Journal: bioRxiv

Article Title: Regulation of the hypertonic stress response by the 3’ mRNA cleavage and polyadenylation complex

doi: 10.1101/2023.01.23.525244

Figure Lengend Snippet: Expression of CRISPR/Cas9-tagged alleles of Tag-RFP::cpf-2 (a) symk-1::gfp (b), and the merged image (c). d-f – higher resolution images of hypodermal (hyp arrows) and germline (gl) nuclei revealing the non-nucleolar nucleoplasmic concentration of tagged SYMK-1 and CPF-2 proteins. Dotted lines delineate the boundaries of the germline. g-i – Exposure of animals to 600 mM NaCl for 1 hour leads to reorganization of SYMK-1 and CPF-2 into subnuclear foci, primarily in the hypodermis. j-l – higher resolution of hypodermal nuclei with SYMK-1 and CPF-2 foci. m-o-higher resolution of hypodermal nuclei with SYMK-1 and CPF-2 carrying the G42E Nio point mutation.

Article Snippet: For CRISPR editing, we injected purified and assembled Cas9/gRNA/tracrRNA complexes with the purified repair template (all from IDT) and the rol-6 marker plasmid into the germlines of day 1 adult hermaphrodites.

Techniques: Expressing, CRISPR, Concentration Assay, Mutagenesis

Journal: Developmental biology

Article Title: FACT complex gene duplicates exhibit redundant and non-redundant functions in C. elegans

doi: 10.1016/j.ydbio.2018.10.002

Figure Lengend Snippet: A homozygous hmg-3(tm2539) mutants (GFP-negative) from heterozygous parents (hmg-3(tm2539)/hT2) exhibit a sterile phenotype, whereas homozygous hmg-4(tm1873) or spt-16(tm6354) mutants from heterozygous parents develop no further than L2 stage. Sample size indicated above the bar for each genotype. B hmg-3(RNAi) treatment of wild-type hermaphrodites (Maternal RNAi) results in sterile offspring, whereas treatment with hmg-4(RNAi) or spt-16(RNAi) results in animals that arrest as young larvae (hmg-4(RNAi)) or embryos (spt-16(RNAi); also see Figure 3, where each is evaluated directly for embryonic lethality). Seeding wild-type eggs onto RNAi plates (Larval RNAi) results in fertility for a majority of hmg-3(RNAi) and spt-16(RNAi) animals, and most hmg-4(RNAi) animals survive to sterile adulthood. Sample size indicated above the bar for each condition. C RNAi treatment of wild-type hermaphrodites (Maternal RNAi) reduces the intensity of fluorescent signal in hmg-3::GFP, hmg-4::GFP, and spt-16::GFP strains. The values represent average pixel signal intensity (arbitrary units) in the nucleus of the most mature oocyte in adult animals treated with RNAi for 24 hours (treatment starting in the L4 stage). * indicates p<0.005. n.s. indicates p>0.05; two tailed t-test. n>=8 for each condition.

Article Snippet: Reagent or resource Source Identifier Antibodies none Bacterial and Virus Strains OP50 E. coli Caenorhabditis Genetics Center Wormbase ID: OP50 HT115(DE3) E. coli Caenorhabditis Genetics Center Wormbase ID: HT115(DE3) I-2N19 (hmg-3 (RNAi) ) Kamath et al., 2003 https://www.sourcebioscience.com III-2P10 ( hmg-4(RNAi) ) Kamath et al., 2003 https://www.sourcebioscience.com Biological Samples none Chemicals, Peptides, and Recombinant Proteins none Critical Commercial Assays none Deposited Data none Experimental Models: Cell Lines none Experimental Models: Organisms/Strains FX18523 hmg-3(tm2539) I/hT2[bli-4(e937) qIs48] hT2[bli-4(e937) qIs48] National Bioresource Project for the Nematode Wormbase ID: WBVar00251408 FX16756 hmg-4(tm1873) III/ hT2[bli-4(e937) qIs48] National Bioresource Project for the Nematode Wormbase ID: WBVar00250836 FX14839 spt-16(tm6354) I/ hT2[bli-4(e937) qIs48 National Bioresource Project for the Nematode Wormbase ID: WBVar01474360 RB1524 F55A3.7(ok1829) I Caenorhabditis Genetics Center Wormbase ID: RB1524 SL438 spe-9(eb19) I; him-5(e1490) V; ebEx126[YAC Y47H9 [spe-9(+) + rol-6(su1006)] Caenorhabditis Genetics Center Wormbase ID: SL438 CM2680 hmg-3(tm2539) I;hmg-4(tm1873) III/ hT2[bli-4(e937) qIs48] This paper N/A SM481 pxIs10 [pha-4::GFP::CAAX + (pRF4) rol-6(su1006)] Caenorhabditis Genetics Center Wormbase ID: SM481 RW10705 unc-119(ed3) III; zuIs178 [his-72(1kb 5’ UTR)::his-72::SRPVAT::GFP::his-72 (1KB 3’ UTR) + 5.7 kb XbaI - HindIII unc-119(+)] V; stIs10024 [pie-1::H2B::GFP::pie-1 3’ UTR + unc-119(+)]; stIs10499 [tbx-37::H1-mCherry + unc-119(+)] Caenorhabditis Genetics Center Wormbase ID: RW10705 CM2450 unc-119(e2498); guEx1457 This paper N/A CM2689 hmg-3(gu244[hmg-3::gfp]) I This paper N/A CM2690 hmg-4(gu245[hmg-4::gfp]) III This paper N/A CM2691 hmg-4(gu246[hmg-4::gfp]) III This paper N/A CM2692 spt-16(gu247[spt-16::gfp]) I This paper N/A Oligonucleotides Primers are listed in Supplemental Table 1 This paper N/A Recombinant DNA L4440/pPD129.36 Fire Lab Vector Kit, 1999 Addgene.org/1654 Software and Algorithms Trackmate/ImageJ Tinevez et al., 2016 https://imagej.net/TrackMate TrackScheme/ImageJ https://imagej.net/TrackScheme Other Open in a separate window KEY RESOURCES TABLE

