Table 3.

Genes that are similarly responsive in the GLDT_Ft:NAC052 line and CRISPR/Cas line, but not responsive in the activation-tagged line and in the GLDT_Ft::5'truncatedNAC052 line

	Gene ID	Gene description	Abbreviated gene name	Acti-vation tagged	CRISPR/Cas	GLDT::5'truncatedNAC052	GLDT::NAC052
1	AT1G02640*	Encodes a protein similar to a beta-xylosidase located in the extracellular matrix (AT5G49360). This is a member of glycosyl hydrolase family 3 and has six other closely related members.	BXL2	0.5<FC<2.0	0.36	0.5<FC<2.0	0.46
2	AT1G26820	Encodes ribonuclease RNS3. Involved in RNA catabolic process and ageing.	RNS3	0.5<FC<2.0	0.34	0.5<FC<2.0	0.50
3	AT1G66040	ORTH4, ORTHRUS 4, VARIANT IN METHYLATION 4, VIM4 Involved in chromatin organization, maintenance of DNA methylation, protein ubiquitination. Protein located in nucleus.	VIM4	0.5<FC<2.0	0.26	0.5<FC<2.0	0.44
4	AT1G70985	Hydroxyproline-rich glycoprotein family protein, protein located in anchored component of membrane. Expressed in seeds of first silique		0.5<FC<2.0	0.44	0.5<FC<2.0	0.50
5	AT1G78450*	SOUL haem-binding family protein, protein located in chloroplast, expressed in hypocotyl and siliques.		0.5<FC<2.0	0.41	0.5<FC<2.0	0.39
6	AT2G29300	NAD(P)-binding Rossmann-fold superfamily protein, protein location unknown, expressed in seeds of first silique.		0.5<FC<2.0	0.44	0.5<FC<2.0	0.48
7	AT3G13000	Ubiquinone biosynthesis protein, expressed in young leaf and young flower. Protein located in nucleus and vacuole.		0.5<FC<2.0	0.48	0.5<FC<2.0	0.50
8	AT3G54720	ALTERED MERISTEM PROGRAM 1, AMP1, encodes glutamate carboxypeptidase. Various alleles show increased cotyledon number and rate of leaf initiation, show transformation of leaves to cotyledons, altered flowering time and photomorphogenesis, and an increased level of cytokinin biosynthesis. Protein located in endoplasmic reticulum. Involved in leaf vascular tissue pattern formation.	AMP1	0.5<FC<2.0	0.47	0.5<FC<2.0	0.39
9	AT3G62070	Hypothetical protein expressed in guard cell.		0.5<FC<2.0	0.48	0.5<FC<2.0	0.39
10	AT4G03610	Metallo-hydrolase/oxidoreductase superfamily protein, protein located in nucleus, expressed in plant embryo.		0.5<FC<2.0	0.19	0.5<FC<2.0	0.45
11	AT4G20820	FAD-binding Berberine family protein, electron transfer activity, protein located in chloroplast, expressed in collective leaf structure, cotyledon, guard cell, hypocotyl, root, stem, vascular leaf.	ATBBE18	0.5<FC<2.0	0.29	0.5<FC<2.0	0.34
12	AT4G26288	Hypothetical protein, expressed in silique, protein located in nucleus		0.5<FC<2.0	0.47	0.5<FC<2.0	0.42
13	AT4G34790	SAUR-like auxin-responsive protein family, protein located in mitochondrion. Expressed in guard cell.	SAUR3	0.5<FC<2.0	0.27	0.5<FC<2.0	0.33
14	AT4G40090	Arabinogalactan protein 3, involved in multicellular organism development, protein located in anchored component of membrane, expressed in hypocotyl, plant egg cell, root, root hair cell, shoot apex, trichoblast.	AGP3	0.5<FC<2.0	0.49	0.5<FC<2.0	0.42
15	AT5G49360*	Encodes a bifunctional (beta)-d-xylosidase/(alpha)-l-arabinofuranosidase required for pectic arabinan modification. Located in the extracellular matrix. Gene is expressed specifically in tissues undergoing secondary wall thickening. This is a member of glycosyl hydrolase family 3 and has six other closely related members.	BXL1	0.5<FC<2.0	0.50	0.5<FC<2.0	0.46

Fold changes are compared with the reference line. Gene IDs in bold are involved in either chromatin organization, leaf vascular tissue pattern formation, or arabinogalactan functioning; gene IDs that include ‘*’ overlap with up-regulated genes after NAC050/052-RNAi (Ning et al., 2015); gene IDs underlined overlap with differentially expressed genes between total leaf and bundle sheath only (Aubry et al., 2014); fold changes in red are decreased compared with the reference line (P=0.05)