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Microarray expression profiles of 19 fluorescently sorted GFP-marked
lines were analyzed (3–9, 23, 24). The colors associated with each marker
line reflect the developmental stage and cell types sampled. Thirteen
transverse sections were sampled along the root's longitudinal axis (red
lines) (10). CC, companion cells.
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(A) The majority of enriched GO terms (hierarchically clustered) are associated
with individual cell types (blue bar). A smaller number are present across multiple
cell types (green bar). (fig. S2) (B) GO category enrichment for hair cells
confirms a previous report (15). Enriched cis-elements and an enriched TF family
were also identified. (C) From the top 50% of varying probe sets, 51 dominant
radial patterns were identified. Pattern expression values were mean-normalized
(rows) and log2 transformed to yield relative expression indices for each marker
line (columns). Marker line order is the same for all figures; see table S1 for
marker line abbreviations. (D) Pattern expression peaks were found across one
to five cell types. (E to G) Patterns where expression is enriched in single and
multiple cell types support transcriptional regulation of auxin flux and synthesis. In
all heat maps with probe sets, expression values were mean-normalized and log2
transformed. Expression is false-colored in representations of a root transverse
section, a cut-away of a root tip, and in a lateral root primordium. (E) Auxin
biosynthetic genes (CYP79B2, CYP79B3, SUPERROOT1, and SUPERROOT2)
are transcriptionally enriched in the QC, lateral root primordia, pericycle, and
phloem-pole pericycle (P = 1.99E–11, pattern 5). All AGI identifiers and TAIR
descriptions are found in table S14. (F) Auxin amido-synthases GH3.6 and
GH3.17 that play a role in auxin homeostasis show enriched expression in the
columella, just below the predicted auxin biosynthetic center of the QC (P =
8.82E–4, pattern 13). (G) The expression of the auxin transporter, PINFORMED2,
and auxin transport regulators (PINOID, WAG1) are enriched in the
columella, hair cells, and cortex (P = 1.03E–4, pattern 31).
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(A) The majority of enriched GO terms (hierarchically clustered) are associated
with individual cell types (blue bar). A smaller number are present across multiple
cell types (green bar). (fig. S2) (B) GO category enrichment for hair cells
confirms a previous report (15). Enriched cis-elements and an enriched TF family
were also identified. (C) From the top 50% of varying probe sets, 51 dominant
radial patterns were identified. Pattern expression values were mean-normalized
(rows) and log2 transformed to yield relative expression indices for each marker
line (columns). Marker line order is the same for all figures; see table S1 for
marker line abbreviations. (D) Pattern expression peaks were found across one
to five cell types. (E to G) Patterns where expression is enriched in single and
multiple cell types support transcriptional regulation of auxin flux and synthesis. In
all heat maps with probe sets, expression values were mean-normalized and log2
transformed. Expression is false-colored in representations of a root transverse
section, a cut-away of a root tip, and in a lateral root primordium. (E) Auxin
biosynthetic genes (CYP79B2, CYP79B3, SUPERROOT1, and SUPERROOT2)
are transcriptionally enriched in the QC, lateral root primordia, pericycle, and
phloem-pole pericycle (P = 1.99E–11, pattern 5). All AGI identifiers and TAIR
descriptions are found in table S14. (F) Auxin amido-synthases GH3.6 and
GH3.17 that play a role in auxin homeostasis show enriched expression in the
columella, just below the predicted auxin biosynthetic center of the QC (P =
8.82E–4, pattern 13). (G) The expression of the auxin transporter, PINFORMED2,
and auxin transport regulators (PINOID, WAG1) are enriched in the
columella, hair cells, and cortex (P = 1.03E–4, pattern 31).
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Schematic flowchart of the Human Protein Atlas. For each gene, a signature
sequence (PrEST) is defined from the human genome sequence, and following
RT-PCR, cloning and production of recombinant protein fragments, subsequent
immunization and affinity purification of antisera results inmunospecific
antibodies. The produced antibodies are tested and validated in various
immunoassays. Approved antibodies are used for protein profiling in cells
(immunofluorescence) and tissues (immunohistochemistry) to generate the
images and protein expression data that are presented in the Human Protein
Atlas (Ponten et al., J Int Med, 2011).
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Excample of an output of transcriptional profiling study using Illumina
sequencing performed in our lab. Shown is just a tiny fragment of the complete
list, copmprising about 7K genes revealing differential expression in the studied
mutant.
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In the figure, there is simplified scheme of vesicle trafficking pathways, regulated by
GNOM and its closest relative, GNOM-LIKE1 (GNL1).
Secretory and membrane proteins are synthesised at the ER (blue) and passed onto the
Golgi apparatus (green) by anterograde trafficking in COPII-coated vesicles.
The retrograde route from the Golgi apparatus to the ER is regulated by the ARF-GEFs
GNOM (GN) and GNL1, which regulate the recruitment of COPI coats to the Golgi
membrane. On the secretory route, proteins are transported to the sorting station, the
trans-Golgi network (TGN; lilac).
From there, proteins are either transported to the vacuole (grey) via multivesicular
bodies (MVB, also called prevacuolar compartment, PVC, which corresponds to the late
endosome; deep blue) or trafficked to the plasma membrane (PM).
Plasma membrane proteins like the auxin efflux carrier PIN1 (red), which accumulates at
the basal PM at steady state, are continually internalised and trafficked to the TGN,
which resembles the early endosome (EE) in plants.
From the TGN, PIN1 is recycled to the plasma membrane via the recycling endosome
(RE; light blue). This pathway is regulated by the ARF-GEF GNOM.
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