Title : Deciphering human functional genome using Massively Parallel Reporter Assays

 

Abstract:

98% of our genome is non-coding, and its function remains largely unknown. The non-coding genome contains a variety of enhancers that play crucial roles in gene regulation. Mutations and variations in enhancers are thought to be a major source of human diseases, individual differences, and evolution. 

lentivirus-based massively parallel reporter assay (lentiMPRA), a cutting-edge technology that enables high-throughput functional characterization of enhancers at single-nucleotide resolution by quantifying transcribed barcodes. We have leveraged the lentiMPRA technology to dissect enhancer function in the genome and understand the molecular basis of gene regulation underlying complex biological phenomena, such as cell differentiation, disease and evolution. 

In my presentation, I will introduce the lentiMPRA methodology and various applications, and discuss the future direction of functional genomics.

 

Reference:

Whalen, S.*, Inoue, F.*, Ryu, H., Fair, T., Markenscoff-Papadimitriou, E., Keough, K., Kircher, M., Martin, B., Alvarado, B., Elor, O., et al. (2023).

Machine learning dissection of human accelerated regions in primate neurodevelopment.

Neuron 111, 857-873.e8. https://doi.org/10.1016/j.neuron.2022.12.026.

 

Klein, J.C.*, Agarwal, V.*, Inoue, F.*, Keith, A.*, Martin, B., Kircher, M., Ahituv, N., and Shendure, J. (2020).

A systematic evaluation of the design and context dependencies of massively parallel reporter assays.

Nature Methods, 1–9. https://doi.org/10.1038/s41592-020-0965-y.

 

Gordon, M.G.*, Inoue, F.*^, Martin, B.*, Schubach, M.*, Agarwal, V., Whalen, S., Feng, S., Zhao, J., Ashuach, T., Ziffra, R., et al. (2020).

lentiMPRA and MPRAflow for high-throughput functional characterization of gene regulatory elements.

Nature Protoc. 15, 2387–2412. https://doi.org/10.1038/s41596-020-0333-5.

 

Inoue, F.*, Kreimer, A.*, Ashuach, T., Ahituv, N., and Yosef, N. (2019).

Identification and Massively Parallel Characterization of Regulatory Elements Driving Neural Induction.

Cell Stem Cell 25, 713-727.e10. https://doi.org/10.1016/J.STEM.2019.09.010.

 

Inoue, F.*, Kircher, M.*, Martin, B., Cooper, G.M., Witten, D.M., McManus, M.T., Ahituv, N., and Shendure, J. (2017).

A systematic comparison reveals substantial differences in chromosomal versus episomal encoding of enhancer activity.

Genome Res. https://doi.org/10.1101/gr.212092.116.