Abstract
Rapid responses to changes within subcellular compartments of highly polarized cells, such as neuron axons, depend on local translation and post-transcriptional regulation. The mechanism by which microRNAs (miRNAs) regulate this process is not fully understood. Here, using live cell imaging and RNA sequencing analysis, we demonstrated how miRNAs can differentially control hundreds of transcripts at the subcellular level. We demonstrated that the seed match length of the miRNA target-sequence regulates both mRNA stability and protein translation rates. While longer seed matches have an increased inhibitory effect, transcriptome analysis did not reveal differences in seed match length between axonal and somata mRNAs of motor neurons. However, mRNA variants with longer 3′UTR are enriched in axons and contain multiple repeats of specific miRNA target sequences. Finally, we demonstrated that the long 3′UTR mRNA variant of the motor protein Kif5b is enriched explicitly in motor neuron axons and contains multiple sequence repeats for binding miR-129-5p. This subsequently results in the differential post-transcriptional regulation of kif5b and its synthesis in axons. Thus, we suggest that the number of miRNA binding sites at the 3′UTR of the mRNA, rather than the miRNA seed match length, regulates the axonal transcriptome.
Funder
HFSP
Ministry of health
State of Israel—JPND program, Israel Science Foundation
Radala Foundation for ALS research
Ministry of Science and Technology, State of Israel
Kirschman Dvora Eleonora Fund for Parkinson’s Disease studies
Edmond J. Safra Center for Bioinformatics at Tel-Aviv University
Tel Aviv University Center for Combating Pandemics (TCCP); Horizon 2020—Research and Innovation Framework Programme, PSY-PGx
The Edmond J. Safra Center for Bioinformatics at Tel Aviv University
The Koret-UC Berkeley-Tel Aviv University Initiative in Computational Biology and Bioinformatics
The QBI/UCSF-Tel Aviv University joint Initiative in Computational Biology and Drug Discovery
Israeli Ministry of Defense, Office of Assistant Minister of Defense for Chemical, Biological, Radiological and Nuclear (CBRN) Defense
Foundation Fighting Blindness; Collaborative clinical Bioinformatics research of the Edmond J. Safra Center for Bioinformatics and Faculty of Medicine at Tel Aviv University
Israeli Ministry of Science and Technology, Israeli–Russia
Kodesz Institute for Technologies in Healthcare
Tel Aviv University Healthy Longevity Research Center
Djerassi-Elias Institute of Oncology
Canada-Montreal Friends of Tel Aviv University
Donations from Harold H. Marcus, Amy Friedkin, Natalio Garber, Tal Zohar
Kirschman Dvora Eleonora Fund for Parkinson’s Disease
Joint funding between Tel Aviv University and Yonsei University
Tel Aviv University Innovation Laboratories