Rapid nuclear deadenylation of mammalian messenger RNA
Jonathan Alles,
Ivano Legnini,
Maddalena Pacelli,
Nikolaus Rajewsky
Affiliations
Jonathan Alles
Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Laboratory for Systems Biology of Gene Regulatory Elements, Hannoversche Str. 28, 10115 Berlin, Germany; Humboldt-Universität zu Berlin, Institute of Biology, Unter den Linden 6, 10099 Berlin, Germany
Ivano Legnini
Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Laboratory for Systems Biology of Gene Regulatory Elements, Hannoversche Str. 28, 10115 Berlin, Germany
Maddalena Pacelli
Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Laboratory for Systems Biology of Gene Regulatory Elements, Hannoversche Str. 28, 10115 Berlin, Germany
Nikolaus Rajewsky
Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Laboratory for Systems Biology of Gene Regulatory Elements, Hannoversche Str. 28, 10115 Berlin, Germany; Humboldt-Universität zu Berlin, Institute of Biology, Unter den Linden 6, 10099 Berlin, Germany; Corresponding author
Summary: Poly(A) tails protect RNAs from degradation and their deadenylation rates determine RNA stability. Although poly(A) tails are generated in the nucleus, deadenylation of tails has mostly been investigated within the cytoplasm. Here, we combined long-read sequencing with metabolic labeling, splicing inhibition and cell fractionation experiments to quantify, separately, the genesis and trimming of nuclear and cytoplasmic tails in vitro and in vivo. We present evidence for genome-wide, nuclear synthesis of tails longer than 200 nt, which are rapidly shortened after transcription. Our data suggests that rapid deadenylation is a nuclear process, and that different classes of transcripts and even transcript isoforms have distinct nuclear tail lengths. For example, many long-noncoding RNAs retain long poly(A) tails. Modeling deadenylation dynamics predicts nuclear deadenylation about 10 times faster than cytoplasmic deadenylation. In summary, our data suggests that nuclear deadenylation might be a key mechanism for regulating mRNA stability, abundance, and subcellular localization.
