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Singer, R. H.

Publications and source records attributed to Singer, R. H..

5 recordsLinked to original sources

Re-targeting of macroH2A following mitosis to cytogenetic-scale heterochromatic domains

The heritability of chromatin states through cell division is a potential contributor to the epigenetic maintenance of cellular memory of prior states. The macroH2A histone variant has properties of a regulator of epigenetic cell memory, including roles controlling gene silencing and cell differentiation. Its mechanisms of regional genomic targeting and maintenance through cell division are unknown. Here we combined in vivo imaging with biochemical and genomic approaches to show that human macroH2A is incorporated into chromatin in the G1 phase of the cell cycle following DNA replication. The newly-incorporated macroH2A re-targets the same, large heterochromatic domains where macroH2A was already enriched in the previous cell cycle. It remains heterotypic, targeting individual nucleosomes that do not already contain a macroH2A molecule. The pattern observed resembles that of new deposition of centromeric histone variants during the cell cycle, indicating mechanistic similarities for macrodomain-scale regulation of epigenetic properties of the cell.

biochemistry

PBAF’s genomic binding dynamics are regulated via bromodomain-acetyl-lysine interactions and select chromatin states

Transcriptional bursting involves genes rapidly switching between active and inactive states. Chromatin remodelers actively target arrays of acetylated nucleosomes at select enhancers and promoters to facilitate or shut down the repeated recruitment of RNA Pol II during transcriptional bursting. It is unknown how acetylated chromatin is dynamically targeted and regulated by chromatin remodelers such as PBAF. Thus, we sought to understand how PBAF targets acetylated chromatin using live-cell single molecule fluorescence microscopy. Our work reveals chromatin hubs throughout the nucleus where PBAF rapidly cycles on and off the genome. Deletion of PBAFs bromodomains impairs targeting, stable engagement and persistent binding on chromatin in hubs. Interestingly, PBAF has a higher probability to stably engage chromatin inside hubs indicating that hubs contain a unique nucleosomal scaffold compared to global chromatin. Dual color imaging of PBAF in hubs near H3.3 or HP1 reveals that PBAF targets both euchromatic and heterochromatic regions with distinct genome binding kinetics that mimic chromatin stability. Removal of PBAFs bromodomains stabilizes H3.3 and HP1 binding within chromatin indicating that bromodomains may play a direct role in remodeling of the nucleosome. Our data, suggests that PBAF differentially and dynamically engages a variety of chromatin structures involved in both activation and repression of transcription via bromodomains. Furthermore, PBAFs binding stability on chromatin may reflect the chromatin remodeling potential of different bound chromatin states. Statement of SignificanceTranscriptional bursting involves a gene rapidly switching between transcriptionally active and inactive states. To regulate transcriptional bursting, chromatin must interchange between euchromatin and heterochromatin to permit or restrict access of transcription factors including RNA Polymerase II to enhancer and gene promoters. However, little is known regarding how chromatin remodelers dynamically read a rapidly changing 4D epigenome. We used live-cell single molecule imaging to characterize the spatiotemporal chromatin binding dynamics of PBAF, a chromatin remodeler that accesses both euchromatin and heterochromatin to regulate transcription. PBAF cycles on and off chromatin hubs in select nuclear regions where it distinctly engages euchromatin and heterochromatin via bromodomains in its BAF180 subunit. Our study provides the framework to understand how the 4D epigenome is regulated.

cell biology

Intercellular mRNA Trafficking Via Membrane Nanotubes In Mammalian Cells

RNAs have been shown to undergo transfer between mammalian cells, though the mechanism behind this phenomenon and its overall importance to cell physiology is not well understood. Numerous publications have suggested that RNAs (microRNAs and incomplete mRNAs) undergo transfer via extracellular vesicles (e.g. exosomes). However, in contrast to a diffusion-based transfer mechanism, we find that full-length mRNAs undergo direct cell-cell transfer via cytoplasmic extensions, called membrane nanotubes (mNTs), which connect donor and acceptor cells. By employing a simple co-culture experimental model and using single-molecule imaging, we provide quantitative data showing that mRNAs are transferred between cells in contact. Examples of mRNAs that undergo transfer include those encoding GFP, mouse {beta}-actin, and human Cyclin D1, BRCA1, MT2A, and HER2. We show that intercellular mRNA transfer occurs in all co-culture models tested (e.g. between primary cells, immortalized cells, and in co-cultures of immortalized human and murine cells). Rapid mRNA transfer is dependent upon actin, but independent of de novo protein synthesis, and is modulated by stress conditions and gene expression levels. Hence, this work supports the hypothesis that full-length mRNAs undergo transfer between cells through a refined structural connection. Importantly, unlike the transfer of miRNA or RNA fragments, this process of communication transfers genetic information that could potentially alter the acceptor cell proteome. This phenomenon may prove important for the proper development and functioning of tissues, as well as host-parasite or symbiotic interactions.\n\nSignificanceMessenger RNA (mRNA) molecules convey genetic information within cells, beginning from genes in the nucleus to ribosomes in the cell body, where they are translated into proteins. Here, we show a novel mode of transferring genetic information from one cell to another. Contrary to previous publications suggesting that mRNAs transfer via extracellular vesicles, we provide visual and quantitative data showing that mRNAs transfer via membrane nanotubes and direct cell-to-cell contact. We predict that this process has a major role in regulating local cellular environments with respect to tissue development and maintenance, cellular responses to stress, interactions with parasites, tissue transplants, and the tumor microenvironment.\n\nAuthor contributionsG.H., A.R. and R.H.S. conceived the research and designed the experiments; C.M.E. performed and analyzed the experiments with WM983b+/-GFP, including transwell and exosomes; M.C.D. and E.E. performed and analyzed the WM983b/NIH393 co-culture experiments; G.H. performed and analyzed all other experiments; and G.H., J.E.G, A.R. and R.H.S. wrote the paper.

cell biology

Nuclear Microenvironments Modulate Transcription From Low-Affinity Enhancers

Transcription factors regulate gene expression by binding to DNA for short durations and by often binding to low-affinity DNA sequences. It is not clear how such temporally brief, low-affinity interactions can drive efficient transcription. Here we report that the transcription factor Ultrabithorax (Ubx) functionally utilizes low-affinity binding sites in the Drosophila melanogaster shavenbaby (svb) locus in nuclear microenvironments of relatively high Ubx concentration. By manipulating the affinity of svb enhancers, we revealed an inverse relationship between enhancer affinity and Ubx concentration required for transcriptional activation. A Ubx cofactor, Homothorax (Hth), was enriched together with Ubx near enhancers that require Hth, even though Ubx and Hth did not co-localize throughout the nucleus. These results suggest that low affinity sites overcome their kinetic inefficiency by utilizing microenvironments with high concentrations of transcription factors and cofactors. Mechanisms that generate these microenvironments are likely to be a general feature of eukaryotic transcriptional regulation.

cell biology

Quantitative mRNA Imaging Throughout the Entire Drosophila Brain

We describe a fluorescence in situ hybridization method that permits detection of the localization and abundance of single mRNAs (smFISH) in cleared whole-mount adult Drosophila brains. The approach is rapid, multiplexable and does not require molecular amplification; it allows facile mRNA expression quantification with subcellular resolution on a standard confocal microscope. Using a custom Bessel Beam-Structured Illumination microscope (BB-SIM), we further demonstrate single-mRNA detection across the entire brain sample.

neuroscience