Table 1.
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] |
† Flybase, †2 Wormbase * Mammalian Orthologs from referenced work or from OrthoDB database. ** Contribution to chromatin structure/transcription. Source: referenced work, OrthoDB, NCBI, or UniProt databases. *** Potentially by acting directly on TDP-43 acetylation. Histone PTM stands for histone post-transcriptional modification.