scholarly journals Comparison of reprogramming factor targets reveals both species-specific and conserved mechanisms in early iPS cells

2017 ◽  
Author(s):  
Kai Fu ◽  
Constantinos Chronis ◽  
Abdenour Soufi ◽  
Giancarlo Bonora ◽  
Miguel Edwards ◽  
...  
Keyword(s):  
Regulatory Networks ◽  
Target Genes ◽  
Human Fibroblasts ◽  
Mouse Cell ◽  
Binding Motifs ◽  
Reprogramming Factors ◽  
Early Mouse ◽  
Species Specific ◽  
Human And Mouse ◽  
Syntenic Regions

AbstractBoth human and mouse fibroblasts can be reprogrammed to pluripotency with Oct4, Sox2, Klf4, and c-Myc (OSKM) transcription factors. While both systems generate pluripotency, human reprogramming takes considerably longer than mouse. To assess additional similarities and differences, we sought to compare the binding of the reprogramming factors between the two systems. In human fibroblasts, the OSK factors initially target many more closed chromatin sites compared to mouse. Despite this difference, the intra- and intergenic distribution of target sites, target genes, primary binding motifs, and combinatorial binding patterns between the reprogramming factors are largely shared. However, while many OSKM binding events in early mouse cell reprogramming occur in syntenic regions, only a limited number is conserved in human. In summary, these findings suggest similar general effects of OSKM binding across these two species, even though the detailed regulatory networks have diverged significantly.

scholarly journals Genome-Wide microRNA Profiling Using Oligonucleotide Microarray Reveals Regulatory Networks of microRNAs in Nicotiana benthamiana During Beet Necrotic Yellow Vein Virus Infection

Viruses ◽  
2020 ◽  
Vol 12 (3) ◽  
pp. 310 ◽  
Author(s):  
Junying Liu ◽  
Huiyan Fan ◽  
Ying Wang ◽  
Chenggui Han ◽  
Xianbing Wang ◽  
...  
Keyword(s):  
Nicotiana Benthamiana ◽  
Regulatory Networks ◽  
Target Genes ◽  
Tobacco Rattle Virus ◽  
Yellow Vein ◽  
Differentially Expressed ◽  
Virus Induced Gene Silencing ◽  
Developmental Defects ◽  
Differentially Expressed Mirnas ◽  
Species Specific

Beet necrotic yellow vein virus (BNYVV) infections induce stunting and leaf curling, as well as root and floral developmental defects and leaf senescence in Nicotiana benthamiana. A microarray analysis with probes capable of detecting 1596 candidate microRNAs (miRNAs) was conducted to investigate differentially expressed miRNAs and their targets upon BNYVV infection of N. benthamiana plants. Eight species-specific miRNAs of N. benthamiana were identified. Comprehensive characterization of the N. benthamiana microRNA profile in response to the BNYVV infection revealed that 129 miRNAs were altered, including four species-specific miRNAs. The targets of the differentially expressed miRNAs were predicted accordingly. The expressions of miR164, 160, and 393 were up-regulated by BNYVV infection, and those of their target genes, NAC21/22, ARF17/18, and TIR, were down-regulated. GRF1, which is a target of miR396, was also down-regulated. Further genetic analysis of GRF1, by Tobacco rattle virus-induced gene silencing, assay confirmed the involvement of GRF1 in the symptom development during BNYVV infection. BNYVV infection also induced the up-regulation of miR168 and miR398. The miR398 was predicted to target umecyanin, and silencing of umecyanin could enhance plant resistance against viruses, suggesting the activation of primary defense response to BNYVV infection in N. benthamiana. These results provide a global profile of miRNA changes induced by BNYVV infection and enhance our understanding of the mechanisms underlying BNYVV pathogenesis.

