scholarly journals Small Activating RNAs: Towards the Development of New Therapeutic Agents and Clinical Treatments

Cells ◽  
2021 ◽  
Vol 10 (3) ◽  
pp. 591
Author(s):  
Hossein Ghanbarian ◽  
Shahin Aghamiri ◽  
Mohamad Eftekhary ◽  
Nicole Wagner ◽  
Kay-Dietrich Wagner
Keyword(s):  
Gene Expression ◽  
Dna Sequences ◽  
Cultured Cells ◽  
Exogenous Dna ◽  
Evolutionarily Conserved ◽  
Rna Activation ◽  
Endogenous Genes ◽  
Cellular Machinery ◽  
Eukaryotic Organisms ◽  
Activate Gene

Small double-strand RNA (dsRNA) molecules can activate endogenous genes via an RNA-based promoter targeting mechanism. RNA activation (RNAa) is an evolutionarily conserved mechanism present in diverse eukaryotic organisms ranging from nematodes to humans. Small activating RNAs (saRNAs) involved in RNAa have been successfully used to activate gene expression in cultured cells, and thereby this emergent technique might allow us to develop various biotechnological applications, without the need to synthesize hazardous construct systems harboring exogenous DNA sequences. Accordingly, this thematic issue aims to provide insights into how RNAa cellular machinery can be harnessed to activate gene expression leading to a more effective clinical treatment of various diseases.

scholarly journals Polycombs and microRNA-223 regulate human granulopoiesis by transcriptional control of target gene expression

Blood ◽  
2012 ◽  
Vol 119 (17) ◽  
pp. 4034-4046 ◽  
Author(s):  
Giuseppe Zardo ◽  
Alberto Ciolfi ◽  
Laura Vian ◽  
Linda M. Starnes ◽  
Monia Billi ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Sequences ◽  
Transcriptional Control ◽  
Transcriptional Level ◽  
Seed Region ◽  
Mrna Targets ◽  
Epigenetic Events ◽  
Evolutionarily Conserved ◽  
Lineage Decision ◽  
Chromatin Remodeling Complexes

Abstract Epigenetic modifications regulate developmental genes involved in stem cell identity and lineage choice. NFI-A is a posttranscriptional microRNA-223 (miR-223) target directing human hematopoietic progenitor lineage decision: NFI-A induction or silencing boosts erythropoiesis or granulopoiesis, respectively. Here we show that NFI-A promoter silencing, which allows granulopoiesis, is guaranteed by epigenetic events, including the resolution of opposing chromatin “bivalent domains,” hypermethylation, recruitment of polycomb (PcG)–RNAi complexes, and miR-223 promoter targeting activity. During granulopoiesis, miR-223 localizes inside the nucleus and targets the NFI-A promoter region containing PcGs binding sites and miR-223 complementary DNA sequences, evolutionarily conserved in mammalians. Remarkably, both the integrity of the PcGs-RNAi complex and DNA sequences matching the seed region of miR-223 are required to induce NFI-A transcriptional silencing. Moreover, ectopic miR-223 expression in human myeloid progenitors causes heterochromatic repression of NFI-A gene and channels granulopoiesis, whereas its stable knockdown produces the opposite effects. Our findings indicate that, besides the regulation of translation of mRNA targets, endogenous miRs can affect gene expression at the transcriptional level, functioning in a critical interface between chromatin remodeling complexes and the genome to direct fate lineage determination of hematopoietic progenitors.

scholarly journals TRANSFECTION OF EXOGENOUS DNA IN CHICKEN OVIDUCT CELLS IN VITRO

2015 ◽  
Vol 14 (1) ◽  
pp. 29-31
Author(s):  
A. V. Samoilov ◽  
N. M. Suraeva
Keyword(s):  
Gene Expression ◽  
Epithelial Cells ◽  
Primary Culture ◽  
Cultured Cells ◽  
Expression System ◽  
Enzyme Treatment ◽  
Exogenous Dna ◽  
Chicken Oviduct ◽  
Development In Vitro

