The Dark Matter Project
@darkmatterproject.bsky.social
Studying The Dark Matter of the Genome - everything noncoding 🧬
A collaborative scientific project at NYU Langone.
Account managed by Ran Brosh.
A collaborative scientific project at NYU Langone.
Account managed by Ran Brosh.
We're thrilled to publish 2 exciting preprints today on the molecular pathology of X-linked Dystonia Parkinsonism!
biorxiv.org/content/10.1...
AND
biorxiv.org/content/10.1...
@nyulangone.bsky.social
biorxiv.org/content/10.1...
AND
biorxiv.org/content/10.1...
@nyulangone.bsky.social
October 29, 2025 at 3:30 AM
This recombination fuses mouse Taf1's exons 1-24 with human TAF1's exons 25-38 to form a fully functional gene that encodes mouse TAF1 protein. The recombination also removes all marker cassettes, making the final "converted" allele scarless.
October 29, 2025 at 3:30 AM
This recombination fuses mouse Taf1's exons 1-24 with human TAF1's exons 25-38 to form a fully functional gene that encodes mouse TAF1 protein. The recombination also removes all marker cassettes, making the final "converted" allele scarless.
The final step of engineering is what we call "conversion". It includes introducing Cre enzyme that induces recombination between the 1st loxP site in mouse Taf1 intron 24, and a 2nd loxP site located in human TAF1 intron 24.
October 29, 2025 at 3:30 AM
The final step of engineering is what we call "conversion". It includes introducing Cre enzyme that induces recombination between the 1st loxP site in mouse Taf1 intron 24, and a 2nd loxP site located in human TAF1 intron 24.
This feat of engineering was performed using a variant of a method we recently published called mSwAP-In (mammalian switching antibiotic resistance markers progressively for integration).
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Mouse genome rewriting and tailoring of three important disease loci - Nature
This study describes a method to insert large stretches of exogenous DNA into mammalian genomes, which is used to insert human ACE2 loci into mouse to produce a model of human SARS-CoV-2 infection.
www.nature.com
October 29, 2025 at 3:30 AM
This feat of engineering was performed using a variant of a method we recently published called mSwAP-In (mammalian switching antibiotic resistance markers progressively for integration).
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Next, we engineered mouse embryonic stem cells (mESCs), first with a loxP site in Taf1's intron 24, followed by integration of a marker cassette (a landing pad) downstream of the gene, and finally we replaced this cassette with the 78-kb human fragment.
October 29, 2025 at 3:30 AM
Next, we engineered mouse embryonic stem cells (mESCs), first with a loxP site in Taf1's intron 24, followed by integration of a marker cassette (a landing pad) downstream of the gene, and finally we replaced this cassette with the 78-kb human fragment.
Using CREEPY (CRISPR-mediated editing of synthetic episomes in yeast) we've substituted every amino acid that is different between humans and mice so that the expressed protein would be identical to mouse TAF1.
doi.org/10.1093/nar/...
doi.org/10.1093/nar/...
CREEPY: CRISPR-mediated editing of synthetic episomes in yeast
Abstract. Use of synthetic genomics to design and build ‘big’ DNA has revolutionized our ability to answer fundamental biological questions by employing a
doi.org
October 29, 2025 at 3:30 AM
Using CREEPY (CRISPR-mediated editing of synthetic episomes in yeast) we've substituted every amino acid that is different between humans and mice so that the expressed protein would be identical to mouse TAF1.
doi.org/10.1093/nar/...
doi.org/10.1093/nar/...
But we were worried that the human TAF1 protein would be incompatible when expressed in mice (TAF1 is the largest subunit of the TFIID complex, a large protein group that is essential for initiating transcription of most genes).
October 29, 2025 at 3:30 AM
But we were worried that the human TAF1 protein would be incompatible when expressed in mice (TAF1 is the largest subunit of the TFIID complex, a large protein group that is essential for initiating transcription of most genes).
We assembled this region from an XDP patient-derived BAC, using the superpower of S. cerevisiae (yeast), into a delivery-ready vector.
October 29, 2025 at 3:30 AM
We assembled this region from an XDP patient-derived BAC, using the superpower of S. cerevisiae (yeast), into a delivery-ready vector.
