Transposable elements and gene expression during the evolution of amniotes

AbstractBackgroundTransposable elements (TEs) are primarily responsible for the changes in genome sequences that occur over time within and between species. TEs themselves evolve, with clade specific LTR/ERV, LINEs and SINEs responsible for the bulk of species specific genomic features. Because TEs can contain regulatory motifs, they can be exapted as regulators of gene expression. While TE insertions can provide evolutionary novelty for the regulation of gene expression, their overall impact on the evolution of gene expression is unclear. Previous investigators have shown that tissue specific gene expression in amniotes is more similar across species than within species, supporting the existence of conserved developmental gene regulation. In order to understand how species specific TE insertions might affect the evolution/conservation of gene expression, we have looked at the association of gene expression in six tissues with TE insertions in six representative amniote genomes (human, opossum, platypus, anole lizard, bearded dragon and chicken).ResultsWe have used a novel bootstrapping approach to minimise the conflation of effects of repeat types on gene expression. We compared the expression of orthologs containing different types of recent TE insertions to orthologs that contained older TE insertions and found significant differences in gene expression associated with TE insertions. Likewise, we compared the expression of non-ortholog genes containing different types of recent TE insertions to non-orthologs with older TE insertions and found significant differences in gene expression associated with TE insertions. As expected TEs were associated with species-specific changes in gene expression, but the magnitude and direction of change of expression changes were unexpected. Overall, orthologs containing clade specific TEs were associated with lower gene expression, while in non-orthologs, non clade-specific TEs were associated with higher gene expression. Exceptions were SINE elements in human and chicken, which had an opposite association with gene expression compared to other species.ConclusionsOur observed species-specific associations of TEs with gene expression support a role for TEs in speciation/response to selection by species. TEs do not exhibit consistent associations with gene expression and observed associations can vary depending on the age of TE insertions. Based on these observations, it would be prudent to refrain from extrapolating these and previously reported associations to distantly related species.

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Functional evaluation of transposable elements as transcriptional enhancers in mouse embryonic and trophoblast stem cells

10.1101/500322 ◽

2018 ◽

Author(s):

Christopher D. Todd ◽

Özgen Deniz ◽

Miguel R. Branco

Keyword(s):

Gene Expression ◽

Stem Cells ◽

Gene Regulation ◽

Transposable Elements ◽

Regulation Of Gene Expression ◽

Embryonic Stem ◽

Specific Gene ◽

Functional Evaluation ◽

Trophoblast Stem Cells ◽

Trophoblast Stem

AbstractThe recurrent invasion and expansion of transposable elements (TEs) throughout evolution brought with it a vast array of coding and non-coding sequences that can serve as substrates for natural selection. Namely, TEs are thought to have contributed to the establishment of gene regulatory networks via their cis-acting elements. Both the embryonic and extraembryonic lineages of the early mouse embryo are thought to have benefited from the co-option of TEs as distal enhancer elements. However, there is little to no evidence that these particular TEs play significant roles in the regulation of gene expression. Here we tested for roles of TEs as enhancers in mouse embryonic and trophoblast stem cells by combining bioinformatic analyses with genetic and epigenetic editing experiments. Epigenomic and transcriptomic data from wildtype cells suggested that a large number of TEs played a role in the establishment of highly tissue-specific gene expression programmes. Through genetic editing of individual TEs we confirmed a subset of these regulatory relationships. However, a wider survey via CRISPR interference of RLTR13D6 elements in embryonic stem cells revealed that only a minority play significant roles in gene regulation. Our results suggest that a small proportion of TEs contribute to the mouse pluripotency regulatory network, and highlight the importance of functional experiments when evaluating the role of TEs in gene regulation.

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ARID2 Chromatin Remodeler in Hepatocellular Carcinoma

Cells ◽

10.3390/cells9102152 ◽

2020 ◽

Vol 9 (10) ◽

pp. 2152

Author(s):

Robin Loesch ◽

Linda Chenane ◽

Sabine Colnot

Keyword(s):

Gene Expression ◽

Hepatocellular Carcinoma ◽

Associated Factors ◽

Regulation Of Gene Expression ◽

Specific Gene ◽

Chromatin Remodeler ◽

Chromatin Remodelers ◽

Genes Encoding ◽

Gene Alterations

Chromatin remodelers are found highly mutated in cancer including hepatocellular carcinoma. These mutations frequently occur in ARID (AT-rich Interactive Domain) genes, encoding subunits of the ATP-dependent SWI/SNF remodelers. The increasingly prevalent complexity that surrounds the functions and specificities of the highly modular BAF (BG1/BRM-associated factors) and PBAF (polybromo-associated BAF) complexes, including ARID1A/B or ARID2, is baffling. The involvement of the SWI/SNF complexes in diverse tissues and processes, and especially in the regulation of gene expression, multiplies the specific outcomes of specific gene alterations. A better understanding of the molecular consequences of specific mutations impairing chromatin remodelers is needed. In this review, we summarize what we know about the tumor-modulating properties of ARID2 in hepatocellular carcinoma.

