Reversing the Central Dogma: RNA-guided control of DNA in epigenetics and genome editing

LncRNAs, RNA Therapeutics, and Emerging Technologies in Liver Pathobiology

The field of ribonucleic acid (RNA) biology has revealed an array of noncoding RNA species, particularly long noncoding RNAs (lncRNAs), which play crucial roles in liver disease pathogenesis. This review explores the diverse functions of lncRNAs in liver pathology, including metabolic-associated steatotic liver disease, hepatocellular carcinoma, alcohol-related liver disease, and cholangiopathies such as primary sclerosing cholangitis and cholangiocarcinoma. We highlight key lncRNAs that regulate lipid metabolism, inflammation, fibrosis, and oncogenesis in the liver, demonstrating their diagnostic and therapeutic potential. Emerging RNA-based therapies, such as mRNA therapy, RNA interference, and antisense oligonucleotides, offer approaches to modulate lncRNA activity and address liver disease at a molecular level. Advances in sequencing technologies and bioinformatics pipelines are simultaneously enabling the identification and functional characterization of novel lncRNAs, driving innovation in personalized medicine. In conclusion, this review highlights the potential of lncRNAs as biomarkers and therapeutic targets in liver disease and emphasizes the need for further research into their regulatory mechanisms and clinical applications.

Dynamic properties of transcriptional condensates modulate CRISPRa-mediated gene activation

CRISPR activation (CRISPRa) is a powerful tool for endogenous gene activation, yet the mechanisms underlying its optimal transcriptional activation remain unclear. By monitoring real-time transcriptional bursts, we find that CRISPRa modulates both burst duration and amplitude. Our quantitative imaging reveals that CRISPR-SunTag activators, with three tandem VP64-p65-Rta (VPR), form liquid-like transcriptional condensates and exhibit high activation potency. Although visible CRISPRa condensates are associated with some RNA bursts, the overall levels of phase separation do not correlate with transcriptional bursting or activation strength in individual cells. When the number of SunTag scaffolds is increased to 10 or more, solid-like condensates form, sequestering co-activators such as p300 and MED1. These condensates display low dynamicity and liquidity, resulting in ineffective gene activation. Overall, our studies characterize various phase-separated CRISPRa systems for gene activation, highlighting the foundational principles for engineering CRISPR-based programmable synthetic condensates with appropriate properties to effectively modulate gene expression.

Characterizing heterologous protein burden in Komagataella phaffii

Yeast is a widely utilized chassis for heterologous protein production, with Komagataella phaffii well-established as a prominent nonconventional yeast in this field. Despite its widespread recognition, there remains considerable potential to further optimize these cell factories to meet high production demands in a cost-effective and sustainable manner. Understanding the cellular response to the challenges of heterologous protein production can equip genetic engineers with crucial knowledge to develop enhanced strategies for constructing more efficient cell factories. In this study, we explore the molecular response of various K. phaffii strains that produce either the human insulin precursor or Mambalgin-1, examining changes in transcription and changes in intra- and extracellular protein levels. Our findings provide valuable insights into the molecular mechanisms that regulate the behaviour of K. phaffii production strains under the stress of producing different heterologous proteins. We believe that these results will serve as a foundation for identifying new genetic targets to improve strain robustness and productivity. In conclusion, we present new cellular and molecular insights into the response of K. phaffii cell factories to the challenges of burdensome heterologous protein production and our findings point to different engineering strategies for improved cell factory performance.

Proximity-activated guide RNA of CRISPR-Cas12a for programmable diagnostic detection and gene regulation

The flexibility and programmability of CRISPR-Cas technology have made it one of the most popular tools for biomarker diagnostics and gene regulation. Especially, the CRISPR-Cas12 system has shown exceptional clinical diagnosis and gene editing capabilities. Here, we discovered that although the top loop of the 5' handle of guide RNA can undergo central splitting, deactivating CRISPR-Cas12a, the segments can dramatically restore CRISPR function through nucleic acid self-assembly or interactions with small molecules and aptamers. This discovery forms the basis of an engineered Cas12a system with a programmable proximity-activated guide RNA (PARC-Cas12a) that links targets of interest to dsDNA. Leveraging the efficient trans- and cis-cleavage of Cas12, our findings further inspired a detection platform design for RNAs or non-nucleic acid biomarkers, enabling highly sensitive and multiplexed analysis. We further demonstrated the feasibility of RNA-controllable gene knockout/knockdown in Escherichia coli. Notably, we successfully validated the gene regulatory capabilities of the PARC-Cas12a system within mammalian cell systems by utilizing the classical theophylline molecule-aptamer system. Our results introduce a programmable toolbox for precise diagnostics and cell regulation, allowing the development of versatile diagnostic tools, complex synthetic biological circuits, and cellular biosensors.

