chromatin-accessibility-profiling-whole-caenorhabditis-elegans-l4

Chromatin Accessibility Profiling in Whole <em>Caenorhabditis elegans</em> L4 Larvae

Chromatin accessibility plays essential roles in transcription, DNA repair, and chromosome segregation. Hyper-accessible regions usually correlate with ...

Universidad Nacional Autónoma de México (UNAM)

Cholesterol is an essential compound in mammalian cells because it is involved in a wide range of functions, including as a key component of membranes, precursor of important molecules such as hormones, bile acids and vitamin D. The cholesterol transport across the circulatory system is a well-known process in contrast to the intracellular cholesterol transport, which is poorly understood. Recently in our laboratory, we identified a novel protein in C. elegans involved in dietary cholesterol uptake, which we have named ChUP-1. Insillicoanalysis identified two putative orthologue candidate proteins in mammals. The proteins SIDT1 and SIDT2 share identity and conserved cholesterol binding (CRAC) domains with C. elegans ChUP-1. Both mammalian proteins are annotated as RNA transporters in databases. In the present study, we show evidence indicating that SIDT1 and SIDT2 not only do not transport RNA, but they are involved in cholesterol transport. Furthermore, we show that single point mutations directed to disrupt the CRAC domains of both proteins prevent FRET between SIDT1 and SIDT2 and the cholesterol analogue dehydroergosterol (DHE) and alter cholesterol transport.

A novel family of mammalian transmembrane proteins involved in cholesterol transport.

Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is a method designed to detect interactions between chromatin and the proteins bound to it. This method has been widely used for characterizing epigenetic landscapes in many cell types; however, a limiting factor has been the requirement of a high number of cells. Here, we describe a protocol for ChIP in epidermal cells from a newborn mouse, purified by fluorescence-activated cell sorting (FACS). This protocol has been optimized specifically for prefixed, low cell numbers, resulting in enough immunoprecipitated DNA suitable for genome-wide analysis.

Chromatin Immunoprecipitation of Low Number of FACS-Purified Epidermal Cells.

SARS-CoV-2 is the causal agent of COVID-19 disease. Currently, infection with SARS-CoV-2 has been the cause of death of over 2.5 million people globally, and there is still no effective curative treatment. Clinically, the severe symptoms caused by COVID-19, in addition to pneumonia, are associated with the development of hyperinflammatory syndrome and thrombosis. It is urgent to expand our understanding of the molecular mechanisms involved in the pathophysiology of COVID-19. This article discusses the potential role that the chemokine CX3CL1 could have in the development of COVID-19-associated thrombosis. CX3CL1 is abundantly expressed by activated endothelium and is an important regulator of many aspects of endothelial function and dysfunction, including thrombosis. The generation of hypotheses about molecules that could be relevant in well-defined aspects of the pathophysiology of COVID-19 encourages the development of basic and clinical studies, that could help find effective and much needed treatments.

Could SARS-CoV-2 blocking of ACE2 in endothelial cells result in upregulation of CX3CL1, promoting thrombosis in COVID-19 patients?

Massive testing is a cornerstone in efforts to effectively track infections and stop COVID-19 transmission, including places with good vaccination coverage. However, SARS-CoV-2 testing by RT-qPCR requires specialized personnel, protection equipment, commercial kits, and dedicated facilities, which represent significant challenges for massive testing in resource-limited settings. It is therefore important to develop testing protocols that are inexpensive, fast, and sufficiently sensitive. Here, we optimized the composition of a buffer (PKTP), containing a protease, a detergent, and an RNase inhibitor, which is compatible with the RT-qPCR chemistry, allowing for direct SARS-CoV-2 detection from saliva without extracting RNA. PKTP is compatible with heat inactivation, reducing the biohazard risk of handling samples. We assessed the PKTP buffer performance in comparison to the RNA-extraction-based protocol of the US Centers for Disease Control and Prevention in saliva samples from 70 COVID-19 patients finding a good sensitivity (85.7% for the N1 and 87.1% for the N2 target) and correlations (R = 0.77, p < 0.001 for N1, and R = 0.78, p < 0.001 for N2). We also propose an auto-collection protocol for saliva samples and a multiplex reaction to minimize the PCR reaction number per patient and further reduce costs and processing time of several samples, while maintaining diagnostic standards in favor of massive testing.

Development and Testing of a Low-Cost Inactivation Buffer That Allows for Direct SARS-CoV-2 Detection in Saliva.

Diabetes complications such as nephropathy, retinopathy, or cardiovascular disease arise from vascular dysfunction. In this context, it has been observed that past hyperglycemic events can induce long-lasting alterations, a phenomenon termed "metabolic memory." In this study, we evaluated the genome-wide gene expression and chromatin accessibility alterations caused by transient high-glucose exposure in human endothelial cells (ECs) in vitro. We found that cells exposed to high glucose exhibited substantial gene expression changes in pathways known to be impaired in diabetes, many of which persist after glucose normalization. Chromatin accessibility analysis also revealed that transient hyperglycemia induces persistent alterations, mainly in non-promoter regions identified as enhancers with neighboring genes showing lasting alterations. Notably, activation of the NRF2 pathway through NRF2 overexpression or supplementation with the plant-derived compound sulforaphane, effectively reverses the glucose-induced transcriptional and chromatin accessibility memories in ECs. These findings underscore the enduring impact of transient hyperglycemia on ECs' transcriptomic and chromatin accessibility profiles, emphasizing the potential utility of pharmacological NRF2 pathway activation in mitigating and reversing the high-glucose-induced transcriptional and epigenetic alterations.

