The submission process this year is different than in previous years, since the RNA-SIG is part of the main conference. More details about the restructuring of ISMB can be found here. If you would like to submit unpublished work as a paper to the ISMB proceedings for topics covered by the RNA-SIG you should use the central ISMB proceedings portal and designate the RNA-SIG as your SIG of choice. The deadline for submission to the conference proceedings is January 29th (see more details and submission link here). Even if your paper is not accepted to the ISMB proceedings, you can still submit it as an abstract to the SIG as described below.
Submission process and format has changed this year. All abstracts are submitted via the ISMB main portal where you should designate RNA as your SIG/COSI of choice. See the new submission guidelines and related info here.