Techniques: Two Tailed Test

Journal: Developmental biology

Article Title: FACT complex gene duplicates exhibit redundant and non-redundant functions in C. elegans

doi: 10.1016/j.ydbio.2018.10.002

Figure Lengend Snippet: Embryonic lethality associated with single and double knockdown of FACT components, using RNA interference (RNAi). hmg-3(RNAi) or hmg-4(RNAi) treatment of hermaphrodites caused limited embryonic lethality among offspring but hmg-3(RNAi); hmg-4(RNAi) in combination resulted in high embryonic lethality, indicating an essential embryonic function that is redundant between these two genes. spt-16(RNAi) treatment resulted in a high level of embryonic lethality whereas embryos derived from mothers homozygous for the deletion allele F55A3.7(ok1829) are viable. This indicates spt-16 is essential for embryonic development. Data represent at least 100 offspring from 3 trials. Error bars correspond to +/− one standard deviation.

Article Snippet: Reagent or resource Source Identifier Antibodies none Bacterial and Virus Strains OP50 E. coli Caenorhabditis Genetics Center Wormbase ID: OP50 HT115(DE3) E. coli Caenorhabditis Genetics Center Wormbase ID: HT115(DE3) I-2N19 (hmg-3 (RNAi) ) Kamath et al., 2003 https://www.sourcebioscience.com III-2P10 ( hmg-4(RNAi) ) Kamath et al., 2003 https://www.sourcebioscience.com Biological Samples none Chemicals, Peptides, and Recombinant Proteins none Critical Commercial Assays none Deposited Data none Experimental Models: Cell Lines none Experimental Models: Organisms/Strains FX18523 hmg-3(tm2539) I/hT2[bli-4(e937) qIs48] hT2[bli-4(e937) qIs48] National Bioresource Project for the Nematode Wormbase ID: WBVar00251408 FX16756 hmg-4(tm1873) III/ hT2[bli-4(e937) qIs48] National Bioresource Project for the Nematode Wormbase ID: WBVar00250836 FX14839 spt-16(tm6354) I/ hT2[bli-4(e937) qIs48 National Bioresource Project for the Nematode Wormbase ID: WBVar01474360 RB1524 F55A3.7(ok1829) I Caenorhabditis Genetics Center Wormbase ID: RB1524 SL438 spe-9(eb19) I; him-5(e1490) V; ebEx126[YAC Y47H9 [spe-9(+) + rol-6(su1006)] Caenorhabditis Genetics Center Wormbase ID: SL438 CM2680 hmg-3(tm2539) I;hmg-4(tm1873) III/ hT2[bli-4(e937) qIs48] This paper N/A SM481 pxIs10 [pha-4::GFP::CAAX + (pRF4) rol-6(su1006)] Caenorhabditis Genetics Center Wormbase ID: SM481 RW10705 unc-119(ed3) III; zuIs178 [his-72(1kb 5’ UTR)::his-72::SRPVAT::GFP::his-72 (1KB 3’ UTR) + 5.7 kb XbaI - HindIII unc-119(+)] V; stIs10024 [pie-1::H2B::GFP::pie-1 3’ UTR + unc-119(+)]; stIs10499 [tbx-37::H1-mCherry + unc-119(+)] Caenorhabditis Genetics Center Wormbase ID: RW10705 CM2450 unc-119(e2498); guEx1457 This paper N/A CM2689 hmg-3(gu244[hmg-3::gfp]) I This paper N/A CM2690 hmg-4(gu245[hmg-4::gfp]) III This paper N/A CM2691 hmg-4(gu246[hmg-4::gfp]) III This paper N/A CM2692 spt-16(gu247[spt-16::gfp]) I This paper N/A Oligonucleotides Primers are listed in Supplemental Table 1 This paper N/A Recombinant DNA L4440/pPD129.36 Fire Lab Vector Kit, 1999 Addgene.org/1654 Software and Algorithms Trackmate/ImageJ Tinevez et al., 2016 https://imagej.net/TrackMate TrackScheme/ImageJ https://imagej.net/TrackScheme Other Open in a separate window KEY RESOURCES TABLE

Techniques: Derivative Assay, Standard Deviation

Journal: Developmental biology

Article Title: FACT complex gene duplicates exhibit redundant and non-redundant functions in C. elegans

doi: 10.1016/j.ydbio.2018.10.002

Figure Lengend Snippet: A, B Phylogenetic trees for SSRP1 and SPT16 in model organisms generated by Treefam (Ruan et al., 2008) identify an inferred duplication of genes encoding SSRP1 and SPT16 in the C. elegans genome. C Comparison of amino acid similarities of the three major protein domains found in human SSRP1 (Hsa-SSRP1) to the predicted C. elegans orthologs. Domains are indicated by boxes; the name for each domain is noted above the topmost row. Numbers inside domain boxes indicate percent amino acid similarity between the protein and the one(s) below it; numbers on the left correspond to domain similarity with that of Cel-HMG −3, the right is similarity with Cel-HMG-4. Overall, Cel-HMG −3 and Cel -HMG-4 share 81% amino acid sequence identity, and the genes share 81% nucleotide sequence identity within the coding region. Genomic and RNA-seq data support two full length C. elegans SSRP1 orthologs. D Protein sequence comparison of the three major domains of human SPT16 (Hsa-SPT16) and C. elegans orthologs. Numbers inside the domain boxes indicate the amino acid similarity between the protein and the one(s) below it; numbers on the left correspond to domain similarity with Cel -SPT-16, the right is similarity with Cel-F55A3.7. Cel-SPT-16 has all four domains present in Hsa-SPT16, but F55A3.7 includes only the Nlob and Spt16 protein domains. NA (not applicable) is indicated in the boxes for these two domains for the comparison to F55A3.7. This gene structure, combined with RNA-seq data that identify limited transcript abundance of F55A3.7, has resulted in classification of F55A3.7 as a psuedogene. These data suggest that SPT-16 is the C. elegans SPT16 ortholog.

