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non-coding regulatory elements: Potential roles in disease and the case of epilepsy

NEUROPATHOLOGY AND APPLIED NEUROBIOLOGY 2022年第3期48卷 e12775-e12775页

作者： Pagni, Susanna Mills, James D. Frankish, Adam Mudge, Jonathan M. Sisodiya, Sanjay M. UCL Queen Sq Inst Neurol Dept Clin & Expt Epilepsy Box 29Queen Sq London WC1N 3BG England Chalfont Ctr Epilepsy Gerrards Cross England Univ Amsterdam Dept Neuro Pathol Amsterdam Neurosci Amsterdam UMC Amsterdam Netherlands European Bioinformat Inst European Mol Biol Lab Cambridge England

non-coding dna (ncdna) refers to the portion of the genome that does not code for proteins and accounts for the greatest physical proportion of the human genome. ncdna includes sequences that are transcribed into RNA molecules, such as ribosomal RNAs (rRNAs), microRNAs (miRNAs), long non-coding RNAs (lncRNAs) and un-transcribed sequences that have regulatory functions, including gene promoters and enhancers. Variation in non-coding regions of the genome have an established role in human disease, with growing evidence from many areas, including several cancers, Parkinson's disease and autism. Here, we review the features and functions of the regulatory elements that are present in the non-coding genome and the role that these regions have in human disease. We then review the existing research in epilepsy and emphasise the potential value of further exploring non-coding regulatory elements in epilepsy. In addition, we outline the most widely used techniques for recognising regulatory elements throughout the genome, current methodologies for investigating variation and the main challenges associated with research in the field of non-coding dna.

关键词： epilepsy gene regulation non-coding dna non-coding mutations regulatory sequences

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Pleiotropic Enhancers are Ubiquitous Regulatory Elements in the Human Genome

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GENOME BIOLOGY AND EVOLUTION 2022年第6期14卷 evac071页

作者： Laiker, Ian Frankel, Nicolas Consejo Nacl Invest Cient & Tecn CONICET Inst Fisiol Biol Mol & Neurociencias IFIBYNE RA-1428 Buenos Aires DF Argentina Univ Buenos Aires UBA RA-1428 Buenos Aires DF Argentina Univ Buenos Aires UBA Fac Ciencias Exactas & Nat FCEN Dept Ecol Genet & Evoluc RA-1428 Buenos Aires DF Argentina

Enhancers are regulatory elements of genomes that determine spatio-temporal patterns of gene expression. The human genome contains a vast number of enhancers, which largely outnumber protein-coding genes. Historically, enhancers have been regarded as highly tissue-specific. However, recent evidence has demonstrated that many enhancers are pleiotropic, with activity in multiple developmental contexts. Yet, the extent and impact of pleiotropy remain largely unexplored. In this study we analyzed active enhancers across human organs based on the analysis of both eRNA transcription (FANTOM5 consortium data sets) and chromatin architecture (ENCODE consortium data sets). We show that pleiotropic enhancers are pervasive in the human genome and that most enhancers active in a particular organ are also active in other organs. In addition, our analysis suggests that the proportion of context-specific enhancers of a given organ is explained, at least in part, by the proportion of context-specific genes in that same organ. The notion that such a high proportion of human enhancers can be pleiotropic suggests that small regions of regulatory dna contain abundant regulatory information and that these regions evolve under important evolutionary constraints.

关键词： human genome non-coding dna gene regulation CRE enhancer pleiotropy

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Contribution of introns to the species diversity associated with the apicomplexan parasite, Neospora caninum

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PARASITOLOGY RESEARCH 2020年第2期119卷 431-445页

作者： Calarco, Larissa Ellis, John Univ Technol Sydney Sch Life Sci POB 123 Ultimo NSW 2007 Australia

