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. 2023 Mar 2;223(3):iyad005.
doi: 10.1093/genetics/iyad005.

SPR-1/CoREST facilitates the maternal epigenetic reprogramming of the histone demethylase SPR-5/LSD1

Brandon S Carpenter  1 , Alyssa Scott  2 , Robert Goldin  3 , Sindy R Chavez  2 , Juan D Rodriguez  2 , Dexter A Myrick  2 , Marcus Curlee  2 , Karen L Schmeichel  4 , David J Katz  2
Affiliations

SPR-1/CoREST facilitates the maternal epigenetic reprogramming of the histone demethylase SPR-5/LSD1

Brandon S Carpenter et al. Genetics. .

Abstract

Maternal reprogramming of histone methylation is critical for reestablishing totipotency in the zygote, but how histone-modifying enzymes are regulated during maternal reprogramming is not well characterized. To address this gap, we asked whether maternal reprogramming by the H3K4me1/2 demethylase SPR-5/LSD1/KDM1A, is regulated by the chromatin co-repressor protein, SPR-1/CoREST, in Caenorhabditis elegans and mice. In C. elegans, SPR-5 functions as part of a reprogramming switch together with the H3K9 methyltransferase MET-2. By examining germline development, fertility, and gene expression in double mutants between spr-1 and met-2, as well as fertility in double mutants between spr-1 and spr-5, we find that loss of SPR-1 results in a partial loss of SPR-5 maternal reprogramming function. In mice, we generated a separation of function Lsd1 M448V point mutation that compromises CoREST binding, but only slightly affects LSD1 demethylase activity. When maternal LSD1 in the oocyte is derived exclusively from this allele, the progeny phenocopy the increased perinatal lethality that we previously observed when LSD1 was reduced maternally. Together, these data are consistent with CoREST having a conserved function in facilitating maternal LSD1 epigenetic reprogramming.

Keywords: COREST; LSD1; SPR-1; SPR-5; histone methylation; maternal epigenetic reprogramming.