Article Snippet: Reagent or resource Source Identifier Antibodies none Bacterial and Virus Strains OP50 E. coli Caenorhabditis Genetics Center Wormbase ID: OP50 HT115(DE3) E. coli Caenorhabditis Genetics Center Wormbase ID: HT115(DE3) I-2N19 (hmg-3 (RNAi) ) Kamath et al., 2003 https://www.sourcebioscience.com III-2P10 ( hmg-4(RNAi) ) Kamath et al., 2003 https://www.sourcebioscience.com Biological Samples none Chemicals, Peptides, and Recombinant Proteins none Critical Commercial Assays none Deposited Data none Experimental Models: Cell Lines none Experimental Models: Organisms/Strains FX18523 hmg-3(tm2539) I/hT2[bli-4(e937) qIs48] hT2[bli-4(e937) qIs48] National Bioresource Project for the Nematode Wormbase ID: WBVar00251408 FX16756 hmg-4(tm1873) III/ hT2[bli-4(e937) qIs48] National Bioresource Project for the Nematode Wormbase ID: WBVar00250836 FX14839 spt-16(tm6354) I/ hT2[bli-4(e937) qIs48 National Bioresource Project for the Nematode Wormbase ID: WBVar01474360 RB1524 F55A3.7(ok1829) I Caenorhabditis Genetics Center Wormbase ID: RB1524 SL438 spe-9(eb19) I; him-5(e1490) V; ebEx126[YAC Y47H9 [spe-9(+) + rol-6(su1006)] Caenorhabditis Genetics Center Wormbase ID: SL438 CM2680 hmg-3(tm2539) I;hmg-4(tm1873) III/ hT2[bli-4(e937) qIs48] This paper N/A SM481 pxIs10 [pha-4::GFP::CAAX + (pRF4) rol-6(su1006)] Caenorhabditis Genetics Center Wormbase ID: SM481 RW10705 unc-119(ed3) III; zuIs178 [his-72(1kb 5’ UTR)::his-72::SRPVAT::GFP::his-72 (1KB 3’ UTR) + 5.7 kb XbaI - HindIII unc-119(+)] V; stIs10024 [pie-1::H2B::GFP::pie-1 3’ UTR + unc-119(+)]; stIs10499 [tbx-37::H1-mCherry + unc-119(+)] Caenorhabditis Genetics Center Wormbase ID: RW10705 CM2450 unc-119(e2498); guEx1457 This paper N/A CM2689 hmg-3(gu244[hmg-3::gfp]) I This paper N/A CM2690 hmg-4(gu245[hmg-4::gfp]) III This paper N/A CM2691 hmg-4(gu246[hmg-4::gfp]) III This paper N/A CM2692 spt-16(gu247[spt-16::gfp]) I This paper N/A Oligonucleotides Primers are listed in Supplemental Table 1 This paper N/A Recombinant DNA L4440/pPD129.36 Fire Lab Vector Kit, 1999 Addgene.org/1654 Software and Algorithms Trackmate/ImageJ Tinevez et al., 2016 https://imagej.net/TrackMate TrackScheme/ImageJ https://imagej.net/TrackScheme Other Open in a separate window KEY RESOURCES TABLE

Techniques: Generated, Sequencing, RNA Sequencing Assay

Journal: Developmental biology

Article Title: FACT complex gene duplicates exhibit redundant and non-redundant functions in C. elegans

doi: 10.1016/j.ydbio.2018.10.002

Figure Lengend Snippet: A Cell cycle duration for all cells of the AB, MS and E lineages through the 6th division of AB. The graph shows medial, maximal and minimal cell cycle durations for control (blue), hmg-3(RNAi); hmg-4(RNAi) (green) and spt-16(RNAi) (orange). N=3 animals for each condition. Missing information (e.g. for spt-16(RNAi) at AB6, or hmg-3(RNAi); hmg-4(RNAi) at E3) indicates some cells failed to divide. Average (and standard deviation) of cell cycle length at AB6 for wild type, hmg-3(RNAi); hmg-4(RNAi), and spt-16(RNAi) in minutes was 33.4 (2.3; n=96), 47.8 (17.4; n=82), and 69.3 (19.0; n=36), respectively, with both hmg-3(RNAi); hmg-4(RNAi) and spt-16(RNAi) statistically different from wild type (two tailed t-test, p<<0.01). B Cell division defects observed at the 6th division of AB. Cells were classified based on whether they executed a relatively normal mitosis (Normal Division), did not initiate a division (No attempt), or initiated mitosis but resulted in morphological defects (Metaphase to either a single apparent nucleus, or a bilobed nucleus rather than the normal two distinct nuclei). Sample size is 96 cells each condition (32 cells each of three animals).