Evolution of miRNA binding sites and regulatory networks in cichlids

2021 ◽  
Author(s):  
Tarang K Mehta ◽  
Luca Penso-Dolfin ◽  
Will K Nash ◽  
Sushmita Roy ◽  
Federica Di Palma ◽  
...  
Keyword(s):  
Binding Site ◽  
Binding Sites ◽  
Regulatory Networks ◽  
Target Genes ◽  
Phenotypic Diversity ◽  
Regulatory Regions ◽  
Adaptive Trait ◽  
Regulatory Variants ◽  
Key Driver ◽  
Species Specific

The divergence of regulatory regions and gene regulatory network (GRN) rewiring is a key driver of cichlid phenotypic diversity. However, the contribution of miRNA binding site turnover has yet to be linked to GRN evolution across cichlids. Here, we extend our previous studies by analysing the selective constraints driving evolution of miRNA and transcription factor (TF) binding sites of target genes, to infer instances of cichlid GRN rewiring associated with regulatory binding site turnover. Comparative analyses identified increased species-specific networks that are functionally associated to traits of cichlid phenotypic diversity. The evolutionary rewiring is associated with differential models of miRNA snd TF binding site turnover, driven by a high proportion of fast-evolving polymorphic sites in adaptive trait genes compared to subsets of random genes. Positive selection acting upon discrete mutations in these regulatory regions is likely to be an important mechanism in rewiring GRNs in rapidly radiating cichlids. Regulatory variants of functionally associated miRNA and TF binding sites of visual opsin genes differentially segregate according to phylogeny and ecology of Lake Malawi species, identifying both rewired e.g. clade-specific and conserved network motifs of adaptive trait associated GRNs. Our approach revealed several novel candidate regulators, regulatory regions and three-node motifs across cichlid genomes with previously reported associations to known adaptive evolutionary traits.

scholarly journals Critical microRNAs and regulatory motifs in cleft palate identified by a conserved miRNA–TF–gene network approach in humans and mice

2019 ◽  
Vol 21 (4) ◽  
pp. 1465-1478 ◽  
Author(s):  
Aimin Li ◽  
Peilin Jia ◽  
Saurav Mallik ◽  
Rong Fei ◽  
Hiroki Yoshioka ◽  
...  
Keyword(s):  
Cleft Palate ◽  
Regulatory Networks ◽  
Target Genes ◽  
Regulatory Mechanisms ◽  
Network Approach ◽  
Regulatory Motifs ◽  
Gene Regulatory ◽  
Regulatory Loop ◽  
Tf Gene ◽  
Human And Mouse

Abstract Cleft palate (CP) is the second most common congenital birth defect. The etiology of CP is complicated, with involvement of various genetic and environmental factors. To investigate the gene regulatory mechanisms, we designed a powerful regulatory analytical approach to identify the conserved regulatory networks in humans and mice, from which we identified critical microRNAs (miRNAs), target genes and regulatory motifs (miRNA–TF–gene) related to CP. Using our manually curated genes and miRNAs with evidence in CP in humans and mice, we constructed miRNA and transcription factor (TF) co-regulation networks for both humans and mice. A consensus regulatory loop (miR17/miR20a–FOXE1–PDGFRA) and eight miRNAs (miR-140, miR-17, miR-18a, miR-19a, miR-19b, miR-20a, miR-451a and miR-92a) were discovered in both humans and mice. The role of miR-140, which had the strongest association with CP, was investigated in both human and mouse palate cells. The overexpression of miR-140-5p, but not miR-140-3p, significantly inhibited cell proliferation. We further examined whether miR-140 overexpression could suppress the expression of its predicted target genes (BMP2, FGF9, PAX9 and PDGFRA). Our results indicated that miR-140-5p overexpression suppressed the expression of BMP2 and FGF9 in cultured human palate cells and Fgf9 and Pdgfra in cultured mouse palate cells. In summary, our conserved miRNA–TF–gene regulatory network approach is effective in detecting consensus miRNAs, motifs, and regulatory mechanisms in human and mouse CP.

scholarly journals Conserved cell types with divergent features between human and mouse cortex

2018 ◽  
Author(s):  
Rebecca D Hodge ◽  
Trygve E Bakken ◽  
Jeremy A Miller ◽  
Kimberly A Smith ◽  
Eliza R Barkan ◽  
...  
Keyword(s):  
Rna Sequencing ◽  
Cognitive Abilities ◽  
Cell Types ◽  
Mouse Cell ◽  
Middle Temporal Gyrus ◽  
Cellular Architecture ◽  
Mouse Cortex ◽  
Single Nucleus ◽  
Species Specific ◽  
Human And Mouse

