An organization writes its acronym in lower-case - do I have to, too?

First, two general principles:

• Consistency with other publications is useful. Consistency within a publication is also useful. So write a style guide that documents your house style.
• Your house style does not necessarily have to match the stylization of a wordmark.

An acronym is an abbreviation pronounced as a word. Many publications write acronyms with all capital letters, like other initialisms. But some publications capitalize acronyms as ordinary proper nouns to help distinguish the pronounciation of "Nasa" from that of the spelled-out initialism "FBI". The Guardian mentions this in its style guide, and BBC News tends toward this as well. The New York Times has a compromise: acronyms up to four letters are set in capital letters, while longer ones are set as proper nouns to avoid the "shouting". For example, N.Y.T. style contrasts "F.B.I." (spelled-out with periods), "NATO" (short acronym with all caps), and "Unicef" (long acronym with title case).

Speaking of Unicef, I had a look at its web site. Unicef's logo uses all lowercase ("unicef"), while the text uses all capitals ("UNICEF"). This difference in stylization between the wordmark and the appearance in running text is common; the logo of Facebook uses a lowercase ''f'', and Twitter used all lowercase before a June 2012 redesign dumped the wordmark entirely for the birdmark. AOL is a spelled-out initialism rendered as "AOL" in text, even though its wordmark resembles "Aol." with the period.

Related questions on other Stack Exchange sites:

• Proper capitalization of commonly used acronyms