Cathepsin L proteolytically processes histone H3 during mouse embryonic stem cell differentiation

Abstract

Chromatin undergoes developmentally-regulated structural and chemical changes as cells differentiate, which subsequently lead to differences in cellular function by altering patterns of gene expression. To gain insight into chromatin alterations that occur during mammalian differentiation, we turned to a mouse embryonic stem cell (ESC) model. Here we show that histone H3 is proteolytically cleaved at its N-terminus during ESC differentiation. We map the sites of H3 cleavage and identify Cathepsin L as a protease responsible for proteolytically processing the N-terminal H3 tail. In addition, our data suggest that H3 cleavage may be regulated by covalent modifications present on the histone tail itself. Our studies underscore the intriguing possibility that histone proteolysis, brought about by Cathepsin L and potentially other family members, plays a role in development and differentiation that was not previously recognized.

Figure 1. A distinct histone H3 species is detected in chromatin during ESC differentiation

(A) Undifferentiated (und) ESCs were differentiated with RA in a monolayer, harvested for WCEs at the time points indicated, and analyzed by immunoblotting with the antibodies indicated to the right of each panel; H3gen refers to the H3 general C-terminal antibody unless otherwise indicated. Molecular weights (in kD) are indicated to the left in all subsequent gels and immunoblots. (B) Chromatin was isolated from undifferentiated ESCs and ESCs differentiated with RA for 3 days, digested with micrococcal nuclease for the indicated times, and analyzed by immunoblotting; P=chromatin pellet input, P’=post-Mnase pellet. (C) ESCs were differentiated using three basic methods: monolayer differentiation with RA (left), monolayer differentiation with LIF withdrawal (middle), and embryoid body (EB) formation by cell aggregation (right); WCEs were analyzed for both a marker of pluripotency (Oct 3/4) and the histone H3 sub-band (H3gen).

Figure 2. Histone H3 is N-terminally cleaved during ESC differentiation

(A) RP-HPLC fractions were screened for the H3 sub-band by immunoblotting (left). Equal amounts of fractions 52–55 were then pooled, separated by SDS-PAGE, and blotted to PVDF (middle). Each sub-band (asteriks) was excised and subjected to Edman degradation, which suggested that H3 had been N-terminally cleaved between residues A21 and T22 and between K27 and S28 (right). Residues not clearly identified in the generated sequence are denoted “X.” (B) Sample in fraction 54 was digested with GluC to generate intact, N-terminal peptides that terminate with E50; peptides were then analyzed by MS. Six highly modified, truncated fragments of the GluC-generated 1–50 peptide were observed (right). Note that the two sequences detected by Edman degradation were also detected by MS (asterisks). All six of the truncated 1–50 peptides contain Ala at position 31 (underlined) and are thus derived from the H3 isoform H3.2. Three highly modified forms of the complementary N-terminal fragments, A1-A21, A1-K23, and A1-R26 (left) are also present in the same HPLC fraction. (C) The sequence of the mammalian histone H3 tail and the cleavage sites mapped in (A) and (B); the bold solid line indicates the “primary” cleavage site mapped by both Edman degradation and MS (H3.cs1); additional significant cleavage sites are marked with regular solid lines; less abundant sites are marked by dashed lines. Lysines found by MS to be highly acetylated (ac) or methylated (me) are marked by a triangle or circle, respectively (see Supplemental Figure S2 for details).

Figure 3. The cysteine protease Cathepsin L is detected in fractions enriched for histone H3 cleavage activity

(A) Schematic of in vitro H3 cleavage assay (see text for details). (B) A representative example of the H3 cleavage assay comparing soluble cytosolic + nuclear protein extract (S) and solubilized chromatin extract (C) from undifferentiated to those prepared from 3 days + RA differentiating ESCs. (C) Schematic of extract fractionation for protease enrichment. (D) H3 cleavage assay of hydroxyapatite fractions generated by scheme shown in (C); assay reactions were analyzed by immunoblotting with both HIS-HRP and H3.cs1 antibodies. (E) Hydroxyapatite fractions assayed in (D) were analyzed for the presence of Cathepsin L by immunoblotting with Cathepsin L antibody; # designates proprotein (~37kD), • indicates intermediate processed form (~30kD), and * indicates mature processed form (~25kD).

