EMBO/soda-nel huggingface dataset:
Vesicle sub-pool organization at inner hair cell ribbon synapses (2018)
Figure 6

Fig 6: The abundance of non-tethered and single-tethered MP-SVs change at wild-type and OtofPga/Pga ribbon synapses upon stimulation

(A) Depicts the fraction of non-tethered and single-tethered MP-SVs per ribbon. Data are presented in mean ± SEM. The fraction of non-tethered SVs reduces in wild-type and OtofPga/Pga after stimulation and the fraction of single membrane-attached tethers increases in wild-type upon stimulation. In resting wild-type, most single-tethered SVs are attached to the presynaptic density. P-values are calculated by one-way ANOVA followed by Tukey's test; p-values of the trends are shown, * p < 0.05, ** p < 0.01, *** p < 0.001 and ns p > 0.05. Values: Appendix Table S5. The red dotted lines represent the mean fraction of MP-SVs in resting wild-type for each sub-pool.

(B-G) 3D reconstructions of the MP-SV pool: AZ-membrane (blue), presynaptic density (PD, pink), non-tethered (yellow), tethered (orange), docked SVs (light orange). Scale bar, 100 nm. (B-D) Wild-type ribbon synapse upon inhibition (B), rest (C) and stimulation (D); (E-G) OtofPga/Pga ribbon synapse upon inhibition (E), rest (F) and stimulation (G).

(H-I) Schematic summary: wild-type (H) and OtofPga/Pga ribbon synapse (I) upon stimulation. Not drawn to scale; color coded similar to the legend in B, frequently observed events are highlighted with a black asterisk, no changes are indicated by green (=). The arrows show the sequence of events taking place in wild-type and OtofPga/Pga when stimulated.
Vesicle sub-pool organization at inner hair cell ribbon synapses (2018)
Figure 7

Fig 7: Occurrence of MP-multiple-tethered and docked SVs in wild-type compared to OtofPga/Pga IHC ribbon synapses

(A-D) Example tomographic virtual sections from inhibitory: wild-type (A) and OtofPga/Pga (B); stimulatory: wild-type (C) and OtofPga/Pga (D). Tethered SVs are highlighted in orange with orange tether(s); single-tethers (with orange arrowhead) and multiple-tethers (with brown arrowhead). The number of tethers per SV is indicated. Magnification: 12,000x; scale bar, 40 nm.

(E-H) Virtual sections from inhibitory: wild-type (E) and OtofPga/Pga (F); stimulatory: wild-type (G) and OtofPga/Pga (H). Docked SVs at the AZ-membrane (blue line) are highlighted (orange asterisk). Some docked SVs are localized close to the presynaptic density (PD, pink outline), anchoring the ribbon (R). Magnification: 12,000x; scale bar, 100 nm.

(I) Percentage of multiple-tethered MP-SVs per ribbon of the total MP-SV pool show more multiple-tethered SVs in OtofPga/Pga IHCs.

(J) Percentage of docked MP-SVs per ribbon of the total MP-pool. The number of docked SVs is significantly increased at OtofPga/Pga inhibited and specifically at stimulated AZs. P-values for (I) and (J) are calculated by Fisher's exact Chi-square test, wild-type: inhib, n = 102 SVs; rest, n = 82 SVs; stim, n = 99 SVs; OtofPga/Pga: inhib, n = 123 SVs; rest, n = 96 SVs; stim, n = 111 SVs; ns p > 0.05, ** p < 0.01, *** p < 0.001, **** p < 0.0001

(K-N) 3D reconstructions from a stimulated wild-type (K,M) and OtofPga/Pga (L,N) ribbon synapse, showing examples of peripheral multiple-tethered (K,L, brown) and docked SVs (M,N, light orange). Distances of the peripheral SVs are depicted. Scale bar, 200 nm.

