25 papers · ranked by Valyu relevance
Lucy W. Barrett, Sue Fletcher, Steve D. Wilton
There is now compelling evidence that the complexity of higher organisms correlates with the relative amount of non-coding RNA rather than the number of protein-coding genes. Previously dismissed as “junk DNA”, it is the non-coding regions of the genome that are responsible for regulation, facilitating complex temporal…
Wenying He, Ying Ju, Xiangxiang Zeng, Xiangrong Liu + 1 more
With the rapid development of high-speed sequencing technologies and the implementation of many whole genome sequencing project, research in the genomics is advancing from genome sequencing to genome synthesis. Synthetic biology technologies such as DNA-based molecular assemblies, genome editing technology, directional…
Dana Cohen, Stefano Lonardi
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 transcription regulation. The specific rules and sequence codes that…
Ning Lu, Xin Gao, Michael C. Lanz, Marianna E. Estrada + 3 more
Genome size varies widely across eukaryotes, largely because of differences in non-coding DNA, but the physiological consequences of this variation remain unclear. To directly test how non-coding DNA abundance influences cellular physiology, we engineered a scalable genome-expansion system in the budding yeast S.…
Sarangdhar Nayak, Pawan K. Dhar
The dark genome comprising of non-expressing, non-translating, and extinct DNA sequences has remained a largely unexplored genomic space. Using computational and experimental approaches, novel insights into the dark matter genome have recently been gained, revealing the presence of a vast and unexplored resource.…
Ruchi Joshi, Anushka Roy, Relestina Lopes, Laxmi Kata + 6 more
Cell-free chromatin particles (cfChPs), primarily derived from non-coding DNA (ncDNA) and released from apoptotic cells into the bloodstream, can be horizontally transferred into living cells^1^. However, their potential role in generating ncDNA within recipient cells remains unknown. We previously reported that…
Valentina Agoni
Many efforts have been done in order to explain the role of junk DNA, but its function remain to be elucidated. In addition the GC-content variations among species still represent an enigma. Both these two mysteries can have a common explanation: we hypothesize that the role of junk DNA is to preserve the mutations…
William A. Haseltine, Roberto Patarca, Alfonso Baldi
Human genome projects in the 1990s identified about 20,000 protein-coding sequences. We are now in the RNA revolution, propelled by the realization that genes determine phenotype beyond the foundational central molecular biology dogma, stating that inherited linear pieces of DNA are transcribed to RNAs and translated…
Joseph L. Tsenum
Long non-coding RNAs (lncRNAs) can perform their regulatory roles by forming triple helices through RNA-DNA interaction. Although this has been verified by few in vivo and in vitro methods, in silico approaches that seek to predict the potentials of lncRNAs and DNA sites becoming a triplex forming structure is…
Joseph L. Tsenum, Maria Poptsova
Long non-coding RNAs (lncRNAs) can perform their regulatory roles by forming triple helices through RNA-DNA interaction. Although this has been verified by few in vivo and in vitro methods, in silico approaches that seek to predict the potentials of lncRNAs and DNA sites becoming a triplex forming structure is…
Jasdeep Kaur Dhanoa, Ram Saran Sethi, Ramneek Verma, Jaspreet Singh Arora + 1 more
The central dogma of gene expression propounds that DNA is transcribed to mRNA and finally gets translated into protein. Only 2-3% of the genomic DNA is transcribed to protein-coding mRNA. Interestingly, only a further minuscule part of genomic DNA encodes for long non-coding RNAs (lncRNAs) which are characteristically…
Daniel Frías-Lasserre, Cristian A. Villagra
Neo-Darwinian explanations of organic evolution have settled on mutation as the principal factor in producing evolutionary novelty. Mechanistic characterizations have been also biased by the classic dogma of molecular biology, where only proteins regulate gene expression. This together with the rearrangement of genetic…
Chen Zhang-Ren
The genome sizes of organisms vary widely (C-value paradox). There are non-transcribing regions in the genome that neither encode proteins nor RNA entities. There are several hypotheses about the function of these regions: one suggests that they are unannotated functional areas, while another views them as genomic…
