Methods and compositions for modifying target DNA directed RNA and modulation of transcription directed RNA

A composition comprising: (a) a chimeric Cas9 protein, or a polynucleotide encoding said chimeric Cas9 protein, wherein the Cas9 chimeric protein comprises a Cas9 modified protein having nuclease activity reduced compared to Cas9 type corresponding wild, and comprises a heterologous polypeptide: (i) modifying activity is DNA, or (ii) shows the ability to increase or decrease transcription, or (iii) has enzymatic activity that modifies a polypeptide associated with DNA; and (b) an RNA directed DNA, or one or more polynucleotides encoding DNA said RNA directed DNA, wherein said RNA directed DNA comprises: (i) a segment address to DNA comprising a nucleotide sequence is complementary to a sequence in a target DNA, and (ii) a segment binding protein which interacts with said chimeric Cas9 protein, wherein the segment binding protein comprises two complementary nucleotide stretches that hybridize to form a duplex RNA double stranded (dsRNA).