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Differential Regulation of Gene Expression of Alveolar Epithelial Cell Markers in Human Lung Adenocarcinoma-Derived A549 Clones

Stem Cells International ◽

10.1155/2015/165867 ◽

2015 ◽

Vol 2015 ◽

pp. 1-20 ◽

Cited By ~ 8

Author(s):

Hiroshi Kondo ◽

Keiko Miyoshi ◽

Shoji Sakiyama ◽

Akira Tangoku ◽

Takafumi Noma

Keyword(s):

Gene Expression ◽

Epithelial Cell ◽

Mapk Pathway ◽

Alveolar Epithelial Cell ◽

Marker Gene ◽

Regulation Of Gene Expression ◽

Surfactant Protein ◽

Specific Gene ◽

Expression Levels ◽

Alveolar Epithelial

Stem cell therapy appears to be promising for restoring damaged or irreparable lung tissue. However, establishing a simple and reproducible protocol for preparing lung progenitor populations is difficult because the molecular basis for alveolar epithelial cell differentiation is not fully understood. We investigated anin vitrosystem to analyze the regulatory mechanisms of alveolus-specific gene expression using a human alveolar epithelial type II (ATII) cell line, A549. After cloning A549 subpopulations, each clone was classified into five groups according to cell morphology and marker gene expression. Two clones (B7 and H12) were further analyzed. Under serum-free culture conditions,surfactant protein C(SPC), an ATII marker, was upregulated in both H12 and B7.Aquaporin 5(AQP5), an ATI marker, was upregulated in H12 and significantly induced in B7. When the RAS/MAPK pathway was inhibited,SPCandthyroid transcription factor-1(TTF-1) expression levels were enhanced. After treatment with dexamethasone (DEX), 8-bromoadenosine 3′5′-cyclic monophosphate (8-Br-cAMP), 3-isobutyl-1-methylxanthine (IBMX), and keratinocyte growth factor (KGF),surfactant protein BandTTF-1expression levels were enhanced. We found that A549-derived clones have plasticity in gene expression of alveolar epithelial differentiation markers and could be useful in studying ATII maintenance and differentiation.

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Profile of a mammalian sperm receptor

Development ◽

10.1242/dev.108.1.1 ◽

1990 ◽

Vol 108 (1) ◽

pp. 1-17 ◽

Cited By ~ 2

Author(s):

P.M. Wassarman

Keyword(s):

Gene Expression ◽

Zona Pellucida ◽

Specific Gene ◽

Mammalian Development ◽

Unique Nature ◽

Mammalian Fertilization ◽

Species Specific ◽

Available Information ◽

Mammalian Eggs ◽

Sperm Receptor

Complementary molecules on the surface of eggs and sperm are responsible for species-specific interactions between gametes during fertilization in both plants and animals. In this essay, several aspects of current research on the mouse egg receptor for sperm, a zona pellucida glycoprotein called ZP3, are addressed. These include the structure, synthesis, and functions of the sperm receptor during oogenesis and fertilization in mice. Several conclusions are drawn from available information. These include (I) ZP3 is a member of a unique class of glycoproteins found exclusively in the extracellular coat (zona pellucida) of mammalian eggs. (II) ZP3 gene expression is an example of oocyte-specific and, therefore, sex-specific gene expression during mammalian development. (III) ZP3 is a structural glycoprotein involved in assembly of the egg extracellular coat during mammalian oogenesis. (IV) ZP3 is a sperm receptor involved in carbohydrate-mediated gamete recognition and adhesion during mammalian fertilization. (V) ZP3 is an inducer of sperm exocytosis (acrosome reaction) during mammalian fertilization. (VI) ZP3 participates in the secondary block to polyspermy following fertilization in mammals. (VII) The extracellular coat of other mammalian eggs contains a glycoprotein that is functionally analogous to mouse ZP3. The unique nature, highly restricted expression, and multiple roles of ZP3 during mammalian development make this glycoprotein a particularly attractive subject for investigation at both the cellular and molecular levels.