The cellular RNA-dependent RNA polymerases in plants

RNA-dependent RNA Polymerases (RdRPs) synthesize double-stranded RNA (dsRNA) from a single-stranded RNA (ssRNA) template. In plants, dsRNAs produced by RdRPs can be further processed into small interfering RNA (siRNAs) with different lengths, ranging from 21 to 24 nucleotides (nt). These siRNAs play a pivotal role in various biological processes, including antiviral responses, transposable elements silencing, DNA methylation, and the regulation of plant reproduction and development. Recent research has reported significant progress in uncovering the molecular mechanisms of plant RNA-DEPENDENT RNA POLYMERASE 2 (RDR2), a representative RdRP involved in the RNA-directed DNA methylation (RdDM) pathway. These discoveries provide a molecular basis underlying the principles of RdRP function and offer insights into potential advancements in crop breeding and antiviral defense strategies.

KHDRBS3 facilitates self-renewal and temozolomide resistance of glioblastoma cell lines

Glioblastoma is a deadly tumor which possesses glioblastoma stem cell populations involved in temozolomide (TMZ) resistance. To gain insight into the mechanisms of self-renewing and therapy-resistant cancer stem cells, subcellular proteomics was utilized to identify proteins whose expression is enriched in U251-derived glioblastoma stem-like cells. The KH RNA Binding Domain Containing, Signal Transduction Associated 3, KHDRBS3, was successfully identified as a gene up-regulated in the cancer stem cell population compared with its differentiated derivatives. Depletion of KHDRBS3 by RNA silencing led to a decrease in cell proliferation, neurosphere formation, migration, and expression of genes involved in glioblastoma stemness. Importantly, TMZ sensitivity can be induced by the gene knockdown. Collectively, our results highlight KHDRBS3 as a novel factor associated with self-renewal of glioblastoma stem-like cells and TMZ resistance. As a consequence, targeting KHDRBS3 may help eradicate glioblastoma stem-like cells.

Epigenetic mechanisms in cardiovascular complications of diabetes: towards future therapies

The pathophysiological mechanisms of cardiovascular disease and microvascular complications in diabetes have been extensively studied, but effective methods of prevention and treatment are still lacking. In recent years, DNA methylation, histone modifications, and non-coding RNAs have arisen as possible mechanisms involved in the development, maintenance, and progression of micro- and macro-vascular complications of diabetes. Epigenetic changes have the characteristic of being heritable or deletable. For this reason, they are now being studied as a therapeutic target for the treatment of diabetes and the prevention or for slowing down its complications, aiming to alleviate the personal and social burden of the disease.This review addresses current knowledge of the pathophysiological links between diabetes and cardiovascular complications, focusing on the role of epigenetic modifications, including DNA methylation and histone modifications. In addition, although the treatment of complications of diabetes with "epidrugs" is still far from being a reality and faces several challenges, we present the most promising molecules and approaches in this field.

Phenotyping Tumor Heterogeneity through Proteogenomics: Study Models and Challenges

Tumor heterogeneity refers to the diversity observed among tumor cells: both between different tumors (inter-tumor heterogeneity) and within a single tumor (intra-tumor heterogeneity). These cells can display distinct morphological and phenotypic characteristics, including variations in cellular morphology, metastatic potential and variability treatment responses among patients. Therefore, a comprehensive understanding of such heterogeneity is necessary for deciphering tumor-specific mechanisms that may be diagnostically and therapeutically valuable. Innovative and multidisciplinary approaches are needed to understand this complex feature. In this context, proteogenomics has been emerging as a significant resource for integrating omics fields such as genomics and proteomics. By combining data obtained from both Next-Generation Sequencing (NGS) technologies and mass spectrometry (MS) analyses, proteogenomics aims to provide a comprehensive view of tumor heterogeneity. This approach reveals molecular alterations and phenotypic features related to tumor subtypes, potentially identifying therapeutic biomarkers. Many achievements have been made; however, despite continuous advances in proteogenomics-based methodologies, several challenges remain: in particular the limitations in sensitivity and specificity and the lack of optimal study models. This review highlights the impact of proteogenomics on characterizing tumor phenotypes, focusing on the critical challenges and current limitations of its use in different clinical and preclinical models for tumor phenotypic characterization.

