Skip to main content

Table 2 Differentially abundant proteins associated with RNA metabolism and proteostasis

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

Gene name

Protein description

FC

p-value

General putative function

RNA metabolism

H2afy2

Core histone macro-H2A.2 (mH2A2)

1.8

0.050

Gene repression

Cdc5l

Cell division cycle 5-like protein

2.2

0.013

mRNA splicing

Cd2bp2

CD2 antigen cytoplasmic tail-binding protein 2

1.8

0.072

mRNA splicing

Hnrnpa0

Heterogeneous nuclear ribonucleoprotein (hnRNP) A0

2.0

0.076

RNA-binding protein

Hnrnpd

Heterogeneous nuclear ribonucleoprotein (hnRNP) D0

1.4

0.029

RNA-binding protein

Hnrnpdl

Heterogeneous nuclear ribonucleoprotein (hnRNP) D-like

2.1

0.024

RNA-binding protein

Hnrnph2

Heterogeneous nuclear ribonucleoprotein (hnRNP) H2

1.5

0.034

RNA-binding protein

Hnrnpl

Heterogeneous nuclear ribonucleoprotein (hnRNP) L

1.8

0.077

RNA-binding protein

Cirbp

Cold-inducible RNA-binding protein

4.3

0.047

RNA-binding protein

Ddx21

Nucleolar RNA helicase 2

2.9

0.009

rRNA transcription, processing, and modification

Hp1bp3

Heterochromatin protein 1-binding protein 3

2.1

0.057

Transcription regulation

Proteostasis

Impact

Protein IMPACT

1.8

0.002

Translational activation

Uchl5

Ubiquitin carboxyl-terminal hydrolase isozyme L5

1.6

0.037

Deubiquitylation

Adrm1

Proteasomal ubiquitin receptor ADRM1

3.0

0.007

Enhances Uchl5

Ublcp1

Ubiquitin-like domain-containing CTD phosphatase 1

3.5

0.068

Nuclear proteasome activity

Cryab

Alpha-crystallin B chain

−2.1

0.003

Chaperone-like activity

Hspb1

Heat shock protein beta-1 (HspB1)

−1.7

0.020

Chaperone for protein folding maintenance

Hsph1*

Heat shock protein 105 kDa

−2.1

0.004

Chaperone activity regulation

Hsp90aa1

Heat shock protein HSP 90-alpha (HSP90α)

−1.5

0.058

ATP-dependent chaperone

Hsp90ab1

Heat shock protein HSP 90-beta (HSP90β)

−1.4

0.056

ATP-dependent chaperone

Hspa4

Heat shock 70 kDa protein 4

−1.5

0.067

Molecular chaperone

Ahsa1

Activator of 90 kDa heat shock protein ATPase homolog 1

−1.3

0.059

Chaperone binding

  1. Significant proteins (p < 0.1) that are associated with either RNA metabolism (top half of table) or proteostasis (bottom half of table) are listed by gene name (first column), followed by the full protein name (second column). For each protein, the fold change (“FC”) and p-value is provided (third and fourth columns, respectively), along with a brief description regarding the putative function of that protein (“General Putative Function”). Information regarding the putative function of each protein was obtained from the UniProtKB/Swiss-Prot database [131]. Gene names with an asterisk (“*”) indicates that the corresponding gene was also identified as significantly, differentially expressed (DE) in the transcriptome by a q < 0.05. Bold proteins indicate that the respective protein has been previously identified as a RTT hit and/or MeCP2 interacting protein (see text for references)