EMBO/SourceData huggingface dataset:
Figure legend: "(B) The expression level of FAM210A mRNA in 15 human organs from the GTEx Portal database. TPM: transcripts per million of reads. The central band shows the median value and the box indicates the first and third quartiles. The sample size of human samples used for quantification in GTEx Portal database (from testis to pancreas): n=361/429/432/555/803/240/432/226/406/578/241/202/85/328/755."
NCBI gene IDs:
"FAM210A: 125228"
Figure legend: "(F,G) Protein expression of mitochondrial ETC component genes was measured in AC16 cells after following treatments in comparison with control cells: (F) siRNA knockdown of FAM210A. (G) FAM210A overexpression."
NCBI gene IDs:
"FAM210A: 125228"
Figure legend: "(A) miR-574-5p and miR-574-3p overexpression reduced FAM210A mRNA expression in AC16 cells (n=3 in each group). (B) miR-574-5p and miR-574-3p inhibition increased FAM210A mRNA expression in AC16 cells (n=3 in each group). "
NCBI gene IDs:
"FAM210A: 125228
miR-574-3p: RF00929
miR-574-5p: 693159"
Figure legend: "(C,D) Protein expression of mitochondrial ETC component genes was measured in AC16 cells after following treatments in comparison with control cells: (C) miR-574-5p or miR-574-3p overexpression. (D) Transfection of anti-miR-574-5p or anti-miR-574-3p inhibitor."
NCBI gene IDs:
"miR-574-3p: RF00929
miR-574-5p: 693159"
Figure legend: "(E,F) Mitochondrial membrane potential and ATP production in AC16 cells under ISO treatment (10 μM for 24 hr) with overexpression of miR-574-5p or miR-574-3p. &gt;120 cells/group were quantified in (E) and n=4 biological replicates in (F). The dashed line in the violin plot shows medium value for the group and the dotted lines represent two quartile lines in each group."
NCBI gene IDs:
"miR-574-3p: RF00929
miR-574-5p: 693159"
Figure legend: "(G,H) Mitochondrial membrane potential and ATP production in primary mouse ACMs isolated from WT and miR-574-/- mice under ISO treatment. Scale bar: 10 μm. &gt;110 cells/group were quantified in bottom panel of (G) and n=5 in (H)."
NCBI gene IDs:
"miR-574: 100124451"
Figure legend: "(I) transfection of miR-574-5p/3p in the absence or presence of FAM210A overexpression. All the Western blot images were provided as representative data from 3-4 biologically replicated experiments."
NCBI gene IDs:
"FAM210A: 125228
miR-574-5p: 693159"
Figure legend: "(J) Increased protein expression of FAM210A and ND1 in miR-574 KO hearts compared to WT hearts upon TAC surgery. N=5 hearts (~110-150 CM cells) were measured per group. The dashed line in the violin plot shows medium value for the group and the dotted lines represent two quartile lines in each group."
NCBI gene IDs:
"miR-574: 100124451"
Figure legend: "(H, I) Induction of Ctcflos and  Ucp1 in vivo during cold-induced iWAT browning. Relative expression levels  of (H) Ctcflos transcript 1 and (I) Ucp1 in iWAT  of C57BL/6J  mice held at 5°C for one week compared to age and weight matched mice held at 30°C  or 23°C, assessed by  quantitative PCR (qPCR). Mean and individual values, n=7 (biological replicates), one-way ANOVA (Šídák-test), **p&lt; 0.01, ****p&lt;0.0001."
NCBI gene IDs:
"Ctcflos: 74161
Ucp1: 22227"
Figure legend: "(D) Relative transcript levels of Ctcflos and Ucp1  in various tissues of 129S6 mice, assessed by  qPCR. Mean values ± SD, n=1 (biological replicate) for Ucp1n=3 (biological replicates) for Ctcflos ."
