Introduction to Genome Biology and Diversity

Repetitive DNA sequence detection and its role in the human genome

Repetitive DNA sequences playing critical roles in driving evolution, inducing variation, and regulating gene expression. In this review, we summarized the definition, arrangement, and structural characteristics of repeats. Besides, we introduced diverse biological functions of repeats and reviewed existing methods for automatic repeat detection, classification, and masking. Finally, we analyzed the type, structure, and regulation of repeats in the human genome and their role in the induction of complex diseases. We believe that this review will facilitate a comprehensive understanding of repeats and provide guidance for repeat annotation and in-depth exploration of its association with human diseases.

Pulmonary Pathogen-Induced Epigenetic Modifications

Epigenetics generally involves genetic control by factors other than our own DNA sequence. Recent research has focused on delineating the mechanisms of two major epigenetic phenomena: DNA methylation and histone modification. As epigenetics involves many cellular processes, it is no surprise that it can also influence disease-associated gene expression. A direct link between respiratory infections, host cell epigenetic regulations, and chronic lung diseases is still unknown. Recent studies have revealed bacterium- or virus-induced epigenetic changes in the host cells. In this review, we focused on respiratory pathogens (viruses, bacteria, and fungi) induced epigenetic modulations (DNA methylation and histone modification) that may contribute to lung disease pathophysiology by promoting host defense or allowing pathogen persistence.

Protein Is an Intelligent Micelle

Interpreting biological phenomena at the molecular and cellular levels reveals the ways in which information that is specific to living organisms is processed: from the genetic record contained in a strand of DNA, to the translation process, and then to the construction of proteins that carry the flow and processing of information as well as reveal evolutionary mechanisms. The processing of a surprisingly small amount of information, i.e., in the range of 1 GB, contains the record of human DNA that is used in the construction of the highly complex system that is the human body. This shows that what is important is not the quantity of information but rather its skillful use-in other words, this facilitates proper processing. This paper describes the quantitative relations that characterize information during the successive steps of the "biological dogma", illustrating a transition from the recording of information in a DNA strand to the production of proteins exhibiting a defined specificity. It is this that is encoded in the form of information and that determines the unique activity, i.e., the measure of a protein's "intelligence". In a situation of information deficit at the transformation stage of a primary protein structure to a tertiary or quaternary structure, a particular role is served by the environment as a supplier of complementary information, thus leading to the achievement of a structure that guarantees the fulfillment of a specified function. Its quantitative evaluation is possible via using a "fuzzy oil drop" (FOD), particularly with respect to its modified version. This can be achieved when taking into account the participation of an environment other than water in the construction of a specific 3D structure (FOD-M). The next step of information processing on the higher organizational level is the construction of the proteome, where the interrelationship between different functional tasks and organism requirements can be generally characterized by homeostasis. An open system that maintains the stability of all components can be achieved exclusively in a condition of automatic control that is realized by negative feedback loops. This suggests a hypothesis of proteome construction that is based on the system of negative feedback loops. The purpose of this paper is the analysis of information flow in organisms with a particular emphasis on the role of proteins in this process. This paper also presents a model introducing the component of changed conditions and its influence on the protein folding process-since the specificity of proteins is coded in their structure.

A tetramerization domain in prokaryotic and eukaryotic transcription regulators homologous to p53

Transcriptional regulation usually requires the action of several proteins that either repress or activate a promotor of an open reading frame. These proteins can counteract each other, thus allowing tight regulation of the transcription of the corresponding genes, where tight repression is often linked to DNA looping or cross-linking. Here, the tetramerization domain of the bacterial gene repressor Rco from Bacillus subtilis plasmid pLS20 (Rco_pLS20) has been identified and its structure is shown to share high similarity to the tetramerization domain of the well known p53 family of human tumor suppressors, despite lacking clear sequence homology. In Rco_pLS20, this tetramerization domain is responsible for inducing DNA looping, a process that involves multiple tetramers. In accordance, it is shown that Rco_pLS20 can form octamers. This domain was named TetD_loop and its occurrence was identified in other Bacillus species. The TetD_loop fold was also found in the structure of a transcriptional repressor from Salmonella phage SPC32H. It is proposed that the TetD_loop fold has evolved through divergent evolution and that the TetD_loop originates from a common ancestor predating the occurrence of multicellular life.

Increasing Genomic Literacy Through National Genomic Projects

Genomics is an advancing field of medicine, science, ethics, and legislation. Keeping up to date with this challenging discipline requires continuous education and exchange of knowledge between many target groups. Specific challenges in genomic education include tailoring complex topics to diverse audiences ranging from the general public and patients to highly educated professionals. National genomic projects face many of the same challenges and thus offer many opportunities to highlight common educational strategies for improving genomic literacy. We have reviewed 41 current national genomic projects and have identified 16 projects specifically describing their approach to genomic education. The following target groups were included in the educational efforts: the general public (nine projects), patients (six projects), and genomic professionals (16 projects), reflecting the general overall aims of the projects such as determining normal and pathological genomic variation, improving infrastructure, and facilitating personalized medicine. The national genomic projects aim to increase genomic literacy through supplementing existing national education in genomics as well as independent measures specifically tailored to each target group, such as training events, research collaboration, and online resources for healthcare professionals, patients, and patient organizations. This review provides the current state of educational activities within national genomic projects for different target groups and identifies good practices that could contribute to patient empowerment, public engagement, proficient healthcare professionals, and lend support to personalized medicine.

Comparative transcriptome analysis reveals key epigenetic targets in SARS-CoV-2 infection

COVID-19 is an infection caused by SARS-CoV-2 (Severe Acute Respiratory Syndrome coronavirus 2), which has caused a global outbreak. Current research efforts are focused on the understanding of the molecular mechanisms involved in SARS-CoV-2 infection in order to propose drug-based therapeutic options. Transcriptional changes due to epigenetic regulation are key host cell responses to viral infection and have been studied in SARS-CoV and MERS-CoV; however, such changes are not fully described for SARS-CoV-2. In this study, we analyzed multiple transcriptomes obtained from cell lines infected with MERS-CoV, SARS-CoV, and SARS-CoV-2, and from COVID-19 patient-derived samples. Using integrative analyses of gene co-expression networks and de-novo pathway enrichment, we characterize different gene modules and protein pathways enriched with Transcription Factors or Epifactors relevant for SARS-CoV-2 infection. We identified EP300, MOV10, RELA, and TRIM25 as top candidates, and more than 60 additional proteins involved in the epigenetic response during viral infection that has therapeutic potential. Our results show that targeting the epigenetic machinery could be a feasible alternative to treat COVID-19.