A fluorescent assay for cryptic transcription in Saccharomyces cerevisiae reveals novel insights into factors that stabilize chromatin structure on newly replicated DNA

The disruption of chromatin structure can result in transcription initiation from cryptic promoters within gene bodies. While the passage of RNA polymerase II is a well-characterized chromatin-disrupting force, numerous factors, including histone chaperones, normally stabilize chromatin on transcribed genes, thereby repressing cryptic transcription. DNA replication, which employs a partially overlapping set of histone chaperones, is also inherently disruptive to chromatin, but a role for DNA replication in cryptic transcription has never been examined. In this study, we tested the hypothesis that, in the absence of chromatin-stabilizing factors, DNA replication can promote cryptic transcription in Saccharomyces cerevisiae. Using a novel fluorescent reporter assay, we show that multiple factors, including Asf1, CAF-1, Rtt106, Spt6, and FACT, block transcription from a cryptic promoter, but are entirely or partially dispensable in G1-arrested cells, suggesting a requirement for DNA replication in chromatin disruption. Collectively, these results demonstrate that transcription fidelity is dependent on numerous factors that function to assemble chromatin on nascent DNA.

43rd International Asilomar Chromatin, Chromosomes, and Epigenetics Conference

The 43rd Asilomar Chromatin, Chromosomes, and Epigenetics Conference was held in an entirely online format from December 9-11, 2021. The conference enabled presenters at various career stages to share promising new findings, and presentations covered modern chromatin research across an array of model systems. Topics ranged from the fundamental principles of nuclear organization and transcription regulation to key mechanisms underlying human disease. The meeting featured five keynote speakers from diverse backgrounds and was organized by: Juan Ausió, University of Victoria (British Columbia, Canada), James Davie, University of Manitoba (Manitoba, Canada), Philippe T. Georgel, Marshall University (West Virginia, USA), Michael Goldman, San Francisco State University (California, USA), LeAnn Howe, University of British Columbia (British Columbia, Canada), Jennifer A. Mitchell, University of Toronto (Ontario, Canada), and Sally G. Pasion, San Francisco State University (California, USA).

Pterostilbene leads to DNMT3B-mediated DNA methylation and silencing of OCT1-targeted oncogenes in breast cancer cells

Transcription factor (TF)-mediated regulation of genes is often disrupted during carcinogenesis. The DNA methylation state of TF-binding sites may dictate transcriptional activity of corresponding genes. Stilbenoid polyphenols, such as pterostilbene (PTS), have been shown to exert anticancer action by remodeling DNA methylation and gene expression. However, the mechanisms behind these effects still remain unclear. Here, the dynamics between oncogenic TF OCT1 binding and de novo DNA methyltransferase DNMT3B binding in PTS-treated MCF10CA1a invasive breast cancer cells has been explored. Using chromatin immunoprecipitation (ChIP) followed by next generation sequencing, we determined 47 gene regulatory regions with decreased OCT1 binding and enriched DNMT3B binding in response to PTS. Most of those genes were found to have oncogenic functions. We selected three candidates, PRKCA, TNNT2, and DANT2, for further mechanistic investigation taking into account PRKCA functional and regulatory connection with numerous cancer-driving processes and pathways, and some of the highest increase in DNMT3B occupancy within TNNT2 and DANT2 enhancers. PTS led to DNMT3B recruitment within PRKCA, TNNT2, and DANT2 at loci that also displayed reduced OCT1 binding. Substantial decrease in OCT1 with increased DNMT3B binding was accompanied by PRKCA promoter and TNNT2 and DANT2 enhancer hypermethylation, and gene silencing. Interestingly, DNA hypermethylation of the genes was not detected in response to PTS in DNMT3B-CRISPR knockout MCF10CA1a breast cancer cells. It indicates DNMT3B-dependent methylation of PRKCA, TNNT2, and DANT2 upon PTS. Our findings provide a better understanding of mechanistic players and their gene targets that possibly contribute to the anticancer action of stilbenoid polyphenols.

The Function and Evolution of Motile DNA Replication Systems in Ciliates

DNA replication is a ubiquitous and conserved cellular process. However, regulation of DNA replication is only understood in a small fraction of organisms that poorly represent the diversity of genetic systems in nature. Here we used computational and experimental approaches to examine the function and evolution of one such system, the replication band (RB) in spirotrich ciliates, which is a localized, motile hub that traverses the macronucleus while replicating DNA. We show that the RB can take unique forms in different species, from polar bands to a "replication envelope," where replication initiates at the nuclear periphery before advancing inward. Furthermore, we identify genes involved in cellular transport, including calcium transporters and cytoskeletal regulators, that are associated with the RB and may be involved in its function and translocation. These findings highlight the evolution and diversity of DNA replication systems and provide insights into the regulation of nuclear organization and processes.