NCBI gene IDs:
"Ctcflos: 74161
Ucp1: 22227"
Figure legend: "(E) Ctcflos, 45SrRNA and 12SrRNA transcript abundance in  nuclear, cytosolic and mitochondrial subfractions of primary  brite adipocytes of 129S6 mice, assessed by qPCR. Mean values ± SD, n=6 (biological replicates), two-way ANOVA (Tukey-test), ****p&lt; 0.0001."
NCBI gene IDs:
"Ctcflos: 74161"
Figure legend: "(E) Relative Ucp1 transcript levels in response to Ctcflos tr1, 3 and 4 KD by ASO 1, 3, 4 and 2, 5 6, respectively, compared to nontargeting controls, assessed by  qPCR. Mean values ± SD, n=3-4 (biological replicates), one-way ANOVA (Šídák-test), ***p&lt;0.001, ****p&lt;0.0001."
NCBI gene IDs:
"Ctcflos: 74161
Ucp1: 22227"
Figure legend: "(F) Relative expression levels of cell death-inducing DNA fragmentation factor alpha-like effector A  (Cidea) and cytochrome c oxidase subunit 7a1 (Cox7a1) in Ctcflos tr1, 3 and 4 KD compared to control samples, assessed by qPCR. Mean values ± SD, n=3 (biological replicates)-4, unpaired t tests or in grey parenthesis two-way ANOVA (Šídák-test), n.s. p&gt;0.05, *p&lt;0.05, **p&lt;0.01, ***p&lt;0.001."
NCBI gene IDs:
"cell death-inducing DNA fragmentation factor alpha-like effector A: 12683
Cidea: 12683
Cox7a1: 12865
cytochrome c oxidase subunit 7a1: 12865
Ctcflos: 74161"
Figure legend: "(H)  Immunocytochemistry of UCP1 protein in response to Ctcflos tr1 KD by ASO 1 (UCP1 (red); DNA staining  by DAPI (green); phase contrast (PC) (gray))."
NCBI gene IDs:
"Ctcflos: 74161"
Figure legend: "Impact of Ctcflos KD on  mitochondrial  biogenesis. (R) Microscopic images of Mito Tracker stained brite adipocytes (Mito tracker (blue); DNA staining by DAPI (green);  phase contrast  (PC) (gray))"
NCBI gene IDs:
"Ctcflos: 74161"
Figure legend: "(D) Relative  expression levels of  brite adipocyte marker genes uncoupling protein 1 (Ucp1), cell death-inducing DNA fragmentation factor alpha-like effector A (Cidea), cytochrome c oxidase subunit 7a1 (Cox7a1), peroxisome proliferator activated receptor γ coactivator 1α  (Pgc1a) and elongation of very long chain fatty acids-like 3 (Elovl3), comparing Ctcflos tr1 (ASO 1) and tr 3 and 4 (ASO 2) KD with their respective controls. Mean values ± SD, n=6 (biological replicates), unpaired t tests or in grey parenthesis two-way ANOVA (Šídák-test) n.s. p&gt;0.05, **p&lt;0.01, ***p&lt;0.001, ****p&lt;0.0001."
