tissues, termed cerebral organoids.

Only 10 days are required for the appearance of neural identity and 20-30 days for defined brain regions to form. The organoids reach the maximum size in two months, but they can be kept in culture indefinitely.

We will couple this system with single cell genomics and genome editing. More specifically, single cell genomic techniques (single-cell RNA-seq and single-cell ATAC-seq) will be employed to assess which SVAs are active in every individual cell during brain organoid generation, and which genes they control. Additionally, we will employ CRISPR-interference, which is a modification of the CRISPR-Cas9 technology that has been optimized to recruit proteins that repress specific genomic sites.

In this case, the CRISPR-interference will be used to repress ALL the human SVAs at different time-points during organoid generation and assess the consequences on the development of the different brain cell types.

In addition to the work performed on organoids, we will harness publicly available human whole genome sequences to profile genetic and structural variation in SVA-derived neurodevelopmental enhancers and will interpret this variation in the context of Genome Wide Association Studies (GWASs) that have been performed by others to predict genetic variants associated with specific human neurodevelopmental traits.

Together these experiments will provide novel insights into human neurodevelopment, specifically unveiling novel mechanisms by which genes are turned on and off during the development of all the different brain components.