**3.1 Application of GE in functional genomics**

NHEJ- or HDR-mediated repair of DSBs generated by programmed nucleases leads to the appearance of insertions /deletions, which shift the reading frame [7–10], while the single base changes by ODM [33] or BE [39] promotes targeted replacement of nucleotides. These events lead to changes in the genes activity due to the effects of gene-knockout or gene-knockin, that can be used to reveal their function [17, 29, 34, 42, 43].

Besides gene-knockout and gene-knockin, GE technologies can also be used to regulate gene expression. In this case, genes repression and activation achieved by combining repressors or activators of transcription with the DNA-binding domains of programmed nucleases is most often used [7].

Unlike technologies targeted introducing changes in the DNA nucleotide sequence, gene regulation by GE methods is carried out at the level of transcripts. It allows to reveal the functions of many non-canonical non-coding transcripts without open reading frames [16].

Moreover, the CRISPR/Cas using makes it possible to simultaneously introduce into cells several genetic constructs targeted different regions of the genome [15, 16]. It allows to have an effect on the work of several genes simultaneously and to study intergenic interactions. In this wise, it is possible, for example, to determine the genes involved in the process of crop domestication [29].

In addition, the CRISPR/dCas9 system combined with epigenetic regulatory factors involved in histone acetylation or DNA methylation, can be efficiently used to modulate chromatin activity and gene expression patterns involved in plant development and adaptation to the environment [29].