Effective production of pharmaceutical proteins using transgenic poultry may be achieved only from a construction of expression vector for chicken oviduct bioreactor. This study was focused on development of temporary expression system by using primary oviduct epithelial cells in which transfected gene expression can be studied. The present work was aimed to study three manners for preparation of primary oviduct cells, but only one was effective. Selective digestion of chicken oviduct tissue pieces in trypsin at 38° C and mechanical withdrawal of upper cell layer resulted in the isolation of purity primary culture. Experiments indicated that monolayer cultured for 2-3 d were fit to be passaged. Then after 1-2-d, the cells were transfected. Based on our result with primary culture, we did not used complicated enzyme treatment and extra equipment in order to increase the purity of epithelial cells. Liposomes «Lipofectine® 2000» were used for primary oviduct cells transfection of a plasmid designed based on the pIRES EGFP2 vector (Clontech, United States). The ratio of cells carrying GFP activity was 5-8% of the total number of cultured cells. This researches was focused on development in vitro of temporary expression system in which transfected gene expression can be tested for 4-5 d.

scholarly journals Homology arms of targeting vectors for gene insertions and CRISPR/Cas9 technology: size does not matter; quality control of targeted clones does

2015 ◽  
Vol 20 (5) ◽  
Author(s):  
Silvia Petrezselyova ◽  
Slavomir Kinsky ◽  
Dominika Truban ◽  
Radislav Sedlacek ◽  
Ingo Burtscher ◽  
...  
Keyword(s):  
Quality Control ◽  
Dna Sequences ◽  
Genome Engineering ◽  
Southern Hybridization ◽  
Embryonic Stem ◽  
Fluorescent Reporter ◽  
Exogenous Dna ◽  
Knock Out ◽  
Endogenous Genes ◽  
Pcr Method

AbstractClustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated 9 (Cas9) technology has brought rapid progress in mammalian genome editing (adding, disrupting or changing the sequence of specific sites) by increasing the frequency of targeted events. However, gene knock-in of DNA cassettes by homologous recombination still remains difficult due to the construction of targeting vectors possessing large homology arms (from 2 up to 5 kb). Here, we demonstrate that in mouse embryonic stem cells the combination of CRISPR/Cas9 technology and targeting vectors with short homology arms (~ 0.3 kb) provides sufficient specificity for insertion of fluorescent reporter cassettes into endogenous genes with similar efficiency as those with large conventional vectors. Importantly, we emphasize the necessity of thorough quality control of recombinant clones by combination of the PCR method, Southern hybridization assay and sequencing to exclude undesired mutations. In conclusion, our approach facilitates programmed integration of exogenous DNA sequences at a target locus and thus could serve as a basis for more sophisticated genome engineering approaches, such as generation of reporters and conditional knock-out alleles.

scholarly journals A novel core promoter element induces bidirectional transcription in CpG island

2017 ◽  
Author(s):  
Amin Mahpour ◽  
Dominic Smiraglia ◽  
Benjamin S. Scruggs ◽  
Irwin H. Gelman ◽  
Toru Ouchi
Keyword(s):  
Gene Expression ◽  
Cpg Island ◽  
Core Promoter ◽  
Consensus Sequence ◽  
Cpg Islands ◽  
Housekeeping Genes ◽  
Bidirectional Transcription ◽  
Evolutionarily Conserved ◽  
Active Research ◽  
Activate Gene

AbstractHow TATA-less promoters such as those within CpG islands (CGI) control gene expression is still a subject of active research. Here, we have identified the “CGCG element”, a ten-base pair motif with a consensus sequence of TCTCGCGAGA present in a group of promoter-associated CGIs of ribosomal protein and housekeeping genes. This element is evolutionarily conserved in vertebrates, found in DNase-accessible regions and employs RNA polymerase 2 to activate gene expression. Through extensive analysis of several endogenous promoters, we demonstrate that this element activates bidirectional transcription through divergent start sites. Methylation of this element abrogates the associated promoter activity. When coincident with a TATA-box directional transcription remains CGCG-dependent. Because the CGCG element is sufficient to drive transcription, we propose that its unmethylated form functions as a core promoter of TATA-less CGI-associated promoters.

