Extranucleosomal DNA enhances the activity of the LSD1/CoREST histone demethylase complex

Kim, Sang Ah; Chatterjee, Nilanjana; Jennings, Matthew J.; Bartholomew, Blaine; Tan, Song

doi:10.1093/nar/gkv388

Cited by 39 publications

(46 citation statements)

References 37 publications

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“…LSD2 lacks this tower domain, does not complex with CoREST, and has distinct biological roles (Fang et al, 2012). Recent biochemical and structural studies on the LSD1/CoREST heterodimer suggest the multilayer interactions of the demethylase with its native nucleosome substrate that include an interaction between one section of the SANT2 domain and nucleosomal DNA (Kim, Chatterjee, Jennings, Bartholomew, & Tan, 2015; Pilotto et al, 2015). Using purified LSD1, it is established that a minimum of about 20 residues of the histone H3 tail are necessary for efficient LSD1-catalyzed demethylation (Forneris, Binda, Antonietta Vanoni, Battaglioli, & Mattevi, 2005; Forneris et al, 2006).…”

Section: Introductionmentioning

confidence: 99%

LSD1 Histone Demethylase Assays and Inhibition

Hayward¹,

Cole²

2016

Methods in Enzymology

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The lysine-specific demethylase (LSD1) is a flavin-dependent amine oxidase that selectively removes one or two methyl groups from histone H3 at the Lys4 position. Along with histone deacetylases 1 and 2, LSD1 is involved in epigenetically silencing gene expression. LSD1 has been implicated as a potential therapeutic target in cancer and other diseases. In this chapter, we discuss several approaches to measure LSD1 demethylase activity and their relative strengths and limitations for inhibitor discovery and mechanistic characterization. In addition, we review the principal established chemical functional groups derived from monoamine oxidase inhibitors that have been investigated in the context of LSD1 as demethylase inhibitors. Finally, we highlight a few examples of recently developed LSD1 mechanism-based inactivators and their biomedical applications.

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Section: Introductionmentioning

confidence: 99%

LSD1 Histone Demethylase Assays and Inhibition

Hayward¹,

Cole²

2016

Methods in Enzymology

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“…Linker DNA can be recognized by the DNA binding regions mostly in a DNA-sequence-independent manner. In many cases, linker DNA interaction is essential for chromatin binding such as for the histone deacetylase Rpd3S and the Lsd1/CoREST demethylase complexes (11,12). (iv) The spacing between nucleosomes contributes.…”

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confidence: 99%

Homodimeric PHD Domain-containing Rco1 Subunit Constitutes a Critical Interaction Hub within the Rpd3S Histone Deacetylase Complex

Ruan

Cui

Lee

et al. 2016

Journal of Biological Chemistry

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Recognition of histone post-translational modifications is pivotal for directing chromatin-modifying enzymes to specific genomic regions and regulating their activities. Emerging evidence suggests that other structural features of nucleosomes also contribute to precise targeting of downstream chromatin complexes, such as linker DNA, the histone globular domain, and nucleosome spacing. However, how chromatin complexes coordinate individual interactions to achieve high affinity and specificity remains unclear. The Rpd3S histone deacetylase utilizes the chromodomain-containing Eaf3 subunit and the PHD domain-containing Rco1 subunit to recognize nucleosomes that are methylated at lysine 36 of histone H3 (H3K36me). We showed previously that the binding of Eaf3 to H3K36me can be allosterically activated by Rco1. To investigate how this chromatin recognition module is regulated in the context of the Rpd3S complex, we first determined the subunit interaction network of Rpd3S. Interestingly, we found that Rpd3S contains two copies of the essential subunit Rco1, and both copies of Rco1 are required for full functionality of Rpd3S. Our functional dissection of Rco1 revealed that besides its known chromatin-recognition interfaces, other regions of Rco1 are also critical for Rpd3S to recognize its nucleosomal substrates and function in vivo. This unexpected result uncovered an important and understudied aspect of chromatin recognition. It suggests that precisely reading modified chromatin may not only need the combined actions of reader domains but also require an internal signaling circuit that coordinates the individual actions in a productive way.It is now widely accepted that histone post-translational modifications (PTMs) 2 and other structural features of chromatin, such as variant histones and DNA modifications, mainly serve as signal platforms to direct downstream regulatory events (1, 2). In general, four major components of chromatin structure contribute to the signals that can be interpreted by downstream chromatin regulators. (i) Histone peptides that carry certain PTMs contribute. Specifically modified histone peptides can be recognized by protein domains/motifs that are commonly referred as PTM "readers." A large repertoire of such domain/PTM interactions have been documented, and they are essential for targeting downstream factors to a given genomic locus (3). Reader domains not only distinguish different types of modifications and the locations of PTMs but also the specific states of modifications. However, due to relatively weak affinity, it is unclear whether these interactions are sufficient to mediate the recruitment of chromatin complexes. For example, although histone H3 methylation at residue Lys-36 (H3K36me) is an essential signal for the histone deacetylase Rpd3S, the contact between the chromodomain of the Eaf3 subunit (CHD Eaf3 ) of Rpd3S and H3K366me only contributes to the binding specificity but not to the overall affinity (4). (ii) Histone globular domains contribute. Because PTMs are mostly cl...

