TY - JOUR
T1 - Massively parallel identification of mRNA localization elements in primary cortical neurons
AU - Mendonsa, Samantha
AU - von Kügelgen, Nicolai
AU - Dantsuji, Sayaka
AU - Ron, Maya
AU - Breimann, Laura
AU - Baranovskii, Artem
AU - Lödige, Inga
AU - Kirchner, Marieluise
AU - Fischer, Meret
AU - Zerna, Nadja
AU - Bujanic, Lucija
AU - Mertins, Philipp
AU - Ulitsky, Igor
AU - Chekulaeva, Marina
N1 - N.v.K. is supported by the MDC PhD fellowship; S.M. by the DAAD PhD fellowship; S.D. by the Honjo International PhD; and L. Breimann by the MDC, the Joachim Herz Foundation (850022) and the NIH/NHGRI (RM1HG011016). Work in the Igor Ulitsky laboratory was supported by Israeli Science Foundation grant ISF 852/19 and the Nella and Leon Benoziyo Center for Neurological Diseases. This work is supported by a grant from the German Israeli Foundation to I.U. and M.C. and a Deutsche Forschungsgemeinschaft (DFG) grant to M.C. We thank R. Hodge for comments on the manuscript. The funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript.
PY - 2023/3
Y1 - 2023/3
N2 - Cells adopt highly polarized shapes and form distinct subcellular compartments in many cases due to the localization of many mRNAs to specific areas, where they are translated into proteins with local functions. This mRNA localization is mediated by specific cis-regulatory elements in mRNAs, commonly called 'zipcodes'. Although there are hundreds of localized mRNAs, only a few zipcodes have been characterized. Here we describe a novel neuronal zipcode identification protocol (N-zip) that can identify zipcodes across hundreds of 3' untranslated regions. This approach combines a method of separating the principal subcellular compartments of neurons-cell bodies and neurites-with a massively parallel reporter assay. N-zip identifies the let-7 binding site and (AU) motif as de novo zipcodes in mouse primary cortical neurons. Our analysis also provides, to our knowledge, the first demonstration of an miRNA affecting mRNA localization and suggests a strategy for detecting many more zipcodes.
AB - Cells adopt highly polarized shapes and form distinct subcellular compartments in many cases due to the localization of many mRNAs to specific areas, where they are translated into proteins with local functions. This mRNA localization is mediated by specific cis-regulatory elements in mRNAs, commonly called 'zipcodes'. Although there are hundreds of localized mRNAs, only a few zipcodes have been characterized. Here we describe a novel neuronal zipcode identification protocol (N-zip) that can identify zipcodes across hundreds of 3' untranslated regions. This approach combines a method of separating the principal subcellular compartments of neurons-cell bodies and neurites-with a massively parallel reporter assay. N-zip identifies the let-7 binding site and (AU) motif as de novo zipcodes in mouse primary cortical neurons. Our analysis also provides, to our knowledge, the first demonstration of an miRNA affecting mRNA localization and suggests a strategy for detecting many more zipcodes.
UR - https://www.scopus.com/pages/publications/85149663534
U2 - 10.1038/s41593-022-01243-x
DO - 10.1038/s41593-022-01243-x
M3 - Article
C2 - 36646877
SN - 1097-6256
VL - 26
SP - 394
EP - 405
JO - Nature Neuroscience
JF - Nature Neuroscience
IS - 3
ER -