TDP-43 Epigenetic Facets and Their Neurodegenerative Implications
Abstract
:1. Introduction
2. TDP-43 Role in Chromatin Remodeling and Transcription
2.1. TDP-43 Is a Global Chromatin Modifier
2.2. TDP-43 and Local/Specific Gene Transcriptional Regulation
2.3. TDP-43 and Genome-Wide Transcriptional Regulation
2.4. TDP-43 and DNA Repair
2.5. TDP-43 and Regulation of the Genome Dark Matter
2.5.1. The Singular Case of Human HERV-K Env Protein Activated by TDP-43
2.5.2. TDP-43 Control of LINE1 Retrotransposition
2.5.3. Conservation of TDP-43/TDPH Regulation of TE in Drosophila
2.6. ALS and Epigenetic Functionality of TDP-43 Short Splicing Isoforms
2.7. Epigenetic Role of TDP-43 Alternative Forms
2.8. Epigenetic Landscape Modifications Associated with TDP-43 Mutants
3. TARDBP/TDP-43 Autonomous/Non-autonomous Regulation
3.1. TDP-43 Autoregulation
3.2. Production of Alternatively Spliced Protein-Coding Isoforms
3.3. Promoter Control of Pan TARDBP Expression
4. Potential Druggable Targets
5. Concluding Remarks
6. Resources for the Review
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Gene Symbol | Name | Mammalian Orthologs *, Alias | Gene Ontology Function | Contribution to Chromatin Structure/Transcription | Toxicity Modulation upon Knockdown | Refs. |
---|---|---|---|---|---|---|
Chd1 † | Chromodomain-helicase-DNA binding protein 1 | CHD1, CHD2 | Chromatin remodeling | SILENCING | suppresses/ameliorates | [52] |
e(y)3 † | Enhancer of yellow 3 | PHF10 | Chromatin remodeling | OPENING | suppresses/ameliorates | [52] |
polybromo † | Polybromo | BAF180 | Chromatin remodeling | OPENING | suppresses/ameliorates | [52] |
ash1 † | Absent, small, or homeotic discs 1 | ASH1L | Chromatin remodeling | OPENING | suppresses/ameliorates | [52] |
enok † | Enoki mushroom | KAT6A | Chromatin remodeling | OPENING | suppresses/ameliorates | [52] |
br † | Broad | - | Chromatin remodeling | OPENING | suppresses/ameliorates | [52] |
Br140 † | Bromodomain-containing protein, 140kD | BRPF1 | Chromatin remodeling | OPENING | suppresses/ameliorates | [52] |
mor † | Moira | BAF170S/MARCC2 | Chromatin remodeling | OPENING | suppresses/ameliorates | [52] |
MED8 † | Mediator complex subunit 8 | MED8 | Mediator complex | TF–RNA Pol interaction | suppresses/ameliorates | [52] |
MED11 † | Mediator complex subunit 11 | MED11 | Mediator complex | TF–RNA Pol interaction | suppresses/ameliorates | [52] |
MED15 † | Mediator complex subunit 15 | MED15 | Mediator complex | TF–RNA Pol interaction | suppresses/ameliorates | [52] |
MED21 † | Mediator complex subunit 21 | MED21 | Mediator complex | TF–RNA Pol interaction | suppresses/ameliorates | [52] |
MED22 † | Mediator complex subunit 22 | MED22 | Mediator complex | TF–RNA Pol interaction | suppresses/ameliorates | [52] |
MED27 † | Mediator complex subunit 27 | MED27 | Mediator complex | TF–RNA Pol interaction | suppresses/ameliorates | [52] |
MED28 † | Mediator complex subunit 28 | MED28 | Mediator complex | TF–RNA Pol interaction | suppresses/ameliorates | [52] |
MED31 † | Mediator complex subunit 31 | MED31 | Mediator complex | TF–RNA Pol interaction | suppresses/ameliorates | [52] |
e(y)1 † | Enhancer of yellow 1 | TAF9 | Transcription Factor | Transcription | suppresses/ameliorates | [52] |
TAF1 † | TBP-associated factor 1 | TAF1 | Transcription Factor | Transcription | suppresses/ameliorates | [52] |
Tomb † | tombola | LIN54/TESMIN ** | Male meiosis | Transcription | suppresses/ameliorates | [52] |
Su(Tpl) † | Suppressor of Triplolethal | ELL, ELL2 | Elongator | Transcription | suppresses/ameliorates | [52] |
SF2 † | Splicing factor 2 | SRSF1 | Splicing | Transcription | suppresses/ameliorates | [52] |