Article Snippet: Reagent or resource Source Identifier Antibodies none Bacterial and Virus Strains OP50 E. coli Caenorhabditis Genetics Center Wormbase ID: OP50 HT115(DE3) E. coli Caenorhabditis Genetics Center Wormbase ID: HT115(DE3) I-2N19 (hmg-3 (RNAi) ) Kamath et al., 2003 https://www.sourcebioscience.com III-2P10 ( hmg-4(RNAi) ) Kamath et al., 2003 https://www.sourcebioscience.com Biological Samples none Chemicals, Peptides, and Recombinant Proteins none Critical Commercial Assays none Deposited Data none Experimental Models: Cell Lines none Experimental Models: Organisms/Strains FX18523 hmg-3(tm2539) I/hT2[bli-4(e937) qIs48] hT2[bli-4(e937) qIs48] National Bioresource Project for the Nematode Wormbase ID: WBVar00251408 FX16756 hmg-4(tm1873) III/ hT2[bli-4(e937) qIs48] National Bioresource Project for the Nematode Wormbase ID: WBVar00250836 FX14839 spt-16(tm6354) I/ hT2[bli-4(e937) qIs48 National Bioresource Project for the Nematode Wormbase ID: WBVar01474360 RB1524 F55A3.7(ok1829) I Caenorhabditis Genetics Center Wormbase ID: RB1524 SL438 spe-9(eb19) I; him-5(e1490) V; ebEx126[YAC Y47H9 [spe-9(+) + rol-6(su1006)] Caenorhabditis Genetics Center Wormbase ID: SL438 CM2680 hmg-3(tm2539) I;hmg-4(tm1873) III/ hT2[bli-4(e937) qIs48] This paper N/A SM481 pxIs10 [pha-4::GFP::CAAX + (pRF4) rol-6(su1006)] Caenorhabditis Genetics Center Wormbase ID: SM481 RW10705 unc-119(ed3) III; zuIs178 [his-72(1kb 5’ UTR)::his-72::SRPVAT::GFP::his-72 (1KB 3’ UTR) + 5.7 kb XbaI - HindIII unc-119(+)] V; stIs10024 [pie-1::H2B::GFP::pie-1 3’ UTR + unc-119(+)]; stIs10499 [tbx-37::H1-mCherry + unc-119(+)] Caenorhabditis Genetics Center Wormbase ID: RW10705 CM2450 unc-119(e2498); guEx1457 This paper N/A CM2689 hmg-3(gu244[hmg-3::gfp]) I This paper N/A CM2690 hmg-4(gu245[hmg-4::gfp]) III This paper N/A CM2691 hmg-4(gu246[hmg-4::gfp]) III This paper N/A CM2692 spt-16(gu247[spt-16::gfp]) I This paper N/A Oligonucleotides Primers are listed in Supplemental Table 1 This paper N/A Recombinant DNA L4440/pPD129.36 Fire Lab Vector Kit, 1999 Addgene.org/1654 Software and Algorithms Trackmate/ImageJ Tinevez et al., 2016 https://imagej.net/TrackMate TrackScheme/ImageJ https://imagej.net/TrackScheme Other Open in a separate window KEY RESOURCES TABLE

Techniques: Standard Deviation, Two Tailed Test

Journal: Developmental biology

Article Title: FACT complex gene duplicates exhibit redundant and non-redundant functions in C. elegans

doi: 10.1016/j.ydbio.2018.10.002

Figure Lengend Snippet: A-D Comparison of the terminal phenotype of hmg-3(RNAi); hmg-4(RNAi) or spt-16(RNAi) embryos with late stage control embryos (hmg-3(RNAi) or hmg-4(RNAi)). Black brackets indicate the posterior bulb of the pharynx. In hmg-3(RNAi); hmg-4(RNAi) or spt-16(RNAi) embryos animals, no anterior pharynx is apparent, and embryos do not elongate. E-H Fluorescence from myo-2::mCherry (a marker for differentiated pharyngeal cells) is seen in the pharynx in single hmg-3(RNAi) or hmg-4(RNAi) larvae but only in posterior pharynx cells corresponding to the grinder (marked by brackets) in hmg-3(RNAi); hmg-4(RNAi) or spt-16(RNAi) embryos. Thirty-five of 38 transgene-bearing hmg-3(RNAi); hmg-4(RNAi) and 19 of 19 spt-16(RNAi) animals exhibited expression in a region consistent with the posterior pharynx similar to that in the image. I-N Expression of the early pharyngeal-intestinal marker PHA-4::GFP is observed only in intestine and posterior pharynx in hmg-3(RNAi); hmg-4(RNAi) or spt-16(RNAi) embryos, whereas it identifies the anterior pharynx in control animals. Scale = 20 µm.

