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DNA methylation is an important epigenetic mark implicated in selective rRNA gene expression, but the DNA methylation readers and effectors remain largely unknown. Here, we report a protein complex that reads DNA methylation to regulate variant-specific 45S ribosomal RNA (rRNA) gene expression in Arabidopsis (Arabidopsis thaliana). The complex, consisting of METHYL-CpG-BINDING DOMAIN PROTEIN5 (MBD5), MBD6, ALPHA-CRYSTALLIN DOMAIN PROTEIN15.5 (ACD15.5), and ACD21.4, directly binds to 45S rDNA. While MBD5 and MBD6 function redundantly, ACD15.5 and ACD21.4 are indispensable for variant-specific rRNA gene expression. These 4 proteins undergo phase separation in vitro and in vivo and are interdependent for their phase separation. The α-crystallin domain of ACD15.5 and ACD21.4, which is essential for their function, enables phase separation of the complex, likely by mediating multivalent protein interactions. The effector MICRORCHIDIA6 directly interacts with ACD15.5 and ACD21.4, but not with MBD5 and MBD6, and is recruited to 45S rDNA by the MBD–ACD complex to regulate variant-specific 45S rRNA expression. Our study reveals a pathway in Arabidopsis through which certain 45S rRNA gene variants are silenced, while others are activated. The METHYL-CpG-BINDING DOMAIN–ALPHA-CRYSTALLIN DOMAIN protein complex reads CG DNA methylation and recruits the effector protein MICRORCHIDIA6 to regulate variant-specific 45S rRNA expression. [ABSTRACT FROM AUTHOR]

Summary: Adenine base editors (ABEs) have been exploited to introduce targeted adenine (A) to guanine (G) base conversions in various plant genomes, including rice, wheat and Arabidopsis. However, the ABEs reported thus far are all quite inefficient at many target sites in rice, which hampers their applications in plant genome engineering and crop breeding. Here, we show that unlike in the mammalian system, a simplified base editor ABE‐P1S (Adenine Base Editor‐Plant version 1 Simplified) containing the ecTadA*7.10‐nSpCas9 (D10A) fusion has much higher editing efficiency in rice compared to the widely used ABE‐P1 consisting of the ecTadA‐ecTadA*7.10‐nSpCas9 (D10A) fusion. We found that the protein expression level of ABE‐P1S is higher than that of ABE‐P1 in rice calli and protoplasts, which may explain the higher editing efficiency of ABE‐P1S in different rice varieties. Moreover, we demonstrate that the ecTadA*7.10‐nCas9 fusion can be used to improve the editing efficiency of other ABEs containing SaCas9 or the engineered SaKKH‐Cas9 variant. These more efficient ABEs will help advance trait improvements in rice and other crops. [ABSTRACT FROM AUTHOR]