Hsp70B (Ba/Bb/Bbb/Bc) † | Heat-shock-protein-70B (Ba/Bb/Bbb/Bc) | HSPA1A | Heat shock Factor | Transcription | suppresses/ameliorates | [52] |
Chd1 † | Chromodomain-helicase-DNA-binding protein 1 | CHD1 | Chromatin remodeling | TDP-1/TDP-43 impedes Chd1 binding | strongly enhances | [51] |
dom † | Domino | SRCAP ** | Chromatin remodeling | strongly enhances | [51] | |
mi-2 † | Mi-2 | CHD3; CHD4; CHD5 ** | Chromatin remodeling | enhances | [51] | |
kis † | Kismet | CHD6, CHD7, CHD8, CHD9 ** | Chromatin remodeling | enhances | [51] | |
asf1 † | Anti-silencing factor 1 | ASF1A; ASF1B | Chromatin remodeling | suppresses | [51] | |
Snr1 † | Snf5-related 1 | SMARCB1 | Chromatin remodeling | suppresses | [51] | |
mor † | Moira | SMARRC1; SMARCC2 ** | Chromatin remodeling | suppresses | [51] | |
Dalao † | Brahma associated protein 111kD, Bap111 | SMARCE1 ** | Chromatin remodeling | suppresses | [51] | |
Chd3 † | Chd3 | CHD3 | Chromatin remodeling | suppresses | [51] | |
Bap60 † | Brahma associated protein 60kD | SMARCD1 | Chromatin remodeling | strongly suppresses | [51] | |
MBD-R2 † | MBD-R2 | PHF20; PHF20L1 | Histone Lysine acetyltransferase | OPENING | enhances | [51] |
Tip60 † | Tat interactive protein 60kDa | KAT5; KAT7; KAT8 ** | Histone Lysine acetyltransferase | OPENING | enhances | [51] |
CG2051 † | Histone acetyltransferase 1 | HAT1 | Histone Lysine acetyltransferase | OPENING | suppresses | [51] |
HDAC3 † | Histone deacetylase 3 | HDAC3 | Histone Lysine deacetylase | SILENCING | enhances | [51] |
Mta1-like † | Metastasis associated 1-like | MTA2; MTA3 | Histone Lysine deacetylase | SILENCING | enhances | [51] |
Sirt4 † | Sirtuin 4 | SIRT4 | Histone Lysine deacetylase | SILENCING | suppresses | [51] |
HDAC6 † | Histone deacetylase 6 | HDAC6 | Histone Lysine deacetylase | SILENCING | suppresses * | [51] |
Scm † | Sex comb on midleg | L3MBTL3; PHC2; SCML1; THAP10 | Transcription Factor | Transcription | suppresses | [51] |
Spt6 † | Spt6 | SUPT6H | Transcription Factor | Transcription | suppresses | [51] |
lid † | Little imaginal discs | KDM 4A; 4B; 4D; 4E; 4F; 5A; 5B; 5C; 5D; | Histone Lysine demethylase (H3K4) | SILENCING | strongly suppresses | [51] |
Utx † | Utx histone demethylase | KDM6A; 6B; UTY | Histone Lysine demethylase (H3K27) | OPENING | suppresses | [51] |
Asx † | Additional sex combs | ASXL1-3 | Chromatin regulator | SILENCING | suppresses | [51] |
Ncoa6 † | Nuclear receptor coactivator 6 | NCOA6 | co-activator | Transcription | suppresses | [51] |
Su(var)3-9 † | Suppressor of variegation 3-9 | SUV39H1 | Histone Lysine methyltransferase (H3K9) | SILENCING | suppresses | [51] |
ash2 † | Absent, small, or homeotic discs 2 | ASH2L | Histone Lysine methyltransferase (H3K4) | OPENING | enhances | [51] |
Su(z)2 † | Suppressor of zeste 2 | BMI1; PCGF1; 2; 5; 6; RING1B; RNF2 | Histone Lysine methyltransferase, histone monoubiquitination (H2A-K119) | OPENING | enhances | [51] |
Set1 † | SET domain containing 1 | KMT2B | Histone Lysine methyltransferase (H3K4) | OPENING | enhances | [51] |
Wdr82 † | WD repeat domain 82 | WDR82 | Histone Lysine methyltransferase (H3K4) | OPENING | enhances | [51] |
HPL-2 †2 | Heterochromatin Protein-like 2 | HPL1 | Chromatin remodeling | TDP-1 bridges HPL-2 to chromatin | n.d. | [53] |
nBAF complex | Neuronal Brg1/BRM Associated factor | SS18L1, NBAF; CREST; SYT homolog 1 | Neuronal chromatin remodeling complex nBAF component | n.d. | [57] | |
sgg † | Shaggy | GSK3 | Control of cellular pathways and metabolism | suppresses | [50] | |
htk † | Hat-trick | Chromatin remodeling | suppresses | [50] | ||
xmas-2 † | Xmas-2 | Transcription and RNA export | suppresses | [50] | ||
