Hypothes.is Annotation tool
Runestone allows annotations using Hypothes.is which is built-in. Hypothes.is can be used for independent or collaborative online annotations.
Click on the < on the top right of a course to open the annotations window.
You can set up a new private group for your class and invite your students to join it.
Then, you or students can highlight text and annotate it to make a comment or ask a question about it and reply to each other.