AbstractElucidating the cellular architecture of the human neocortex is central to understanding our cognitive abilities and susceptibility to disease. Here we applied single nucleus RNA-sequencing to perform a comprehensive analysis of cell types in the middle temporal gyrus of human cerebral cortex. We identify a highly diverse set of excitatory and inhibitory neuronal types that are mostly sparse, with excitatory types being less layer-restricted than expected. Comparison to a similar mouse cortex single cell RNA-sequencing dataset revealed a surprisingly well-conserved cellular architecture that enables matching of homologous types and predictions of human cell type properties. Despite this general conservation, we also find extensive differences between homologous human and mouse cell types, including dramatic alterations in proportions, laminar distributions, gene expression, and morphology. These species-specific features emphasize the importance of directly studying human brain.

scholarly journals NfiS, a species-specific regulatory noncoding RNA of Pseudomonas stutzeri, enhances oxidative stress tolerance in Escherichia coli

AMB Express ◽  
2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Guihua Hu ◽  
Tao Hu ◽  
Yuhua Zhan ◽  
Wei Lu ◽  
Min Lin ◽  
...  
Keyword(s):  
Oxidative Stress ◽  
Escherichia Coli ◽  
Stress Responses ◽  
Noncoding Rna ◽  
Regulatory Networks ◽  
Target Genes ◽  
Pseudomonas Stutzeri ◽  
Bacterial Strains ◽  
E Coli ◽  
Species Specific

Abstract Noncoding RNAs (ncRNAs) can finely control the expression of target genes at the posttranscriptional level in prokaryotes. Regulatory small RNAs (sRNAs) designed to control target gene expression for applications in metabolic engineering and synthetic biology have been successfully developed and used. However, the effect on the heterologous expression of species- or strain-specific ncRNAs in other bacterial strains remains poorly understood. In this work, a Pseudomonas stutzeri species-specific regulatory ncRNA, NfiS, which has been shown to play an important role in the response to oxidative stress as well as osmotic stress in P. stutzeri A1501, was cloned and transferred to the Escherichia coli strain Trans10. Recombinant NfiS-expressing E. coli, namely, Trans10-nfiS, exhibited significant enhancement of tolerance to oxidative stress. To map the possible gene regulatory networks mediated by NfiS in E. coli under oxidative stress, a microarray assay was performed to delineate the transcriptomic differences between Trans10-nfiS and wild-type E. coli under H2O2 shock treatment conditions. In all, 1184 genes were found to be significantly altered, and these genes were divided into mainly five functional categories: stress response, regulation, metabolism related, transport or membrane protein and unknown function. Our results suggest that the P. stutzeri species-specific ncRNA NfiS acts as a regulator that integrates adaptation to H2O2 with other cellular stress responses and helps protect E. coli cells against oxidative damage.

scholarly journals Divergence of regulatory networks governed by the orthologous transcription factors FLC and PEP1 in Brassicaceae species

2017 ◽  
Vol 114 (51) ◽  
pp. E11037-E11046 ◽  
Author(s):  
Julieta L. Mateos ◽  
Vicky Tilmes ◽  
Pedro Madrigal ◽  
Edouard Severing ◽  
René Richter ◽  
...  
Keyword(s):  
Stress Responses ◽  
Regulatory Networks ◽  
Target Genes ◽  
Gene Transcript ◽  
Mads Box ◽  
Core Motif ◽  
The Core ◽  
Brassicaceae Species ◽  
Carg Box ◽  
Species Specific