Sequence-Based Deep Learning Frameworks on Enhancer-Promoter Interactions Prediction

2020 ◽  
Vol 26 ◽  
Author(s):  
Xiaoping Min ◽  
Fengqing Lu ◽  
Chunyan Li
Keyword(s):  
Gene Expression ◽  
Deep Learning ◽  
Dna Sequences ◽  
Experimental Methods ◽  
Learning Methods ◽  
Comprehensive Review ◽  
Genomic Features ◽  
Disease Mechanisms ◽  
Evaluation Strategies ◽  
Learning Frameworks

: Enhancer-promoter interactions (EPIs) in the human genome are of great significance to transcriptional regulation which tightly controls gene expression. Identification of EPIs can help us better deciphering gene regulation and understanding disease mechanisms. However, experimental methods to identify EPIs are constrained by the fund, time and manpower while computational methods using DNA sequences and genomic features are viable alternatives. Deep learning methods have shown promising prospects in classification and efforts that have been utilized to identify EPIs. In this survey, we specifically focus on sequence-based deep learning methods and conduct a comprehensive review of the literatures of them. We first briefly introduce existing sequence-based frameworks on EPIs prediction and their technique details. After that, we elaborate on the dataset, pre-processing means and evaluation strategies. Finally, we discuss the challenges these methods are confronted with and suggest several future opportunities.

scholarly journals The crest phenotype in domestic chicken is caused by a 197 bp duplication in the intron of HOXC10

2021 ◽  
Author(s):  
Jingyi Li ◽  
Mi-Ok Lee ◽  
Brian W Davis ◽  
Ping Wu ◽  
Shu-Man Hsieh-Li ◽  
...  
Keyword(s):  
Gene Expression ◽  
Whole Genome Sequencing ◽  
Diagnostic Test ◽  
Genome Sequencing ◽  
Ectopic Expression ◽  
Body Region ◽  
Whole Genome ◽  
Dorsal Skin ◽  
Conserved Sequence ◽  
Evolutionarily Conserved

Abstract The Crest mutation in chicken shows incomplete dominance and causes a spectacular phenotype in which the small feathers normally present on the head are replaced by much larger feathers normally present only in dorsal skin. Using whole genome sequencing, we show that the crest phenotype is caused by a 197 bp duplication of an evolutionarily conserved sequence located in the intron of HOXC10 on chromosome 33. A diagnostic test showed that the duplication was present in all 54 crested chickens representing eight breeds and absent from all 433 non-crested chickens representing 214 populations. The mutation causes ectopic expression of at least five closely linked HOXC genes, including HOXC10, in cranial skin of crested chickens. The result is consistent with the interpretation that the crest feathers are caused by an altered body region identity. The upregulated HOXC gene expression is expanded to skull tissue of Polish chickens showing a large crest often associated with cerebral hernia, but not in Silkie chickens characterized by a small crest, both homozygous for the duplication. Thus, the 197 bp duplication is required for the development of a large crest and susceptibility to cerebral hernia because only crested chicken show this malformation. However, this mutation is not sufficient to cause herniation because this malformation is not present in breeds with a small crest, like Silkie chickens.

scholarly journals Binding of an X-Specific Condensin Correlates with a Reduction in Active Histone Modifications at Gene Regulatory Elements

Genetics ◽  
2019 ◽  
Vol 212 (3) ◽  
pp. 729-742 ◽  
Author(s):  
Lena Annika Street ◽  
Ana Karina Morao ◽  
Lara Heermans Winterkorn ◽  
Chen-Yu Jiao ◽  
Sarah Elizabeth Albritton ◽  
...  
Keyword(s):  
Gene Expression ◽  
Histone Modifications ◽  
Chromatin Immunoprecipitation ◽  
Protein Complexes ◽  
Regulatory Elements ◽  
Evolutionarily Conserved ◽  
Chromatin Immunoprecipitation Sequencing ◽  
Gene Regulatory Elements ◽  
Gene Regulatory ◽  
Regulatory Sites