NCBI gene IDs:
"cell death-inducing DNA fragmentation factor alpha-like effector A: 12683
Cidea: 12683
Cox7a1: 12865
cytochrome c oxidase subunit 7a1: 12865
Ctcflos: 74161
elongation of very long chain fatty acids-like 3: 12686
Elovl3: 12686
peroxisome proliferator activated receptor γ coactivator 1α: 19017
Pgc1a: 19017
Ucp1: 22227
uncoupling protein 1: 22227"
Figure legend: "(K-M) Rescue of Ctcflos KD impact on Ucp1 gene transcription by Prdm16 overexpression. Primary iWAT cells infected with Prdm16- or turbo green fluorescent protein (GFP)-expressing viral particles at the second day of  proliferation, followed by reverse transfection at the first day of differentiation using nontargeting control (NC) or Ctcflos-targeting ASO1. Gene expression  analyzed 72 hours later by qPCR (K)  Transcript levels  of Ctcflos tr1 relative to Fabp4 (L) Transcript levels  of  Prdm16 relative to  Fabp4 (M)  Transcript levels of Ucp1  relative to Fabp4. Mean and individual values. Each graph presents pooled data from two experiments slightly varying virus titers. RM One-way ANOVA (Tukey-test), n.s. p&gt;0.05, *p&lt;0.05, **p&lt;0.01, ***p&lt;0.001. "
NCBI gene IDs:
"GFP: 
green fluorescent protein: 
Ctcflos: 74161
Fabp4: 11770
Prdm16: 70673
Ucp1: 22227"
Figure legend: "(B-D) Impact of splicing inhibition by different concentrations of general splicing inhibitor isoginkgetin on brite adipogenesis, (B) expressed as  Ucp1  relative to Fabp4 mRNA levels, (C) Ucp1 relative to  Gtf2b and (D) Fabp4  relative to Gtf2b. Mean values ± SD, n=3 (biological replicates), one-way ANOVA (Šídák-test), n.s. p&gt;0.05, *p&lt;0.05, **p&lt;0.01, ***p&lt;0.001, ****p&lt;0.0001."
NCBI gene IDs:
"Fabp4: 11770
Gtf2b: 229906
Ucp1: 22227"
Figure legend: "Effect of Ctcflos KD on  Serine/Arginine rich Splicing factor 2 (SC35/SRSF2) and nuclear speckle abundance in Ctcflos tr1 (ASO 1) KD and control cells (KD day 1 of differentiation, analysis after 48h). (E) Immunocytochemistry of SC35. SC35 signal (blue) alone (middle images) and SC35 (blue),  DNA staining by DAPI (green) and phase contrast (PC) (gray) combined (outer  images)."
NCBI gene IDs:
"Ctcflos: 74161"
Figure legend: "Influence of Ctcflos  KD on Prdm16 alternative splicing. (O) Relative Prdm16  total, (P) Relative Prdm16 long  transcript levels 24 hours after Ctcflos  KD, comparing Ctcflos tr1 (ASO1) and tr3, 4 (ASO2) KD and control samples, assessed by  qPCR, Mean values ± SD, n=3-4 (biological replicates), unpaired t tests, n.s. p&gt;0.05, * p&lt;0.05, **p&lt;0.01, ***p&lt;0.001."
NCBI gene IDs:
"Ctcflos: 74161
Prdm16: 70673"
Figure legend: "Influence of Ctcflos  KD on  Prdm16 alternative splicing. (R, S) Fold change of Prdm16 short and Prdm16 long (R) ASO1 to NC and (S) ASO2 and NC 24 hours after Ctcflos KD, n=3-4 (biological replicates), unpaired t tests, n.s. p&gt;0.05, ** p&lt;0.01."
NCBI gene IDs:
"Ctcflos: 74161
Prdm16: 70673"
Figure legend: "(A) Neutralization assay of FD20 using SARS-CoV-2 pp harboring spike derived from four Variants of Concern as indicated. Mean ± s.d. are plotted (n = 3 biological replicates). Numbers in brackets indicate IC50 values in nM."
NCBI gene IDs:
"spike: 43740568"
Figure legend: "(C) Northern analysis of EVD RNA isoforms using a probe for the GAG region or for ACTIN2 (ACT2) as a loading control."
NCBI gene IDs:
"GAG: 
ACT2: 821411
ACTIN2: 821411
EVD: 3770632"
Figure legend: "(D) qPCR quantification of shGAG and flGAG-POL normalized to ACT2 and to GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE C SUBUNIT (GAPC) levels. qPCR was performed on n=3 biological replicates; bars: standard error. (**) = p-value &lt; 0.01 (two-sided t-test between indicated values)."
NCBI gene IDs:
"shGAG: 
ACT2: 821411
flGAG-POL: 2745586
GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE C SUBUNIT: 819567
GAPC: 819567"
Figure legend: "(F-G) sRNA-seq profiles from EVD de-repressed in the ddm1 (F) or ddm1 dcl1 (G) backgrounds. Different siRNA size categories are stacked. Nomenclature as in (B)."
