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Lykke-Andersen, J.

Publications and source records attributed to Lykke-Andersen, J..

2 recordsLinked to original sources

The Conserved CNOT1 Interaction Motif of Tristetraprolin Regulates ARE-mRNA Decay Independently of the p38 MAPK-MK2 Kinase Pathway

Regulation of the mRNA decay activator Tristetraprolin (TTP) by the p38 mitogen-activated protein kinase (MAPK) pathway during the mammalian inflammatory response represents a paradigm for the regulation of mRNA turnover by signaling. Phosphorylation of TTP by p38 MAPK-activated kinase 2 (MK2) inhibits the association of TTP with the CCR4-NOT deadenylase complex and represses TTP-mediated mRNA decay. Here we present evidence that TTP remains active in the presence of activated MK2 due to its highly conserved CNOT1 Interacting Motif (CIM), which remains unphosphorylated and capable of promoting deadenylation and decay. The CIM recruits the CCR4-NOT complex cooperatively with previously identified conserved tryptophan residues of TTP and deletion of the CIM strongly represses residual association with the deadenylase complex and activity of TTP in conditions of active MK2. A conserved serine in the CIM is not a target of MK2 but is instead phosphorylated by other kinases including the PKC pathway and regulates TTP activity independently of MK2. These results suggest that kinase pathways regulate TTP activity in a cooperative manner and that the p38 MAPK-MK2 pathway relies on the activation of additional kinase pathway(s) to fully control TTP function.

molecular biology↗

Tailer: A Pipeline for Sequencing-Based Analysis of Non-Polyadenylated RNA 3' End Processing

Post-transcriptional trimming and tailing of RNA 3 ends play key roles in the processing and quality control of non-coding RNAs (ncRNAs). However, bioinformatic tools to examine changes in the RNA 3 "tailome" are sparse and not standardized. Here we present Tailer, a bioinformatic pipeline in two parts that allows for robust quantification and analysis of tail information from next generation sequencing experiments that preserve RNA 3 end information. The first part of Tailer, Tailer-Processing, uses genome annotation or reference FASTA gene sequences to quantify RNA 3 ends from SAM-formatted alignment files or FASTQ sequence read files produced from sequencing experiments. The second part, Tailer-Analysis, uses the output of Tailer-Processing to identify statistically significant RNA targets of trimming and tailing and create graphs for data exploration. We apply Tailer to RNA 3 end sequencing experiments from three published studies and find that it accurately and reproducibly recapitulates key findings. Thus, Tailer should be a useful and easily accessible tool to globally investigate tailing dynamics of non-polyadenylated RNAs and conditions that perturb them.

molecular biology↗