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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])
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