Why genome editing technologies

It allows us to rethink our approach to serious challenges in agriculture, food and pharma. We now have the ability to precisely edit the DNA of a living plant, opening up the possibility of correcting and optimizing genetic material at their source. These efforts ultimately contribute to solving global challenges such as the need for improved nutritional value or reduced pesticide use. This is how we create more sustainable future.

Why Hudson River Biotechnology

HRB is an agricultural biotech platform specialized in optimizing plants that are used to produce high value compounds. We employ the latest genetic technology and state-of-art science to optimize plants. Our team is made up of enthusiastic minds from science and business community.

HRB gene-editing technology platform enables full spectrum of development, end-to-end solution, from a concept to a modified crop ready for field or greenhouse testing. This consist of target identification, including the unique and proprietary SuRE platform or other target selection methods, allowing to identify target sites for genetic modification in gene sequences as well as in gene regulatory elements (promoters and enhancers). We can genetically alter such targets through a targeted mutagenesis approach with CRISPR-Cas9 or through TILLING.

Targeted mutagenesis via CRISPR

In genetics, clustered regulatory interspaced short palindromic repeats (CRISPRs) are loci that contain multiple short direct repeats, and that provide acquired immunity to bacteria and archaea through sequence-specific silencing of invading foreign DNA. So-called CRISPR-associated systems (CAS) are a family of proteins (including for example Cas9, Cpf1 and Cms1) that can serve as RNA-guided DNA endonucleases for targeted mutagenesis in plants and other organisms. These endonucleases cleave DNA upon target recognition by their guide RNA (gRNA) sequences. The gRNA, connects to the endonuclease and identifies, in a highly specific manner, the correct location in the genome where a cut is to be made. Together, the endonuclease and gRNA form the RNA-protein complex that performs targeted mutagenesis. The cell’s innate DNA damage repair machinery (for example, non-homologous end joining, NHEJ) repairs the break made in the DNA by the endonuclease, but introduces errors (mutations) in the process that cause altered function of the targeted gene. As such, CRISPR enables a novel form of targeted mutagenesis, which allows us to modify a specific gene of interest.

SuRE Platform

Gen-Xa spin-off from the Netherlands Cancer Institute has developed SuRE and validated the platform in mammalian cell culture systems1.

Van Arensbergen et al. (2016) Nature Biotechnology

Hudson River Biotechnology (HRB) has partnered with Gen-X for exclusive access to the SuRE technology for agricultural applications, and for validation of the technology in plants. SuRE is a technology that assays small fragments of a sheared genome for their ability to autonomously drive transcription. A plasmid library of random, 0.2-2kb genomic fragments upstream of a 20-bp barcode is constructed, and decoded by paired-end sequencing. This library is used to transfect cells, and barcodes in transcribed RNA are quantified by high-throughput sequencing. Over 50-fold genome coverage can be reached, allowing mapping of autonomous promoter activity to a genome, or parts of a sequenced genome. By computational modeling we can further delineate sub-regions within promoters that are relevant for their activity.

Why SuRE Platform?

Numerous valuable agricultural applications:

  • Unbiased identification of gene regulatory elements that can serve as targets for CRISPR-Cas9 or TILLING approaches to mutagenesis. Modifying these elements rather than the genes themselves allows for partial down-regulation or even up-regulation of gene activity, rather than complete knockout, and leaves the gene sequence intact. In addition, elements may be identified that regulate gene expression in a manner that is tissue or time specific, enabling genetic optimizations that are even more specifically targeted or that circumvent off-target effects.
  • Genomes of closely related lines can be compared to pinpoint differences in traits (e.g. disease resistance) that are due to differing levels of gene expression rather than sequence variations within genes.
  • Protoplasts containing the SuRE plasmid library can be differentially exposed to e.g. (a)biotic stressors to identify the genomic elements that mediate the stress response; such elements may function as targets for modification to confer resistance to the stressor.
  • Identification of unique promoter/enhancer regions that can serve as strong, endogenous promoters. These are highly valuable for strong and sustained transgene expression with reduced risk of silencing.
Other Target Selection Methods

In addition to identifying gene regulatory elements, we also screen for gene sequences as targets for modification. Depending on existing knowledge and tools available (e.g., a sequenced genome), we take a tailored approach to target gene selection. For example, comparing gene expression profiles of different, closely related lines, usually via RNAseq. If a reference genome is not yet available for your species of interest we still have several options for this, such as CAGE (Cap Analysis Gene Expression) and SAGE (Serial Analysis of Gene Expression), or mapping RNAseq data to genomic sequences of related species.

In addition to these unbiased approaches, target genes will be researched based on literature study and interviews with academic groups active in the field. Combined with SuRE, this will result in a candidate list for mutagenesis that we prioritize and then pursue via targeted mutagenesis, and/or TILLING.