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Table 2 Genes with altered mRNA processing patterns in the neocortex of TDP-43 cKO mice

From: Transcriptomopathies of pre- and post-symptomatic frontotemporal dementia-like mice with TDP-43 depletion in forebrain neurons

  Gene Location Strand Significant Δmisoψ White et al. [86] References
     3 Months 12 Months 3 Months 12 Months 5 Months 20 Months  
Cryptic Cdh22 Ch2:165183239-165183371 - 0.61 0.54    Jeong et al. [37]
Cryptic Camk1g Ch1:193368867-193368952 - 0.46 0.59    Jeong et al. [37]
Cryptic Slc45a1 Ch4:150630400-150630454 - 0.32 0.13    Jeong et al. [37]
Cryptic Synj2bp Ch12:81509828-81510051 - 0.39 0.30    Jeong et al. [37]
Cryptic Hgsnat Ch8:25945949-25945996 - 0.22 0.19    Jeong et al. [37]
Cryptic Adnp2 Ch18:80138153-80138304 - 0.45 0.49    Jeong et al. [37]
Cryptic Abca8b Ch11:109975240-109975477 - 0.18 0.18    
Cryptic Upf3a Ch8:13789928-13789967 +   0.17 0.07    
Cryptic Letm1 Ch5:33779574-33779604 -   0.13 0.04    Jeong et al. [37]
Inclusion Sort1 Ch3:108355472-108355570 + 0.35 0.40 (exclusion) (exclusion) Polymenidou et al. [58]
Inclusion Islr2-02 Ch9:58200272-58200461 - 0.36 0.37    
Inclusion Islr2-01 Ch9:58200272-58200443 - 0.30 0.29    
Inclusion Bsg Ch10:80136663-80136743 - 0.25 0.13    
Inclusion Vps13d Ch4:145099352-145099463 - 0.23 0.18   (inclusion)  
Inclusion Smg5 Ch3:88340649-88340763 + 0.20 0.10    
Inclusion Smarca4 Ch9:21677953-21678051 + 0.20 0.24    
Inclusion Uggt2 Ch14:119043908-119044028 - 0.19 0.08    
Inclusion Elac2 Ch11:65005454-65005505 - 0.15 0.12    
Inclusion Kcnmb4 Ch10:116443772-116443912 - 0.11 0.08    
Inclusion Dnajc5 Ch2:181548926-181549000 + 0.10 0.13    Polymenidou et al. [58]
Inclusion Sun1 Ch5:139230773-139230838 + -0.14 0.32    
Inclusion Pdp1-01 Ch4:11965614-11965648 -   0.40 0.24    
Inclusion Tmem2 Ch19:21780171-21780252 +   0.40 0.19    
Inclusion Zfp30 Ch7:29788049-29788175 +   0.32 -0.04    
Inclusion Zkscan16 Ch4:58943943-58944160 +   0.29 0.18    
Inclusion Nfia-02 Ch4:98081725-98081816 +   0.12 0.02    
Inclusion Lrrk2 Ch15:91785371-91785527 +   0.06 -0.01    
Inclusion Atxn1 Ch13:45849519-45849588 -   0.10 0.09    Polymenidou et al. [58]
Inclusion Ranbp17 Ch11:33283908-33283990 -   -0.17 0.28    
Inclusion Srr Ch11:74919437-74919662 -   0.11 0.22    
Inclusion Atad2b Ch12:4970406-4970468 +   -0.03 0.15    
Inclusion Kctd10 Ch5:114376771-114376866 -   0.05 0.06    
Inclusion Pdp1-02 Ch4:11965614-11965648 -   #REF! 0.05    
Inclusion Mettl22 Ch16:8482127-8482167 +   0.00 0.03    
Exclusion Cobl Ch11:12306958-12307128 - -0.34 -0.41 (inclusion)   
Exclusion Scamp1 Ch13:94210577-94210678 - -0.31 -0.26    
Exclusion Ddx50 Ch10:62627521-62627682 - -0.27 -0.37    
Exclusion Kcnip2-02 Ch19:45797091-45797186 - -0.23 -0.29    
Exclusion Dtwd1 Ch2:126158410-126158553 + -0.27 -0.19    
Exclusion Nlgn3 ChX:101307075-101307134 + -0.22 -0.15    