Reversal of high-glucose-induced transcriptional and epigenetic memories through NRF2 pathway activation.

Cadmium (Cd) is a heavy metal that is highly toxic to humans and animals. Its adverse effects have been widely associated with mitochondrial alterations. However, there are not many treatments that target mitochondria. This study aimed to evaluate the impact of sulforaphane (SFN) pre-exposure against cadmium chloride (CdCl)-induced toxicity and mitochondrial alterations in the nematode  (), by exploring the role of the insulin/insulin-like growth factor signaling pathway (IIS). The results revealed that prior exposure to SFN protected against CdCl-induced mortality and increased lifespan, body length, and mobility while reducing lipofuscin levels. Furthermore, SFN prevented mitochondrial alterations by increasing mitochondrial membrane potential (Δψm) and restoring mitochondrial oxygen consumption rate, thereby decreasing mitochondrial reactive oxygen species (ROS) production. The improvement in mitochondrial function was associated with increased mitochondrial mass and the involvement of the  and  genes of the IIS signaling pathway. In conclusion, exposure to SFN before exposure to CdCl mitigates toxic effects and mitochondrial alterations, possibly by increasing mitochondrial mass, which may be related to the regulation of the IIS pathway. These discoveries open new possibilities for developing therapies to reduce the damage caused by Cd toxicity and oxidative stress in biological systems, highlighting antioxidants with mitochondrial action as promising tools.

Sulforaphane Exposure Prevents Cadmium-Induced Toxicity and Mitochondrial Dysfunction in the Nematode  by Regulating the Insulin/Insulin-like Growth Factor Signaling (IIS) Pathway.

Despite its economic and population status, Mexico's scientific output remains under 1% of global production because of low spending on science. Yet, additional challenges, including over-reliance on expensive imported technology, brain drain, and limited private sector investment, further hinder its progress. Nonetheless, significant opportunities exist, such as fostering local biotechnology, enhancing policy continuity, and leveraging new leadership to boost scientific growth. Although focused on Mexico, these insights hold relevance for the broader region of Latin America, a region that shares vast untapped scientific potential.

Science in Mexico: a rising force amid adversity.

Polycomb domains safeguard cell identity by maintaining lineage-specific chromatin states enriched in repressive histone modifications, preserving the epigenetic memory of cell lineages. While Polycomb Repressive Complex 2 (PRC2) can re-establish its occupancy after perturbation, the mechanisms that guide  Polycomb recruitment remain unclear. To address this, we engineered an auxin-inducible degradation system to reversibly deplete and reintroduce the endogenous PRC2 core subunit Suz12 in mouse embryonic stem cells (mESCs). Genome-wide profiling at an early recovery time point revealed ~1,100 PRC2 nucleation sites, characterized by rapid Suz12 and histone H3K27me3 re-accumulation with strong signal, with minimal impact on gene expression. These sites were significantly enriched at bivalent promoters, coinciding with unmethylated CpG islands and chromatin states associated with developmental regulation, and were largely conserved in differentiated cells. Motif analysis identified G/C-rich DNA sequences associated with E2F and zinc-finger proteins, alongside strong co-occupancy with MTF2 and JARID2, two PRC2 cofactors previously implicated in Polycomb targeting. Notably, a subset of nucleation sites overlapped with long-range chromatin interaction anchors in histone H3K27me3 HiChIP datasets. These findings reveal that PRC2  nucleation sites are associated with a combination of chromatin states, DNA sequence features, cofactor co-occupancy and spatial genome organization, suggesting that epigenetic memory can be re-established through defined genomic and chromatin features.

Article	Year
A novel family of mammalian transmembrane proteins involved in cholesterol transport. Scientific reports\| PubMed ID: 28785058	2017
Chromatin Immunoprecipitation of Low Number of FACS-Purified Epidermal Cells. Methods in molecular biology (Clifton, N.J.)\| PubMed ID: 32314219	2020
Could SARS-CoV-2 blocking of ACE2 in endothelial cells result in upregulation of CX3CL1, promoting thrombosis in COVID-19 patients? Medical hypotheses\| PubMed ID: 33836338	2021
Development and Testing of a Low-Cost Inactivation Buffer That Allows for Direct SARS-CoV-2 Detection in Saliva. Vaccines\| PubMed ID: 35632485	2022
Reversal of high-glucose-induced transcriptional and epigenetic memories through NRF2 pathway activation. Life science alliance\| PubMed ID: 38755006	2024
Sulforaphane Exposure Prevents Cadmium-Induced Toxicity and Mitochondrial Dysfunction in the Nematode by Regulating the Insulin/Insulin-like Growth Factor Signaling (IIS) Pathway. Antioxidants (Basel, Switzerland)\| PubMed ID: 38790689	2024
Science in Mexico: a rising force amid adversity. Trends in cell biology\| PubMed ID: 40713302	2025
Mapping early PRC2 nucleation sites upon Suz12 reintroduction reveals features of Polycomb recruitment. bioRxiv : the preprint server for biology\| PubMed ID: 40950132	2025

Victor Julian Valdes

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