Gao-De Li
Till now, in biological sciences, the term, transcription, mainly refers to DNA to RNA transcription. But our recently published experimental findings obtained from Plasmodium falciparum strongly suggest the existence of DNA to DNA transcription in the genome of eukaryotic cells, which could shed some light on the…
Ken Nishikawa, Akira R. Kinjo
The epigenome, i.e. the whole of chromatin modifications, is transferred from mother to daughter cells during cell differentiation. When de novo chromatin modifications (establishment or erasure of, respectively, new or pre-existing DNA methylations and/or histone modifications) are made in a daughter cell, however, it…
Kerim Arioglu, Umut Eser
Non-protein-coding regions of the human genome contain many complex patterns which regulate the cellular activity. Studying the human genome is limited by the lack of understanding of its features and their complex interactions. However, recent advances in Artificial Intelligence research have enabled automatically…
Dan Graur
Noncoding RNA (ncRNA) and long noncoding RNA (lncRNA) are scientifically invalid terms because they define molecular entities according to properties they do not possess and functions they do not perform. Here, I suggest retiring these two terms. Instead, I suggest using an evolutionary classification of genomic…
Neha Periwal, Priya Sharma, Pooja Arora, Saurabh Pandey + 2 more
Classification among coding (CDS) and non-coding RNA (ncRNA) sequences is a challenge and several machine learning models have been developed for the same. Since the frequency of curated coding sequences is many-folds as compared to that of the ncRNAs, we devised a novel approach to work with the complete datasets from…
Janet Sasso, Barbara Ambrose, Rumiana Tenchov, Ruchira Datta + 3 more
In the last decade, there has been a shift in research, clinical development, and commercial activity to exploit the many roles of RNA in physiology for use in medicine. With the rapid success in the development of lipid-RNA nanoparticles for mRNA vaccines against COVID-19 and with several approved RNA-based drugs, RNA…
Бранко Драгович
The genetic code is connection between 64 codons, which are building blocks of the genes, and 20 amino acids, which are building blocks of the proteins. In addition to coding amino acids, a few codons code stop signal, which is at the end of genes, i.e. it terminates process of protein synthesis. This article is a…
Authors not listed
One aim of the international Human Proteome Organization (HUPO) Human Proteome Project (HPP) is to obtain high-confidence translation evidence for every human protein-coding gene established in its target list of 19433 entries based on the protein-coding genes from Ensembl-GENCODE. However, 76 are annotated in…
Hirotake Udono, Minzhi Fan, Yoko Saito, Hirohisa Ohno + 4 more
Programmable droplets, artificial liquid-like condensates of nucleic acids, are intelligent out-of-equilibrium systems that allow the critical aspects of their biological counterparts to be harnessed programmably, such as molecular sensing and phase-state change. While DNA has been central to the previous efforts, less…
HANIYEH ABDOLLAHZADEH, Tonya Peeples, Mohammad Shahcheraghi
DNA-based nanomaterials have shown great potential in numerous applications, thanks to their unique properties including DNA's various molecular interactions, programmability, and versatility with biological modules. Meanwhile, the DNA origami platforms have shown promise in the creation of drug carriers. This…
S. M. Hossein Tabatabaei Yazdi, Han Mao Kiah, Eva Ruiz Garcia, Jian Ma + 2 more
'Jian Ma' 'Huimin Zhao' 'Olgica Milenković'] Abstract—We provide an overview of current approaches to DNA-based storage system design and accompanying synthesis, sequencing and editing methods. We also introduce and analyze a suite of new constrained coding schemes for both archival and random access DNA storage…
Authors not listed
Synthetic DNA strands are programmable and biocompatible building blocks that can be combined through hybridization to form user-defined nanostructures, but their assembly traditionally requires cell-incompatible conditions, imposing a lengthy ex situ fabrication step before any application with living matter. Here we…