Article Snippet: Reagent or resource Source Identifier Antibodies none Bacterial and Virus Strains OP50 E. coli Caenorhabditis Genetics Center Wormbase ID: OP50 HT115(DE3) E. coli Caenorhabditis Genetics Center Wormbase ID: HT115(DE3) I-2N19 (hmg-3 (RNAi) ) Kamath et al., 2003 https://www.sourcebioscience.com III-2P10 ( hmg-4(RNAi) ) Kamath et al., 2003 https://www.sourcebioscience.com Biological Samples none Chemicals, Peptides, and Recombinant Proteins none Critical Commercial Assays none Deposited Data none Experimental Models: Cell Lines none Experimental Models: Organisms/Strains FX18523 hmg-3(tm2539) I/hT2[bli-4(e937) qIs48] hT2[bli-4(e937) qIs48] National Bioresource Project for the Nematode Wormbase ID: WBVar00251408 FX16756 hmg-4(tm1873) III/ hT2[bli-4(e937) qIs48] National Bioresource Project for the Nematode Wormbase ID: WBVar00250836 FX14839 spt-16(tm6354) I/ hT2[bli-4(e937) qIs48 National Bioresource Project for the Nematode Wormbase ID: WBVar01474360 RB1524 F55A3.7(ok1829) I Caenorhabditis Genetics Center Wormbase ID: RB1524 SL438 spe-9(eb19) I; him-5(e1490) V; ebEx126[YAC Y47H9 [spe-9(+) + rol-6(su1006)] Caenorhabditis Genetics Center Wormbase ID: SL438 CM2680 hmg-3(tm2539) I;hmg-4(tm1873) III/ hT2[bli-4(e937) qIs48] This paper N/A SM481 pxIs10 [pha-4::GFP::CAAX + (pRF4) rol-6(su1006)] Caenorhabditis Genetics Center Wormbase ID: SM481 RW10705 unc-119(ed3) III; zuIs178 [his-72(1kb 5’ UTR)::his-72::SRPVAT::GFP::his-72 (1KB 3’ UTR) + 5.7 kb XbaI - HindIII unc-119(+)] V; stIs10024 [pie-1::H2B::GFP::pie-1 3’ UTR + unc-119(+)]; stIs10499 [tbx-37::H1-mCherry + unc-119(+)] Caenorhabditis Genetics Center Wormbase ID: RW10705 CM2450 unc-119(e2498); guEx1457 This paper N/A CM2689 hmg-3(gu244[hmg-3::gfp]) I This paper N/A CM2690 hmg-4(gu245[hmg-4::gfp]) III This paper N/A CM2691 hmg-4(gu246[hmg-4::gfp]) III This paper N/A CM2692 spt-16(gu247[spt-16::gfp]) I This paper N/A Oligonucleotides Primers are listed in Supplemental Table 1 This paper N/A Recombinant DNA L4440/pPD129.36 Fire Lab Vector Kit, 1999 Addgene.org/1654 Software and Algorithms Trackmate/ImageJ Tinevez et al., 2016 https://imagej.net/TrackMate TrackScheme/ImageJ https://imagej.net/TrackScheme Other Open in a separate window KEY RESOURCES TABLE

Techniques: Fluorescence, Marker, Expressing

Journal: Developmental biology

Article Title: FACT complex gene duplicates exhibit redundant and non-redundant functions in C. elegans

doi: 10.1016/j.ydbio.2018.10.002

Figure Lengend Snippet: A-H HMG-3::GFP is nuclear-localized and present broadly in early embryos (A, two cell embryo; B-D, gastrulation through ventral cleft closure) Over developmental time, the somatic protein intensity is reduced compared to that in the germ cells, and in late embryonic stages it is absent from somatic cells (D, ventral cleft closure; E, comma stage; F, elongated embryo; arrowhead indicates germ cell(s)). Presence of the protein in the germline persists through adulthood in both sexes (G, adult hermaphrodite, H, adult male). I-P HMG-4::GFP is present broadly and in both somatic and germ cells from embryonic (I, two cell embryo; J-L, gastrulation through ventral cleft closure; M, comma stage; N, elongated embryo) through adult stages in both hermaphrodites (O) and males (P). Q-X Like HMG-4::GFP, SPT-16::GFP is seen in both somatic and germ cells from early embryonic stages (Q, two cell embryo; R-T, gastrulation through ventral cleft closure; U, comma stage; V, elongated embryo) through adult stages (W, adult hermaphrodite; X, adult male). Scale = 20 µm. Scale in D, L, and T is for all embryonic images (A-F, I-N, Q-V, taken with 100x objective) and scale in G, O, and W is for all adult images (G-H, O-P, W-X, taken with 40x objective).

Article Snippet: Reagent or resource Source Identifier Antibodies none Bacterial and Virus Strains OP50 E. coli Caenorhabditis Genetics Center Wormbase ID: OP50 HT115(DE3) E. coli Caenorhabditis Genetics Center Wormbase ID: HT115(DE3) I-2N19 (hmg-3 (RNAi) ) Kamath et al., 2003 https://www.sourcebioscience.com III-2P10 ( hmg-4(RNAi) ) Kamath et al., 2003 https://www.sourcebioscience.com Biological Samples none Chemicals, Peptides, and Recombinant Proteins none Critical Commercial Assays none Deposited Data none Experimental Models: Cell Lines none Experimental Models: Organisms/Strains FX18523 hmg-3(tm2539) I/hT2[bli-4(e937) qIs48] hT2[bli-4(e937) qIs48] National Bioresource Project for the Nematode Wormbase ID: WBVar00251408 FX16756 hmg-4(tm1873) III/ hT2[bli-4(e937) qIs48] National Bioresource Project for the Nematode Wormbase ID: WBVar00250836 FX14839 spt-16(tm6354) I/ hT2[bli-4(e937) qIs48 National Bioresource Project for the Nematode Wormbase ID: WBVar01474360 RB1524 F55A3.7(ok1829) I Caenorhabditis Genetics Center Wormbase ID: RB1524 SL438 spe-9(eb19) I; him-5(e1490) V; ebEx126[YAC Y47H9 [spe-9(+) + rol-6(su1006)] Caenorhabditis Genetics Center Wormbase ID: SL438 CM2680 hmg-3(tm2539) I;hmg-4(tm1873) III/ hT2[bli-4(e937) qIs48] This paper N/A SM481 pxIs10 [pha-4::GFP::CAAX + (pRF4) rol-6(su1006)] Caenorhabditis Genetics Center Wormbase ID: SM481 RW10705 unc-119(ed3) III; zuIs178 [his-72(1kb 5’ UTR)::his-72::SRPVAT::GFP::his-72 (1KB 3’ UTR) + 5.7 kb XbaI - HindIII unc-119(+)] V; stIs10024 [pie-1::H2B::GFP::pie-1 3’ UTR + unc-119(+)]; stIs10499 [tbx-37::H1-mCherry + unc-119(+)] Caenorhabditis Genetics Center Wormbase ID: RW10705 CM2450 unc-119(e2498); guEx1457 This paper N/A CM2689 hmg-3(gu244[hmg-3::gfp]) I This paper N/A CM2690 hmg-4(gu245[hmg-4::gfp]) III This paper N/A CM2691 hmg-4(gu246[hmg-4::gfp]) III This paper N/A CM2692 spt-16(gu247[spt-16::gfp]) I This paper N/A Oligonucleotides Primers are listed in Supplemental Table 1 This paper N/A Recombinant DNA L4440/pPD129.36 Fire Lab Vector Kit, 1999 Addgene.org/1654 Software and Algorithms Trackmate/ImageJ Tinevez et al., 2016 https://imagej.net/TrackMate TrackScheme/ImageJ https://imagej.net/TrackScheme Other Open in a separate window KEY RESOURCES TABLE