NCBI gene IDs:
"EVD: 3770632
ddm1: 836808
dcl1: 839574"
Figure legend: "(B) Expression levels of shGFP (spliced) and GFP-EVDint/ter-GUS (unspliced) transcripts, relative to ACT2 and AT4G26410 (RHIP1), in the WT or rdr6 background. qPCR was performed on three biological replicates and error bars represent the standard error on. (*) = p-value &lt; 0.05 (two-sided t-test against corresponding controls)."
NCBI gene IDs:
"shGFP: 
GFP: 
GUS: 
ACT2: 821411
AT4G26410: 828747
RHIP1: 828747
EVD: 3770632
rdr6: 824112"
Figure legend: "(C) sRNA-seq profile mapped on the genomic 35S:GFP-EVDint/ter-GUS locus. (RPM) Reads per million. Positions indicated in nucleotides (nt) from the start of the 35S sequence. Dashed vertical lines: shGFP and GFP-GUS 3' ends."
NCBI gene IDs:
"shGFP: 
GFP: 
GUS: 
EVD: 3770632"
Figure legend: "(D) Relative expression levels of spliced and unspliced transcripts in the three EVD constructs relative to ACT2. qPCR was performed on three biological replicates and error bars represent the standard error. (ns.) = non-significant, (*) = p-value &lt; 0.05, (**) = p-value &lt; 0.01, (two-sided t-test between indicated samples/targets)."
NCBI gene IDs:
"ACT2: 821411
EVD: 3770632"
Figure legend: "(E) High and low molecular-weight RNA analysis of EVD GAG (GAG-ex1) and EVD intron (GAG-in) in two independent T1 bulks from each indicated line. The filled arrows on the right hand-side or with an asterisk on the blots correspond to the transcripts depicted in (A-C). ACT2: loading control for mRNAs; tasiR255, miR173 and U6: loading controls for sRNAs. Hybridizations for GAG-ex2 and POL probes are found in Supp. Fig.5A."
NCBI gene IDs:
"GAG: 
tasiR255: 
ACT2: 821411
EVD: 3770632
miR173: 28719308
POL: 819306
U6: 28719273"
Figure legend: "(B) Boxplots of RNA expression levels of TEs in ddm1 from the quartiles in (A)."
NCBI gene IDs:
"ddm1: 836808"
Figure legend: "(A) Comparison of RNA isoforms and sRNA patterns generated by 35S:GFP-GUS and 35S:GFP-EVDint/ter-GUS. High and low molecular-weight RNA analysis using a GFP or GUS probe in two independent transgenic lines from each construct in the WT or rdr6 background. mRNA isoforms are indicated with arrows and correspond to the transcripts depicted in Fig.2A. EtBr staining of the agarose gel and miR171 probe serve as loading control for mRNAs and sRNAs, respectively."
NCBI gene IDs:
"GFP: 
GUS: 
miR171: 
EVD: 3770632
rdr6: 824112"
Figure legend: "(C) Nucleo-cytosolic distribution of 35S:EVD and 35S:GFP-EVDint/ter-GUS RNA isoforms in rdr6 relative to that of ACT2 analyzed by qPCR. RNA extracted from Total, nuclear (Nucl) and cytoplasmic (Cyto) fractions was reverse transcribed with random hexamers and oligo(dT). snoRNA U5 is shown as a nuclear-only RNA control. (D) Same as in (C) but using exclusively oligo(dT) to reverse transcribe poly(A)+ RNAs."
NCBI gene IDs:
"GUS: 
ACT2: 821411
EVD: 3770632
rdr6: 824112"
Figure legend: "(B) RIBO-seq coverage profiles from 35S:EVD in WT or rdr6. RPM: Reads per million. (C) Ribosomal footprints on shGAG in rdr6 displaying codon occupancy at P-sites to calculate codon coverage. The coverage observed at each codon position was divided by the expected mean coverage along the entire GAG coding sequence."