Neospora caninum is an intracellular parasite considered a leading cause of bovine reproduction failure worldwide, and a serious neurological disease of canines. Transplacental transmission in intermediate hosts is considered the most efficient means of transmission, which strictly involves asexual reproduction. nonetheless, extensive genetic diversity has been reported within the species. What is yet to be elucidated are the major drivers of such diversity, and their impact on important parasite phenotypes such as virulence. Instead of protein-encoding sequences, genome and transcriptome data were used to investigate SNPs in introns between two distinct N. caninum isolates, with reported differences in pathogenicity. Variant analysis identified 840 and 501 SNPs within intergenic regions and introns, respectively, distinctly concentrated on chromosomes VI and XI, whereas the rest of the genome was monomorphic in comparison. Gene ontologies for SNP-dense intron-containing genes included ATP binding, transmembrane transport, protein kinase activity, and transcription and translation processes. This study shows that variation in non-coding dna is contributing to N. caninum intraspecies genetic diversity, and potentially influencing and contributing to important parasite mechanisms. Finally, we present an assembled and annotated N. caninum apicoplast genome and show that this essential organelle is highly conserved between the two isolates, and related Coccidia.

关键词： Transcriptomics Genomics Structural variation non-coding dna Apicoplast SNPs

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Bioinformatic Evaluation of Features on Cis-regulatory Elements at 6q25.1

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BIOINFORMATICS AND BIOLOGY INSIGHTS 2023年 17卷

作者： Sreekar, N. Shrestha, Smeeta Dayananda Sagar Univ Sch Basic & Appl Sci Dept Genet Bengaluru India Nanyang Technol Univ NTU Lee Kong Chian Sch Med Singapore 636921 Singapore

Eukaryotic non-coding regulatory features contribute significantly to cellular plasticity which on aberration leads to cellular malignancy. Enhancers are cis-regulatory elements that contribute to the development of resistance to endocrine therapy in estrogen receptor (ER)-positive breast cancer leading to poor clinical outcome. ER is vital for therapeutic targets in ER-positive breast cancer. Here, we review and report the different regulatory features present on ER with the objective to delineate potential mechanisms which may contribute to development of resistance. The UCSC Genome Browser, data mining, and bioinformatics tools were used to review enhancers, transcription factors (TFs), histone marks, long non-coding RNAs (lncRNAs), and variants residing in the non-coding region of the ER gene. We report 7 enhancers, 3 of which were rich in TF-binding sites and histone marks in a cell line-specific manner. Furthermore, some enhancers contain estrogen resistance variants and sites for lncRNA. Our review speculates putative models suggesting potential aberrations in gene regulation and expression if these regulatory landscapes and assemblies are altered. This review gives an interesting perspective in designing integrated in vitro studies including non-coding elements to study development of endocrine resistance in ER-positive breast cancer.

关键词： Estrogen receptor non-coding dna gene regulation enhancer estrogen resistance transcription factors RNA chromatin state

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Characterizing intergenic transcription at RNA polymerase II binding sites in normal and cancer tissues

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CELL GENOMICS 2023年第10期3卷 100411-100411页

作者： de Langen, Pierre Hammal, Fayrouz Gueret, Elise Mouren, Jean-Christophe Spinelli, Lionel Ballester, Benoit Aix Marseille Univ INSERM TAGC Marseille France

Intergenic transcription in normal and cancerous tissues is pervasive but incompletely understood. To inves-tigate this, we constructed an atlas of over 180,000 consensus RNA polymerase II (RNAPII)-bound intergenic regions from 900 RNAPII chromatin immunoprecipitation sequencing (ChIP-seq) experiments in normal and cancer samples. Through unsupervised analysis, we identified 51 RNAPII consensus clusters, many of which mapped to specific biotypes and revealed tissue-specific regulatory signatures. We developed a meta -clus-tering methodology to integrate our RNAPII atlas with active transcription across 28,797 RNA sequencing (RNA-seq) samples from The Cancer Genome Atlas (TCGA), Genotype-Tissue Expression (GTEx), and Ency-clopedia of dna Elements (ENCODE). This analysis revealed strong tissue-and disease-specific intercon-nections between RNAPII occupancy and transcriptional activity. We demonstrate that intergenic transcrip-tion at RNAPII-bound regions is a novel per-cancer and pan-cancer biomarker. This biomarker displays genomic and clinically relevant characteristics, distinguishing cancer subtypes and linking to overall survival. Our results demonstrate the effectiveness of coherent data integration to uncover intergenic transcriptional activity in normal and cancer tissues.