Figure 4. Cathepsin L cleaves histone H3 in vitro and associates with chromatin in vivo

(A) Hydroxyapatite fraction #23 (Figure 3D) was assayed +/− protease inhibitors in the H3 cleavage assay; cysteine protease inhibitor E64 is a potent inhibitor of the H3 protease activity in fraction #23. (B) Immobilized E64 was incubated with both an active hydroxyapatite fraction (23) and one without enzymatic activity (20); control resin was incubated with each fraction in parallel. Resins were then analyzed for bound proteins by immunoblotting (bottom panel) and the supernatant was tested for H3 protease activity (top panel). (C) Hydroxyapatite fraction #23 (Figure 3D) was assayed with various rH3-HIS point mutants in the H3 cleavage assay. (D) Chromatin from undifferentiated ESCs and ESCs differentiated +RA for the number of days indicated was digested with micrococcal nuclease; the solubilized mononucleosomes were analyzed by immunoblotting with Cathepsin L antibody.

Figure 5. rCathepsin L cleaves histone H3 in vitro

(A) Recombinant Cathepsin L cleaves rH3 in vitro at both pH 5.5 and pH 7.4 and generates a fragment that is recognized by both α-HIS-HRP (top panel) and α-H3.cs1 (middle panel) antibodies. (B) Recombinant mouse Cathepsin L was incubated with recombinant H3-HIS at both pH 5.5 and pH 7.4; after 2 hours, the reaction products were subjected to analysis by mass spectrometry. Both N-terminal (left) and C-terminal (right) fragments of the rH3 cleavage were detected; note the similarity to the pattern of in vivo cleavage shown in Figure 2B. (C) Recombinant Cathepsins B, K, and L were pre-activated and incubated with recombinant H3-HIS at both pH 5.5 and pH 7.4 for 15 minutes; the reactions were separated by SDS-PAGE and analyzed by immunoblotting.

Figure 6. Both RNAi and chemical inhibition of Cathepsin L reduce histone H3 cleavage in vivo

(A) Control and Ctsl RNAi cells lines were differentiated with RA as usual and harvested at the indicated time points; WCEs were then separated by SDS-PAGE and analyzed for both Cathepsin L expression (upper panel) and histone H3 cleavage (lower panel) by immunoblotting. (B) A serial two-fold dilution of samples from day 3 post-induction with RA were resolved by SDS-PAGE gel and analyzed by immunoblotting as in (A). (C) The addition of Cathepsin L Inhibitor I to the cell media of differentiating ESCs (left side) inhibits the processing of Cathepsin L itself (a) as well as that of histone H3 (b, c) as compared to DMSO alone treated control cells (right side). Loss of pluripotency marker Oct 3/4 was not affected (d) nor was the self-processing of another cathepsin family member, Cathepsin B (e).

Figure 7. Covalent histone modifications modulate Cathepsin L activity and its downstream effects

(A) rCathepsin L was incubated with each of four rH3 substrates: 1= rH3 unmodified, 2= rH3 alkylated to K27me2, 3= rH3 pan-acetylated with acetic anhydride, 4= rH3+K27me2 pan-acetylated with acetic anhydride. (B) H3 cleavage reactions were performed as in (A) using synthesized peptides that represent the H3 tail from amino acids 15 to 31. Reactions were incubated with ~250pmol peptide and quenched with 0.1% TFA before being plated in duplicate for ELISA with the H3cs.1 antibody. Signal was normalized to that of mock reactions for each peptide. Results represent the mean of three independent experiments ± SD. (C) Peptide pull-down assays were performed with the chromodomain of mouse CBX7 and the PHD finger of human BPTF. (D) Fluorescence anisotropy Cbx7-CD protein binding to non-cleaved peptide (18–37) vs. cleaved peptide (22–37); binding decreases 3 fold with cleaved peptide, p<0.01. K_ds are in µM±SEM. Data points represent the mean±SD.