It has been shown in recent years that many repeated sequences in the genome are expressed as RNA transcripts, although the role of such RNAs is poorly understood. Some isolated and tandem repeats (satellites) have been found to be transcribed, such...
The advent of long-read sequencing offers a new assessment method of detecting genomic structural variation (SV) in numerous rare genetic diseases. For autism spectrum disorders (ASD) cases where pathogenic variants fail to be found in the protein-co...
Numerous pan-genomic studies identified alterations in protein-coding genes and signaling pathways involved in bladder carcinogenesis, while non-coding somatic alterations remain weakly explored. The goal of this study was to identify clinical biomar...
Resistance to chemotherapy is a leading cause of treatment failure. Drug resistance mechanisms involve mutations in specific proteins or changes in their expression levels. It is commonly understood that resistance mutations happen randomly prior to...
Porcine reproductive and respiratory syndrome (PRRS) is a vertically transmitted reproductive disorder that is typically characterized by miscarriage, premature birth, and stillbirth in pregnant sows after infection. Such characteristics indicate tha...
The portion of the mosquito genome that does not code for proteins contains regulatory elements that likely underlie variation for important phenotypes including resistance and susceptibility to infection with arboviruses and Apicomplexan parasites....
Plant genomes are punctuated by repeated bouts of proliferation of transposable elements (TEs), and these mobile bursts are followed by silencing and decay of most of the newly inserted elements. As such, plant genomes reflect TE-related genome expan...
Protein encoding genes constitute a small fraction of mammalian genomes. In addition to the protein coding genes, there are other functional units within the genome that are transcribed, but not translated into protein, the so called non-coding RNAs....
The majority of the human genome is comprised of non-protein-coding genes, but the relevance of non-coding RNAs in complex diseases has yet to be fully elucidated. One class of non-coding RNAs is long non-coding RNAs or lncRNAs, many of which have be...
The contribution of the non-coding genome to disease and its therapeutic potential have been largely unexplored. Recently, several epigenetic drugs developed for cancer treatment have been described to mediate therapeutic effects through the reactiva...
This study seeks to investigate distinct signatures and codes within different genomic sequence locations of the human genome. The promoter and other non-coding regions contain sites for the binding of biological particles, for processes such as tran...
The red cusk-eel (Genypterus chilensis) is an endemic Chilean teleost fish of significant importance to fisheries and aquaculture; however, no reference genome is available for this species. In this study, we present the first hybrid genome assembly...
The advent of Whole Genome Sequencing (WGS) broadened the genetic variation detection range, revealing the presence of variants even in non-coding regions of the genome, which would have been missed using targeted approaches. One of the most challeng...
A large part of the genome is known to be transcribed as non-coding DNA including some tandem repeats (satellites) such as telomeric/centromeric satellites in different species. However, there has been no detailed study on the eventual transcription...
Long non-coding, tandem-repetitive regions in mitochondrial (mt) genomes of many metazoans have been notoriously difficult to characterise accurately using conventional sequencing methods. Here, we show how the use of a third-generation (long-read) s...
Coffea canephora grains are highly traded commodities worldwide. Non-coding RNAs (ncRNAs) are transcriptional products involved in genome regulation, environmental responses, and plant development. There is not an extensive genome-wide analysis that...
Introns represent almost half of the human genome, yet their vast majority is eliminated from eukaryotic transcripts through RNA splicing. Nevertheless, they feature key elements and functions that deserve further interest. At the level of DNA, intro...
Long human ultra-conserved non-coding elements (UCNEs) do not have any sequence similarity to each other or other characteristics that make them unalterable during vertebrate evolution. We hypothesized that UCNEs have unique dinucleotide (DN) composi...
Multiple myeloma (MM) is a plasma cell malignancy whereby a single clone of plasma cells over-propagates in the bone marrow, resulting in the increased production of monoclonal immunoglobulin. While the complex genetic architecture of MM is well char...
Age-related macular degeneration (AMD) is a progressive neurodegenerative disease that is the world’s leading cause of blindness in the aging population. Although the clinical stages and forms of AMD have been elucidated, more specific prognost...
Mucosal melanomas (MM) are rare aggressive cancers in humans, and one of the most common forms of oral cancers in dogs. Similar biological and histological features are shared between MM in both species, making dogs a powerful model for comparative o...
The size of the mitogenome varies greatly in angiosperms from different species, but the causes of expansion remain unclear. Species from the Zingiberaceae family often carry exceptionally large mitogenomes, where this phenomenon can be readily studi...
There are more than 350 species of amphipods (Crustacea) in Lake Baikal, which have emerged predominantly through the course of endemic radiation. This group represents a remarkable model for studying various aspects of evolution, one of which is the...
Genome-wide association studies have identified numerous genetic variants statistically significantly associated with body mass index (BMI). However, the functional mechanisms underlying most associations between single nucleotide polymorphisms (SNPs...
Bacterial regulatory non-coding RNAs control numerous mRNA targets that direct a plethora of biological processes, such as the adaption to environmental changes, growth and virulence. Recently developed high-throughput techniques, such as genomic til...
Cardiovascular disease (CVD) is one of the biggest threats to public health worldwide. Identifying key genetic contributors to CVD enables clinicians to assess the most effective treatment course and prognosis, as well as potentially inform family me...
