Primary transcripts: From the discovery of RNA processing to current concepts of gene expression - Review

METTL3 as a master regulator of translation in cancer: mechanisms and implications

Translational regulation is an important step in the control of gene expression. In cancer cells, the orchestration of both global control of protein synthesis and selective translation of specific mRNAs promote tumor cell survival, angiogenesis, transformation, invasion and metastasis. N6-methyladenosine (m6A), the most prevalent mRNA modification in higher eukaryotes, impacts protein translation. Over the past decade, the development of m6A mapping tools has facilitated comprehensive functional investigations, revealing the involvement of this chemical mark, together with its writer METTL3, in promoting the translation of both oncogenes and tumor suppressor transcripts, with the impact being context-dependent. This review aims to consolidate our current understanding of how m6A and METTL3 shape translation regulation in the realm of cancer biology. In addition, it delves into the role of cytoplasmic METTL3 in protein synthesis, operating independently of its catalytic activity. Ultimately, our goal is to provide critical insights into the interplay between m6A, METTL3 and translational regulation in cancer, offering a deeper comprehension of the mechanisms sustaining tumorigenesis.

Is RNA the working genome in eukaryotes ? The 60 year evolution of a conceptual challenge

About 80 years ago, in 1943, after a century of biochemical and genetic research, DNA was established as the carrier of genetic information. At the onset of Molecular Biology around 1960, the genome of living organisms embodied 3 basic, still unknown paradigms: its composition, organisation and expression. Between 1980 and 1990, its replication was understood, and ideas about its 3D-organisation were suggested and finally confirmed by 2010. The basic mechanisms of gene expression in higher organisms, the synthesis of precursor RNAs and their processing into functional RNAs, were also discovered about 60 years ago in 1961/62. However, some aspects were then, and are still now debated, although the latest results in post-genomic research have confirmed the basic principles. When my history-essay was published in 2003, describing the discovery of RNA processing 40 years earlier, the main facts were not yet generally confirmed or acknowledged. The processing of pre-rRNA to 28 S and 18 S rRNA was clearly demonstrated, confirmed by others and generally accepted as a fact. However, the "giant" size of pre-mRNA 10-100 kb-long and pervasive DNA transcription were still to be confirmed by post-genomic methods. It was found, surprisingly, that up to 90% of DNA is transcribed in the life cycle of eukaryotic organisms thus showing that pervasive transcription was the general rule. In this essay, we shall take a journey through the 60-year history of evolving paradigms of gene expression which followed the emergence of Molecular Biology, and we will also evoke some of the "folklore" in research throughout this period. Most important was the growing recognition that although the genome is encoded in DNA, the Working Genome in eukaryotic organisms is RNA.

Cancer Epigenetics: An Overview

Cancer is a complex disease caused by genetic and epigenetic alterations in the control of cell division. Findings from the field of cancer genomics and epigenomics have increased our understanding of the origin and evolution of tumorigenic processes, greatly advancing our knowledge of the molecular etiology of cancer. Consequently, any contemporary view of cancer research must consider tumorigenesis as a cellular phenomenon that is a result of the interplay between genetic and epigenetic mutations and their interaction with environmental factors, including our microbiome, that influences cellular metabolism and proliferation rates. The integration and better knowledge of these processes will help us to improve diagnosis, prognosis, and future genetic and epigenetic therapies. Here, I present an overview of the epigenetic processes that are affected in cancer and how they contribute to the onset and progression of the disease. Finally, I discuss how the development of sophisticated experimental approaches and computational tools, including novel ways to exploit large data sets, could contribute to the better understanding and treatment of cancer.