Genome-wide landscapes of transcription factor (TF) binding sites (BSs) diverge during evolution, conferring species-specific transcriptional patterns. The rate of divergence varies in different metazoan lineages but has not been widely studied in plants. We identified the BSs and assessed the effects on transcription of FLOWERING LOCUS C (FLC) and PERPETUAL FLOWERING 1 (PEP1), two orthologous MADS-box TFs that repress flowering and confer vernalization requirement in the Brassicaceae species Arabidopsis thaliana and Arabis alpina, respectively. We found that only 14% of their BSs were conserved in both species and that these contained a CArG-box that is recognized by MADS-box TFs. The CArG-box consensus at conserved BSs was extended compared with the core motif. By contrast, species-specific BSs usually lacked the CArG-box in the other species. Flowering-time genes were highly overrepresented among conserved targets, and their CArG-boxes were widely conserved among Brassicaceae species. Cold-regulated (COR) genes were also overrepresented among targets, but the cognate BSs and the identity of the regulated genes were usually different in each species. In cold, COR gene transcript levels were increased in flc and pep1-1 mutants compared with WT, and this correlated with reduced growth in pep1-1. Therefore, FLC orthologs regulate a set of conserved target genes mainly involved in reproductive development and were later independently recruited to modulate stress responses in different Brassicaceae lineages. Analysis of TF BSs in these lineages thus distinguishes widely conserved targets representing the core function of the TF from those that were recruited later in evolution.

scholarly journals Authentication, characterization and contamination detection of cell lines, xenografts and organoids by barcode deep NGS sequencing

2020 ◽  
Vol 2 (3) ◽  
Author(s):  
Xiaobo Chen ◽  
Wubin Qian ◽  
Zhenzhen Song ◽  
Qi-Xiang Li ◽  
Sheng Guo
Keyword(s):  
Cell Lines ◽  
Low Cost ◽  
Human Cell Line ◽  
Mouse Cell ◽  
Single Nucleotide ◽  
And Gender ◽  
Species Specific ◽  
Human And Mouse ◽  
Higher Sensitivity ◽  
Short Tandem

Abstract Misidentification and contamination of biobank samples (e.g. cell lines) have plagued biomedical research. Short tandem repeat (STR) and single-nucleotide polymorphism assays are widely used to authenticate biosamples and detect contamination, but with insufficient sensitivity at 5–10% and 3–5%, respectively. Here, we describe a deep NGS-based method with significantly higher sensitivity (≤1%). It can be used to authenticate human and mouse cell lines, xenografts and organoids. It can also reliably identify and quantify contamination of human cell line samples, contaminated with only small amount of other cell samples; detect and quantify species-specific components in human–mouse mixed samples (e.g. xenografts) with 0.1% sensitivity; detect mycoplasma contamination; and infer population structure and gender of human samples. By adopting DNA barcoding technology, we are able to profile 100–200 samples in a single run at per-sample cost comparable to conventional STR assays, providing a truly high-throughput and low-cost assay for building and maintaining high-quality biobanks.

C-banding plus fluorochrome staining shows differences in C-, G-, and R-bands in human and mouse metaphase chromosomes

Genome ◽  
1995 ◽  
Vol 38 (5) ◽  
pp. 864-868 ◽  
Author(s):  
J. L. Bella ◽  
J. Gosálvez ◽  
J. L. Fernández
Keyword(s):  
Mouse Cell ◽  
Structural Factors ◽  
Metaphase Chromosomes ◽  
Fluorochrome Staining ◽  
Banding Patterns ◽  
C Banding ◽  
Dapi Banding ◽  
Species Specific ◽  
L929 Mouse ◽  
Human And Mouse

C-banded slides stained with DAPI or chromomycin A3 show different banding patterns between human and L929 mouse cell line metaphase chromosomes, which are also different from those obtained with standard Giemsa C-banding or fluorochrome staining. Human metaphase chromosomes pretreated for C-banding and stained with DAPI show simultaneous C– and DA–DAPI banding patterns, whilst the mouse metaphase chromosomes show both C-banding and G/Q banding like patterns. However, the chromomycin A3 staining of pre-C-banded metaphase chromosomes reveals conspicuous R-banding in man that is absent in mouse. Chromatin species-specific structural factors would explain these results, which prevent simple comparisons of R-, G-, and C-bands among different organisms. The markers induced by this technique may be of practical use for chromosome identification in human–mouse somatic cell hybridization cultures.Key words: mammalian cytogenetics, chromosome structure, chromosome banding, fluorochrome staining.