NCBI gene IDs:
"shGAG: 
GAG: 
EVD: 3770632
rdr6: 824112"
Figure legend: "B Competitive inhibition of mitochondrial protein import by clogger proteins inhibits cell growths. Yeast cells expressing clogger proteins (cytochrome b2-DHFR and cytochrome b2∆19-DHFR) or cytosolic DHFR for comparison under control of the galactose-inducible promoter were grown to mid-log phase on lactate medium. Ten-fold serial dilutions were dropped on lactate (no induction) or lactate with 0.5% galactose medium (induction). MTS, matrix-targeting signal."
NCBI gene IDs:
"cytochrome b2: 854950
DHFR: 854411"
Figure legend: "E Levels of the proteasome protein Pre6 were detected upon expression of cytosolic DHFR or clogger by Western blotting and quantified from three replicates. Cells were grown in lactate medium and clogger expression was induced for 4.5 h with 0.5% galactose before samples were harvested and lysed. Data are displayed as mean ± standard deviations from n = 3 independent biological replicates."
NCBI gene IDs:
"DHFR: 854411"
Figure legend: "A The clogger was expressed in wild type (WT) and ∆rpn4 (∆) cells for 4.5 h with medium containing 0.5% galactose. Medium was exchanged for a non-inducing lactate medium. Precursor (pre) and mature (m) forms of the b2∆-DHFR clogger were visualized by Western blotting using a DHFR-specific antibody."
NCBI gene IDs:
"rpn4: 851542"
Figure legend: "G Signals of Hsp104 and Hsp42 before and after clogger induction in wild type and ∆rpn4 cells. The cytosolic soluble DHFR protein was expressed for control. The strains were grown in lactate medium and clogger expression was induced with 0.5% galactose for 6 h."
NCBI gene IDs:
"DHFR: 854411
rpn4: 851542"
Figure legend: "A Cytosolic DHFR (control) or the clogger protein b2-DHFR were expressed in wild type and ∆rpn4 cells for 4.5 h. The distribution of constitutively expressed Hsp104-GFP was visualized by fluorescence microscopy. Diameter of Hsp104-GFP-bound aggregates were quantified. . Data are displayed as mean ± standard deviations from n = 36 independent biological replicates. Significance was assessed using two-sided, paired Student's t-test. P values are indicated as asterisks ** p ≤ 0.01, **** p ≤ 0.0001. See also Fig. EV4A for quantification of the number of aggregates per cell."
NCBI gene IDs:
"b2: 854950
DHFR: 854411
rpn4: 851542"
Figure legend: "A The mitochondrial proteins Pdb1, Mam33 and Aim17 were co-expressed for 4.5 h with clogger as fusions with the red fluorescent protein RFP (mCherry). Fluorescence microscopic images of the indicated mitochondrial proteins visualized 4.5 h after induction of the clogger or cytosolic DHFR for control. For quantification of colocalization B Mutants lacking Hsp104 and Hsp42 were transformed with Aim17-expressing plasmids and grown to mid-log phase in lactate medium. Clogger expression was induced for 4.5 h with 0.5 % galactose before microscopy was perfomed. Please note that in the absence of Hsp42 and Hsp104, no Aim17-RFP-containing granules are formed. C Wild type cells were transformed with plasmids for the simultaneous expression of the clogger and an N-terminally truncated version of Mam33-RFP (both under control of GAL promoter) together with constitutively expressed Hsp104-GFP (TPI promoter) . The cells were grown on lactate plus 0.5% galactose-containing medium for 4.5 h. The distribution of the fluorescent proteins was visualized by microscopy."
NCBI gene IDs:
"Aim17: 856365
DHFR: 854411
GAL: 855828
Hsp104: 850633
Hsp42: 851751
TPI: 851620"
Figure legend: "E Clogger and Mam33-HA were co-expressed for 4.5 h in wild type and ∆hsp42 cells. Mitochondria were isolated and subjected to Western blotting to detect mature (m) and precursor (pre) forms of Mam33-HA. The matrix protein Tim16 served as loading control."
