The Chromatin Reader ZMYND8 Regulates Igh Enhancers to Promote Immunoglobulin Class Switch Recombination

Class switch recombination (CSR) is a DNA recombination reaction that diversifies the effector component of antibody responses. CSR is initiated by activation-induced cytidine deaminase (AID), which targets transcriptionally active immunoglobulin heavy chain (Igh) switch donor and acceptor DNA. The 3′ Igh super-enhancer, 3′ regulatory region (3′RR), is essential for acceptor region transcription, but how this function is regulated is unknown. Here, we identify the chromatin reader ZMYND8 as an essential regulator of the 3′RR. In B cells, ZMYND8 binds promoters and super-enhancers, including the Igh enhancers. ZMYND8 controls the 3′RR activity by modulating the enhancer transcriptional status. In its absence, there is increased 3′RR polymerase loading and decreased acceptor region transcription and CSR. In addition to CSR, ZMYND8 deficiency impairs somatic hypermutation (SHM) of Igh, which is also dependent on the 3′RR. Thus, ZMYND8 controls Igh diversification in mature B lymphocytes by regulating the activity of the 3′ Igh super-enhancer.

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ZMYND8 is required for GLT of acceptor S regions and Class Switch Recombination

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ZMYND8 supports efficient somatic hypermutation of the Igh variable regions

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ZMYND8 binds B cell super-enhancers, including the 3′ Igh enhancer

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ZMYND8 modulates the transcriptional status and activity of the 3′ Igh enhancer

A pipeline for determining protein-protein interactions and proximities in the cellular milieu

It remains extraordinarily challenging to elucidate endogenous protein-protein interactions and proximities within the cellular milieu. The dynamic nature and the large range of affinities of these interactions augment the difficulty of this undertaking. Among the most useful tools for extracting such information are those based on affinity capture of target bait proteins in combination with mass spectrometric readout of the co-isolated species. Although highly enabling, the utility of affinity-based methods is generally limited by difficulties in distinguishing specific from nonspecific interactors, preserving and isolating all unique interactions including those that are weak, transient, or rapidly exchanging, and differentiating proximal interactions from those that are more distal. Here, we have devised and optimized a set of methods to address these challenges. The resulting pipeline involves flash-freezing cells in liquid nitrogen to preserve the cellular environment at the moment of freezing; cryomilling to fracture the frozen cells into intact micron chunks to allow for rapid access of a chemical reagent and to stabilize the intact endogenous subcellular assemblies and interactors upon thawing; and utilizing the high reactivity of glutaraldehyde to achieve sufficiently rapid stabilization at low temperatures to preserve native cellular interactions. In the course of this work, we determined that relatively low molar ratios of glutaraldehyde to reactive amines within the cellular milieu were sufficient to preserve even labile and transient interactions. This mild treatment enables efficient and rapid affinity capture of the protein assemblies of interest under nondenaturing conditions, followed by bottom-up MS to identify and quantify the protein constituents. For convenience, we have termed this approach Stabilized Affinity Capture Mass Spectrometry. Here, we demonstrate that Stabilized Affinity Capture Mass Spectrometry allows us to stabilize and elucidate local, distant, and transient protein interactions within complex cellular milieux, many of which are not observed in the absence of chemical stabilization.

Ferrocenylbutadiyne

The title compound, [Fe(C₅H₅)(C₉H₅)], crystallizes in a form of a π–π-stacked assembly formed as a result of strong inter­molecular π–π inter­actions between (a) the triple bonds of two neighboring butadiyne substituents overlapping in a ‘head-to-tail’ fashion [characterized by C⋯C short contacts of 3.622 (5), 3.567 (6) and 3.556 (6) Å] and (b) the triple bonds of the butadiyne substituent and substituted cyclo­pendadiene ring of neighboring mol­ecules [C⋯C = 3.474 (5) and 3.492 (6) Å]. The linear butadiyne substituent has alternating C—C triple and single bonds, while the unsubstituted cyclo­penta­diene ring is slightly positionally disordered (although the structure reported here was solved as non-disordered) and retains a close to eclipsed conformation.

Mixed-valence states formation in conformationally flexible metal-free 5,10,15,20-tetraferrocenylporphyrin and 5,10-bisferrocenyl-15,20-bisphenylporphyrin

Metal-free 5,10,15,20-tetraferrocenylporphyrin and 5,10-bisferrocenyl-15,20-bisphenylporphyrin have been prepared and characterized by UV-Vis, MCD, (1)H, (13)C, and variable-temperature NMR, APCI- and ESI-MS, and Mössbauer spectroscopy, while their redox properties were investigated using electrochemical (cyclic voltammetry and differential pulse voltammetry), spectroelectrochemical, and chemical oxidation approaches. The electronic structure calculations at Density Functional Theory level reveal that both compounds adopt saddle conformations and the HOMOs in both complexes are predominantly metal-centered, while the LUMOs predominantly consist of porphyrin pi* orbitals. In spite of the rotational freedom of ferrocenyl substituents at room temperature, both metal-free 5,10,15,20-tetraferrocenylporphyrin and 5,10-bisferrocenyl-15,20-bisphenylporphyrin are able to form mixed-valence states upon the successive ferrocene-based two- and one-electron oxidations, respectively, as confirmed by UV-Vis, MCD, Mössbauer, electro-, and spectroelectrochemical methods, and thus, the earlier suggested (Boyd et al. Chem. Commun., 1999, 637) requirements for the formation of mixed-valence states in ferrocene-containing porphyrins should be revised.