H3C14 | H3S10Ph-K14Ac: Histone 3 (serine 10 phosphorylation/lysine 14 acetylation) | H3 | Histone tail PTM | Transcriptional activation/repression | n.d. | [58] |
H3C14 | H3K9me3: Histone 3 (methylation of lysine 9) | H3 | Histone tail PTM | Transcriptional repression | n.d. | [58] |
HDAC1 | Histone deacetylase 1 | HDAC1 | Histone/Protein Lysine deacetylase | SILENCING *** | n.d. | [48] |
H2b | Histone cluster 1, H2bp | HIST1H2BP | Nucleosome assembly | Downregulated in the TDPΔNLS | n.d. | [63] |
H3d | Histone cluster 1, H3d | HIST1H3D | Nucleosome assembly | Downregulated in the TDPΔNLS | n.d. | [63] |
H4a/H4b/H4c/H4h | Histone cluster 1, H4a, b, c, h | HIST1H4 | Nucleosome assembly | Downregulated in the TDPΔNLS | n.d. | [63] |
Nap1l1 | Nucleosome assembly protein 1-like1 | NAP1L1 | Nucleosome assembly | Upregulated in the TDPΔNLS | n.d. | [63] |
Med20 | Mediator Complex subunit 20 | MED20; SRB2; TRFP; PRO0213 | Mediator Complex/transcriptional coactivator | Transcriptional activation | n.d. | [64] |
Usp49 | Ubiquitin specific processing protease 49 | USP49 | H2B Histone deubiquitinase | Transcriptional activation/regulation of mRNA splicing | n.d. | [64] |
HUWE1 | HECT, UBA, WWE domain Containing E3 Ubiquitin Protein ligase 1 | HUWE1 | Histone/protein Ubiquitination | n.d. | [65] | |
YY1 | Yin and Yang 1 transcription Factor | YY-1; INO80S | Transcription factor | Transcriptional activation/repression | n.d. | [65] |
MORF4L2 | Mortality Factor 4-like 2 | MRGX; KIAA0026; MORF-Related Gene X | Heterochromatin assembly/histone modification | Transcriptional activation | n.d. | [65] |
HMGN1 | High-Mobility Group Nucleosome Binding Domain 1 | HMG14; MGC104230; FLJ27265 | Chromatin remodeling | n.d. | [65] | |
PRKDC | Protein Kinase, DNA-Activated, Catalytic subunit | DNA-PKcs; DNPK1; P460; DNAPKc; XRCC7; P350 | DNA repair and recombination | n.d. | [65] | |
UIMC1 | Ubiquitin Interaction Motif Containing 1 | RAP80; Retinoid X Receptor-Interacting Protein 110 | DNA repair | Ubiquitination/Transcription repression | n.d. | [65] |
POLB | DNA Pol Beta | DNA Pol Beta | DNA excision and repair | n.d. | [65] | |
SFPQ | Splicing Factor Proline and Glutamine Rich | PSF; PPP1R140; HPOMp100; POMP100 | Splicing | Enables DNA binding activity | n.d. | [65] |
MSH3 | MutS Homolog 3 | MRP1; DUP; HMSH3; Mismatch Repair Protein | DNA mismatch repair system (MMR) | Postreplicative DNA mismatch repair | n.d. | [65] |
XRCC5 | X-Ray Repair Cross Complementing 5 | Ku86; KARP-1; KU80; KUB2 | DNA repair | DNA DSB repair by NHEJ | n.d. | [65] |
XRCC6 | X-RAY Repair Cross Complementing 6 | KU70; Cells6; G22P1; ML8 | DNA repair | DNA DSB repair by NHEJ | n.d. | [65] |
STAG2 | Stromal Antigen 2 | SA2; SCC3B; SA-2; Cohesin Subunit SA-2 | Chromatin remodeling | Cohesion of sister chromatids after DNA replication | n.d. | [77,78] |
Ell, Su(Tpl) † | Elongation Factor for RNA Pol II | ELL; ELL2; C19orf17; PPP1R68 | Elongator | Transcription regulation | enhances | [52,79] |
TDP-43 Mutation | Epigenomic Alterations | Cellular Context | Refs. | |
---|---|---|---|---|
G294V | DNA damage/DSB TC-DSB | Mislocalization; | SH-S5Y5 | [97] |
R-loop accumulation; R-loop-dependent increased DSBs | ||||
Accumulation of FANCD2 repair foci (replication blockage). | ||||
G298S | DNA methylation | Hyper- and hypo-methylated regions related to controls with common and specific DMRs related to other ALS hIPSCs-derived MNs (C9orf72-, TARDBP-, SOD1-, and FUS-mutation carriers). | hIPSCs-derived MNs from G298S carrier | [74] |
A315T | Chromatin remodeling | Diminution of nBAF chromatin-remodeling complex components (Brg1, BAF53b, and CREST). | Cultured mouse MNs | [57] |
