Abstract: To reduce the total amount of linear sequence (DNA, RNA or other medium) required to encode a set of genetic elements, the present disclosure describes a computational method for compressing genetic information by finding one or more sequences that each mutually encode multiple genetic elements in the same stretch of sequence (a “co-encoding”). The computational method encodes each of the genetic elements in respective directed acyclic graphs (DAGs) or finite automatons (FAs), then encodes overlapping sequences between the DAGs or FAs in a second DAG or FA. Additional DAGs or FAs may be encoded for overlapping sequences that result from shifting the reading frame of the genetic elements relative to one another and switching the orientation of the elements.

Abstract: The present disclosure provides (i) RNA-guided polypeptides (e.g., circular permuted Cas9 proteins) in which the N-terminal end of an N-terminal fragment of a parent RNA-guided polypeptide (e.g., a parent Cas9 protein) is fused (e.g., via linker) to the C-terminal end of the C-terminal fragment (thereby generating new N- and C-termini), (ii) conditionally active RNA-guided polypeptides (e.g., conditionally active circular permuted Cas9 proteins), and (iiii) Cas9 fusion polypeptides that include an internal insertion of a heterologous polypeptide; as well as methods that employ the above polypeptides.

Abstract: The present disclosure provides an RNA-guided effector polypeptide having a length that is less than Streptococcus pyogenes Cas9, and that retains the ability, when complexed with a guide RNA, to bind to a target nucleic acid. The present disclosure provides a fusion polypeptide comprising: i) an RNA-guided effector polypeptide of the present disclosure; and ii) a fusion partner. The present disclosure further provides nucleic acids encoding an RNA-guided effector polypeptide, or a fusion polypeptide, of the present disclosure. Methods of using an RNA-guided effector polypeptide, or a fusion polypeptide, of the present disclosure are also provided.