(O-P) Bar-plots show the distance of multiple-tethered (O) and docked (P) SVs from presynaptic density (PD), 0-100 nm: MP-SV pool (dark blue); 100-500 nm: peripheral SV pool (light blue). Upon stimulation, multiple-tethered and docked SVs are localized significantly closer to the PD in OtofPga/Pga. P-values for (O) and (P) are calculated by Wilcoxon Rank test, * p < 0.05, *** p < 0.001, ns p > 0.05 and Ø inconclusive statistics because occurrence of docked SVs in wild-type resting condition is extremely rare. Multiple-tethered SVs, wild-type: inhib, n = 3 SVs; rest, n = 13 SVs; stim, n = 3 SVs; OtofPga/Pga: inhib, n = 21 SVs; rest, n = 34 SVs; stim, n = 16 SVs; docked SVs, wild-type: inhib, n = 2 SVs; rest, n = 1 SVs; stim, n = 7 SVs; OtofPga/Pga: inhib, n = 20 SVs; rest, n = 4 SVs; stim, n = 18 SVs.

(Q) The illustration highlights the position of multiple-tethered (M, brown) and docked (D, light orange) SVs relative to PD (pink), indicating a depletion upon prolonged stimulation in wild-type.
Vesicle sub-pool organization at inner hair cell ribbon synapses (2018)
Figure 8

Fig 8: OtofPga/Pga ribbon synapses exhibit shorter tethers in the MP-SV pool upon stimulation

(A,B) Example virtual sections depict SVs with single membrane- (orange arrowhead) and presynaptic density (pink arrowhead) -attached tethers in resting wild-type. Magnification 12,000x; scale bar, 40 nm.

(A',B') 3D reconstructions of same tethered SVs (orange) as shown in (A) and (B); membrane-attached (A', yellow tether) and presynaptic density (PD) -attached (B', pink tether). Individual tether lengths are depicted. For clarity, ribbon (R) and AZ-membrane are shown in transparent. Scale bar, 20 nm.

(C) The graph depicts the mean length of single membrane-, presynaptic density-attached and multiple-tethers. Data are presented as mean ± SEM. Stimulated OtofPga/Pga synapses exhibit a shorter average tether length compared to stimulated wild-type.

(D) The cumulative probability distribution of MP-SVs plotted against the tether length.

(E) Total mean tether length in the MP-SV pool. Data are presented as mean ± SEM. Longer tethers are present upon stimulation in wild-type. Resting OtofPga/Pga ribbon synapses harbor the longest tethers, and tether where shorter at stimulated OtofPga/Pga synapses compared to wild-type.

For (C) and (E), p-values are calculated by K-W test corrected for multiple-comparison; * p < 0.05, *** p < 0.001, **** p < 0.0001, ns p > 0.05 and Ø no multiple-tethered SVs are observed in the MP-SV pool of wild-type ribbon synapse. The red dotted lines in (D) and (E) represent the mean MP tether length in resting wild-type for each sub-pool.
Molecular basis for cytoplasmic RNA surveillance by uridylation-triggered decay in Drosophila (2016)
Figure 1

Figure 1. Identification of the terminal RNA uridylation-mediated processing (TRUMP) complex.

A. Model for uridylation-triggered RNA decay. 3′ terminal uridylation by the TUTase Tailor may trigger the degradation of RNA species by unknown reader enzyme(s).

B. Protein interaction analysis by Nano LC-MS. Unique peptide counts and protein sequence coverage, as well as signal intensities (PSI) for Tailor (bait) and CG16940/dmDis3l2 in control IP (FLAG-GFP) and FLAG-Tailor IP are indicated. A.u., arbitrary units.

C. Protein domain architecture of Tailor/CG1091 and dmDis3l2/CG16940. DUF1439, domain of unknown function; NTase, nucleotidyltransferase; PAP assoc, polyA polymerase associated; CC, predicted coiled-coil motif; CSD, cold-shock domain; S1, RNA binding domain;

D. Co-immunoprecipitation of FLAG-dmDis3l2 (bait) and GFP-Tailor full-length and truncations expressed in Drosophila S2 cells. GFP-Nibbler (Nbr) served as negative control. Domain architecture of GFP-Tailor truncations are indicated.

E- G. Recombinant protein interaction analysis using the indicated epitope tags and purification methods. Domain architecture of bait and prey are indicated.

H and I. Immunostaining and imaging of Myc-Tailor and GFP-dmDis3l2 (H) or endogenous dmDis3l2 (I) in S2 cells. Single color channel images show total inversions. Scale bar = 5 µm.
Molecular basis for cytoplasmic RNA surveillance by uridylation-triggered decay in Drosophila (2016)
Figure 2

Figure 2. DmDis3l2/CG16940 is a 3′ terminal-uridylation-triggered, processive 3′-to-5′ exoribonuclease.

