Collaborate with us — nominate a locus for study:

We seek collaborators interested in the biology, genetics and genomics of human and other loci and invite you to consider being our collaborator on one or more loci of interest.

Specifically, we are focusing on three types of projects (or loci):

Synthetic Haplotypes:
A comprehensive way to study complex disease-associated haplotypes by combinatorial manipulation of genetic variants with an emphasis on regulatory variants (e.g. SNPs at DNase-hypersensitive sites).
Examples: CLU, CACNA1C, IRF5 and HTRA1/ARMS2.

Synthetic Hypervariation:
A comprehensive way to probe the network of regulatory sites controlling a gene of interest by combinatorial manipulation of regulatory elements (e.g. enhancers, CTCF sites, transposons, non-coding RNAs etc).
Examples: Hoxa, Sox2, H19/Igf2 and α-Globin.

Humanized mice:

We can deliver hundreds of kb of human DNA (or any other DNA) site-specifically to the mouse genome and generate mice rapidly and efficiently. See more info below,

Examples: TAF1 and ACE2

The Locus Nomination Board:

Our Locus Nomination Board (LNB) aids us in identifying and scoring potential loci. To help guide you and the LNB in this process, we list below the ideal characteristics of such loci.

Preferable Project Properties:

General properties:

Size: The entire region should be <200 kb. Notably, the locus of interest can be >200 kb, as long as we are focusing our manipulations within a defined ~200 kb region. Alternatively, we can engineer >200 kb loci iteratively, but with a cost of integrating fewer variants and and/or higher cost.
Interest: Locus should be of special interest due to disease relevance, genomic location, molecular mechanisms, evolutionary origin, population-specific aspects, etc.

Undesirable Properties:

Highly-repetitive regions (e.g. large 100% identical repeats). The “usual” amount of repetitiveness of mammalian DNA is not a problem. To determine how repetitive your locus is, you can follow these instructions.
Readouts that involve developing the methods for differentiating ESCs, or using a differentiation protocol that is poorly described or inefficient at producing a single cell type of interest.

Readout and follow-up:

Investigator(s) willing to commit to in-depth phenotypic analyses in their lab(s), or alternatively, suggest additional suitable collaborator(s).
If the readout is performed in a specialized cell type (not ES cells) then either [a] a simple, short and robust differentiation protocol (from ES cells) is available, or [b] the readout cell type is amenable to genomic engineering (e.g. high transfection efficiency, high proliferation rate etc).
Accessibility for analysis in a particularly easily-manipulated model organism (e.g. Zebrafish, Ciona) is a plus.

Synthetic haplotypes projects - Locus and disease properties:

Locus harbors one or more genes whose RNA abundance or structure (e.g. splicing) is known to be affected by the risk haplotype. The larger the amplitude of transcript variation, the better, as this makes readout more reliable, especially in cases of potential combinatorial/epistatic effects.
Large effect size (e.g. odds ratio), which is not readily explained by coding variants.
High frequency of the risk haplotype.
Disease is amenable to (e.g. CRISPR-based) gene therapy.

Humanized mice projects - considerations:

Essentiality: Humanizing nonessential genes and especially genes that are not expressed nor functional in mESCs will be easier and FASTER.
Delivery site: we can delivery the human DNA to an ectopic site (a safe harbor like Hprt) or alternatively, we can also replace the mouse gene with the human counterpart. Ectopic delivery to the mouse Hprt would be FASTEST. Delivery to any locus on the X chromosome would be faster than to an autosome.
Variants:
- Delivering a single “base construct” is FASTER than multiple variants (“base construct” is the unmodified human locus that can contain multiple contiguous genes, cloned from a human BAC into a delivery-ready vector).
- Base construct consisting of single, unbroken contiguous region FASTER than >1 noncontiguous regions.
- Unmodified gene FASTER than modified, singly modified FASTER than multiply modified (modifications include tagging of proteins, insertion of selectable markers, mutating codons etc).
Genetic background: BL6/J (currently used) is FASTER than custom genetic background (though the latter is also interesting).

How to Nominate a Locus?

