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Interplay Between Uridylation and Deadenylation During Mrna Degradation in Arabidopsis Thaliana

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Interplay Between Uridylation and Deadenylation During Mrna Degradation in Arabidopsis Thaliana $FNQRZOHGJPHQWV &ŝƌƐƚ͕/ǁŽƵůĚůŝŬĞƚŽƚŚĂŶŬaƚĢƉĄŶŬĂsĂŸĄēŽǀĄ ͕ŶĚƌĞĂƐtĂĐŚƚĞƌĂŶĚ&ĂďŝĞŶŶĞDĂƵdžŝŽŶĨŽƌŚĂǀŝŶŐ ĂĐĐĞƉƚĞĚƚŽĞǀĂůƵĂƚĞŵLJǁŽƌŬ͘DĞƌĐŝĠŐĂůĞŵĞŶƚ ĂƵ>ĂďdžEĞƚZEĚ͛ĂǀŽŝƌĨŝŶĂŶĐĠŵĂƚŚğƐĞ͘ :͛ĂŝŵĞƌĂŝƐƌĞŵĞƌĐŝĞƌŵŽŶĚŝƌĞĐƚĞƵƌĚĞƚŚğƐĞ ͕ŽŵŝŶŝƋƵĞ'ĂŐůŝĂƌĚŝ;ͨ'ĂŐͩͿ͕ ĚĞŵ͛ĂǀŽŝƌĂĐĐƵĞŝůůŝ ĂƵƐĞŝŶĚĞƐŽŶĠƋƵŝƉĞĞƚĚĞŵ͛ĂǀŽŝƌƐŽƵƚĞŶƵ ƚŽƵƚĂƵůŽŶŐĚĞŵĂƚŚğƐĞ͘:ĞƚĞƌĞŵĞƌĐŝĞƉŽƵƌƚŽŶ ĞdžƉĞƌƚŝƐĞ͕ƚ ĞƐƉƌĠĐŝĞƵdžĐŽŶƐĞŝůƐĞƚůĞƐ;ůŽŶŐƵĞƐ͙ ͿĚŝƐĐƵƐƐŝŽŶƐƐĐŝĞŶƚŝĨŝƋƵĞƐƋƵŝŵ͛ŽŶƚďĞĂƵĐŽƵƉ ĂƉƉŽƌƚĠĞƚĂŝĚĠăĚĠǀĞůŽƉƉĞƌŵŽŶĞƐƉƌŝƚĐƌŝƚŝƋƵĞĞƚƐĐŝĞŶƚŝĨŝƋƵĞ͘ hŶŐƌĂŶĚŵĞƌĐŝă,ĠůğŶĞƵďĞƌƉŽƵƌƐĂŐĞŶƚŝůůĞƐƐĞĞƚƐĂƉĂƚŝĞŶĐĞĚƵƌĂŶƚĐĞƐϰĂŶŶĠĞƐ͘DĞƌĐŝƉŽƵƌ ƚŽŶ ƐŽƵƚŝĞŶ ŵŽƌĂů Ğƚ ŝŶƚĞůůĞĐƚƵĞů͕ ƚƵ ĂƐ ƚŽƵũŽƵƌƐ ĠƚĠ ůă ƉŽƵƌ ƌĠƉŽŶĚƌĞ ă ŵĞƐ ŝŶŶŽŵďƌĂďůĞƐ ƋƵĞƐƚŝŽŶƐĞƚƚƵĂƐƚŽƵũŽƵƌƐƐƵŵ͛ĞŶĐŽƵƌĂŐĞƌƋƵĂŶĚĕĂŶ͛ĂůůĂŝƚƉĂƐƚƌŽƉ͘ ƚŵĞƌĐŝĂƵƐƐŝƉŽƵƌƚĂ ƉĂƚŝĞŶĐĞ Ğƚ ƚ ĞƐ ďŽŶƐ ĐŽŶƐĞŝůƐ ůŽƌƐ ĚĞ ů͛ĠĐƌŝƚƵƌĞ ĚĞ ĐĞƚƚĞ ƚŚğƐĞ͘ dƵ ĞƐ ƵŶĞ ƉĞƌƐŽŶŶĞ Ğƚ ƵŶĞ ƐĐŝĞŶƚŝĨŝƋƵĞ ƌĞŵĂƌƋƵĂďůĞ͕ ũĞ ƐƵŝƐ ĐŽŶĨŝĂŶƚĞ ƋƵĞ ƚƵ ŝƌĂƐ ůŽŝŶ ĚĂŶƐ ƚĂ ǀŝĞ ƉĞƌƐŽŶŶĞůůĞ Ğƚ ƉƌŽĨĞƐƐŝŽŶŶĞůůĞ͊ ŝŶ ďĞƐŽŶĚĞƌĞƌ ĂŶŬ Őŝůƚ ,ĞŝŬĞ Ĩƺƌ ŝŚƌĞ ĞƚƌĞƵƵŶŐ ƵŶĚ ŝŚƌĞ ŐƵƚĞŶ ZĂƚƐĐŚůćŐĞ͘ /ĐŚ ĚĂŶŬĞ Ěŝƌ ĂƵĨƌŝĐŚƚŝŐĨƺƌĚĞŝŶĞŶŬŽŶƐƚƌƵŬƚŝǀĞŶĞŝƚƌĂŐƵŶĚĚĞŝŶĞƵŶĞƌŵƺĚůŝĐŚĞhŶƚĞƌƐƚƺƚnjƵŶŐ͕ĚŝĞŵŝƌďĞŝĚĞƌ hŵƐĞƚnjƵŶŐĚŝĞƐĞƐDĂŶƵƐŬƌŝƉƚƐƐĞŚƌŐĞŚŽůĨĞŶŚĂďĞŶ͘,ćƚƚĞƐƚĚƵŵŝĐŚĚĂŵĂůƐŶŝĐŚƚĂůƐWƌĂŬƚŝŬĂŶƚŝŶ ŐĞŶŽŵŵĞŶ͕ǁćƌĞŝĐŚǁŽŚůũĞƚnjƚŶŝĐŚƚŚŝĞƌ͘ƵďŝƐƚĞŝŶĞƐĞŚƌĂƵĨŵĞƌŬƐĂŵĞƵŶĚŚŝůĨƐďĞƌĞŝƚĞWĞƌƐŽŶ͕ ĚŝĞŝĐŚƐĞŚƌƐĐŚćƚnjĞƵŶĚŶŝĐŚƚƐŽƐĐŚŶĞůůǀĞƌŐĞƐƐĞŶǁĞƌĚĞ͘ DĞƌĐŝăDĂƌůğŶĞĞƚ,ĠůğŶĞĚ͛ĂǀŽŝƌĠƚĠ ůă͊sŽƵƐġƚĞƐĚĞƐĂŵŝĞƐƉƌĠĐŝĞƵƐĞƐƋƵĞũĞŶĞƐƵŝƐƉĂƐƉƌġƚĞ ăŽƵďůŝĞƌ͊DĞƌĐŝDĂƌůğŶĞƉŽƵƌƚŽŶŐƌĂŝŶĚĞĨŽůŝĞ͕ƚĂďŽŶŶĞŚƵŵĞƵƌĞƚƚŽŶŚŽŶŶġƚĞƚĠ͕ĞƚƉŽƵƌƚŽƵƐ ĐĞƐ ŵŽŵĞŶƚƐ ƉĂƐƐĠƐ ĂƵ ůĂďŽ Ğƚ ƐƵƌƚŽƵƚ ĞŶ ĚĞŚŽƌƐ ĚƵ ůĂďŽ ĂǀĞĐ ,ĠůğŶĞ ͊ DĞƌĐŝ ,ĠůğŶĞ͕ ũĞ Ŷ͛ŽƵďůŝĞƌĂŝƐũĂŵĂŝƐĐĞƐďŽŶƐŵŽŵĞŶƚƐĚĞƌŝƌĞƋƵ͛ŽŶĂ ƉĂƐƐĠƐĞŶƐĞŵďůĞĂƵůĂďŽ͊DĞƌĐŝƉŽƵƌƚŽŶ ƐŽƵƚŝĞŶĞƚƚĂƉƌĠƐĞŶĐĞĚĂŶƐůĞƐŵŽŵĞŶƚƐƵŶƉĞƵŵŽŝŶƐũŽLJĞƵdž͕ĞƚƚŽƵƚĞƚŽŶĂŝĚĞĚƵƌĂŶƚůĂƚŚğƐĞ ƋƵŝ Ŷ͛ĂƵƌĂŝƐƉĂƐĠƚĠůĂŵġŵĞƐĂŶƐƚŽŝ͘:͛ĞƐƉğƌĞƋƵĞƚƵĂƵƌĂ ƐƚŽƵƚĐĞƋƵĞƚƵŵĠƌŝƚĞƐĚĂŶƐƚĂǀŝĞ ƉĞƌƐŽŶŶĞůůĞĞƚƉƌŽĨĞƐƐŝŽŶŶĞůůĞ͕ƚƵĂƐƚŽƵƚĞƐůĞƐĐĂƉĂĐŝƚĠƐƉŽƵƌĂůůĞƌƚƌğƐůŽŝŶ͘ DĞƌĐŝĂƵdžĂƵƚƌĞƐŵĞŵďƌĞƐĂĐƚƵĞůƐ ŽƵĂŶĐŝĞŶƐĚĞů͛ĠƋƵŝƉĞ͕ĂŵŝĞŶ͕ ůĂƌĂ͕EĂƚŬĂ͕WŝĞƌƌĞ͕^ŝŵŽŶ͕ ŶŶĞͲĂƌŽůŝŶĞ͕DĂƌŝĞ͕ƵĚĞĞƚ'ĂĠƚĂŶƉŽƵƌǀŽƚƌĞĂŝĚĞĞƚƉŽƵƌǀŽƚƌĞďŽŶŶĞŚƵŵĞƵƌ͘DĞƌĐŝă>ĂƵƌĞ ƉŽƵƌƚĂŐĞŶƚŝůůĞƐƐĞ͕ƚƵĞƐƚŽƵũŽƵƌƐƉƌġƚĞăĂŝĚĞƌ Ğƚăů͛ĠĐŽƵƚĞ ͘DĞƌĐŝăŵĞƐƐƚĂŐŝĂŝƌĞƐ&ůŽƌĞŶĐĞ͕ DĂƌŝŶĞĞƚYƵĞŶƚŝŶ͕ũĞǀŽƵƐƐŽƵŚĂŝƚĞďĞĂƵĐŽƵƉĚĞƌĠƵƐƐŝƚĞƉŽƵƌůĂƐƵŝƚĞ͘ DĞƌĐŝăů͛ĠƋƵŝƉĞĚĞůĂƉůĂƚĞĨŽƌŵĞĚĞƐĠƋƵĞŶĕĂŐĞƉŽƵƌǀŽƚƌĞĂŝĚĞĞƚĐŽŶƐĞŝůƐ͕ŵĞƌĐŝăƚŽƵƐůĞƐ ŵĞŵďƌĞƐĚĞůĂƉůĂƚĞĨŽƌŵĞĚĞƉƌŽĚƵĐƚŝŽŶĚĞƉůĂŶƚĞ͕DŝĐŚğůĞĚĞůĂůĂǀĞƌŝĞ͕>ĂƵƌĞŶĐĞĚƵŵĂŐĂƐŝŶ͕ ĞƚůĞƐŵĞŵďƌĞƐĚĞůĂƉůĂƚĞĨŽƌŵĞĚĞƉƌŽƚĠŽŵŝƋƵĞĚĞů͛/D ƉŽƵƌǀŽƚƌĞĞdžƉĞƌƚŝƐĞĞƚƉƌĠĐŝĞƵƐĞĂŝĚĞ͘ DĞƌĐŝăƚŽƵƐůĞƐĂƵƚƌĞƐĨŽƌŵŝĚĂďůĞƐƉĞƌƐŽŶŶĞƐƋƵĞũ͛ĂŝƉƵĐŽŶŶĂŝƚƌĞăů͛/DW͕DĂƌŝŽŶ͕DĂƌĐŽ͕ dŚŝďĂƵƚ͕DĂŐĚĂůğŶĞ͕>ƵĐŝĞ͕ŚůŽĠ͕ĚƌŝĞŶ͕sĂůĞŶƚŝŶ͕ ,Ăďŝď͕ƌŶĂƵĚ͕,ĞƌƌĂĚĞ;ĞƚdŚŝďĂƵĚͿ͕yƵĞ͕ ĠĚƌŝĐ͕EŝĐŽůĂƐ͕DĂƌĐĞů͕sŝĂŶŶĞLJ͕DĂƚŚŝůĚĞ͕ŶƚŚŽŶLJ͕ůŽĚŝĞ͕^ĂŶĚƌŝŶĞ͕dŚĂůŝĂ͕ůĠŵĞŶƚŝŶĞ͕<ĂŵĞů͕ ƐƚŚĞƌ͙ĞƚƚŽƵƐůĞƐĂƵƚƌĞƐ ͘ƵdžͨŐƵƌůnjnjnjĞƚďŽLJLJnjnjͩĚĞůĂƐĂůůĞĚĞƌĠĚĂĐƚŝŽŶ͕ŵĞƌĐŝƉŽƵƌǀŽƚƌĞ ƐŽƵƚŝĞŶ͕ǀŽƚƌĞŐĞŶƚŝůůĞƐƐĞĞƚůĞƐďŽŶƐŵŽŵĞŶƚƐƉĂƐƐĠƐĞŶƐĞŵďůĞ͘EĞůąĐŚĞnjƌŝĞŶǀŽƵƐĂůůĞnjƚŽƵƐLJ ĂƌƌŝǀĞnj͊ DĞƌĐŝăŵĞƐďŽŶƐĂŵŝƐĠďŽƌĂŚ͕^ŝŵŽŶ͕EŝĐŽůĂƐ͕zĂŶŶŝĐŬĞƚWŝĞƌƌĞ͕ƋƵŝŽŶƚƚŽƵũŽƵƌƐĠƚĠůăƉŽƵƌ ŵŽŝ͕ Ğƚ ƋƵŝ ;ƐƵƌƚŽƵƚ ă ůĂ ĨŝŶͿ ŵ͛ŽŶƚ ƚŽƵũŽƵƌƐ ƐƵƉƉŽƌƚĠ ŵĂůŐƌĠ ŵĂ ŵĂƵǀĂŝƐĞ ŚƵŵĞƵƌͨŽĐĐĂƐŝŽŶŶĞůůĞͩ ͘ DĞƌĐŝ ă ĐĞƵdž ƋƵĞ ũ͛Ăŝ ĐŽŶŶƵ ă ů͛ƵŶŝǀĞƌƐŝƚĠ͕ >ĠĂ Ğƚ zĂĐŝŶĞ͕ Ğƚ ƉĂƌƚŝĐƵůŝğƌĞŵĞŶƚŵĞƐĂŵŝƐĞƚĂŶĐŝĞŶƐĐĂŵĂƌĂĚĞƐĚĞůŝĐĞŶĐĞ hƌƓĂ͕ EĂĚũǁĂ͕ĂƌŽůĞ͕dŚĠŽ͕ĂŶŝĞů͕ ŚĂƌůĞƐ͕ĞƚƐƵƌƚŽƵƚ ŵŽŶĐŽƵƐŝŶ'ŝůůĞƐĞƚEŝĐŽůĂƐ͘:͛ĂŝƉĂƐƐĠĚĞƐƵƉĞƌďĞƐŵŽŵĞŶƚƐĂǀĞĐǀŽƵƐĞƚũĞ ŶĞǀŽƵƐŽƵďůŝĞƌĂŝƐũĂŵĂŝƐ͘ DĞƌĐŝĚĞŵEĂƚĂƐĐŚĂ͕:ŝůů͕ŶŶŝĐŬ͕>ĂƵƌĞŶƚ͕/ƐĂďĞůůĞĂŶĂƌŽůŝŶĞ͕ĚĂƐƐĚŝĞƌģŵŵĞƌ<ŽŶƚĂŬƚŵĂƚŵŝƌ ŐĞŚĂůĞŶŚƵƚƚŽďǁƵĞůĞĐŚƐćŝƚĞƉƵĞƌ:ŽƌĞŶĞůŽŶĞƚŵĠŝĂŵ>ĂŶĚƐŝŶŶ͘DĞƌĐŝĨŝƌćƌ!