Optimizing functional genomics research tools by aligning their design with the ongoing evolution of the genome.

Part 1 of the Realigning and Remapping Dharmacon research tools series

As genomic science evolves, so must the tools we use to study it. At Revvity, our Dharmacon^™ reagents brand is committed to providing world-class gene modulation and editing reagents that reflect the latest understanding of genomics. The Dharmacon RNAi and CRISPR products combine expertise in synthetic oligonucleotide chemistry and flexible lentiviral vector systems with sophisticated, empirically validated, construct and sequence design algorithms to deliver specificity and functionality across research models. With the rapid advancement of sequencing technologies and database curation, understanding of the genome and transcriptome is continuously evolving. Therefore, it becomes critical for scientists to comprehend and utilize the latest genome assemblies and annotations to ensure biological relevance in their discovery research.

Impact of ever-evolving reference sequence database

The Human Genome Project provided our first static understanding of the genome in the early 2000s, yet this initial view was limited, representing a single composite reference with gaps in complex regions, minimal population diversity, and little functional context. Subsequent advances, incorporated into the NCBI Reference Sequence (RefSeq) collections, addressed many of these gaps by providing comprehensive, integrated, non-redundant, and well-annotated sets of sequences, including genomic DNA, transcripts, and proteins.¹

Three key developments have led to this transformation of the genomic and transcriptomic landscape:

• Expanded sequencing data: Modern Next Generation Sequencing (NGS) technologies have generated unprecedented amounts of data from diverse cell types and tissues routinely over 30x—compared to 1–2x in the early 2000s.
• Advanced long-read sequencing technologies now detect previously missed genetic variations and enable comprehensive coverage of complex genomic regions, such as highly homologous and repetitive sequences, which were inaccessible to short-read methods.
• Confirmed isoform diversity: Updated RNA sequencing has confirmed that genes often produce multiple variant forms (isoforms) in different cell types.

To address this evolution in functional genomics, CRISPR guide RNA and RNAi, siRNA, & shRNA designs should be continuously reannotated and/or re-designed if needed. This means sequences should be re-mapped to the most up-to-date accession information. This approach, along with retiring outdated sequences, is critical for maintaining effective tools required for valuable research.

Reannotation vs. realignment: Staying ahead in a changing genomic landscape

To ensure scientists always have the most accurate and relevant reagents, we take two complementary approaches:

Reannotation: This is about keeping designs current. We remap existing sgRNA and RNAi reagents against the latest genome references, so annotations always reflect today’s best knowledge.

Realignment: This is a deeper refresh. Instead of just updating annotations, we redesign reagents using advanced bioinformatics and the most recent genomic insights. The result is broader and more specific coverage of important gene variants and isoforms through more comprehensive coverage of transcripts. In many cases, this means products now target all or most isoforms of a gene—helping researchers capture the variants that matter most in their specific cell type or experimental model. In some cases re-alignment reduces the instance of false-positives by reducing unintended off-targets due to previously inaccurate genomic data.

Together, these practices replace outdated or misaligned designs with optimized sequences increasing the biological relevance of our products-so your experiments are aligned with the latest science and ready to deliver meaningful results.

What realignment means for your research

If you’re already using our products, rest assured they remain effective. For many well-studied genes, realignment doesn’t change the target region, while for others, updated designs now capture a broader set of isoforms and variants. For further questions, please reach out to our technical support team (technical.horizon@revvity.com).

If you’re starting new projects, realignment gives you greater confidence by covering more gene variants, helping you detect effects that older designs may have missed, especially in screening or novel cell types. Most importantly, all realigned products are built to maintain the same high level of accuracy and functionality you expect.

In short, realignment means your research tools stay as current as the science so you can move forward with confidence.