To enable us and the Locus Nomination Board to fully assess the potential and feasibility of the proposed project, please try to provide as much detail as possible when suggesting a locus, with an emphasis on the following:

What is the special significance of this locus? Please write 1-3 paragraphs indicating what the “payoff” would be of having this particular locus and its variants synthesized by our SyRGe center. Think of this as the “background and significance” section of a grant proposal.
Indicate whether you have the resources available, ideally in the form of a trainee or technician in your group to carry out the proposed analyses on those cells and whether you prefer to do the genomics at your site or have our CEGS perform the genomic analyses. Indicate the nature of the genomic analyses to be carried out on cells carrying the base assemblon and its variants.
What cell type and species do you wish to study? Keep in mind that currently, we can relatively efficiently deliver assemblons of up to ~200 kb into mouse ESCs. We are working on doing so in human ESCs, but that method is not yet in routine use. It is very important to tell us how readily you and/or your collaborators can go from mouse or human ESCs to a cell type of interest. Important factors to consider are:
- How long/complex is the process from stem cell to differentiated cell?
- What is the conversion efficiency to the cell type of interest in your hands?
Provide genomic coordinates of the locus and of relevant elements (e.g. risk-associated SNPs in the case of Synthetic Haplotypes projects and known enhancers/CTCF sites and other elements of interest in the case of Synthetic Hypervariation projects). Please paste these coordinates in a BED file format into the submission form (and make sure to match the genome version specified). Here’s an example.
For “Synthetic Hypervariation” projects, list at least ten potential variants of the proposed locus and what they will tell us (e.g., inverting the distal enhancer cluster, deleting the transposable element in intron 2 etc). For “Synthetic Haplotype” projects, indicate the number of known variants in the risk haplotype. We can build dozens (or even more) variants, but we would like to know which (and how many) variants are of the highest priority.
Describe what sort of material would you like to receive from us. This could be, for example, synthetic DNA (we build, you integrate and analyze in your lab), engineered human/mouse ES cells (you differentiate and analyze in your lab), differentiated engineered cells (you only analyze) etc.
Provide references with your nomination (e.g. for “Synthetic haplotypes” GWAS papers or for Synthetic hypervariation key papers describing regulatory elements/regions).
If you’d like to send us accompanying material, you can mail us at syrge@nyulangone.org

See the Frequently Asked Questions page for more info!

Nominate a locus - humanized mice

Name

First Name

Last Name

Institute

Project Title

Source Locus

Please use official human gene symbol. Note that more than one contiguous gene is fine; keep in mind our practical limit right now is around 200-300 kb.

Genome assembly used

Source locus coordinates

Essential gene?

Target locus name

Specify the site of delivery in mESCs. It can be the locus corresponding to human source, or different locus e.g. insertion into a safe harbor. Consider our favorite existing safe harbor landing pad, immediately adjacent to mouse Hprt (animals will be Hprt+). Because it is on the X, all (male) animals will be hemizygous for human locus, obviating screening for biallelic payloads, meaning project will be completed faster

Target locus coordinates

We can either replace a mouse gene(s) with the source DNA or insert the DNA into a specific ectopic position. Please specify this explicitly by providing coordinates for replacement or write “insert to Hprt”.

Mono/bi-allelic

If we’re engineering autosomes, will we be making homozygotes or heterozygotes?

Modifications

Describe any modification of the source DNA needed before payload delivery. If none, we will deliver full human locus unmodified. The more modifications, the longer it will take.

Variants

Please describe variants of the locus you would like built and delivered to the mouse. These variants can include some or all of the modifications listed in the previous field. Please note that increasing number of variants will increase cost, you may also list variants as “optional future components” to indicate this is long term planning.

Significance

Please write 1-3 paragraphs indicating what the “payoff” would be of having this particular locus and, optionally, its variants synthesized by our CEGS group. Think of this as the “background and significance” section of a grant proposal. Please include references.

Requested Material

Describe what sort of material would you like to receive from us. This could be, for example, synthetic DNA (we build, you integrate and make mice in your lab), engineered mouse ES cells (you make mice in your lab) or engineered mice. Typically it would be the latter.

Available Resources

Indicate whether you have the resources available, ideally in the form of a trainee or technician in your group to carry out the proposed downstream analyses on the engineered DNA/cells/mice

References

You can also download this form and email it to syrge@nyulangone.org

Become a SyRGe Fellow:

We have funds to host a SyRGe Fellow each summer. SyRGe Fellows will spend the summer in our facility working with the assembly or delivery/readout teams and perhaps seeding a CEGS collaborative project with their home institution. Contact us if you’re interested.