A. Sequence of RNA substrate used for in vitro exoribonuclease assays. N, randomized nucleotide.

B. In vitro exoribonuclease assay using 5′ radiolabeled RNA substrate and immunopurified wild-type (WT) or catalytic mutant (CM) FLAG-dmDis3l2 (mutation indicated in Figure 1C), incubated for the indicated time and separated on a 15 % polyacrylamide gel followed by phosphorimaging. Quantification of degraded substrate in percent is indicated.

C. Change in abundance of 256 different substrate RNAs as determined by high-throughput sequencing of substrates in experiment shown in (B).

D. Decay rates of 256 different substrate RNAs. Data shown in (C) was normalized to overall decrease in substrate abundance as determined by phosphorimaging (as shown in B) and fit to the indicated model for exponential decay. Apparent decay rate of all substrates, as determined by phosphorimaging is indicated in red.

E. Selected examples for individual substrates shown in (D). Values report the observed decay rate (kobs) in min-1.

F. Overview of decay rates (kobs) of all 256 different substrate RNAs, as determined in (D). Error represents SEM of curve fit.

G. Impact of RNA secondary structures, as determined by RNAfold (Gruber et al, 2008), and reported as effective free energy (EFE, kcal/mol), on decay rates (kobs) are shown. Error bars represent SEM of curve fit. Grey boxes represent tukey boxplot of individual EFE groups. White line indicates median. P-Value was determined by Mann-Whitney test comparing individual EFE groups against all substrates. Unstructured substrates used for subsequent analysis are indicated (EFE groups 4 to 6).

H. Nucleotide content of single-stranded RNA substrates, ranked from slow (top) to fast (bottom) decay by dmDis3l2.

I. Cumulative distribution of decay rates for RNA substrates with the indicated nucleotide at each one of four randomized position at the 3′ end of the substrate RNA. P-Value was determined by Mann-Whitney test comparing individual nts against all.

J. Functional coupling between two base positions within the randomized 3′ end of substrate RNA. Red squares show average increase in decay rate compared to all substrates. Black squares show no or negative effect.

K. Boxplot decay rates of substrates containing no, one, two, or three uridine(s) within the randomized 3′ end of the substrate RNA. Median decay rates SEM of fit are indicated.

L. Decay rate of all substrates, or substrates containing no, one, two, or three uridine(s) within the randomized 3′ end of the substrate RNA. Median and quartile ranges are indicated. P-values were determined by Mann-Whitney test. Substrate containing 4 uridines (4U) is indicated.
Molecular basis for cytoplasmic RNA surveillance by uridylation-triggered decay in Drosophila (2016)
Figure 3

Figure 3. Uridylation-triggered RNA decay of mirtron hairpins by Tailor and dmDis3l2 in vitro

A. RNA decay assay using synthetic, 5′ radiolabeled pre-miR-1003, immunopurified dmDis3l2 and wild-type (WT) or catalytic mutant (CM) Tailor. Reactions were incubated for the indicated time and separated by 15% denaturing polyacrylamide gel electrophoresis and subjected to phosphorimaging.

B. Quantification of at least three independent replicates of experiment shown in A. Data represent mean SD. Half-life was determined by fitting data to single exponential (dmDis3l2 and dmDis3l2/TailorCM) or sigmoidal (dmDis3l2/TailorWT) reaction kinetics.

C. RNA decay assay using synthetic, 5′ radiolabeled pre-miR-1003 containing the indicated number or uridine residues at the 3′ end and immunopurified dmDis3l2.

D. Quantification of three independent replicates of experiment shown in C. Data represent mean SD. Data were fit to single exponential reaction kinetics.

E. Reaction kinetics (kobs) determined in D plotted against number of 3′ terminal uridine residues. Error of fit is shown as SEM.

F. Two-step-model for the regulation of mirtron hairpin maturation in Drosophila. Mirtron hairpins are generated by splicing and lariat debranching. Upon export from the nucleus, Tailor uridylates mirtron hairpins by recognizing the 3′ guanine, a hallmark of splice-acceptor sequences. Short uridylation masks the 2nt 3′ overhang required for Dicer-1 to recognize pre-miRNAs. Extended uridine-tails eventually trigger processive, 3′-to-5′ exoribonucleolytic decay by dmDis3l2, resulting in mirtron clearance.
Molecular basis for cytoplasmic RNA surveillance by uridylation-triggered decay in Drosophila (2016)
Figure 4

Figure 4. In vitro uridylation assay in S2 cell lysate recapitulates uridylation-triggered RNA decay of cellular RNA transcripts.