Techniques:

Journal: Developmental biology

Article Title: FACT complex gene duplicates exhibit redundant and non-redundant functions in C. elegans

doi: 10.1016/j.ydbio.2018.10.002

Figure Lengend Snippet: A-C Homozygous hmg-3(tm2539); hmg-4(tm1873) and spt-16(tm6354) mutant larvae derived from heterozygous mothers have normal pharynges, indicating that maternal gene activity is sufficient for normal pharyngeal development. Scale = 20 µm. D. hmg-3(tm2539); hmg-4(tm1873) double mutants hatch at the same frequency as single mutants. Both genes are balanced by hT2, which is marked with a myo-2::GFP transgene. The percent of GFP-negative L1 larvae derived from heterozygous mother was evaluated, and no significant difference in survivability was observed. Data represent at least 125 offspring from at least 2 trials. Error bars correspond to +/− one standard deviation.

Article Snippet: Reagent or resource Source Identifier Antibodies none Bacterial and Virus Strains OP50 E. coli Caenorhabditis Genetics Center Wormbase ID: OP50 HT115(DE3) E. coli Caenorhabditis Genetics Center Wormbase ID: HT115(DE3) I-2N19 (hmg-3 (RNAi) ) Kamath et al., 2003 https://www.sourcebioscience.com III-2P10 ( hmg-4(RNAi) ) Kamath et al., 2003 https://www.sourcebioscience.com Biological Samples none Chemicals, Peptides, and Recombinant Proteins none Critical Commercial Assays none Deposited Data none Experimental Models: Cell Lines none Experimental Models: Organisms/Strains FX18523 hmg-3(tm2539) I/hT2[bli-4(e937) qIs48] hT2[bli-4(e937) qIs48] National Bioresource Project for the Nematode Wormbase ID: WBVar00251408 FX16756 hmg-4(tm1873) III/ hT2[bli-4(e937) qIs48] National Bioresource Project for the Nematode Wormbase ID: WBVar00250836 FX14839 spt-16(tm6354) I/ hT2[bli-4(e937) qIs48 National Bioresource Project for the Nematode Wormbase ID: WBVar01474360 RB1524 F55A3.7(ok1829) I Caenorhabditis Genetics Center Wormbase ID: RB1524 SL438 spe-9(eb19) I; him-5(e1490) V; ebEx126[YAC Y47H9 [spe-9(+) + rol-6(su1006)] Caenorhabditis Genetics Center Wormbase ID: SL438 CM2680 hmg-3(tm2539) I;hmg-4(tm1873) III/ hT2[bli-4(e937) qIs48] This paper N/A SM481 pxIs10 [pha-4::GFP::CAAX + (pRF4) rol-6(su1006)] Caenorhabditis Genetics Center Wormbase ID: SM481 RW10705 unc-119(ed3) III; zuIs178 [his-72(1kb 5’ UTR)::his-72::SRPVAT::GFP::his-72 (1KB 3’ UTR) + 5.7 kb XbaI - HindIII unc-119(+)] V; stIs10024 [pie-1::H2B::GFP::pie-1 3’ UTR + unc-119(+)]; stIs10499 [tbx-37::H1-mCherry + unc-119(+)] Caenorhabditis Genetics Center Wormbase ID: RW10705 CM2450 unc-119(e2498); guEx1457 This paper N/A CM2689 hmg-3(gu244[hmg-3::gfp]) I This paper N/A CM2690 hmg-4(gu245[hmg-4::gfp]) III This paper N/A CM2691 hmg-4(gu246[hmg-4::gfp]) III This paper N/A CM2692 spt-16(gu247[spt-16::gfp]) I This paper N/A Oligonucleotides Primers are listed in Supplemental Table 1 This paper N/A Recombinant DNA L4440/pPD129.36 Fire Lab Vector Kit, 1999 Addgene.org/1654 Software and Algorithms Trackmate/ImageJ Tinevez et al., 2016 https://imagej.net/TrackMate TrackScheme/ImageJ https://imagej.net/TrackScheme Other Open in a separate window KEY RESOURCES TABLE

Techniques: Mutagenesis, Derivative Assay, Activity Assay, Standard Deviation

Journal: Developmental biology

Article Title: FACT complex gene duplicates exhibit redundant and non-redundant functions in C. elegans

doi: 10.1016/j.ydbio.2018.10.002

Figure Lengend Snippet: Males homozygous for HMG-3::GFP, HMG-4::GFP or SPT-16::GFP were mated to spe −9(eb19) hermaphrodites to evaluate the onset of zygotic protein expression. A A comparison of the percent of HMG-3::GFP-positive animals at late embryonic and early larval stages indicates that zygotic expression initiates only in late embryonic/early larval stages, coincident with the initiation of germline cell division. B Offspring from spe-9 hermaphrodites mated with either HMG-4::GFP- or SPT-16::GFP-bearing males were evaluated at different timepoints after the parent had laid eggs for one hour. Zygotic expression for HMG-4::GFP and SPT-16::GFP begins much earlier than for HMG-3::GFP, and is apparent in somatic cells as well as germline. Data represent at least 30 offspring at each timepoint for both panels. Error bars correspond to the 95% confidence interval.