Condensins are evolutionarily conserved protein complexes that are required for chromosome segregation during cell division and genome organization during interphase. In Caenorhabditis elegans, a specialized condensin, which forms the core of the dosage compensation complex (DCC), binds to and represses X chromosome transcription. Here, we analyzed DCC localization and the effect of DCC depletion on histone modifications, transcription factor binding, and gene expression using chromatin immunoprecipitation sequencing and mRNA sequencing. Across the X, the DCC accumulates at accessible gene regulatory sites in active chromatin and not heterochromatin. The DCC is required for reducing the levels of activating histone modifications, including H3K4me3 and H3K27ac, but not repressive modification H3K9me3. In X-to-autosome fusion chromosomes, DCC spreading into the autosomal sequences locally reduces gene expression, thus establishing a direct link between DCC binding and repression. Together, our results indicate that DCC-mediated transcription repression is associated with a reduction in the activity of X chromosomal gene regulatory elements.

scholarly journals Retention of relict satellite DNA sequences in Anemone (Ranunculaceae)

2013 ◽  
Vol 72 (1) ◽  
pp. 1-133 ◽  
Author(s):  
Višnja Besendorfer ◽  
Jelena Mlinarec
Keyword(s):  
Dna Sequences ◽  
Southern Hybridization ◽  
Repeat Unit ◽  
Similar Species ◽  
Genomic Component ◽  
Library Hypothesis ◽  
Species Specific ◽  
Eukaryotic Organisms ◽  
Fish Signal

Abstract Satellite DNAis a genomic component present in virtually all eukaryotic organisms. The turnover of highly repetitive satellite DNAis an important element in genome organization and evolution in plants. Here we study the presence, physical distribution and abundance of the satellite DNAfamily AhTR1 in Anemone. Twenty-two Anemone accessions were analyzed by PCR to assess the presence of AhTR1, while fluorescence in situ hybridization and Southern hybridization were used to determine the abundance and genomic distribution of AhTR1. The AhTR1 repeat unit was PCR-amplified only in eight phylogenetically related European Anemone taxa of the Anemone section. FISH signal with AhTR1 probe was visible only in A. hortensis and A. pavonina, showing localization of AhTR1 in the regions of interstitial heterochromatin in both species. The absence of a FISH signal in the six other taxa as well as weak signal after Southern hybridization suggest that in these species AhTR1 family appears as relict sequences. Thus, the data presented here support the »library hypothesis« for AhTR1 satellite evolution in Anemone. Similar species-specific satellite DNAprofiles in A. hortensis and A. pavonina support the treatment of A. hortensis and A. pavonina as one species, i.e. A. hortensis s.l.

scholarly journals Combinatorial Control of Gene Expression

2013 ◽  
Vol 2013 ◽  
pp. 1-11 ◽  
Author(s):  
Soumya Bhattacharjee ◽  
Kaushik Renganaath ◽  
Rajesh Mehrotra ◽  
Sandhya Mehrotra
Keyword(s):  
Gene Expression ◽  
Short Description ◽  
Controlling Factors ◽  
Environmental Cues ◽  
Control Of Gene Expression ◽  
Environmental Signals ◽  
Combinatorial Control ◽  
Sense And Respond ◽  
Eukaryotic Organisms

The complexity and diversity of eukaryotic organisms are a feat of nature’s engineering. Pulling the strings of such an intricate machinery requires an even more masterful and crafty approach. Only the number and type of responses that they generate exceed the staggering proportions of environmental signals perceived and processed by eukaryotes. Hence, at first glance, the cell’s sparse stockpile of controlling factors does not seem remotely adequate to carry out this response. The question as to how eukaryotes sense and respond to environmental cues has no single answer. It is an amalgamation, an interplay between several processes, pathways, and factors—a combinatorial control. A short description of some of the most important elements that operate this entire conglomerate is given in this paper.

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