The pathogenic SVA insertion is in TAF1's intron 32, but we wanted to generate a partially humanized mouse model, and decided to include a 78 kb human region that spans TAF1 exons 25-38, including all intervening introns and the SVA.
October 29, 2025 at 3:30 AM
The pathogenic SVA insertion is in TAF1's intron 32, but we wanted to generate a partially humanized mouse model, and decided to include a 78 kb human region that spans TAF1 exons 25-38, including all intervening introns and the SVA.
Our solution? A "hybrid-convertible" allele:
October 29, 2025 at 3:30 AM
Our solution? A "hybrid-convertible" allele:
This is the problem we had to tackle when we engineered the first mouse model of X-linked Dystonia Parkinsonism, a disease caused by an SVA (SINE-VNTR-Alu) retrotransposon insertion in the essential TAF1 gene.
October 29, 2025 at 3:30 AM
This is the problem we had to tackle when we engineered the first mouse model of X-linked Dystonia Parkinsonism, a disease caused by an SVA (SINE-VNTR-Alu) retrotransposon insertion in the essential TAF1 gene.
The answer is quite simple of course: make it conditional.
But what if the lethality is induced by a 2.7 kb retrotransposon insertion into an X-linked gene? How would you CONDITIONALLY introduce this element?
But what if the lethality is induced by a 2.7 kb retrotransposon insertion into an X-linked gene? How would you CONDITIONALLY introduce this element?
October 29, 2025 at 3:30 AM
The answer is quite simple of course: make it conditional.
But what if the lethality is induced by a 2.7 kb retrotransposon insertion into an X-linked gene? How would you CONDITIONALLY introduce this element?
But what if the lethality is induced by a 2.7 kb retrotransposon insertion into an X-linked gene? How would you CONDITIONALLY introduce this element?
Read more on our website www.TheDarkMatterProject.org
The Dark Matter Project
The Center for Synthetic Regulatory Genomics at NYU Langone Health is tasked with the study of the genome's Dark Matter - the noncoding DNA and its role in human diseases.
www.TheDarkMatterProject.org
October 8, 2025 at 5:54 PM
Read more on our website www.TheDarkMatterProject.org
Congrats to all authors, including Yu (Jeremy) Zhao, Ran Brosh, @liddelowsa.bsky.social, @jefboeke.bsky.social, Cris Bragg and others. This work was primarily funded by the Collaborative Center for XDP and NHGRI's CEGS program.
October 8, 2025 at 5:54 PM
Congrats to all authors, including Yu (Jeremy) Zhao, Ran Brosh, @liddelowsa.bsky.social, @jefboeke.bsky.social, Cris Bragg and others. This work was primarily funded by the Collaborative Center for XDP and NHGRI's CEGS program.
In the 2nd preprint @pryprk.bsky.social et al. describe deep behavioral and histological analysis of XDP mice and reveal a surprising myelin pathology.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Myelin pathology is a key feature of X-linked Dystonia Parkinsonism
X-linked Dystonia-Parkinsonism (XDP) is a progressive, adult-onset neurodegenerative movement disorder that predominantly affects males of Filipino descent. The disease is caused by the insertion of a...
www.biorxiv.org
October 8, 2025 at 5:54 PM
In the 2nd preprint @pryprk.bsky.social et al. describe deep behavioral and histological analysis of XDP mice and reveal a surprising myelin pathology.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
In the 1st preprint Zhang et al. describe the engineering of the first XDP mouse model and the splicing defects induced by the presence of a pathogenic intronic SVA retrotransposon.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Genome writing to dissect consequences of SVA retrotransposon disease X-Linked Dystonia Parkinsonism
Human retrotransposon insertions are often associated with diseases. In the case of the neurodegenerative X-Linked Dystonia-Parkinsonism (XDP) disease, a human-specific SINE-VNTR-Alu subfamily F (SVA_...
www.biorxiv.org
October 8, 2025 at 5:54 PM
In the 1st preprint Zhang et al. describe the engineering of the first XDP mouse model and the splicing defects induced by the presence of a pathogenic intronic SVA retrotransposon.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Check out more news and publications on our website
www.TheDarkMatterProject.org
www.TheDarkMatterProject.org
September 12, 2025 at 1:53 PM
Check out more news and publications on our website
www.TheDarkMatterProject.org
www.TheDarkMatterProject.org