关键词： enhancers non-coding dna regulatory genomics intergenic RNA Polymerase II gene regulation cancer genomics non-coding transcription

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Association of miR-760 with cancer: An overview

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GENE 2020年 747卷 144648-144648页

作者： Manvati, Monika Kaushik Siddharth Khan, Juveria Verma, Neeraj Dhar, Pawan K. Jawaharlal Nehru Univ Sch Biotechnol New Mehrauli Rd New Delhi 110067 India

MicroRNAs (miRNAs) are small non-coding RNA molecules of around 22 nucleotides in length. They are crucially involved in the post transcriptional regulation and thus play a significant role in the modulation of different diseases. Several studies have suggested that miRNA expression is dysregulated in various cancers through different mechanisms and the dysregulated miRNA in return affects different cancer hallmarks including cell proliferation, cell death suppression, metastasis and angiogenesis. Compilation of the available miRNA data can be a stimulator for proper understanding of the correlation between the miRNA expression and cancer progression. In this review, we have focussed on the role of miR-760 in the progression of different cancer. MicroRNA-760 (miR-760) has been found to be down regulated in various cancers, thus it can be utilized as a possible prognostic marker for cancer detection. Here, we have tried to fill a gap regarding the role of miR-760 in relation to cervical cancer also. Moreover, unravelling the role of miR-760 in different cancers will enlighten the researchers with proper understanding of biology of miR-760 in regulation of different cancers.

关键词： micro RNA Cancer miR-760 non-coding dna Regulation microRNA targets

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The role of codons during a natural selection

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CHEMICAL PHYSICS 2021年 540卷 110986-110986页

作者： Pincak, Richard Bartos, Erik Slovak Acad Sci Inst Expt Phys Watsonova 47 Kosice 04353 Slovakia Joint Inst Nucl Res Bogoliubov Lab Theoret Phys Dubna 141980 Moscow Region Russia Slovak Acad Sci Inst Phys Dubravska Cesta 9 Bratislava 84511 Slovakia

We suggest the origin of coded amino acids in nature by using a new theory on the connection in lattice Pascal's triangle and adding some properties of cohomology theory to biological objects as dna, RNA, and proteins. With the enhancement of the energy-momentum tensor equation for this new theory, we can better understand and explain a new role of codons with their symmetry in gene expression. For the investigation of codon interaction was used model of lattice Pascal's triangle. With this approach we proof the existence of twenty coded amino acids.

关键词： Connection Amino acid Retrotransposon non-coding dna Pascal's triangle

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Application of artificial intelligence for detection of chemico-biological interactions associated with oxidative stress and dna damage

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CHEMICO-BIOLOGICAL INTERACTIONS 2021年 345卷 109533-109533页

作者： Davidovic, Lazar M. Laketic, Darko Cumic, Jelena Jordanova, Elena Pantic, Igor Univ Belgrade Studentski Trg 1 RS-11000 Belgrade Serbia Univ Belgrade Fac Med Inst Anat Niko Miljanic Dr Subotica 4-2 RS-11129 Belgrade Serbia Univ Belgrade Fac Med Clin Ctr Serbia Dr Koste Todorov 8 RS-11129 Belgrade Serbia Univ Belgrade Clin Hosp Ctr Fac Med Vukova 9 RS-11000 Belgrade Serbia Univ Belgrade Fac Med Inst Med Physiol Lab Cellular Physiol Visegradska 26-2 RS-11129 Belgrade Serbia Univ Haifa 199 Abba Hushi Blvd Mt Carmel IL-3498838 Haifa Israel

In recent years, various AI-based methods have been developed in order to uncover chemico-biological interactions associated with dna damage and oxidative stress. Various decision trees, bayesian networks, random forests, logistic regression models, support vector machines as well as deep learning tools, have great potential in the area of molecular biology and toxicology, and it is estimated that in the future, they will greatly contribute to our understanding of molecular and cellular mechanisms associated with dna damage and repair. In this concise review, we discuss recent attempts to build machine learning tools for assessment of radiation - induced dna damage as well as algorithms that can analyze the data from the most frequently used dna damage assays in molecular biology. We also review recent works on the detection of antioxidant proteins with machine learning, and the use of AI-related methods for prediction and evaluation of noncoding dna sequences. Finally, we discuss previously published research on the potential application of machine learning tools in aging research.