Exclusion Lzts1 Ch8:69182213-69182331 - -0.12 -0.15    
Exclusion Nrxn1 Ch17:90701988-90702011 - -0.09 -0.16    
Exclusion Shisa4 Ch1:135373152-135373285 - -0.07 -0.14   (inclusion)  
Exclusion Rdh13 Ch7:4444978-4445122 - 0.08 -0.26    
Exclusion Atp11b Ch3:35843571-35843696 +   -0.44 -0.28   (inclusion)  
Exclusion Gpatch1 Ch7:35281332-35281480 -   -0.36 0.00    
Exclusion Kcnip2-01 Ch19:45796279-45796332 -   -0.21 -0.18    
Exclusion Nfia-01 Ch4:98041551-98041679 +   -0.15 0.00    
Exclusion Dzip3 Ch16:48951543-48952160 -   -0.13 0.01    
Exclusion Cacna1b-01 Ch2:24618255-24618362 -   -0.04 0.01    
Exclusion Tmcc2 Ch1:132380657-132381172 -   -0.05 0.01    
Exclusion Pcm1-01 Ch8:41313302-41313460 +   -0.08 -0.01    
Exclusion Cdk19-02 Ch10:40466638-40466769 +   -0.02 -0.04    
Exclusion Max Ch12:76939430-76939514 -   -0.08 -0.05    
Exclusion Phactr2 Ch10:13253342-13253879 -   -0.16 -0.08    
Exclusion Cdk19-01 Ch10:40454015-40454072 +   0.02 -0.05    
Exclusion Rimbp2 Ch5:128846922-128846991 -   -0.01 -0.09    
Exclusion Clasp1-01 Ch1:118512175-118512222 +   0.02 -0.12    
Exclusion Clasp1-03 Ch1:118541675-118541698 +   0.07 -0.12    
Exclusion Cntln-01 Ch4:84984369-84984500 +   -0.02 -0.20    
Exclusion Agfg1 Ch1:82891460-82891507 +   -0.16 -0.26    
Exclusion Repin1 Ch6:48594862-48594976 +   -0.07 -0.24    
Exclusion Ppp3ca Ch3:136932011-136932040 +   -0.09 -0.11 (inclusion) (inclusion)  
Exclusion Hspa13 Ch16:75758632-75758727 -   0.01 -0.08    
Extension Wbscr22 Ch5:135063781-135063921 - 0.17 0.19    Jeong et al. [37]
Extension Chga Ch12:102558298-102558559 + 0.08 0.06    Jeong et al. [37]
Extension Bptf Ch11:107054456-107055318 - -0.10 -0.11    
PolyA extension Rapgefl1 Ch11:98851076-98857648 - 0.17 0.21    Jeong et al. [37]
PolyA extension Kctd2 Ch11:115430313-115433591 + 0.14 0.11    
PolyA extension Kcnj4 Ch15:79505196-79505875 - 0.09 0.06    
PolyA extension Ergic1 Ch17:26655067-26658770 + 0.05 0.09    
PolyA extension Syt17 Ch7:118378587-118379874 - 0.06 0.16    
PolyA extension Polr1b Ch2: 129125214:129126791 +   0.14 0.13    
PolyA extension Elk1 ChX:20932683-20935548 -   0.19 0.22    
PolyA extension Ppp3cc Ch14:70214901-70215786 -   0.08 0.09    
  1. The ψ (PSI, percentage of spliced in) score was defined as the percentage of transcripts containing the alternative splicing events and/ or alternative poly(A) site usage. The mRNAs with increase of splcing events, i.e. conserved exon inclusion/ exclusion, cryptic exon inclusion, and exon extension, as well as change of poly(A) site usage are indicated by Δ ψ > 0, mRNA with decrease of the processing events are indicated by Δ ψ < 0. Unpaired t test was used to calculate the significance from data of 3 independent samples. Note that changes of the pre-mRNA processing events of several genes including Cob1 in the TDP-43 cKO mice are oppisite to those observed in the TDP-43(Q331K) knock-in mice (White et al. [86])