@article{321ccc5f785444fa98f6ea17301f347a,
title = "PNPT1 Release from Mitochondria during Apoptosis Triggers Decay of Poly(A) RNAs",
abstract = "Widespread mRNA decay, an unappreciated feature of apoptosis, enhances cell death and depends on mitochondrial outer membrane permeabilization (MOMP), TUTases, and DIS3L2. Which RNAs are decayed and the decay-initiating event are unknown. Here, we show extensive decay of mRNAs and poly(A) noncoding (nc)RNAs at the 3′ end, triggered by the mitochondrial intermembrane space 3′-to-5′ exoribonuclease PNPT1, released during MOMP. PNPT1 knockdown inhibits apoptotic RNA decay and reduces apoptosis, while ectopic expression of PNPT1, but not an RNase-deficient mutant, increases RNA decay and cell death. The 3′ end of PNPT1 substrates thread through a narrow channel. Many non-poly(A) ncRNAs contain 3′-secondary structures or bind proteins that may block PNPT1 activity. Indeed, mutations that disrupt the 3′-stem-loop of a decay-resistant ncRNA render the transcript susceptible, while adding a 3′-stem-loop to an mRNA prevents its decay. Thus, PNPT1 release from mitochondria during MOMP initiates apoptotic decay of RNAs lacking 3′-structures.",
keywords = "apoptosis, caspase, DIS3L2, mitochondrial outer membrane permeabilization, PABPC1, PNPT1, RNA decay, RNase, TUTase",
author = "Xing Liu and Rui Fu and Youdong Pan and Meza-Sosa, {Karla F.} and Zhibin Zhang and Judy Lieberman",
note = "Funding Information: Biological duplicate unstranded RNA-seq libraries were prepared using the NEBNext Ultra RNA Library Prep Kit (#E7530S) after initial RNA isolation by TRIzol (ThermoFisher Scientific) and Ribo-Zero (Illumina, #MRZH116) rRNA removal kit. RNA and DNA purity and concentrations were monitored using an Agilent 2100 Bioanalyzer in the BCH IDDRC Molecular Genetic Core, supported by National Institutes of Health award NIH-P30-HD 18655. Libraries were pooled and sequenced on an Illumina NextSeq 500, yielding around 20 million mapped 50 bp single-end reads per sample. Sequences were aligned to the GENCODE v23 GRCh38 human genome annotation by TopHat2 ( Kim et al., 2013 ). Alignment output BAM files were sorted and indexed by SAMtools ( Li et al., 2009 ). After counting reads by HTSeq ( Anders et al., 2015 ) with the options “-s no –m union –nonunique none –I gene_name,” DESeq2 ( Love et al., 2014 ) was used for differential expression analysis and fold change estimation. A set of control genes, RN7SL1 , RPPH1 , RMRP , RNU4-1 , RNU4-2 , RN7SK , SNORA33 , SNORD83A , MT-RNR2 , RNU1-1 , RNU1-2 , SNORD15B , SNORD104 , SNORA2B , that were stable during apoptosis as verified by qRT-PCR, were used to estimate size factors for normalization. DESeq2 automatically implements independent filtering to filter out genes with low mean expression (in this case, the cut-off was 26.6 reads). Only genes that pass filtering were used for dispersion estimation, negative binomial GLM fitting, and Wald test. For analysis of poly(A) versus non-poly(A) ncRNAs, sequence alignment was restricted to the final exon of intron-containing genes or the 3′ quarter length of intron-lacking genes by using a GTF annotation generated by custom python code. Publisher Copyright: {\textcopyright} 2018 Elsevier Inc.",
year = "2018",
month = jun,
day = "28",
doi = "10.1016/j.cell.2018.04.017",
language = "English (US)",
volume = "174",
pages = "187--201.e12",
journal = "Cell",
issn = "0092-8674",
publisher = "Cell Press",
number = "1",
}