As we all know in IPA isn’t used capital letters. There is also the 2nd option for representation acronyms which is to use dots, but in IPA dots is used to represent syllables. And therefore I'd like to figure out how to represent acronyms?
IPA is used to render the pronunciation of a word, so NATO is [ˈnɛɪtʰɔʊ], JPEG is [ˈdʒeɪpɛɡ] and so on. Some people pronounce NATO as [ˈnɛɪɾɔʊ], in which case you'd use a different transcription. IPA isn't a spelling system / general-purpose writing system, it's used to represent pronunciation, thus it doesn't matter if you write IRA or I.R.A (but it does matter if you pronounce it [ɑɪɑɹɛɪ] or [ɑɪɹə]).