ŶŶĞƌƐƚģƚnjƵŶŐĂŶ ćƌƉŽƐŝƚŝǀtŝĞĚĞƌ͘ DŽŶƉůƵƐŐƌĂŶĚŵĞƌĐŝŝƌĂăŵĂĨĂŵŝůůĞƋƵŝŵ͛ĂƚŽƵũŽƵƌƐƐŽƵƚĞŶƵĞ ĞƚĞŶĐŽƵƌĂŐĠ͘DĞƌĐŝăŵĞƐ ƉĂƌĞŶƚƐĞƚŵĞƐƐƈƵƌƐ ƉŽƵƌǀŽƚƌĞƉĂƚŝĞŶĐĞƚŽƵƚŽŶůŽŶŐĚĞŵĂƐĐŽůĂƌŝƚĠ͕ĞƚƉĂƌƚŝĐƵůŝğƌĞŵĞŶƚĚƵƌĂŶƚ ĐĞƐϰĚĞƌŶŝğƌĞƐĂŶŶĠĞƐ͊ DĞƌĐŝĚĞŵ͛ĂǀŽŝƌĂƉƉƌŝƐăġƚƌĞƉĞƌƐĠǀĠƌĂŶƚĞĞƚƉĂƚŝĞŶƚĞĞƚăƚŽƵũŽƵƌƐ ĞƐƐĂLJĞƌĚĞĚŽŶŶĞƌůĞŵĞŝůůĞƵƌĚĞŵŽŝͲŵġŵĞ͘hŶŐƌĂŶĚŵĞƌĐŝă&ůŽƌĞŶƚĚ ͛ĂǀŽŝƌ ƚŽƵũŽƵƌƐĐƌƵĞŶŵŽŝ͕ ƚƵĂƐƚŽƵũŽƵƌƐĠƚĠ ăů͛ĠĐŽƵƚĞĞƚƚƵ ĂƐƚŽƵũŽƵƌƐƐƵ ŵ͛ĞŶĐŽƵƌĂŐĞ ƌ͘DĞƌĐŝƉŽƵƌƚŽƵƚĞƐĐĞƐĚĠĐŽƵǀĞƌƚĞƐ ŵƵƐŝĐĂůĞƐĞƚĐƵůƚƵƌĞůůĞƐƋƵĞŶŽƵƐĂǀŽŶƐƉƵĨĂŝƌĞĐĞƐĚĞƌŶŝğƌĞƐĂŶŶĠĞƐ͘DĞƌĐŝăƚŽŝĞƚŵĂĨĂŵŝůůĞ Ě͛ġƚƌ ĞƚŽƵũŽƵƌƐăŵĞƐĐŽƚĠĞƐ͕ƐĂŶƐ ǀŽƵƐũĞŶĞƐĞƌĂŝƐĂŶƐĚŽƵƚĞƉĂƐĂƌƌŝǀĠĞũƵƐƋƵ͛ŝĐŝ͘ dĂďůĞŽĨĐŽŶƚĞŶƚƐ /ŶƚƌŽĚƵĐƚŝŽŶ͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘ϭ ϭ͘WŽƐƚͲƚƌĂŶƐĐƌŝƉƚŝŽŶĂůZEŵŽĚŝĨŝĐĂƚŝŽŶƐ͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘Ϯ ϭ͘ϭ͘hƌŝĚLJůĂƚŝŽŶ͕ĂǁŝĚĞƐƉƌĞĂĚŵŽĚŝĨŝĐĂƚŝŽŶŽĨŶŽŶͲĐŽĚŝŶŐĂŶĚĐŽĚŝŶŐZEƐ͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘ϯ ϭ͘ϭ͘ϭ͘<ĞLJĨĞĂƚƵƌĞƐŽĨƚĞƌŵŝŶĂůƵƌŝĚLJůLJůƚƌĂŶƐĨĞƌĂƐĞƐ͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘ϯ ϭ͘ϭ͘Ϯ͘dŚĞEͲƚĞƌŵŝŶĂů/ZŽĨƌĂďŝĚŽƉƐŝƐhZdϭŝƐƌĞƋƵŝƌĞĚĨŽƌƚŚĞďŝŶĚŝŶŐŽĨƉĂƌƚŶĞƌƉƌŽƚĞŝŶƐ͘͘͘͘͘͘͘͘͘͘͘͘͘ϱ ϭ͘ϭ͘ϯ͘DŽůĞĐƵůĂƌĨƵŶĐƚŝŽŶƐŽĨZEƵƌŝĚLJůĂƚŝŽŶ͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘ϲ Ϯ͘ƐƐĞŶƚŝĂůƉƌŽƚĞĐƚŝǀĞĞůĞŵĞŶƚƐŽĨĞƵŬĂƌLJŽƚŝĐŵZEƐ͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘ϲϭ Ϯ͘ϭ͘ŽͲƚƌĂŶƐĐƌŝƉƚŝŽŶĂůĂĚĚŝƚŝŽŶŽĨƚŚĞϱΖĐĂƉĂŶĚϯΖƉŽůLJͲƚĂŝůƐ͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘ϲϭ Ϯ͘ϭ͘ϭ͘dŚĞϱ͛ĐĂƉƐƚƌƵĐƚƵƌĞ͘ ͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘ϲϭ Ϯ͘ϭ͘Ϯ͘dŚĞϯ͛ƉŽůLJƚĂŝů͘ ͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘ϲϮ Ϯ͘Ϯ͘dŚĞĐĂƉďŝŶĚŝŶŐĐŽŵƉůĞdžĂŶĚƉŽůLJďŝŶĚŝŶŐƉƌŽƚĞŝŶƐ͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘ϲϯ Ϯ͘Ϯ͘ϭ͘dŚĞŶƵĐůĞĂƌĐĂƉďŝŶĚŝŶŐĐŽŵƉůĞdž͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘ϲϰ Ϯ͘Ϯ͘Ϯ͘EƵĐůĞĂƌƉŽůLJďŝŶĚŝŶŐƉƌŽƚĞŝŶƐWWE͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘ϲϱ Ϯ͘Ϯ͘ϯ͘dŚĞĐLJƚŽƉůĂƐŵŝĐĐĂƉďŝŶĚŝŶŐĐŽŵƉůĞdžĞ/&ϰ&͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘ϲϲ Ϯ͘Ϯ͘ϰ͘LJƚŽƉůĂƐŵŝĐƉŽůLJďŝŶĚŝŶŐƉƌŽƚĞŝŶƐ;WWͿ͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘ϲϳ Ϯ͘Ϯ͘ϱ͘Ğ/&ϰ&ĂŶĚWWƉƌŽŵŽƚĞƚƌĂŶƐůĂƚŝŽŶŝŶŝƚŝĂƚŝŽŶ͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘͘ϲϳ ϯ͘ĞĂĚĞŶLJůĂƚŝŽŶ͕ƚŚĞƌĂƚĞͲůŝŵŝƚŝŶŐƐƚĞƉŽĨďƵůŬŵZEĚĞĐĂLJ .
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    3534–3548 Nucleic Acids Research, 2016, Vol. 44, No. 8 Published online 7 April 2016 doi: 10.1093/nar/gkw222 FAM46 proteins are novel eukaryotic non-canonical poly(A) polymerases Krzysztof Kuchta1,2,†, Anna Muszewska1,3,†, Lukasz Knizewski1, Kamil Steczkiewicz1, Lucjan S. Wyrwicz4, Krzysztof Pawlowski5, Leszek Rychlewski6 and Krzysztof Ginalski1,* 1Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, Zwirki i Wigury 93, 02–089 Warsaw, Poland, 2College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, Banacha 2C, 02–097 Warsaw, Poland, 3Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02–106 Warsaw, Poland, 4Laboratory of Bioinformatics and Biostatistics, M. Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, WK Roentgena 5, 02–781 Warsaw, Poland, 5Department of Experimental Design and Bioinformatics, Warsaw University of Life Sciences, Nowoursynowska 166, 02–787 Warsaw, Poland and 6BioInfoBank Institute, Limanowskiego 24A, 60–744 Poznan, Poland Received December 16, 2015; Accepted March 22, 2016 ABSTRACT RNA metabolism in eukaryotes may guide their fur- ther functional studies. FAM46 proteins, encoded in all known animal genomes, belong to the nucleotidyltransferase (NTase) fold superfamily. All four human FAM46 paralogs (FAM46A, FAM46B, FAM46C, FAM46D) are INTRODUCTION thought to be involved in several diseases, with Proteins adopting the nucleotidyltransferase (NTase) fold FAM46C reported as a causal driver of multiple play crucial roles in various biological processes, such as myeloma; however, their exact functions remain un- RNA stabilization and degradation (e.g. RNA polyadenyla- known. By using a combination of various bioinfor- tion), RNA editing, DNA repair, intracellular signal trans- matics analyses (e.g.
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