NCBI gene IDs:
"HA: 
hsp42: 851751
Mam33: 854740"
Figure legend: "G To measure the toxicity of clogger expression, clogger proteins were induced for 24 h with lactate medium containing 0.5 % galactose in the mutants indicated. Aliquots were removed and the number of living cells were assessed by a plating assay on glucose-containing plates. The resistance of ∆rpn4 to clogger expression depends on Hsp104 and Hsp42. Data are displayed as mean ± standard deviations from n = 3 independent biological replicates."
NCBI gene IDs:
"Hsp104: 850633
Hsp42: 851751
rpn4: 851542"
Figure legend: "B BAK, or BAK with cysteine introduced at the indicated positions (on a BAK∆Cys background) were stably expressed in Bax-/-Bak-/- MEFs and assess for BAK expression by immunoblotting (inset panel; * indicates non-specific band.) and apoptotic activity in response to etoposide treatment."
NCBI gene IDs:
"BAK: 12018
Bak: 12018
Bax: 12028"
Figure legend: "C E24 and R169 are proximal in inactive BAK on mitochondria. Mitochondria-enriched membrane fractions from cells were incubated with oxidant (CuPhe) and induced intramolecular disulphide linkage of BAK was assessed on non-reducing SDS-PAGE."
NCBI gene IDs:
"BAK: 578"
Figure legend: "D E24 and R169 dissociate during BAK activation. Mitochondria-enriched membrane fractions from cells were incubated with cBID (100 nM) prior to oxidant (CuPhe) and the induced intramolecular and intermolecular disulphide linkage of BAK was assessed on non-reducing SDS-PAGE."
NCBI gene IDs:
"BAK: 578"
Figure legend: "C Bax-/-Bak-/- MEFs expressing the indicated BAK variants were treated with doxycycline (Dox, 3 h), incubated for a further 24 h in the presence or absence of BH3-mimetic compounds, and cell death was assessed by PI uptake."
NCBI gene IDs:
"Bak: 12018
BAK: 12018
Bax: 12028"
Figure legend: "D Mutation of BH4 promotes BAK activating conformation change. Cells were treated with doxycycline (3 h) to induce BAK expression followed by incubation with BH3-mimetics where indicated (for 2 h) and conformation change of BAK was assessed by intracellular flow cytometry with an antibody that recognises activated BAK (G3172)."
NCBI gene IDs:
"BAK: 12018"
Figure legend: "D BAK wild-type, or BAK with an engineered α1-α2 loop thrombin cleavage site were stably expressed in Bax-/-Bak-/- MEFs. Membrane fractions were incubated with thrombin prior to incubation with copper phenanthroline (CuPhe) to induce disulphide-linkage. Samples were run on SDS-PAGE under non-reducing or reducing conditions and immunoblotted for BAK with an antibody recognising the BAK N-terminus upstream of the thrombin cleavage site (aa23-38) or an antibody recognising the BH3 domain (4B5) downstream of the cleavage site. Schematic indicates the nature of the BAK protein detected by each antibody. Disulphide-linkage indicated by a hashed line. Note that the N-terminal portion of thrombin cleaved BAK could not be detected with the N-terminal antibody unless it was intramolecularly disulphide-linked. *cBID (100 nM) was added to activate BAK during thrombin cleavage. Data representative of two independent experiments."
NCBI gene IDs:
"BAK: 578
Bak: 12018
Bax: 12028"
Figure legend: "E Cleavage of the BAK α1-α2 loop potentiates MOMP. Membrane fractions from Bax-/-Bak-/- MEFs expressing BAK or BAKthrombin were incubated or not with thrombin in the presence or absence of cBID (10 nM) for the indicated times. Membrane (P) and supernatant (S) fractions were separated and immunoblotted for cytochrome c or BAK 4B5."
