RNA modification has a pivotal role in gene expression regulation. Particularly, mRNA chemical modification directly affects various aspects of mRNA processing, such as mRNA splicing, transcription and decay. The 5' cap modification and internal chemical modifications are critical regulatory elements in determining mRNA destiny. In my thesis, we investigated two proteins, NUDT12 and YTHDC2, that act on mRNA 5' end and 3' UTR, respectively. NUDT12 is a decapping enzyme and preferentially removes NAD-capped mRNAs. It forms a complex with BLMH and regulates circadian gene expression. YTHDC2 is an RNA helicase and is essential for mammalian germ cell development. It interacts with XRN1, an exoribonuclease, both in vivo and in vitro. The helicase activity, instead of its m6A binding capacity, is crucial for mouse fertility.