关键词： Reactive oxygen species Radiation Machine learning non-coding dna Aging

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The decreased exclusion of nuclear eccdna: From molecular and subcellular levels to human aging and age-related diseases

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AGEING RESEARCH REVIEWS 2021年 67卷 101306-101306页

作者： Qiu, Guo-Hua Zheng, Xintian Fu, Mingjun Huang, Cuiqin Yang, Xiaoyan Longyan Univ Key Lab Prevent Vet Med & Biotechnol Coll Life SciFujian Prov Univ Fujian Prov Key Lab Prevent & Control Anim Infect Longyan 364012 Peoples R China

Extrachromosomal circular dna (eccdna) accumulates within the nucleus of eukaryotic cells during physiological aging and in age-related diseases (ARDs) and the accumulation could be caused by the declined exclusion of nuclear eccdna in these states. This review focuses on the formation of eccdna and the roles of some main factors, such as nuclear pore complexes (NPCs), nucleoplasmic reticulum (NR), and nuclear actin, in eccdna exclusion. eccdnas are mostly formed from non-coding dna during dna damage repair. They move to NPCs along nuclear actin and are excluded out of the nucleus through functional NPCs in young and healthy cells. However, it has been demonstrated that defective NPCs, abnormal NPC components and nuclear actin rods are increased in aged cells, various cancers and certain other ARDs such as cardiovascular diseases, premature aging, neurodegenerative diseases and myopathies. Therefore, mainly resulting from the increase of dysfunctional NPCs, the exclusion of nuclear eccdnas may be reduced and eccdnas thus accumulate within the nucleus in aging and the aforementioned ARDs. In addition, the protective function of non-coding dna in tumorigenesis is further discussed.

关键词： eccdnas Aging Cancer Age-related diseases NPC non-coding dna

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Paradoxical evolution of rickettsial genomes

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TICKS AND TICK-BORNE DISEASES 2019年第2期10卷 462-469页

作者： Diop, Awa Raoult, Didier Fournier, Pierre-Edouard Aix Marseille Univ UMR VITROME Inst Hospitalouuniv Mediterranee Infect Assistance Publ Hop MarseilleIRDServ Sante Arme 19-21 Blvd Jean Moulin F-13005 Marseille France Aix Marseille Univ UMR MEPHI Inst Hospitalouuniv Mediterranee Infect Assistance Publ Hop MarseilleIRD Marseille France

Rickettsia species are strictly intracellular bacteria that evolved approximately 150 million years ago from a presumably free-living common ancestor from the order Rickettsiales that followed a transition to an obligate intracellular lifestyle. Rickettsiae are best known as human pathogens vectored by various arthropods causing a range of mild to severe human diseases. As part of their obligate intracellular lifestyle, rickettsial genomes have undergone a convergent evolution that includes a strong genomic reduction resulting from progressive gene degradation, genomic rearrangements as well as a paradoxical expansion of various genetic elements, notably small RNAs and short palindromic elements whose role remains unknown. This reductive evolutionary process is not unique to members of the Rickettsia genus but is common to several human pathogenic bacteria. Gene loss, gene duplication, dna repeat duplication and horizontal gene transfer all have shaped rickettsial genome evolution. Gene loss mostly involved amino-acid, ATP, LPS and cell wall component biosynthesis and transcriptional regulators, but with a high preservation of toxin-antitoxin (TA) modules, recombination and dna repair proteins. Surprisingly the most virulent Rickettsia species were shown to have the most drastically reduced and degraded genomes compared to closely related species of milder pathogenesis. In contrast, the less pathogenic species harbored the greatest number of mobile genetic elements. Thus, this distinct evolutionary process observed in Rickettsia species may be correlated with the differences in virulence and pathogenicity observed in these obligate intracellular bacteria. However, future investigations are needed to provide novel insights into the evolution of genome sizes and content, for that a better understanding of the balance between proliferation and elimination of genetic material in these intracellular bacteria is required.

关键词： Rickettsia Genomics Evolution Virulence Genome rearrangement non-coding dna Gene loss dna repeats

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