A and E. Western blot analysis of genetically modified Drosophila S2 cells. Unmodified S2 cells (wild-type, wt), or S2 cells depleted of Tailor (tailorko) or dmDis3l2 (dmDis3l2ko) by CRISPR/Cas9 or expressing FLAG-tagged Tailor (TailorOE) or catalytic mutant dmDis3l2 (dmDis3l2CM OE) were analyzed. Antibodies are indicated. Note, that panels were assembled from two technical replicates of identical lysates (see source data).

B, C, F and G. Lysate of S2 cells (as characterized in A and E) were incubated with -32P-UTP (B and F) or -32P-ATP (C and G) for the indicated time followed by RNA extraction, denaturing polyacrylamide gel electrophoresis and phosphorimaging.

D and H. Quantification of at least five (D) or seven (H) independent replicates of experiment shown in B/C and F/G, respectively. Uridylation signal intensity for substrate S1 (indicated in B and F) was corrected for adenylation activity and normalized to wild-type 2 min time point. Data represent mean SEM. P-values were determined using Student’s t-test. * p<0.05, ** p<10-2, *** p<10-3, **** p<10-4.
Molecular basis for cytoplasmic RNA surveillance by uridylation-triggered decay in Drosophila (2016)
Figure 6

Figure 6. The TRUMP complex targets unprocessed, 3′ trailer-containing tRNA for decay.

A. 3′ end counts for the indicated locus in the Drosophila melanogaster genome, corresponding to tRNA-Alanine(TGC) in libraries generated from total RNA or dmDis3l2CM-IP. PM, prefix-matching (i.e. tailed); GM, genome-matching.

B. Meta-analysis of 3′ end counts in dmDis3l2CM-IP mapping to the indicated region around the annotated 3′ end of 68 tRNA loci in the Drosophila melanogaster genome. Cumulative relative distribution of 3′ end signal, relative to the annotated 3′ end, is reported (bottom). The average genome thymine (T)-content for the same regions is displayed (top).

C. Northern hybridization experiment using total RNA from adult whole male flies using probes against 3′ trailer or mature tRNAAla(TGC). Wild-type flies (w1118), or flies bearing a homozygous frame-shift mutation in the first coding exon (dmDis3l2-/-) or a homozygous amino acid-exchange mutation in the catalytic site (dmDis3l2CM) in the endogenous dmdis3l2 locus in the same genetic background were used. Probes against 2S rRNA served as loading control.

D. Quantification of four independent biological replicates of experiment shown in C. P-Value determined by Student’s t-test.

E. Exoribonuclease assay using immunopurified dmDis3l2 and in vitro transcribed, 5′ radiolabeled mature tRNA, containing a CCA modification or 3′ trailer-containing tRNA. Reactions were incubated for the indicated time and subjected to polyacrylamide gel electrophoresis and phosphorimaging.

F. Quantification of three independent replicates of experiment shown in E. Data represent mean SD. Decay rates (kobs) SEM of fit were determined upon fitting to single exponential decay kinetics.

G. Model for TRUMP-mediated quality control of tRNA. In the process of tRNA maturation, RNase P removes the 5′ leader and tRNase Z the 3′ trailer sequence, followed by CCA-addition and export. Premature export of unprocessed tRNA results in degradation by dmDis3l2, recognizing the uridine-rich 3′ end of the 3′ trailer, a hallmark of RNA polymerase III terminators. In contrast, mature CCA-modified tRNA is resistant against TRUMP-mediated decay.
Molecular basis for cytoplasmic RNA surveillance by uridylation-triggered decay in Drosophila (2016)
Figure 7

Figure 7. High-throughput biochemical comparison of E. coli RNase R and D. melanogaster Dis3l2.

