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In English figurative meaning of word usually marked with quotation marks like this:

The motherboard is sometimes considered the "brain" of a computer.

I know that in Japanese quotation marks usually used for emphasis. But do they also used to mark figurative meaning or some other method is used?

5

Yes, Japanese quotation marks (「」) can be used to enclose non-literal or figurative expressions.

マザーボードはしばしばコンピュータの「頭脳」と見なされる。

Double corner brackets (『』) and Western-style double-quotes (“ ”)are also commonly used for this purpose. This article seems good.

But please don't think take this as a hard rule. As a matter of fact, Japanese people use brackets fairly loosely. Quotation marks are not strongly associated with sarcasm, either. See the following questions.

(By the way, the "brain" of a PC is usually a CPU, isn't it?)

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Usually 傍点(ぼうてん) is used.
傍点 are small dots used like furigana, and put above or on the side of the word you want to emphasize.

Example:
傍点{・・}

Frequently they can mean sarcasm.
Unfortunately you cannot 傍点 in text files.
Only on computer files that allow furigana, like Word files.

https://dictionary.goo.ne.jp/word/en/傍点/#je-69567
https://www.724685.com/weekly/qa120328.htm
https://dictionary.goo.ne.jp/jn/202293/meaning/m1u/傍点/
https://ja.wikipedia.org/wiki/圏点

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