Regulation of DNA methylation during the testicular development of Shaziling pigs

DNA methylation is one of the key epigenetic regulatory mechanisms in development and spermatogenesis. However, the dynamic regulatory mechanisms of genome-wide DNA methylation during testicular development remain largely unknown. Herein, we generated a single-base resolution DNA methylome and transcriptome atlas of precocious porcine testicular tissues across three developmental stages (1, 75, and 150 days old). The results showed that the dynamic methylation patterns were directly related to the expression of the DNMT3A gene. Conjoint analysis revealed a negative regulatory pattern between promoter methylation and the positive regulation of 3'-untranslated region (3'UTR) methylation. Mechanistically, the decrease in promoter methylation affected the upregulation of meiosis-related genes, such as HORMAD1, SPO11, and SYCE1. Demethylation in the 3'UTR induced the downregulation of the INHBA gene and knockdown of INHBA inhibited cell proliferation by reducing the synthesis of activin A. These findings contribute to exploring the regulatory mechanisms of DNA methylation in testicular development.

Immunopeptidogenomics: Harnessing RNA-Seq to Illuminate the Dark Immunopeptidome

Human leukocyte antigen (HLA) molecules are cell-surface glycoproteins that present peptide antigens on the cell surface for surveillance by T lymphocytes, which contemporaneously seek signs of disease. Mass spectrometric analysis allows us to identify large numbers of these peptides (the immunopeptidome) following affinity purification of solubilized HLA-peptide complexes. However, in recent years, there has been a growing awareness of the "dark side" of the immunopeptidome: unconventional peptide epitopes, including neoepitopes, which elude detection by conventional search methods because their sequences are not present in reference protein databases (DBs). Here, we establish a bioinformatics workflow to aid identification of peptides generated by noncanonical translation of mRNA or by genome variants. The workflow incorporates both standard transcriptomics software and novel computer programs to produce cell line-specific protein DBs based on three-frame translation of the transcriptome. The final protein DB also includes sequences resulting from variants determined by variant calling on the same RNA-Seq data. We then searched our experimental data against both transcriptome-based and standard DBs using PEAKS Studio (Bioinformatics Solutions, Inc). Finally, further novel software helps to compare the various result sets arising for each sample, pinpoint putative genomic origins for unconventional sequences, and highlight potential neoepitopes. We applied the workflow to study the immunopeptidome of the acute myeloid leukemia cell line THP-1, using RNA-Seq and immunopeptidome data. We confidently identified over 14,000 peptides from three replicates of purified HLA peptides derived from THP-1 cells using the conventional UniProt human proteome. Using the transcriptome-based DB generated using our workflow, we recapitulated >85% of these and also identified 1029 unconventional peptides not explained by UniProt, including 16 sequences caused by nonsynonymous variants. Our workflow, which we term "immunopeptidogenomics," can provide DBs, which include pertinent unconventional sequences and allow neoepitope discovery, without becoming too large to search. Immunopeptidogenomics is a step toward unbiased search approaches that are needed to illuminate the dark side of the immunopeptidome.

Non-coding RNAs in chromatin folding and nuclear organization

One of the most intriguing questions facing modern biology concerns how the genome directs the construction of cells, tissues, and whole organisms. It is tempting to suggest that the part of the genome that does not encode proteins contains architectural plans. We are still far from understanding how these plans work at the level of building tissues and the body as a whole. However, the results of recent studies demonstrate that at the cellular level, special non-coding RNAs serve as scaffolds for the construction of various intracellular structures. The term "architectural RNAs" was proposed to designate this subset of non-coding RNAs. In this review, we discuss the role of architectural RNAs in the construction of the cell nucleus and maintenance of the three-dimensional organization of the genome.

Redefining fundamental concepts of transcription initiation in bacteria

Despite enormous progress in understanding the fundamentals of bacterial gene regulation, our knowledge remains limited when compared with the number of bacterial genomes and regulatory systems to be discovered. Derived from a small number of initial studies, classic definitions for concepts of gene regulation have evolved as the number of characterized promoters has increased. Together with discoveries made using new technologies, this knowledge has led to revised generalizations and principles. In this Expert Recommendation, we suggest precise, updated definitions that support a logical, consistent conceptual framework of bacterial gene regulation, focusing on transcription initiation. The resulting concepts can be formalized by ontologies for computational modelling, laying the foundation for improved bioinformatics tools, knowledge-based resources and scientific communication. Thus, this work will help researchers construct better predictive models, with different formalisms, that will be useful in engineering, synthetic biology, microbiology and genetics.