A. Impact of RNA secondary structures on RNA decay rates (kobs) of 256 different RNA substrates subjected to E.coli RNase R (ecoRNaseR)- or Drosophila melanogaster Dis3l2 (dmDis3l2)-directed RNA decay assay as described in Fig. 2. RNA secondary structures were determined by RNAfold (Gruber et al, 2008) and reported as effective free energy (EFE). Error bars represent SEM of curve fit. Grey boxes represent tukey boxplot of individual EFE groups. White line indicates median. P-Value determined by Mann-Whitney test comparing individual EFE groups against all substrates. Unstructured RNA used for subsequent analysis are indicated (EFE groups 4 to 6).

B. Nucleotide content of randomized 3′ end sequence among the indicated number of substrate RNAs, ranked according to decay kinetics from slow (left) to fast (right). Fold-change in abundance for individual nucleotides is reported (bottom). Only unstructured RNA substrates (see A) were considered.

C. Decay rate of the indicated number of sequences, grouped according to individual nucleotide content in the randomized 3′ end sequence. Data is represented as boxplot, outliers are not shown. P-Value reports significant differences compared to all substrates as determined by Mann-Whitney test. Grey area represents the inner quartile range and white line the median of all substrates.

D. RNaseII/R enzymes act as conserved molecular ‘readers’ of destabilizing post-transcriptional modifications. In prokaryotes, e.g. E. coli, structured RNA is marked by a polyA-polymerase (PAPase) for subsequent degradation by RNaseR, 3′-to-5′ exoribonuclease with intrinsic preference for 3′ adenylated RNA. In eukaryotes, e.g. flies or mammals, structured RNA undergoes 3′ terminal uridylation by a terminal uridylyltransferase (TUTase) for subsequent degradation by Dis3l2, a 3′-to-5′ exoribonuclease with intrinsic preference for 3′ uridylated RNA.
LSD1 inhibition induces differentiation and cell death in Merkel cell carcinoma (2020)
Figure 1

Figure 1. LSD1 is required for Merkel cell carcinoma proliferation.

A. Heatmap of IC50 values for cell viability. Human dermal fibroblasts (HDFB) controls and 4 MCC cell lines (PeTa, MKL-1, WaGa, MS-1) were treated with the 43 indicated small molecules targeting epigenetic modifiers. IC50 values are depicted as log10(IC50) in [mM]. n/a, IC50 values could not be calculated. n = 4 technical replicates.

B. Dose-response curves of PeTa cells and control HDFB cells after 6 days of treatment with GSK-LSD1 or ORY-1001. Dose-response curves of 3 other MCC cell lines are displayed in Fig EV1A. n = 4 technical replicates. Data are represented as means ± SD.

C. Calculated IC50 values for reduced growth of PeTa, WaGa, MS-1, MKL-1 as well as HDFB controls based on Fig 1B and Fig EV1A.

D. In vitro competition assay of the 3 MCC cell lines MKL-2, PeTa, and WaGa transduced with either shLSD1.1, shLSD1.2, shRenilla (negative control), or shRPS15 (positive control). Individual graphs are displayed in Fig EV1E.

E. Dependency plot depicting the mean dependency of the 3 MCC cell lines PeTa, MKL-1, MKL-2 of the genes targeted by the compound library in Fig 1A. A score of 0 indicates that a gene is not essential; correspondingly -1 is comparable to the median of all pan-essential genes. Data obtained from DepMap; dependencies for the individual cell lines are displayed in Fig EV1F.

F. Violin plot depicting the LSD1 dependency score in MCC compared to cancer types from 23 tissues, ordered according to mean dependency score. Red horizontal line depicts the median. Data obtained from DepMap RNAi screen. Blood, hematopoietic and lymphoid tissue; U. aerodigestive, upper aerodigestive tract; A. ganglia, autonomic ganglia; CNS, central nervous system.
LSD1 inhibition induces differentiation and cell death in Merkel cell carcinoma (2020)
Figure 4

Figure 4. LSD1 inhibition induces marked transcriptional changes.

A. Photomicrographs of the MCC cell line PeTa after 6 days of 100 nM GSK-LSD1 or DMSO treatment. Scale bar, 100 μm.

B. Metagene plots showing the average CUT&RUN signal for H3K4me1, H3K27ac, and H3K27me3 for differentially expressed genes after 6 days of LSD1i or DMSO treatment. kb, kilobase; TSS, transcription start site; TES transcription end site.

