RNA sequencing and proteomics approaches reveal novel deficits in the cortex of Mecp2-deficient mice, a model for Rett syndrome

Pacheco, Natasha L.; Heaven, Michael R.; Holt, Leanne M.; Crossman, David K.; Boggio, Kristin J.; Shaffer, Scott A.; Flint, Daniel L.; Olsen, Michelle L.

doi:10.1186/s13229-017-0174-4

Molecular Autism

Table 1 Significant DE genes overlapping with previously identified RTT hits

From: RNA sequencing and proteomics approaches reveal novel deficits in the cortex of Mecp2-deficient mice, a model for Rett syndrome

Gene targets: this study	UniProt: function keywords	Fold change	RTT gene hits: direction of expression (with references)
Aacs*	• Molecular function: ligase • Biological process: fatty acid metabolism; lipid metabolism • Ligand: ATP-binding; nucleotide-binding	− 0.79	Decrease⁴
Aldh1a1*	• Molecular function: oxidoreductase • Ligand: NAD	− 0.67	Decrease⁴
*Arhgdig*	• Molecular function: GTPase activation	− 0.69	Decrease ²
Auts2	N/A	1.40	Increase⁷
C1qa	• Biological process: complement pathways; immunity; innate immunity	− 0.76	Decrease⁷
*Cacnb3*	• Molecular function: calcium channel; ion channel; voltage-gated channel • Biological process: calcium transport; ion transport; transport • Ligand: calcium	− 0.79	Increase ²
*Calb1*	• Ligand: calcium; metal-binding; vitamin D	− 0.79	Decrease ⁵
Calr*	• Molecular function: chaperone • Ligand: calcium; lectin; metal-binding	− 0.80	Decrease⁸
Dgkg*	• Molecular function: kinase; transferase • Ligand: ATP-binding; calcium; metal-binding; nucleotide-binding; zinc	1.42	Increase^{4, 8}
Ephx2*	• Molecular function: hydrolase • Biological process: aromatic hydrocarbons catabolism; detoxification; lipid metabolism • Ligand: magnesium; metal-binding	− 0.71	Decrease⁴
*Fabp7*	• Biological process: transport • Ligand: lipid-binding	− 0.39	Decrease ^2,5
*Fkbp5*	• Molecular function: chaperone; isomerase; rotamase	1.81	Increase ^3,4,5,7,8
Gabra3	• Molecular function: chloride channel; ion channel; ligand-gated ion channel; receptor • Biological process: ion transport; transport • Ligand: chloride	− 0.81	Decrease⁶
Gfra1*	• Molecular function: receptor	1.26	Increase^{4, 8}
Grm3*	• Molecular function: G-protein coupled receptor; receptor; transducer	− 0.63	Decrease⁴
Hpcal4*	• Ligand: calcium; metal-binding	− 0.69	Decrease^{4, 8}
Hsph1	• Biological process: stress response • Ligand: ATP-binding; nucleotide-binding	− 0.80	Decrease³
*Itm2a*	N/A	− 0.73	Decrease ⁵
Mecp2	• Molecular function: DNA-binding; repressor • Biological process: transcription; transcription regulation	− 0.66	Decrease^{1, 4}
*Msmo1* / *Sc4mol*	• Molecular function: oxidoreductase • Biological process: lipid biosynthesis; lipid metabolism; steroid biosynthesis; steroid metabolism; steroid biosynthesis; sterol metabolism • Ligand: iron; NAD	− 0.77	Decrease ⁵
Myo1b*	• Molecular function: actin-binding; calmodulin-binding; motor protein; myosin • Ligand: ATP-binding; nucleotide-binding	1.32	Increase^{4, 8}
Pcsk1	• Molecular function: hydrolase; protease; serine protease • Ligand: calcium	− 0.74	Decrease⁶
Pdia4*	• Molecular function: isomerase	− 0.71	Decrease^{4, 8}
*Plagl1*	• Ligand: metal-binding; zinc	1.37	Increase ⁵
Prkcg*	• Molecular function: kinase; serine/threonine-protein kinase; transferase • Biological process: biological rhythms • Ligand: ATP-binding; calcium; metal-binding; nucleotide-binding; zinc	− 0.82	Decrease⁸
*Pvalb*	• Molecular function: muscle protein • Ligand: calcium; metal-binding	1.27	Increase ²
Pygm	• Molecular function: glycosyltransferase; transferase • Biological process: carbohydrate metabolism; glycogen metabolism • Ligand: nucleotide-binding; pyridoxal phosphate	1.29	Increase⁶
Qdpr*	• Molecular function: oxidoreductase • Biological process: tetrahydrobiopterin biosynthesis • Ligand: NADP	− 0.74	Decrease⁴
Rnpep*	• Molecular function: aminopeptidase; hydrolase; metalloprotease; protease • Ligand: metal-binding; zinc	− 0.78	Decrease⁴
*Sgk1*	• Molecular function: kinase; serine/threonine-protein kinase; transferase • Biological process: apoptosis; stress response • Ligand: ATP-binding; nucleotide-binding	1.37	Increase ^2,3
Slc24a4*	• Biological process: antiport; calcium transport; ion transport; olfaction; potassium transport; sensory transduction; sodium transport; symport; transport • Ligand: calcium; potassium; sodium	1.58	Increase⁴
Slc9a3r1*	• Biological process: Wnt signaling pathway	− 0.74	Decrease⁸
Sun2*	• Biological process: meiosis	1.42	Increase⁸
Ugp2*	• Molecular function: nucleotidyltransferase; transferase • Ligand: magnesium; metal-binding	− 0.73	Decrease⁴
Zmat4*	• Molecular function: DNA-binding • Ligand: metal-binding; zinc	1.5	Increase⁸

First column represents the significant DE gene identified in this study, along with the UniProt function keyword(s) for each gene (second column) and the Log₂ fold change expression of the gene in our data set (third column). DE genes with an asterisk (*) represent genes identified in supplemental material from Chahrour et al. [4] and Veeraragavan et al. [34]. All function keywords were found from the UniProtKB/Swiss-Prot database [131] per respective DE gene. DE genes without a published function keyword in the UniProtKB/Swiss-Prot database are represented as “N/A.” The last column represents the previously identified RTT hits’ fold change expression direction, with each superscript representing that gene’s respective references. Superscript references are as follows: (1) Amir et al. [2], (2) Tudor et al. [20], (3) Nuber et al. [21], (4) Chahrour et al. [4], (5) Urdinguio et al. [24], (6) Ben-Shachar et al. [25], (7) Lin et al. [33], and (8) Veeraragavan et al. [34]. Rows in bold font represent previously identified RTT hits that were found to be specifically DE in the cortex

Back to article page

ISSN: 2040-2392

Contact us

General enquiries: journalsubmissions@springernature.com