(635a) A Low-Input Microfluidic Method for Studying Genome-Wide Lncrna Binding Profiles

The percentage of the human genome responsible for coding protein is relatively small at only 1.5%, while most of the genome is transcribed into various types of noncoding RNA. Long noncoding RNA (lncRNA) is noncoding RNA which is >200 bp long and is broadly known to affect gene expression through their binding to proteins and DNA. Differentiation in lncRNA expression has been associated with disease and development, but there is still very little known about how lncRNA functions to regulate genes and how they relate to other epigenetic markers such as histone modifications and transcription factors.

To study lncRNA binding profiles across the genome, one method developed was Chromatin Isolation by RNA Purification following by next generation sequencing (ChIRP-seq). The epigenetics of disease vary highly in vivo vs. in vitro, so to study the role of lncRNA in disease, it is essential to study tissue samples rather than cell lines to get the full picture. Unfortunately, the original ChIRP-seq method requires 20 million cells of input material, whereas tissue samples are usually only available in very small quantities, which renders this method impractical for such studies. With the goal of studying disease tissue, we have developed a microfluidic method that is able to capture comparable DNA quantity and binding sites as the original ChIRP-seq method with as few as 100K cells of input DNA.

Microfluidic ChIRP-seq utilizes a two-step hybridization process which consists of an oscillatory hybridization followed by flow-through hybridization through a packed bed. Following hybridization, we employ a multi-step oscillatory washing procedure on-chip and finally extract the DNA of interest for NGS. Our microfluidic ChIRP-seq can collect a comparable quantity of high-quality enriched ChIRP DNA to the original method with as few as 100K cells of input material.