C. ATAC-seq peak profile around TSS of differentially expressed genes after 6 days of LSD1i or DMSO treatment. kb, kilobase; TSS, transcription start site

D. Volcano plot showing the -log10 (adjusted p-value) and log2 fold-change (log2FC) for transcripts detected by RNAseq analysis of PeTa cells treated with 100 nM GSK-LSD1 or DMSO for 6 days. Significantly down-regulated genes (FDR≤0.05; log2FC≤-1) involved in mitotic cell cycle (GO:0000278) are highlighted in blue.

E. Upstream promoter motif enrichment of the downregulated genes from the dataset in Fig 4D. Top-5 enriched motifs are depicted. TF, transcription factor.

F. Volcano plot showing the -log10 (adjusted p-value) and log2 fold-change (log2FC) for transcripts detected by RNAseq analysis of PeTa cells treated with 100 nM GSK-LSD1 or DMSO after 6 days. Significantly upregulated genes (FDR≤0.05; log2FC≥1) involved in nervous system development (GO:0007399) are highlighted in red.

G. Upstream promoter motif enrichment of the upregulated genes from the dataset in Fig 4F. Top-5 enriched motifs are depicted. TF, transcription factor.
LSD1 inhibition induces differentiation and cell death in Merkel cell carcinoma (2020)
Figure 6

Figure 6. HMG20B is an essential LSD1-CoREST complex subunit necessary for proliferation.

A. Schematics and immunoblot of LSD1 co-immunoprecipitation (coIP) from PeTa cells. IB, Immunoblot; MS, mass spectrometry.

B. Volcano plot displaying the protein-protein binding partners of LSD1. Proteins belonging to the LSD1 complex are marked in red, protein localization in blue and other protein interaction partners in green. FC, fold-change.

C. Protein-protein interaction (PPI) mapping of the identified LSD1 binding partners. Individual complexes and p-values are displayed in Fig EV 6A.

D. Volcano plot depicting the protein-protein binding partners of LSD1 depleting in PeTa cells treated with ORY-1001 versus DMSO. Proteins belonging to the LSD1 complex are marked in red, protein localization in blue and other protein interaction partners in green. FC, fold-change.

E. Violin plot depicting the HMG20B dependency in MCC compared to cancer types from 23 tissues, ordered according to mean. Red horizontal line depicts the median. Data obtained from DepMap RNAi screen. Blood, hematopoietic and lymphoid tissue; U. aerodigestive, upper aerodigestive tract; A. ganglia, autonomic ganglia; CNS, central nervous system.

F. Schematic of TMT-MS experiment. PeTa cells were treated for 24h with 100 nM GSK-LSD1 or DMSO. Cells were fractionated to separate nuclei from cytosol. Nuclei were analyzed by TMT-MS. IB, Immunoblot; TMT-MS, tandem mass tag labeling mass spectrometry.

G. Volcano plot depicting the differentially regulated proteins obtained from Fig 6F. Proteins members of the LSD1-CoREST complex are labeled and highlighted in red. Proteins significantly upregulated (-log10(p-adjusted)≥1; log2FC≥0.75) and involved in nervous system development (GO:0007399) are labelled. FC, fold-change.

H. Left. Immunoblot confirmation of HMG20B downregulation. H3 serves as nuclear fraction control and α-Tubulin as loading control. Right. Immunoblot quantification. HMG20B protein levels are normalized to H3 and relative to DMSO control.

I. Amino acid conservation analysis of HMG20B across species and (bottom) the corresponding domains. DNA interacting amino acids are indicated with a red dot. aa, amino acid; NLS, nuclear localization signal (aa: 55-65); HMG, high-mobility group box (aa: 70-137); cc, coiled-coil domain (aa: 196-251); ALPHA, alpha-helices (aa: 276-312).

J. Schematic of HMG20B domain deletion mutant proteins. WT, wild-type; ΔALPHA, alpha-helices deletion; ΔCC, coiled-coil domain deletion; ΔHMG, HMG box deletion.

K. Bar graph of HMG20B rescue experiment in PeTa cells transduced with either a shRNA targeting HMG20B (shHMG20B) or negative control (shRenilla) and with an overexpression construct expressing either of the HMG20B mutant that cannot be targeted by the shRNA. Cell survival is depicted at day 8 after transduction and normalized to shRenilla. EV, empty vector control, WT, wild-type; ΔALPHA, alpha-helices deletion; ΔCC, coiled-coil domain deletion; ΔHMG, HMG box deletion.