Pan-cancer analysis of RNA 5-methylcytosine reader (ALYREF)

The increasing interest in RNA modifications has significantly advanced epigenomic and epitranscriptomic technologies. This study focuses on the immuno-oncological impact of ALYREF in human cancer through a pan-cancer analysis, enhancing understanding of this gene's role in cancer. We observed differential ALYREF expression between tumor and normal samples, correlating strongly with prognosis in various cancers, particularly kidney renal papillary cell carcinoma (KIRP) and liver hepatocellular carcinoma (LIHC). ALYREF showed a negative correlation with most tumor-infiltrating cells in lung squamous cell carcinoma (LUSC) and lymphoid neoplasm diffuse large B-cell lymphoma (DLBC), while positive correlations were noted in LIHC, kidney chromophobe (KICH), mesothelioma (MESO), KIRP, pheochromocytoma and paraganglioma (PARD), and glioma (GBMLGG). Additionally, ALYREF expression was closely associated with tumor heterogeneity, stemness indices, and a high mutation rate in TP53 across these cancers. In conclusion, ALYREF may serve as an oncogenic biomarker in numerous cancers, meriting further research attention.

Epigenetic regulation of mRNA mediates the phenotypic plasticity of cancer cells during metastasis and therapeutic resistance (Review)

Plasticity, the ability of cancer cells to transition between differentiation states without genomic alterations, has been recognized as a major source of intratumoral heterogeneity. It has a crucial role in cancer metastasis and treatment resistance. Thus, targeting plasticity holds tremendous promise. However, the molecular mechanisms of plasticity in cancer cells remain poorly understood. Several studies found that mRNA, which acts as a bridge linking the genetic information of DNA and protein, has an important role in translating genotypes into phenotypes. The present review provided an overview of the regulation of cancer cell plasticity occurring via changes in the transcription and editing of mRNAs. The role of the transcriptional regulation of mRNA in cancer cell plasticity was discussed, including DNA‑binding transcriptional factors, DNA methylation, histone modifications and enhancers. Furthermore, the role of mRNA editing in cancer cell plasticity was debated, including mRNA splicing and mRNA modification. In addition, the role of non‑coding (nc)RNAs in cancer plasticity was expounded, including microRNAs, long intergenic ncRNAs and circular RNAs. Finally, different strategies for targeting cancer cell plasticity to overcome metastasis and therapeutic resistance in cancer were discussed.

Is epigenome editing non-inheritable? Implications for ethics and the regulation of human applications

Epigenome editing offers ethical advantages with non-inheritable gene expression control. However, concerns arise regarding potential transgenerational effects in humans. Ethical and regulatory evaluation is crucial, considering recent advancements and enhanced understanding of transgenerational epigenetics in both mammals and humans.

PlantIntronDB: a database for plant introns that host functional elements

Although more and more attention has been focused on introns and the important role of plant introns in plant growth and development has been discovered, there is still a lack of an open and comprehensive database on plant introns with functional elements in current research. In order to make full use of large-scale sequencing data and help researchers in related fields to achieve high-throughput functional verification of identified plant introns with functional elements, we designed a database containing five plant species, PlantIntronDB and systematically analyzed 358, 59, 185, 210 and 141 RNA-seq samples from Arabidopsis thaliana (Arabidopsis), Gossypium raimondii (cotton), Zea mays (maize), Brassica napus (oilseed rape) and Oryza sativa Japonica Group (rice). In total, we found 100 126 introns that host functional elements in these five species. Specifically, we found that among all species, the number of introns with functional elements on the positive and negative strands is similar, with a length mostly smaller than 1500 bp, and the Adenine/Thymine (A/T) content is much higher than that of Guanine/Cytosine (G/C). In addition, the distribution of functional elements in introns varies among different species. All the above data can be downloaded for free in this database. This database provides a concise, comprehensive and user-friendly web interface, allowing users to easily retrieve target data based on their needs, using relevant organizational options. The database operation is simple and convenient, aiming to provide strong data support for researchers in related fields to study plant introns that host functional elements, including circular RNAs, lncRNAs, etc. Database URL:  http://deepbiology.cn/PlantIntronDB/.