Table 1 Chromatin and transcription factors regulated by TDP-43
From: Decoding TDP-43: the molecular chameleon of neurodegenerative diseases
Full Name | Gene Symbol | Gene Function | Contribution to Chromatin Structure/Transcription | Reference |
|---|---|---|---|---|
Absent, small, or homeotic discs 1 | ash1 | Chromatin remodeling | Opening | (Azpurua et al., 2021) |
Absent, small, or homeotic discs 2 | ash2 | Histone Lysine methyltransferase (H3K4) | Opening | (Berson et al., 2017) |
Additional sex combs | Asx | Chromatin regulator | Silencing | (Berson et al., 2017) |
Anti-silencing factor 1 | asf1 | Chromatin remodeling | - | (Berson et al., 2017) |
Ash1-like Histone Methyltransferase | ASH1L | Histone methyltransferase | Promotes open chromatin through H3K4 methylation, modulates transcription | (Gimenez et al., 2023) |
Brahma associated protein 60kD | Bap60 | Chromatin remodeling | - | (Berson et al., 2017) |
Brahma associated protein 111kD, | Bap111 | Chromatin remodeling | - | (Berson et al., 2017) |
Broad | br | Chromatin remodeling | Opening | (Azpurua et al., 2021) |
Bromodomain-containing protein, 140kD | Br140 | Chromatin remodeling | Opening | (Azpurua et al., 2021) |
Chd3 | Chd3 | Chromatin remodeling | - | (Berson et al., 2017) |
Chromodomain-helicase-DNA binding protein 1 | Chd1 | Chromatin remodeling | Silencing/TDP-43 impedes Chd1 binding | |
DNA Pol Beta | POLB | DNA excision and repair | - | (Liu et al., 2019) |
Domino | dom | Chromatin remodeling | - | (Berson et al., 2017) |
Elongation Factor for RNA Pol II | Ell, Su(Tpl) | Elongator | Transcription regulation | (Azpurua et al., 2021) |
Enhancer of yellow 1 | e(y)1 | Transcription Factor | Transcription | (Azpurua et al., 2021) |
Enhancer of yellow 3 | e(y)3 | Chromatin remodeling | Opening | (Azpurua et al., 2021) |
Enoki mushroom | enok | Chromatin remodeling | Opening | (Azpurua et al., 2021) |
Hat-trick | htk | Chromatin remodeling | - | (Sreedharan et al., 2015) |
Heat-shock-protein- 70B (Ba/Bb/Bbb/Bc) | Hsp70B(Ba/Bb/Bbb/Bc) | Heat shock Factor | Transcription | (Azpurua et al., 2021) |
HECT, UBA, WWE domain Containing E3 Ubiquitin Protein ligase 1 | HUWE1 | Histone/protein Ubiquitinatio | - | (Liu et al., 2019) |
Heterochromatin Protein-like 2 | HPL-2 | Chromatin remodeling | TDP-1 bridges HPL-2 to chromatin | (Saldi et al., 2018) |
High-Mobility Group Nucleosome Binding Domain 1 | HMGN1 | Chromatin remodeling | - | (Liu et al., 2019) |
Histone acetyltransferase 1 | CG2051 | Histone Lysine acetyltransferase | Opening | (Berson et al., 2017) |
Histone cluster 1, H2bp | H2b | Nucleosome assembly | Downregulated in the TDP∆NLS | (Igaz et al., 2011) |
Histone cluster 1, H4a, b, c, h | H4a/H4b/H4c/H4h | Nucleosome assembly | Downregulated in the TDP∆NLS | (Igaz et al., 2011) |
Histone cluster 1, H3d | H3d | Nucleosome assembly | Downregulated in the TDP∆NLS | (Igaz et al., 2011) |
H3S10Ph-K14Ac: Histone 3 (serine 10 phosphorylation/lysine 14 acetylation) | H3C14 | Histone tail PTM | Transcriptional activation/repression | (Masala et al., 2018) |
Histone deacetylase 1 | HDAC1 | Histone/Protein Lysine deacetylase | Silencing | (Sanna et al., 2020) |
Histone deacetylase 3 | HDAC3 | Histone Lysine acetyltransferase | Silencing | (Berson et al., 2017) |
Histone deacetylase 6 | HDAC6 | Histone Lysine acetyltransferase | Silencing | (Berson et al., 2017) |
High-Mobility Group Nucleosome Binding Domain 1 | HMGN1 | Chromatin remodeling | Nucleosome binding and chromatin structure regulation | (Gimenez et al., 2023) |
Kismet | kis | Chromatin remodeling | - | (Berson et al., 2017) |
Little imaginal discs | lid | Histone Lysine demethylase (H3K4) | Silencing | (Berson et al., 2017) |
MBD-R2 | MBD-R2 | Histone Lysine acetyltransferase | Opening | (Berson et al., 2017) |
Mediator complex subunit 8 | MED8 | Mediator complex | TF–RNA Pol interaction | (Azpurua et al., 2021) |
Mediator complex subunit 11 | MED11 | Mediator complex | TF–RNA Pol interaction | (Azpurua et al., 2021) |
Mediator complex subunit 15 | MED15 | Mediator complex | TF–RNA Pol interaction | (Azpurua et al., 2021) |