Transcription Promotes the Interaction of the FAcilitates Chromatin Transactions (FACT) Complex with Nucleosomes in Saccharomyces cerevisiae

The FACT (FAcilitates Chromatin Transactions) complex is a conserved complex that maintains chromatin structure on transcriptionally active genes. Consistent with this, FACT is enriched on highly expressed genes, but how it is targeted to these regions is unknown. In vitro, FACT binds destabilized nucleosomes, supporting the hypothesis that FACT is targeted to transcribed chromatin through recognition of RNA polymerase (RNAP)-disrupted nucleosomes. In this study, we used high-resolution analysis of FACT occupancy in Saccharomyces cerevisiae to test this hypothesis. We demonstrate that FACT interacts with nucleosomes in vivo and that its interaction with chromatin is dependent on transcription by any of the three RNAPs. Deep sequencing of micrococcal nuclease-resistant fragments shows that FACT-bound nucleosomes exhibit differing nuclease sensitivity compared to bulk chromatin, consistent with a modified nucleosome structure being the preferred ligand for this complex. Interestingly, a subset of FACT-bound nucleosomes may be "overlapping dinucleosomes," in which one histone octamer invades the ∼147-bp territory normally occupied by the adjacent nucleosome. While the differing nuclease sensitivity of FACT-bound nucleosomes could also be explained by the demonstrated ability of FACT to alter nucleosome structure, transcription inhibition restores nuclease resistance, suggesting that it is not due to FACT interaction alone. Collectively, these results are consistent with a model in which FACT is targeted to transcribed genes through preferential interaction with RNAP-disrupted nucleosomes.

Polarization of the endoplasmic reticulum by ER-septin tethering

Polarization of the plasma membrane (PM) into domains is an important mechanism to compartmentalize cellular activities and to establish cell polarity. Polarization requires formation of diffusion barriers that prevent mixing of proteins between domains. Recent studies have uncovered that the endoplasmic reticulum (ER) of budding yeast and neurons is polarized by diffusion barriers, which in neurons controls glutamate signaling in dendritic spines. The molecular identity of these barriers is currently unknown. Here, we show that a direct interaction between the ER protein Scs2 and the septin Shs1 creates the ER diffusion barrier in yeast. Barrier formation requires Epo1, a novel ER-associated subunit of the polarisome that interacts with Scs2 and Shs1. ER-septin tethering polarizes the ER into separate mother and bud domains, one function of which is to position the spindle in the mother until M phase by confining the spindle capture protein Num1 to the mother ER.

Histone acetylation: where to go and how to get there

Transcriptionally active DNA is packaged with histones that are post-translationally acetylated on multiple lysines within their amino termini. While the majority of this acetylation is limited to the promoters of genes, acetylated histones are also found throughout transcribed units. Over the last decade we have uncovered many of the pathways involved in directing histone acetylation to active genes. This review will summarize much of this groundbreaking research as well as discuss some of the outcomes of this important protein post-translational modification.

Choroidal abnormalities in birdshot chorioretinopathy: an indocyanine green angiography study

Birdshot chorioretinopathy is a rare inflammatory disorder with an insidious onset that can slowly progress to severe visual loss. The pathogenesis is unknown. This study used indocyanine green (ICG) angiography to investigate the degree of choroidal vascular involvement with progression of disease and to determine the nature of the birdshot lesions. Seven patients with birdshot chorioretinopathy had ICG angiography performed with a scanning laser ophthalmoscope at various stages of clinical disease. Results were compared with fluorescein fundal angiography (FFA). All large choroidal vessels appeared normal. The birdshot lesions were demonstrated with ICG but not with FFA and were represented by dark areas on ICG angiography. Typically these areas were bordered by large or medium-sized choroidal vessels and their appearance suggested small choroidal vessel hypoperfusion. In disease of recent onset, some lesions masked fluorescence from large underlying choroidal vessels possibly due to inflammatory choroidal infiltrates. In long-standing disease, the choroidal angioarchitecture was relatively normal within the birdshot lesions. This study of birdshot chorioretinopathy demonstrates abnormalities in the small choroidal vessels within the birdshot lesions. ICG angiography detects the birdshot lesions more readily than FFA and may be of benefit in assessing disease activity.