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Evolution of New cis-Regulatory Motifs Required for Cell-Specific Gene Expression in Caenorhabditis

PLoS Genetics ◽

10.1371/journal.pgen.1006278 ◽

2016 ◽

Vol 12 (9) ◽

pp. e1006278 ◽

Cited By ~ 12

Author(s):

Michalis Barkoulas ◽

Amhed M. Vargas Velazquez ◽

Alexandre E. Peluffo ◽

Marie-Anne Félix

Keyword(s):

Gene Expression ◽

Specific Gene ◽

Regulatory Motifs ◽

Specific Gene Expression

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Transposable Elements in the Organization and Diversification of the Genome of Aegilops speltoides Tausch (Poaceae, Triticeae)

International Journal of Genomics ◽

10.1155/2018/4373089 ◽

2018 ◽

Vol 2018 ◽

pp. 1-9 ◽

Cited By ~ 3

Author(s):

Olga Raskina

Keyword(s):

Transposable Elements ◽

Mobile Element ◽

Plant Genome ◽

Aegilops Speltoides ◽

Genome Architecture ◽

Different Types ◽

In The Wild ◽

Species Specific ◽

Current Species

Repetitive DNA—specifically, transposable elements (TEs)—is a prevailing genomic fraction in cereals that underlies extensive genome reshuffling and intraspecific diversification in the wild. Although large amounts of data have been accumulated, the effect of TEs on the genome architecture and functioning is not fully understood. Here, plant genome organization was addressed by means of cloning and sequencing TE fragments of different types, which compose the largest portion of the Aegilops speltoides genome. Individual genotypes were analyzed cytogenetically using the cloned TE fragments as the DNA probes for fluorescence in situ hybridization (FISH). The obtained TE sequences of the Ty1-copia, Ty3-gypsy, LINE, and CACTA superfamilies showed the relatedness of the Ae. speltoides genome to the Triticeae tribe and similarities to evolutionarily distant species. A significant number of clones consisted of intercalated fragments of TEs of various types, in which Fatima (Ty3-gypsy) sequences predominated. At the chromosomal level, different TE clones demonstrated sequence-specific patterning, emphasizing the effect of the TE fraction on the Ae. speltoides genome architecture and intraspecific diversification. Altogether, the obtained data highlight the current species-specific organization and patterning of the mobile element fraction and point to ancient evolutionary events in the genome of Ae. speltoides.

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Differential evolution in 3′UTRs leads to specific gene expression in Staphylococcus

Nucleic Acids Research ◽

10.1093/nar/gkaa047 ◽

2020 ◽

Vol 48 (5) ◽

pp. 2544-2563 ◽

Cited By ~ 2

Author(s):

Pilar Menendez-Gil ◽

Carlos J Caballero ◽

Arancha Catalan-Moreno ◽

Naiara Irurzun ◽

Inigo Barrio-Hernandez ◽

...

Keyword(s):

Gene Expression ◽

Gene Expression Regulation ◽

Bacterial Species ◽

Regulatory Elements ◽

Specific Gene ◽

Species Differentiation ◽

Orthologous Genes ◽

Genome Wide ◽

Sequence Variations ◽

Species Specific

Abstract The evolution of gene expression regulation has contributed to species differentiation. The 3′ untranslated regions (3′UTRs) of mRNAs include regulatory elements that modulate gene expression; however, our knowledge of their implications in the divergence of bacterial species is currently limited. In this study, we performed genome-wide comparative analyses of mRNAs encoding orthologous proteins from the genus Staphylococcus and found that mRNA conservation was lost mostly downstream of the coding sequence (CDS), indicating the presence of high sequence diversity in the 3′UTRs of orthologous genes. Transcriptomic mapping of different staphylococcal species confirmed that 3′UTRs were also variable in length. We constructed chimeric mRNAs carrying the 3′UTR of orthologous genes and demonstrated that 3′UTR sequence variations affect protein production. This suggested that species-specific functional 3′UTRs might be specifically selected during evolution. 3′UTR variations may occur through different processes, including gene rearrangements, local nucleotide changes, and the transposition of insertion sequences. By extending the conservation analyses to specific 3′UTRs, as well as the entire set of Escherichia coli and Bacillus subtilis mRNAs, we showed that 3′UTR variability is widespread in bacteria. In summary, our work unveils an evolutionary bias within 3′UTRs that results in species-specific non-coding sequences that may contribute to bacterial diversity.