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Figures

Fig. 1.
Fig. 1.
Germline mortality in spr-1/CoREST and met-2; spr-1 mutants. a) The average number of total progeny from wild-type (WT), spr-5/lsd1, and spr-1/CoREST mutants over progressive generations. The average number of progeny from spr-1/CoREST mutants (N = 192, N = total number broods counted) is significantly decreased compared with WT animals (N = 92) across 50 generations (unpaired Student t-test, **** P-value <0.0001 between WT and spr-1/CoREST mutants). 10 × differential interference contrast images of F1 met-2; spr-1 mutants scored as either fertile (b), fertile (Egl) (c), or sterile (d). Asterisk denotes hatched larvae outlined by a dashed line inside of a met-2; spr-1 mutant scored as fertile (Egl)(c). e) The average number of total progeny from WT, spr-1/CoREST, met-2 and met-2; spr-1 mutants over progressive generations. f) Percent of animals cloned out for experiment in (e) scored for sterility over progressive generations. In panel f, several of the genotypes have values of zero. spr-1/CoREST mutant progeny were only scored at F1, F4, F7, and F10 generations in (e, f). g) The average number of total progeny from wild-type (WT), spr-5/lsd1, spr-1/CoREST, and spr-5; spr-1 mutants over progressive generations. Error bars in (a, e, and f) represent the standard error of the mean (SEM).
Fig. 2.
Fig. 2.
Transcriptional misregulation in met-2; spr-1 progeny overlaps with that observed in spr-5; met-2 progeny, but is less affected. Overlap between all (a), upregulated (b), and downregulated (c) DEGs in met-2; spr-1 and spr-5; met-2 L1 progeny. Significant over-enrichment in a–c was determined by the hypergeometric test (*P-value < 1.28E-270, *P-value < 2.61E-392, *P-value < 2.16E-72, respectively). Scatter dot plots displaying the log2 fold change of 676 upregulated (d), and 236 downregulated (e) overlapping DEGs between met-2; spr-1 and spr-5; met-2 progeny. d, e) Numbers and solid black lines represent the mean log2 fold change. DEGs in spr-5; met-2 progeny were obtained from (Carpenter et al., 2021). f) Scatter plot displaying the correlation in log2 fold change of all 1,010 overlapping DEGs between met-2; spr-1and spr-5; met-2 L1 progeny. Genes with correlated expression changes are found in the top right and bottom left quadrants, while genes that do not correlate are found in the opposite quadrants. The dotted line represents 1:1 relationship between gene expression changes in met-2; spr-1 vs spr-5; met-2. Less severe gene expression changes fall to the left of the dotted line in the positively correlated quadrant and to the right of the dotted line in the negatively correlated quadrant.
Fig. 3.
Fig. 3.
MES-4 germline genes are enriched in met-2; spr-1 mutants, but less affected compared with spr-5; met-2 mutants. a) Overlap between MES-4 germline genes and differentially expressed genes (DEGs) in met-2; spr-1 L1 progeny. Asterisks denote significant over-enrichment in A as determined by a hypergeometric test (P-value < 1.41E-9). b) Overlap between MES-4 germline genes differentially expressed in met-2; spr-1 and spr-5; met-2 L1 progeny. c) Heatmap of log2 fold change (FC) of all 196 MES-4 germline genes in spr-1/CoREST, met-2, met-2; spr-1 and spr-5; met-2 mutants compared with the wild-type. log2(FC) values are represented in a yellow-to-blue gradient with a range of −2 to 5. Yellow represents genes with negative log2(FC) values and blue represents genes with positive log2FC values compared with the wild-type.
Fig. 4.
Fig. 4.
LSD1 and CoREST are expressed during each stage of mouse oocyte development. Representative immunofluorescence images of various stages of the mouse oocyte: primary (a–c, j-l), secondary (d–f, m-o), and antral (g–i, p-r). DAPI (a, d, g, j, m, p), as distinguished by granulosa cell layers and the amount of antral fluid. LSD1 (b, e, h) CoREST (k, n, q), and Merge (c, f, i, l, o, r). Both LSD1 and CoREST are expressed in the oocyte nucleus and surrounding follicle cells during each stage of oocyte development. Scale bars = 25 um.
Fig. 5.
Fig. 5.
Hypomorphic maternal LSD1 results in perinatal lethality. a) Crystal structure of LSD1 (pink) in complex with CoREST (blue) from Nicholson et al., 2013. The M448V mutation is in a CoREST binding site (star). b–d) Genetic crosses showing wild-type (+), loxP sites (triangles), and M448V (star) alleles. In all cases, P0 females are crossed to wild-type males, so that F1 progeny have normal zygotic LSD1 activity from their paternal allele after transcription begins at the 2-cell stage. b) In the Lsd1M448V cross, P0 mothers are Zp3Cre+, contributing only the hypomorphic allele maternally. c) In the Lsd1+ control cross, P0 mothers are Zp3Cre-, contributing a wild-type and hypomorphic allele, maternally. d) In the Lsd1het control cross, P0 mothers are Zp3Cre+, contributing one wild-type copy of Lsd1 maternally. e) Percent perinatal lethality per litter by experimental condition, n = 154 pups from 24 l (Lsd1+), n = 96 pups from 15 l (Lsd1het), and n = 187 pups from 32 l (Lsd1M448V). See File S1 for the list of individual litters. P-values are calculated using a χ2 test, **** = P < 0.0001, ** = P < 0.01, * = P < 0.05.
Fig. 6.
Fig. 6.
Model of SPR-1/CoREST affects SPR-5/LSD1 maternal reprogramming. a–c) In C. elegans, SPR-5/LSD1 functions with SPR-1/CoREST maternally to erase H3K4me2. This is reinforced by the addition of H3K9me2 by MET-2/SETDB1 (a). In spr-1/CoREST mutants, H3K4me2 erasure is less efficient genome wide, but partially compromised SPR-5/LSD1 reprogramming combined with normal MET-2/SETDB1 reprogramming is sufficient to prevent sterility across generations (b). However, if maternal reprogramming is further compromised in met-2; spr-1 double mutants, H3K4me2 accumulates and results in increasing sterility across generations (c). In mice, disruption of LSD1/SPR-5's ability to bind CoREST/SPR-1 maternally results in less efficient H3K4me2 erasure (d) that is similar to the loss of SPR-1/CoREST in C. elegans (b).
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