Article Snippet: Reagent or resource Source Identifier Antibodies none Bacterial and Virus Strains OP50 E. coli Caenorhabditis Genetics Center Wormbase ID: OP50 HT115(DE3) E. coli Caenorhabditis Genetics Center Wormbase ID: HT115(DE3) I-2N19 (hmg-3 (RNAi) ) Kamath et al., 2003 https://www.sourcebioscience.com III-2P10 ( hmg-4(RNAi) ) Kamath et al., 2003 https://www.sourcebioscience.com Biological Samples none Chemicals, Peptides, and Recombinant Proteins none Critical Commercial Assays none Deposited Data none Experimental Models: Cell Lines none Experimental Models: Organisms/Strains FX18523 hmg-3(tm2539) I/hT2[bli-4(e937) qIs48] hT2[bli-4(e937) qIs48] National Bioresource Project for the Nematode Wormbase ID: WBVar00251408 FX16756 hmg-4(tm1873) III/ hT2[bli-4(e937) qIs48] National Bioresource Project for the Nematode Wormbase ID: WBVar00250836 FX14839 spt-16(tm6354) I/ hT2[bli-4(e937) qIs48 National Bioresource Project for the Nematode Wormbase ID: WBVar01474360 RB1524 F55A3.7(ok1829) I Caenorhabditis Genetics Center Wormbase ID: RB1524 SL438 spe-9(eb19) I; him-5(e1490) V; ebEx126[YAC Y47H9 [spe-9(+) + rol-6(su1006)] Caenorhabditis Genetics Center Wormbase ID: SL438 CM2680 hmg-3(tm2539) I;hmg-4(tm1873) III/ hT2[bli-4(e937) qIs48] This paper N/A SM481 pxIs10 [pha-4::GFP::CAAX + (pRF4) rol-6(su1006)] Caenorhabditis Genetics Center Wormbase ID: SM481 RW10705 unc-119(ed3) III; zuIs178 [his-72(1kb 5’ UTR)::his-72::SRPVAT::GFP::his-72 (1KB 3’ UTR) + 5.7 kb XbaI - HindIII unc-119(+)] V; stIs10024 [pie-1::H2B::GFP::pie-1 3’ UTR + unc-119(+)]; stIs10499 [tbx-37::H1-mCherry + unc-119(+)] Caenorhabditis Genetics Center Wormbase ID: RW10705 CM2450 unc-119(e2498); guEx1457 This paper N/A CM2689 hmg-3(gu244[hmg-3::gfp]) I This paper N/A CM2690 hmg-4(gu245[hmg-4::gfp]) III This paper N/A CM2691 hmg-4(gu246[hmg-4::gfp]) III This paper N/A CM2692 spt-16(gu247[spt-16::gfp]) I This paper N/A Oligonucleotides Primers are listed in Supplemental Table 1 This paper N/A Recombinant DNA L4440/pPD129.36 Fire Lab Vector Kit, 1999 Addgene.org/1654 Software and Algorithms Trackmate/ImageJ Tinevez et al., 2016 https://imagej.net/TrackMate TrackScheme/ImageJ https://imagej.net/TrackScheme Other Open in a separate window KEY RESOURCES TABLE

Techniques: Expressing

Journal: Developmental biology

Article Title: FACT complex gene duplicates exhibit redundant and non-redundant functions in C. elegans

doi: 10.1016/j.ydbio.2018.10.002

Figure Lengend Snippet: Germline of a wild-type L4 lethargus (A) and adult (B) hermaphrodite, with inset of sperm cells. Germline of hmg-3(tm2539) (C) and zygotic (L1 larval) hmg-4(RNAi) (D) adult animals exhibit evidence of germline proliferation and sperm cells (inset), but lack oocytes. Scale = 20 µm. Inset images are 3x the primary image. Quantification of sterile phenotype for hmg-3(tm2539) and hmg-4(RNAi) is in Figure 1.