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Inducible cell-specific mouse models for paired epigenetic and transcriptomic studies of microglia and astroglia

Communications Biology ◽

10.1038/s42003-020-01418-x ◽

2020 ◽

Vol 3 (1) ◽

Cited By ~ 1

Author(s):

Ana J. Chucair-Elliott ◽

Sarah R. Ocañas ◽

David R. Stanford ◽

Victor A. Ansere ◽

Kyla B. Buettner ◽

...

Keyword(s):

Gene Expression ◽

Affinity Purification ◽

Regulation Of Gene Expression ◽

Cell Types ◽

Tissue Level ◽

Cell Phenotype ◽

Specific Gene ◽

Cell Type ◽

A Cell ◽

Cell Type Specific

AbstractEpigenetic regulation of gene expression occurs in a cell type-specific manner. Current cell-type specific neuroepigenetic studies rely on cell sorting methods that can alter cell phenotype and introduce potential confounds. Here we demonstrate and validate a Nuclear Tagging and Translating Ribosome Affinity Purification (NuTRAP) approach for temporally controlled labeling and isolation of ribosomes and nuclei, and thus RNA and DNA, from specific central nervous system cell types. Analysis of gene expression and DNA modifications in astrocytes or microglia from the same animal demonstrates differential usage of DNA methylation and hydroxymethylation in CpG and non-CpG contexts that corresponds to cell type-specific gene expression. Application of this approach in LPS treated mice uncovers microglia-specific transcriptome and epigenome changes in inflammatory pathways that cannot be detected with tissue-level analysis. The NuTRAP model and the validation approaches presented can be applied to any brain cell type for which a cell type-specific cre is available.

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Cohesin-dependent regulation of gene expression during differentiation is lost in cohesin-mutated myeloid malignancies

Blood ◽

10.1182/blood.2019001553 ◽

2019 ◽

Vol 134 (24) ◽

pp. 2195-2208 ◽

Cited By ~ 9

Author(s):

Daniel Sasca ◽

Haiyang Yun ◽

George Giotopoulos ◽

Jakub Szybinski ◽

Theo Evan ◽

...

Keyword(s):

Gene Expression ◽

Acute Myeloid Leukemia ◽

Myeloid Leukemia ◽

Potential Role ◽

Regulation Of Gene Expression ◽

Specific Gene ◽

Myeloid Malignancy ◽

Erythroid Maturation ◽

Acute Myeloid

Cohesin mutations are common in myeloid malignancy. Sasca et al elucidate the potential role of cohesin loss in myelodysplastic syndrome and acute myeloid leukemia (MDS/AML). They demonstrate that cohesin binding is critical for erythroid-specific gene expression and that reduction in cohesin impairs terminal erythroid maturation and promotes myeloid malignancy.

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Roles of Transposable Elements in the Different Layers of Gene Expression Regulation

International Journal of Molecular Sciences ◽

10.3390/ijms20225755 ◽

2019 ◽

Vol 20 (22) ◽

pp. 5755 ◽

Cited By ~ 4

Author(s):

Denise Drongitis ◽

Francesco Aniello ◽

Laura Fucci ◽

Aldo Donizetti

Keyword(s):

Gene Expression ◽

Transposable Elements ◽

Gene Expression Regulation ◽

Regulation Of Gene Expression ◽

Chromatin Modification ◽

Essential Element ◽

Protein Translation ◽

Expression Regulation ◽

Molecular Processes ◽

Eukaryotic Genomes

The biology of transposable elements (TEs) is a fascinating and complex field of investigation. TEs represent a substantial fraction of many eukaryotic genomes and can influence many aspects of DNA function that range from the evolution of genetic information to duplication, stability, and gene expression. Their ability to move inside the genome has been largely recognized as a double-edged sword, as both useful and deleterious effects can result. A fundamental role has been played by the evolution of the molecular processes needed to properly control the expression of TEs. Today, we are far removed from the original reductive vision of TEs as “junk DNA”, and are more convinced that TEs represent an essential element in the regulation of gene expression. In this review, we summarize some of the more recent findings, mainly in the animal kingdom, concerning the active roles that TEs play at every level of gene expression regulation, including chromatin modification, splicing, and protein translation.

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