DNA methylation | Altered 5mC and 5hmC underlying their increased vulnerability to degeneration. | TDP-43A315T mouse CSMNs | [171] | |
DNA damage/DSB | Enhanced vulnerability to DNA damages. | MN-like NSC-34 cells | [95] | |
M323K | Autoregulation | Increased RNA, but not significant for protein. | Mouse TDP-43M323K knock-in | [167] |
Q331K | Autoregulation | Increase in RNA and nuclear protein in frontal cortex and spinal cords of mutant mice, but not in motor neuron. | Mouse TDP-43Q331K knock-in but not transgene | [168,169] |
DNA damage/DSB | Increased cytosolic sequestration of the poly-ubiquitinated and aggregated form, nuclear loss of function DNA damage induction, and DSB repair defects (preventing the nuclear translocation of XRCC4); Contribution to oxidative genome damage accumulation via increased reactive oxygen species (ROS). | Spinal cord of ALS Q331K carriers, SH-S5Y5 | [93] | |
Enhanced vulnerability to DNA damages (increase yH2Ax post damaging agent exposure). | MN-like NSC-34 cells | [95] | ||
M337V | DNA methylation | No global alteration in 5mC | SH-S5Y5 | [58] |
Histone PTMs | Significant decrease in global H3S10Ph-K14Ac; No significant increase in H3K9me3. | |||
DNA damage/DSB | Impairment in the NHEJ DSB repair factors recruitment. | Fibroblasts of human M337V carrier | [95] | |
G348C | Autoregulation | Upstream intron1 promoter region of TARDBP binding but less efficient than WT for its repression; No significant activation of the intron 1 promoter. | HEK293T | [170] |
A382T | DNA Methylation | No global alteration in 5mC. | SH-S5Y5 | [58] |
Histone PTMs | No significant decrease in global H3S10Ph-K14Ac; No significant increase in H3K9me3. | |||
DNA damage/DSB TC-DSB | Increased yH2Ax; R-loop accumulation; R-loop-dependent increased DSBs accumulation of FANCD2 repair foci (replication blockage). | SH-S5Y5 LCL from A382T carriers | [97] | |
Isoforms/fragments | Increased TDP-35 form at chromatin at R-loop. | LCL from A382T carriers | [97] | |
Autoregulation | Upstream intron1 promoter region of TARDBP binding but less efficient than WT for its repression; Able to induce a significant activation of the intron 1 promoter. | HEK293T | [170] | |
N390D | DNA methylation | Hyper- and hypo-methylated regions related to controls with common and specific DMRs related to other ALS hIPSCs-derived MNs (C9orf72-, TARDBP-, SOD1-, and FUS-mutation carriers). | hIPSCs-derived MNs from N390D carrier | [74] |
G418C | Chromatin remodeling | Diminution in nBAF chromatin-remodeling complex components (Brg1, BAF53b and CREST). | Cultured mouse MNs | [57] |
C9orf72 with loss of nuclear TDP-43 | DNA methylation | Altered DNA 5mC and 5hmC in the CSMN without nuclear TDP-43 compared to residual C9orf72 CMSN without TDP-43 nuclear loss. | Residual lower MNs from post-mortem CSMN tissues of C9orf72 carriers | [73] |
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Gimenez, J.; Spalloni, A.; Cappelli, S.; Ciaiola, F.; Orlando, V.; Buratti, E.; Longone, P. TDP-43 Epigenetic Facets and Their Neurodegenerative Implications. Int. J. Mol. Sci. 2023, 24, 13807. https://doi.org/10.3390/ijms241813807
Gimenez J, Spalloni A, Cappelli S, Ciaiola F, Orlando V, Buratti E, Longone P. TDP-43 Epigenetic Facets and Their Neurodegenerative Implications. International Journal of Molecular Sciences. 2023; 24(18):13807. https://doi.org/10.3390/ijms241813807
Chicago/Turabian StyleGimenez, Juliette, Alida Spalloni, Sara Cappelli, Francesca Ciaiola, Valerio Orlando, Emanuele Buratti, and Patrizia Longone. 2023. "TDP-43 Epigenetic Facets and Their Neurodegenerative Implications" International Journal of Molecular Sciences 24, no. 18: 13807. https://doi.org/10.3390/ijms241813807