TFG-maintaining stability of overlooked FANCD2 confers early DNA-damage response

Emerging Fanconi Anemia (FA) signaling in the field of cancer research annotates the extreme importance of its center player, Fanconi Anemia complementation group D2 (FANCD2) in protecting human cells from going awry. However, a previously-unrecognized form of FANCD2, namely FANCD2-V2, is understudied. We report TRK-Fused Gene (TFG) is critical for roles played by FANCD2-V2 in early responses to DNA damage, but not for FANCD2-V1, the long-known form of FANCD2. FANCD2-V2 forms nuclear foci upon DNA damage, and both its focus appearance and disappearance are earlier than FANCD2-V1. The amino acid/aa 5-100 of TFG and the aa1437-1442 of FANCD2-V2 were identified to contribute to their interaction, which maintains the steady-state level of FANCD2-V2 protein. TFGΔaa5-100 or FANCD2-V2Δaa1437-1442-carrying cells could not show timely focus formation of FANCD2-V2 upon DNA damage and gained carcinogenicity over time. This study provides a previously-unknown key to unlock in-depth insights into maintaining genome stability, fostering translational studies on preventing, diagnosing and/or treating related diseases.

The Interchromatin Compartment Participates in the Structural and Functional Organization of the Cell Nucleus

This article focuses on the role of the interchromatin compartment (IC) in shaping nuclear landscapes. The IC is connected with nuclear pore complexes (NPCs) and harbors splicing speckles and nuclear bodies. It is postulated that the IC provides routes for imported transcription factors to target sites, for export routes of mRNA as ribonucleoproteins toward NPCs, as well as for the intranuclear passage of regulatory RNAs from sites of transcription to remote functional sites (IC hypothesis). IC channels are lined by less-compacted euchromatin, called the perichromatin region (PR). The PR and IC together form the active nuclear compartment (ANC). The ANC is co-aligned with the inactive nuclear compartment (INC), comprising more compacted heterochromatin. It is postulated that the INC is accessible for individual transcription factors, but inaccessible for larger macromolecular aggregates (limited accessibility hypothesis). This functional nuclear organization depends on still unexplored movements of genes and regulatory sequences between the two compartments.

Weak interactions in higher-order chromatin organization

The detailed principles of the hierarchical folding of eukaryotic chromosomes have been revealed during the last two decades. Along with structures composing three-dimensional (3D) genome organization (chromatin compartments, topologically associating domains, chromatin loops, etc.), the molecular mechanisms that are involved in their establishment and maintenance have been characterized. Generally, protein-protein and protein-DNA interactions underlie the spatial genome organization in eukaryotes. However, it is becoming increasingly evident that weak interactions, which exist in biological systems, also contribute to the 3D genome. Here, we provide a snapshot of our current understanding of the role of the weak interactions in the establishment and maintenance of the 3D genome organization. We discuss how weak biological forces, such as entropic forces operating in crowded solutions, electrostatic interactions of the biomolecules, liquid-liquid phase separation, DNA supercoiling, and RNA environment participate in chromosome segregation into structural and functional units and drive intranuclear functional compartmentalization.