scholarly journals Independent Transposon Exaptation Is a Widespread Mechanism of Redundant Enhancer Evolution in the Mammalian Genome

2020 ◽  
Vol 12 (3) ◽  
pp. 1-17
Author(s):  
Nicolai K H Barth ◽  
Lifei Li ◽  
Leila Taher
Keyword(s):  
Convergent Evolution ◽  
Regulatory Networks ◽  
Tissue Specificity ◽  
Target Genes ◽  
Mouse Genome ◽  
Intrinsic Property ◽  
Mammalian Genome ◽  
Fine Tuning ◽  
Evolutionary Advantage ◽  
Species Specific

Abstract Many regulatory networks appear to involve partially redundant enhancers. Traditionally, such enhancers have been hypothesized to originate mainly by sequence duplication. An alternative model postulates that they arise independently, through convergent evolution. This mechanism appears to be counterintuitive to natural selection: Redundant sequences are expected to either diverge and acquire new functions or accumulate mutations and become nonfunctional. Nevertheless, we show that at least 31% of the redundant enhancer pairs in the human genome (and 17% in the mouse genome) indeed originated in this manner. Specifically, for virtually all transposon-derived redundant enhancer pairs, both enhancer partners have evolved independently, from the exaptation of two different transposons. In addition to conferring robustness to the system, redundant enhancers could provide an evolutionary advantage by fine-tuning gene expression. Consistent with this hypothesis, we observed that the target genes of redundant enhancers exhibit higher expression levels and tissue specificity as compared with other genes. Finally, we found that although enhancer redundancy appears to be an intrinsic property of certain mammalian regulatory networks, the corresponding enhancers are largely species-specific. In other words, the redundancy in these networks is most likely a result of convergent evolution.

scholarly journals EPEN-21. IMPAIRED NEURONAL-GLIAL FATE SPECIFICATION IN PEDIATRIC EPENDYMOMA REVEALED BY SINGLE-CELL RNA-SEQ

2020 ◽  
Vol 22 (Supplement_3) ◽  
pp. iii311-iii312
Author(s):  
Bernhard Englinger ◽  
Johannes Gojo ◽  
Li Jiang ◽  
Jens M Hübner ◽  
McKenzie L Shaw ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Single Cell ◽  
Regulatory Networks ◽  
Target Genes ◽  
Target Identification ◽  
Rna Seq ◽  
Cell Models ◽  
Pediatric Ependymoma ◽  
Glial Fate ◽  
Anatomic Locations

Abstract Ependymoma represents a heterogeneous disease affecting the entire neuraxis. Extensive molecular profiling efforts have identified molecular ependymoma subgroups based on DNA methylation. However, the intratumoral heterogeneity and developmental origins of these groups are only partially understood, and effective treatments are still lacking for about 50% of patients with high-risk tumors. We interrogated the cellular architecture of ependymoma using single cell/nucleus RNA-sequencing to analyze 24 tumor specimens across major molecular subgroups and anatomic locations. We additionally analyzed ten patient-derived ependymoma cell models and two patient-derived xenografts (PDXs). Interestingly, we identified an analogous cellular hierarchy across all ependymoma groups, originating from undifferentiated neural stem cell-like populations towards different degrees of impaired differentiation states comprising neuronal precursor-like, astro-glial-like, and ependymal-like tumor cells. While prognostically favorable ependymoma groups predominantly harbored differentiated cell populations, aggressive groups were enriched for undifferentiated subpopulations. Projection of transcriptomic signatures onto an independent bulk RNA-seq cohort stratified patient survival even within known molecular groups, thus refining the prognostic power of DNA methylation-based profiling. Furthermore, we identified novel potentially druggable targets including IGF- and FGF-signaling within poorly prognostic transcriptional programs. Ependymoma-derived cell models/PDXs widely recapitulated the transcriptional programs identified within fresh tumors and are leveraged to validate identified target genes in functional follow-up analyses. Taken together, our analyses reveal a developmental hierarchy and transcriptomic context underlying the biologically and clinically distinct behavior of ependymoma groups. The newly characterized cellular states and underlying regulatory networks could serve as basis for future therapeutic target identification and reveal biomarkers for clinical trials.

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