Demethylase-independent roles of LSD1 in regulating enhancers and cell fate transition

The major enhancer regulator lysine-specific histone demethylase 1A (LSD1) is required for mammalian embryogenesis and is implicated in human congenital diseases and multiple types of cancer; however, the underlying mechanisms remain enigmatic. Here, we dissect the role of LSD1 and its demethylase activity in gene regulation and cell fate transition. Surprisingly, the catalytic inactivation of LSD1 has a mild impact on gene expression and cellular differentiation whereas the loss of LSD1 protein de-represses enhancers globally and impairs cell fate transition. LSD1 deletion increases H3K27ac levels and P300 occupancy at LSD1-targeted enhancers. The gain of H3K27ac catalyzed by P300/CBP, not the loss of CoREST complex components from chromatin, contributes to the transcription de-repression of LSD1 targets and differentiation defects caused by LSD1 loss. Together, our study demonstrates a demethylase-independent role of LSD1 in regulating enhancers and cell fate transition, providing insight into treating diseases driven by LSD1 mutations and misregulation.

nature portfolio | reporting summary April 2023 Antibodies Antibodies used
Specificity for use of primary antibodies in Western blotting, ChIP-Rx, and immunofluorescence were either validated as described in the websites of vendors, in the previous literatures that were indicated in the manuscript, or in the current manuscript.
Anti-LSD1 antibody (Abcam ab17721) was validated by the vendor in Western blotting Western blotting, immunocytochemistry, and immunofluorescence. (https://www.abcam.com/products/primary-antibodies/kdm1lsd1-antibody-nuclear-marker-ab17721.html). We have previously validated this antibody in Western blotting and ChIP-seq in (Cao et al., 2018. Sci. Adv.). It was validated again in the current manuscript in Fig. 1 for Western blotting and in Fig. 2 for ChIP-seq.

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V6.5 ESC line is a gift from Rudolf Jaenisch lab. HEK293T cells were purchased from ATCC (https://www.atcc.org/products/ crl-3216) V6.5 ESCs was authenticated genetically by the Jaenisch lab and we indirectly verified their identity by their morphology, growth behavior, and transcriptomic profiles. HEK293T cells were autheticated by ATCC and we indirectly verified their identity by the morphology and growth behavior of the cells. All genetically modified cell lines were validated by PCR, Sanger sequencing, Western blotting, and next generation sequencing.
All cell lines were tested for mycoplasma contamination before the experiments. None of these cell lines are contaminated by mycoplasma.
No commonly misidentified lines was used.
Report on the source of all seed stocks or other plant material used. If applicable, state the seed stock centre and catalogue number. If plant specimens were collected from the field, describe the collection location, date and sampling procedures.
Describe the methods by which all novel plant genotypes were produced. This includes those generated by transgenic approaches, gene editing, chemical/radiation-based mutagenesis and hybridization. For transgenic lines, describe the transformation method, the number of independent lines analyzed and the generation upon which experiments were performed. For gene-edited lines, describe the editor used, the endogenous sequence targeted for editing, the targeting guide RNA sequence (if applicable) and how the editor was applied.
Describe any authentication procedures for each seed stock used or novel genotype generated. Describe any experiments used to assess the effect of a mutation and, where applicable, how potential secondary effects (e.g. second site T-DNA insertions, mosiacism, off-target gene editing) were examined.