Considerable evidence links many neuropsychiatric, neurodevelopmental and neurodegenerative disorders with multiple complex interactions between genetics and environmental factors such as nutrition. Mental health problems, autism, eating disorders, A...
Congenital heart disease (CHD) and neurodevelopmental disorders (NDDs) frequently co-occur, indicating that cardiac and neural phenotypes can arise from shared developmental disturbances rather than exclusively from the physiological consequences of...
Utilizing large-scale epigenomics data, deep learning tools can predict the regulatory activity of genomic sequences, annotate non-coding genetic variants, and uncover mechanisms behind complex traits. However, these tools primarily rely on human or...
Jiviruses are a group of recently described viruses characterized with a tripartite genome and having affinities with Virgaviridae (RNA1 and 2) and Flaviviridae (RNA3). Using a combination of high-throughput sequencing, datamining and RT-PCR approach...
The abundance of mammalian long intergenic non-coding RNA (lincRNA) genes is high, yet their functions remain largely unknown. One possible way to study this important question is to use large-scale comparisons of various characteristics of lincRNA w...
Background/Objectives: Precision medicine requires translation of genetic and molecular variation into clinically actionable therapeutic targets. However, many disease-associated signals identified by genome-wide association studies (GWAS) reside in...
Autoimmune diseases arise from complex interactions between genetic susceptibility, immune regulation, and tissue-specific inflammatory processes, yet most risk variants identified by genome-wide association studies occur in non-coding regions with p...
The advent of next generation sequencing revealed that a fraction of transcribed RNAs (short and long RNAs) is non-coding. Long non-coding RNAs (lncRNAs) have a crucial role in regulating gene expression and in epigenetics (chromatin and histones rem...
Primary mitochondrial disease (MD) is a group of rare genetic diseases reported to have a prevalence of 1:5000 and is currently without a cure. This group of diseases includes mitochondrial encephalopathy, lactic acidosis, and stroke-like episodes (M...
A colorectal adenoma, an aberrantly growing tissue, arises from the intestinal epithelium and is considered as precursor of colorectal cancer (CRC). In this study, we investigated structural and numerical chromosomal aberrations in adenomas, hypothes...
The prevention of muscle atrophy carries with it clinical significance for the control of increased morbidity and mortality following physical inactivity. While major transcriptional events associated with muscle atrophy-recovery processes are the su...
Long non-coding RNAs (lncRNAs) are transcripts longer than 200 nucleotides (nt) that are not translated into known functional proteins. This broad definition covers a large collection of transcripts with diverse genomic origins, biogenesis, and modes...
Transposable elements (TEs) comprise nearly half of the human genome and play an essential role in the maintenance of genomic stability, chromosomal architecture, and transcriptional regulation. TEs are repetitive sequences consisting of RNA transpos...
Small non-coding RNAs have been extensively studied in plants over the last decade. In contrast, genome-wide identification of plant long non-coding RNAs (lncRNAs) has recently gained momentum. LncRNAs are now being recognized as important players in...
Imprinted genes play diverse roles in mammalian development, homeostasis, and disease. Most imprinted chromosomal domains express one or more long non-coding RNAs (lncRNAs). Several of these lncRNAs are strictly nuclear and their mono-allelic express...
Adapting to climate change, providing sufficient human food and nutritional needs, and securing sufficient energy supplies will call for a radical transformation from the current conventional adaptation approaches to more broad-based and transformati...
Numerous sources of evidence suggest that most of the eukaryotic genome is transcribed into protein-coding mRNAs and also into a large number of non-coding RNAs (ncRNAs). Long ncRNAs (lncRNAs), a group consisting of ncRNAs longer than 200 nucleotides...
Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disorder characterized by marked genetic and phenotypic heterogeneity. Although pathogenic variants in major ALS genes, including C9ORF72, SOD1, TARDBP, and FUS, have provided fundament...
Malignant mesothelioma is an aggressive and lethal asbestos-related disease. Diagnosis of malignant mesothelioma is particularly challenging and is further complicated by the lack of disease subtype-specific markers. As a result, it is especially dif...
Genome-wide association studies (GWASs) have identified numerous loci associated with Alzheimer’s disease (AD), yet the effector genes and regulatory mechanisms underlying many of these associations remain unresolved. This challenge is particul...
Breast cancer is a heterogeneous disease that arises as a multi-stage process involving multiple cell types. Patients diagnosed with the same clinical stage and pathological classification may have different prognoses and therapeutic responses due to...
Azoospermia and severe oligozoospermia represent the most extreme forms of male infertility. Despite their prevalence, the genetic foundations of these conditions are not well understood, with only a limited number of genetic factors identified so fa...
Non-coding RNAs (ncRNAs) are conserved in the genome of cells across the three domains of life. They comprise a diverse group that are particularly prominent in metazoans where they provide a crucial interface between genes and proteins, participatin...
Genome-wide long non-coding RNAs (lncRNAs) in low, moderate, and high pyrethroid insecticide-resistant and -susceptible strains of Helicoverpa armigera were identified in this study. Using 45 illumina-based RNA-sequencing datasets, 8394 lncRNAs were...
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