Angiographic abnormalities of experimental autoimmune uveoretinitis

PURPOSE

Experimental autoimmune uveoretinitis (EAU) is an invaluable animal model for studying inflammatory eye disease in humans. Indocyanine green (ICG) is a fluorescent dye that can be used to image both retinal and choroidal vessels. This study was performed to examined the retinal and choroidal vascular abnormalities of a rat model of EAU using ICG and fluorescein as the contrast media to assess the suitability of this model for studying ICG angiographic abnormalities in inflammatory eye disease in humans.

METHODS

Twenty-six black-hooded Lister rats were inoculated with bovine retinal S-antigen plus adjuvant with or without Bordetella pertussis antigen. Fluorescein and ICG angiograms were performed at different stages of clinical disease with a scanning laser ophthalmoscope.

RESULTS

EAU was more severe and primarily choroidal disease in rats given Bordetella pertussis, but no animals showed evidence of dye leakage from large choroidal vessels. There was frank leakage of indocyanine green from retinal vessels. Leakage of both fluorescein and ICG retinal vessels largely correlated with disease activity. Retinal pigment epithelial lesions either corresponded to areas of hypofluorescence on the ICG angiogram alone or were represented by areas of ICG hyperfluorescence that had overlying areas of fluorescein leakage from retinal capillaries.

CONCLUSIONS

This study has demonstrated the vascular abnormalities of this model of EAU using ICG and fluorescein as the contrast media. The suitability of this method for studying ICG angiographic abnormalities in inflammatory eye disease in humans is encouraging.

Choroidal hypoperfusion in acute posterior multifocal placoid pigment epitheliopathy. An indocyanine green angiography study

BACKGROUND

The pathogenesis of acute posterior multifocal placoid pigment epitheliopathy remains obscure. The placoid lesions and characteristic findings on fluorescein angiography have been interpreted as representing either primary disease of the retinal pigment epithelium or disease of the choroidal vasculature. This study used indocyanine green (ICG) choroidal videoangiography to investigate this controversy.

METHODS

Sequential choroidal videoangiography was performed with ICG and a scanning laser ophthalmoscope on patients with acute posterior multifocal placoid pigment epitheliopathy. Image analysis was used to differentiate between masking and ischemia as to the cause of hypofluorescence on the angiograms.

RESULTS

Indocyanine green angiograms of acute posterior multifocal placoid pigment epitheliopathy showed areas of hypofluorescence in both the early and late pictures that correlated with the placoid lesions. Image analysis identified these as areas of choroidal hypoperfusion. Successive films showed partial or complete resolution of these hypofluorescent areas.

CONCLUSIONS

Indocyanine green choroidal videoangiography has shown choroidal hypoperfusion to underlie the pathogenesis of acute posterior multifocal placoid pigment epitheliopathy.

The efficacy of systemic corticosteroids in sight-threatening retinal vasculitis

This study was undertaken to assess the efficacy of a standard regime of high-dose systemic oral corticosteroids in the management of retinal vasculitis. The study was performed because the single most common reason for referral to our specialist clinic is the apparent failure of patients to respond to a course of systemic steroids, which in most cases appeared to be due to an inadequate initial dose. A retrospective study of 29 patients (30 treatment episodes) with sight-threatening retinal vasculitis managed initially with high-dose systemic steroids was evaluated 1 year after treatment. Patients included in the study all started treatment with > or = 1 mg/kg prednisolone and remained on a high steroid dose (> or = 40 mg prednisolone) for at least 5 weeks. No patient was on any other immunosuppressive agent at the start of the study. Therapeutic success for this regime, as judged by improvement in visual acuity, was 60%, improving to 77% with addition of other immunosuppressive agents. Eight patients required additional immunosuppressives. Although documented side-effects of steroids were common (50% of cases managed on steroids alone), in only 5 patients were they therapeutically important. Twelve of the 22 patients managed on high-dose steroids alone were off treatment at 12 months. There was no correlation at any stage between visual acuity, activity index or relapses and the final visual outcome at 12 months. Seven cases had a poor visual outcome and the causes for this included relapse in the twelfth month of follow-up, persistent cystoid macular oedema and lens opacity.(ABSTRACT TRUNCATED AT 250 WORDS)