Article Snippet: Reagent or resource Source Identifier Antibodies none Bacterial and Virus Strains OP50 E. coli Caenorhabditis Genetics Center Wormbase ID: OP50 HT115(DE3) E. coli Caenorhabditis Genetics Center Wormbase ID: HT115(DE3) I-2N19 (hmg-3 (RNAi) ) Kamath et al., 2003 https://www.sourcebioscience.com III-2P10 ( hmg-4(RNAi) ) Kamath et al., 2003 https://www.sourcebioscience.com Biological Samples none Chemicals, Peptides, and Recombinant Proteins none Critical Commercial Assays none Deposited Data none Experimental Models: Cell Lines none Experimental Models: Organisms/Strains FX18523 hmg-3(tm2539) I/hT2[bli-4(e937) qIs48] hT2[bli-4(e937) qIs48] National Bioresource Project for the Nematode Wormbase ID: WBVar00251408 FX16756 hmg-4(tm1873) III/ hT2[bli-4(e937) qIs48] National Bioresource Project for the Nematode Wormbase ID: WBVar00250836 FX14839 spt-16(tm6354) I/ hT2[bli-4(e937) qIs48 National Bioresource Project for the Nematode Wormbase ID: WBVar01474360 RB1524 F55A3.7(ok1829) I Caenorhabditis Genetics Center Wormbase ID: RB1524 SL438 spe-9(eb19) I; him-5(e1490) V; ebEx126[YAC Y47H9 [spe-9(+) + rol-6(su1006)] Caenorhabditis Genetics Center Wormbase ID: SL438 CM2680 hmg-3(tm2539) I;hmg-4(tm1873) III/ hT2[bli-4(e937) qIs48] This paper N/A SM481 pxIs10 [pha-4::GFP::CAAX + (pRF4) rol-6(su1006)] Caenorhabditis Genetics Center Wormbase ID: SM481 RW10705 unc-119(ed3) III; zuIs178 [his-72(1kb 5’ UTR)::his-72::SRPVAT::GFP::his-72 (1KB 3’ UTR) + 5.7 kb XbaI - HindIII unc-119(+)] V; stIs10024 [pie-1::H2B::GFP::pie-1 3’ UTR + unc-119(+)]; stIs10499 [tbx-37::H1-mCherry + unc-119(+)] Caenorhabditis Genetics Center Wormbase ID: RW10705 CM2450 unc-119(e2498); guEx1457 This paper N/A CM2689 hmg-3(gu244[hmg-3::gfp]) I This paper N/A CM2690 hmg-4(gu245[hmg-4::gfp]) III This paper N/A CM2691 hmg-4(gu246[hmg-4::gfp]) III This paper N/A CM2692 spt-16(gu247[spt-16::gfp]) I This paper N/A Oligonucleotides Primers are listed in Supplemental Table 1 This paper N/A Recombinant DNA L4440/pPD129.36 Fire Lab Vector Kit, 1999 Addgene.org/1654 Software and Algorithms Trackmate/ImageJ Tinevez et al., 2016 https://imagej.net/TrackMate TrackScheme/ImageJ https://imagej.net/TrackScheme Other Open in a separate window KEY RESOURCES TABLE

Techniques:

Journal: Developmental biology

Article Title: FACT complex gene duplicates exhibit redundant and non-redundant functions in C. elegans

doi: 10.1016/j.ydbio.2018.10.002

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: Reagent or resource Source Identifier Antibodies none Bacterial and Virus Strains OP50 E. coli Caenorhabditis Genetics Center Wormbase ID: OP50 HT115(DE3) E. coli Caenorhabditis Genetics Center Wormbase ID: HT115(DE3) I-2N19 (hmg-3 (RNAi) ) Kamath et al., 2003 https://www.sourcebioscience.com III-2P10 ( hmg-4(RNAi) ) Kamath et al., 2003 https://www.sourcebioscience.com Biological Samples none Chemicals, Peptides, and Recombinant Proteins none Critical Commercial Assays none Deposited Data none Experimental Models: Cell Lines none Experimental Models: Organisms/Strains FX18523 hmg-3(tm2539) I/hT2[bli-4(e937) qIs48] hT2[bli-4(e937) qIs48] National Bioresource Project for the Nematode Wormbase ID: WBVar00251408 FX16756 hmg-4(tm1873) III/ hT2[bli-4(e937) qIs48] National Bioresource Project for the Nematode Wormbase ID: WBVar00250836 FX14839 spt-16(tm6354) I/ hT2[bli-4(e937) qIs48 National Bioresource Project for the Nematode Wormbase ID: WBVar01474360 RB1524 F55A3.7(ok1829) I Caenorhabditis Genetics Center Wormbase ID: RB1524 SL438 spe-9(eb19) I; him-5(e1490) V; ebEx126[YAC Y47H9 [spe-9(+) + rol-6(su1006)] Caenorhabditis Genetics Center Wormbase ID: SL438 CM2680 hmg-3(tm2539) I;hmg-4(tm1873) III/ hT2[bli-4(e937) qIs48] This paper N/A SM481 pxIs10 [pha-4::GFP::CAAX + (pRF4) rol-6(su1006)] Caenorhabditis Genetics Center Wormbase ID: SM481 RW10705 unc-119(ed3) III; zuIs178 [his-72(1kb 5’ UTR)::his-72::SRPVAT::GFP::his-72 (1KB 3’ UTR) + 5.7 kb XbaI - HindIII unc-119(+)] V; stIs10024 [pie-1::H2B::GFP::pie-1 3’ UTR + unc-119(+)]; stIs10499 [tbx-37::H1-mCherry + unc-119(+)] Caenorhabditis Genetics Center Wormbase ID: RW10705 CM2450 unc-119(e2498); guEx1457 This paper N/A CM2689 hmg-3(gu244[hmg-3::gfp]) I This paper N/A CM2690 hmg-4(gu245[hmg-4::gfp]) III This paper N/A CM2691 hmg-4(gu246[hmg-4::gfp]) III This paper N/A CM2692 spt-16(gu247[spt-16::gfp]) I This paper N/A Oligonucleotides Primers are listed in Supplemental Table 1 This paper N/A Recombinant DNA L4440/pPD129.36 Fire Lab Vector Kit, 1999 Addgene.org/1654 Software and Algorithms Trackmate/ImageJ Tinevez et al., 2016 https://imagej.net/TrackMate TrackScheme/ImageJ https://imagej.net/TrackScheme Other Open in a separate window KEY RESOURCES TABLE

Techniques: Recombinant, Plasmid Preparation, Software