Studying RNA-DNA interactome by Red-C identifies noncoding RNAs associated with various chromatin types and reveals transcription dynamics

Non-coding RNAs (ncRNAs) participate in various biological processes, including regulating transcription and sustaining genome 3D organization. Here, we present a method termed Red-C that exploits proximity ligation to identify contacts with the genome for all RNA molecules present in the nucleus. Using Red-C, we uncovered the RNA-DNA interactome of human K562 cells and identified hundreds of ncRNAs enriched in active or repressed chromatin, including previously undescribed RNAs. Analysis of the RNA-DNA interactome also allowed us to trace the kinetics of messenger RNA production. Our data support the model of co-transcriptional intron splicing, but not the hypothesis of the circularization of actively transcribed genes.

Molecular characteristics and functional differences of anti-PM/Scl autoantibodies and two other distinct and unique supramolecular structures known as "EXOSOMES"

The term "exosome" has been applied to three distinct supramolecular entities, namely the PM/Scl autoantibodies or "RNA exosomes", transforming DNA fragments termed "DNA exosomes", and small size extracellular vesicles knows as "exosomes". Some of the molecular components of the "PM/Scl exosome complex" or "RNA exosome" are recognized by specific autoantibodies present in the serum from some Systemic Sclerosis (SSc), polymyositis (PM) and polymyositis SSc (PM/Scl) overlap syndrome patients. On the other hand, one of the most active focuses of laboratory investigation in the last decade has been the biogenesis and role of extracellular vesicles known as "exosomes". The remarkable ability of these "exosome" vesicles to alter the cellular phenotype following fusion with target cells and the release of their macromolecular cargo has revealed a possible role in the pathogenesis of numerous diseases, including malignant, inflammatory, and autoimmune disorders and may allow them to serve as theranostic agents for personalized and precision medicine. The indiscriminate use of the term "exosome" to refer to these three distinct molecular entities has engendered great confusion in the scientific literature. Here, we review the molecular characteristics and functional differences between the three molecular structures identified as "exosomes". Given the rapidly growing scientific interest in extravesicular exosomes, unless a solution is found the confusion in the literature resulting from the use of the term "exosomes" will markedly increase.

Executive functions

First, executive functions are defined. Then the development of executive functions in children, from infancy to 10-11 years of age, is briefly described. The relation between the speed of processing and the development of executive functions is addressed. Finally, tools and pointers for evaluating executive functioning in younger and older children are discussed. A cautionary note is sounded, in that almost no executive function measure requires only one executive function. A child might fail a working memory task because of problems with inhibitory control (not working memory), fail an inhibitory control task because of working memory problems, or fail a cognitive flexibility, planning, or reasoning task because of problems with inhibitory control or working memory.

Extracellular Matrix Composition and Remodeling: Current Perspectives on Secondary Palate Formation, Cleft Lip/Palate, and Palatal Reconstruction

Craniofacial development comprises a complex process in humans in which failures or disturbances frequently lead to congenital anomalies. Cleft lip with/without palate (CL/P) is a common congenital anomaly that occurs due to variations in craniofacial development genes, and may occur as part of a syndrome, or more commonly in isolated forms (non-syndromic). The etiology of CL/P is multifactorial with genes, environmental factors, and their potential interactions contributing to the condition. Rehabilitation of CL/P patients requires a multidisciplinary team to perform the multiple surgical, dental, and psychological interventions required throughout the patient's life. Despite progress, lip/palatal reconstruction is still a major treatment challenge. Genetic mutations and polymorphisms in several genes, including extracellular matrix (ECM) genes, soluble factors, and enzymes responsible for ECM remodeling (e.g., metalloproteinases), have been suggested to play a role in the etiology of CL/P; hence, these may be considered likely targets for the development of new preventive and/or therapeutic strategies. In this context, investigations are being conducted on new therapeutic approaches based on tissue bioengineering, associating stem cells with biomaterials, signaling molecules, and innovative technologies. In this review, we discuss the role of genes involved in ECM composition and remodeling during secondary palate formation and pathogenesis and genetic etiology of CL/P. We also discuss potential therapeutic approaches using bioactive molecules and principles of tissue bioengineering for state-of-the-art CL/P repair and palatal reconstruction.