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“…This result supports the idea that KDM1A catalytic activity is modular in nature, as it often exists as a member of multiprotein complexes that dictate function. 19 We should note that KDM1A catalytic efficiency and substrate specificity might be further altered if chromatin or nucleosomes are utilized as substrates. 22 In fact, Tan and co-workers recently illustrated that the KDM1A/CoREST-C complex has a >25-fold increase in catalytic efficiency when site-specifically methylated nucleosomes with extranucleosomal DNA are used as substrates, a phenomenon driven by K m app .…”

Section: Discussionmentioning

confidence: 99%

“…22 In fact, Tan and co-workers recently illustrated that the KDM1A/CoREST-C complex has a >25-fold increase in catalytic efficiency when site-specifically methylated nucleosomes with extranucleosomal DNA are used as substrates, a phenomenon driven by K m app . 19 Despite this evidence, there appears to be further confounding aspects to the regulation of KDM1A activity. For example, CoREST paralogs (CoREST2/RCOR2 and CoREST3/RCOR3) were recently shown to alter KDM1A activity toward nucleosomal substrates as assessed by their DNA binding ability and also affected catalytic efficiency toward peptide substrates.…”

Section: Discussionmentioning

confidence: 99%

“…12–15 Interestingly, CoREST endows KDM1A with the ability to demethylate nucleosomal substrates as a noncatalytic domain donor with DNA binding ability bridging the gap between KDM1A and its substrates. 15–19 On the other hand, the SWIRM domain of KDM1A, which is found in multiple chromatin-associated proteins, 20 is a bundle of α -helices with a central helix that is joined by two smaller helix–turn–helix motifs (Figure 1B). 11 Moreover, consistent with other flavin-dependent oxidoreductases, the AOD of KDM1A houses a noncovalently bound flavin adenine dinucleotide (FAD) cofactor and can be further subdivided into an expanded Rossman fold for cofactor binding and the substrate-binding lobe (Figure 1B).…”

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confidence: 99%

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Lysine-Specific Demethylase 1A (KDM1A/LSD1): Product Recognition and Kinetic Analysis of Full-Length Histones

et al. 2016

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Lysine-specific demethylase 1A (KDM1A/LSD1) is a FAD-dependent enzyme that catalyzes the oxidative demethylation of histone H3K4me1/2 and H3K9me1/2 repressing and activating transcription, respectively. Although the active site is expanded compared to that of members of the greater amine oxidase superfamily, it is too sterically restricted to encompass the minimal 21-mer peptide substrate footprint. The remainder of the substrate/product is therefore expected to extend along the surface of KDM1A. We show that full-length histone H3, which lacks any posttranslational modifications, is a tight-binding, competitive inhibitor of KDM1A demethylation activity with a Ki of 18.9 ± 1.2 nM, a value that is approximately 100-fold higher than that of the 21-mer peptide product. The relative H3 affinity is independent of preincubation time, suggesting that H3 rapidly reaches equilibrium with KDM1A. Jump dilution experiments confirmed the increased binding affinity of full-length H3 was at least partially due to a slow off rate (koff) of 1.2 × 10−3 s−1, corresponding to a half-life (t1/2) of 9.63 min, and a residence time (τ) of 13.9 min. Independent affinity capture surface plasmon resonance experiments confirmed the tight-binding nature of the H3/KDM1A interaction, revealing a Kd of 9.02 ± 2.3 nM, a kon of (9.3 ± 1.5) × 104 M−1 s−1, and a koff of (8.4 ± 0.3) × 10−4 s−1. Additionally, no other core histones exhibited inhibition of KDM1A demethylation activity, which is consistent with H3 being the preferred histone substrate of KDM1A versus H2A, H2B, and H4. Together, these data suggest that KDM1A likely contains a histone H3 secondary specificity element on the enzyme surface that contributes significantly to its recognition of substrates and products.

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Extranucleosomal DNA enhances the activity of the LSD1/CoREST histone demethylase complex

Cited by 39 publications

References 37 publications

LSD1 Histone Demethylase Assays and Inhibition

LSD1 Histone Demethylase Assays and Inhibition

Homodimeric PHD Domain-containing Rco1 Subunit Constitutes a Critical Interaction Hub within the Rpd3S Histone Deacetylase Complex

Lysine-Specific Demethylase 1A (KDM1A/LSD1): Product Recognition and Kinetic Analysis of Full-Length Histones

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