Mediator complex subunit 21 | MED21 | Mediator complex | TF–RNA Pol interaction | (Azpurua et al., 2021) |
Mediator complex subunit 22 | MED22 | Mediator complex | TF–RNA Pol interaction | (Azpurua et al., 2021) |
Mediator complex subunit 28 | MED28 | Mediator complex | TF–RNA Pol interaction | (Azpurua et al., 2021) |
Mediator Complex subunit 20 | Med20 | Mediator Complex/transcriptional coactivator | Transcriptional activation | (Liu et al., 2019) |
Mediator complex subunit 31 | MED31 | Mediator complex | TF–RNA Pol interaction | (Azpurua et al., 2021) |
Metastasis associated 1-like | Mta1-like | Histone Lysine acetyltransferase | Silencing | (Berson et al., 2017) |
Mi-2 | mi-2 | Chromatin remodeling | - | (Berson et al., 2017) |
MutS Homolog 3 | MSH3 | DNA mismatch repair system (MMR) | Postreplicative DNA mismatch repair | (Liu et al., 2019) |
Moira | mor | Chromatin remodeling | Opening | |
Mortality Factor 4-like 2 | MORF4L2 | Heterochromatin assembly/histone modification | Transcriptional activation | (Liu et al., 2019) |
Neuronal Brg1/BRM Associated factor | nBAF complex | Neuronal chromatin remodeling complex nBAF component | - | (Tibshirani et al., 2017) |
Nuclear receptor coactivator 6 | Ncoa6 | co-activator | Transcription | (Berson et al., 2017) |
Nucleosome assembly protein 1-like1 | Nap1l1 | Nucleosome assembly | Upregulated in the TDP∆NLS | (Igaz et al., 2011) |
Polybromo | polybromo | Chromatin remodeling | Opening | (Azpurua et al., 2021) |
Protein Kinase, DNA-Activated, Catalytic subunit | PRKDC | DNA repair and recombination | - | (Liu et al., 2019) |
SET domain containing 1 | Set1 | Histone Lysine methyltransferase (H3K4) | Opening | (Berson et al., 2017) |
Sex comb on midleg | Scm | Transcription Factor | Transcription | (Berson et al., 2017) |
Shaggy | sgg | Control of cellular pathways and metabolism | - | (Sreedharan et al., 2015) |
Sirtuin 4 | Sirt4 | Histone Lysine acetyltransferase | Silencing | (Berson et al., 2017) |
Splicing Factor Proline and Glutamine Rich | SFPQ | Splicing | Enables DNA binding activity | (Liu et al., 2019) |
Splicing factor 2 | SF2 | Splicing | Transcription | (Azpurua et al., 2021) |
Spt6 | Spt6 | Transcription Factor | Transcription | (Berson et al., 2017) |
Snf5-related 1 | Snr1 | Chromatin remodeling | - | (Berson et al., 2017) |
Stromal Antigen 2 | STAG2 | Chromatin remodeling | Cohesion of sister chromatids after DNA replication | (Appocher et al., 2017) |
Suppressor of Triplolethal | Su(Tpl) | Elongator | Transcription | (Azpurua et al., 2021) |
Suppressor of variegation 3–9 | Su(var)3–9 | Histone Lysine methyltransferase (H3K9) | Silencing | (Berson et al., 2017) |
Suppressor of zeste 2 | Su(z)2 | Histone Lysine methyltransferase, histone monoubiquitination (H2A-K119) | Opening | (Berson et al., 2017) |
Tat interactive protein 60Â kDa | Tip60 | Histone Lysine acetyltransferase | Opening | (Berson et al., 2017) |
TBP-associated factor 1 | TAF1 | Transcription Factor | Transcription | (Azpurua et al., 2021) |
tombola | Tomb | Male meiosis | Male meiosis | (Azpurua et al., 2021) |
Ubiquitin Interaction Motif Containing 1 | UIMC1 | DNA repair | Ubiquitination/Transcription repression | (Liu et al., 2019) |
Ubiquitin specific processing protease 49 | Usp49 | H2B Histone deubiquitinase | Transcriptional activation/regulation of mRNA splicing | (Amlie-Wolf et al., 2015) |
UNC13A (Unc-13 homolog A) | UNC13A | Synaptic vesicle release | - | (Koike et al., 2023) |
Utx histone demethylase | Utx | Histone Lysine demethylase (H3K27) | Opening | (Berson et al., 2017) |
WD repeat domain 82 | Wdr82 | Histone Lysine methyltransferase (H3K4) | Opening | (Gimenez et al., 2023) |
Xmas-2 | xmas-2 | Transcription and RNA export | - | (Sreedharan et al., 2015) |
X-Ray Repair Cross Complementing 5 | XRCC5 | DNA repair | DNA DSB repair by NHEJ | (Liu et al., 2019) |
X-RAY Repair Cross Complementing 6 | XRCC6 | DNA repair | DNA DSB repair by NHEJ | (Liu et al., 2019) |
Yin and Yang 1 transcription Factor | YY1 | Transcription factor | Transcriptional activation/repression | (Liu et al., 2019) |