NCBI gene IDs:
"Bak: 12018
BAK: 578
Bax: 12028"
Figure legend: "(E) Weight  and survival curves  of neutrophil  specific  Nlrp3A350VneoR Gsdmd-/- mice. n≥18"
NCBI gene IDs:
"Gsdmd: 69146
Nlrp3: 216799"
Figure legend: "(A,B) MPO staining  of liver  issue used as a marker for  myeloid cells including monocytes  in both  Nlrp3D301N-MRP8 and Nlrp3A350V-MRP8 mutant (n≥3 mice  per genotype, representative images shown, bar indicates 250 μM). H&amp;E staining  of liver  tissue with histologic  scoring of  liver  inflammation (bar indicates 100 μM, representative images are shown). TUNEL staining  of liver  tissue (Representative images shown, bar indicates 250 μM). Data information: n≥6 mice  per genotype, significance determined by unpaired t test (* p &lt; 0.05; ** p &lt; 0.01; *** p &lt; 0.001), data are expressed as mean +/− SD, dots represent individual biological replicats"
NCBI gene IDs:
"MRP8: 
Nlrp3: 216799"
Figure legend: "(A) Immunohistochemical staining  of  F4/80, a marker for resident macrophages, and mRNA expression  of F4/80  in liver  tissue. Data information: Representative images shown, bar indicates 250 μM for F4/80  n≥6 mice  per genotype, significance determined by unpaired t test (** p &lt; 0.01; *** p &lt; 0.001), data are expressed as mean +/− SD, dots represent individual biological replicats"
NCBI gene IDs:
"F4/80: 13733"
Figure legend: "(B) Immunofluorescence staining  of CLEC4F, a specific marker of  Kupffer cells, and gene expression of CLEC4F  in liver  tissue. Data information: Representative images shown, bar indicates 100 μM for CLEC4F, n≥6 mice  per genotype, significance determined by unpaired t test (** p &lt; 0.01; *** p &lt; 0.001), data are expressed as mean +/− SD, dots represent individual biological replicats"
NCBI gene IDs:
"CLEC4F: 51811"
Figure legend: "Telomeric lncRNA levels in the indicated deletion strains as analyzed by dot blot (top) or Northern blot hybridization (bottom) using a double‐stranded telomeric probe. Telomeric dot blot signals are expressed as fold increase relative to wtA after normalization through U6 snRNA. Bars and error bars are averages and s.d. from 4 independent experiments. U6 and 18S rRNA are shown as loading controls for Northern blotting. The asterisk indicates unspliced U6. Molecular weights are on the left in kilobases."
NCBI gene IDs:
"18S: 
U6: "
Figure legend: "ARRET and αARRETNorthern blot analysis of the indicated strains using strand‐specific probes."
NCBI gene IDs:
"ARRET: 
αARRET: "
Figure legend: "Chromosome maps of differentially expressed genes in cay1Δ cells shown as fold enrichment over wt. Red dots are overexpressed genes and Tf2 retrotransposons, blue dots are overexpressed LTR sequences."
NCBI gene IDs:
"Tf2: 
cay1: 2540353"
Figure legend: "Northern blot analysis of tlh1/2+, Tf2 retrotransposons, and 18S rRNA (loading control) in wt, cay1Δ, and trichostatin A (TSA)‐treated wt cells. Black arrowhead indicates tlh1/2+ mRNA; red arrowhead unprocessed Tf2 transcripts; and blue arrowhead processed Tf2 transcripts."
NCBI gene IDs:
"18S: 
Tf2: 
cay1: 2540353
tlh1: 2541932"
Figure legend: "ChIP analysis of Cay1‐Myc binding to the indicated genomic loci. subtel: subtelomeres; Tf2: Tf2 retrotransposon genes; LTR: Tf2 LTR sequences; Tlh: tlh1/2+ genes; cen: centromeres. Immunoprecipitated DNA is normalized to input DNA and expressed as fold increase over untagged strains (unt)."
NCBI gene IDs:
"Tf2: 
tlh1: 2541932"