scholarly journals Correlation in Expression between LTR Retrotransposons and Potential Host Cis-Targets during Infection of Antherea pernyi with ApNPV Baculovirus

Viruses ◽  
2019 ◽  
Vol 11 (5) ◽  
pp. 421 ◽  
Author(s):  
Min Feng ◽  
Feifei Ren ◽  
Yaohong Zhou ◽  
Nan Zhang ◽  
Qiuyuan Lu ◽  
...  
Keyword(s):  
Full Length ◽  
Differentially Expressed ◽  
Ltr Retrotransposons ◽  
Mtor Signaling Pathway ◽  
Regulation Of Expression ◽  
Solo Ltrs ◽  
In Cis ◽  
The Relationship ◽  
Go Terms ◽  
Gene Element

The published genome sequence of Antheraea yamamai (Saturnnidae) was used to construct a library of long terminal repeat (LTR)-retrotransposons that is representative of the wild silkmoth (Antherea) genus, and that includes 22,666 solo LTRs and 541 full-length LTRs. The LTR retrotransposons of Antheraea yamamai (AyLTRs) could be classified into the three canonical groups of Gypsy, Copia and Belpao. Eleven AyLTRs contained the env gene element, but the relationship with the env element of baculovirus, particularly A. yamamai and pernyi nucleopolyhedrovirus (AyNPV and ApNPV), was distant. A total of 251 “independent” full-length AyLTRs were identified that were located within 100 kb distance (downstream or upstream) of 406 neighboring genes in A. yamamai. Regulation of these genes might occur in cis by the AyLTRs, and the neighboring genes were found to be enriched in GO terms such as “response to stimulus”, and KEGG terms such as “mTOR signaling pathway” among others. Furthermore, the library of LTR-retrotransposons and the A. yamamai genome were used to identify and analyze the expression of LTR-retrotransposons and genes in ApNPV-infected and non-infected A. pernyi larval midguts, using raw data of a published transcriptome study. Our analysis demonstrates that 93 full-length LTR-retrotransposons are transcribed in the midgut of A. pernyi of which 12 significantly change their expression after ApNPV infection (differentially expressed LTR-retrotransposons or DELs). In addition, the expression of differentially expressed genes (DEGs) and neighboring DELs on the chromosome following ApNPV infection suggests the possibility of regulation of expression of DEGs by DELs through a cis mechanism, which will require experimental verification. When examined in more detail, it was found that genes involved in Notch signaling and stress granule (SG) formation were significantly up-regulated in ApNPV-infected A. pernyi larval midgut. Moreover, several DEGs in the Notch and SG pathways were found to be located in the neighborhood of particular DELs, indicating the possibility of DEG-DEL cross-regulation in cis for these two pathways.

scholarly journals Reactivation of transposable elements following hybridization in fission yeast

2021 ◽  
pp. gr.276056.121
Author(s):  
Sergio Tusso ◽  
Fang Suo ◽  
Yue Liang ◽  
Li-Lin Du ◽  
Jochen B.W Wolf
Keyword(s):  
Transposable Elements ◽  
Fission Yeast ◽  
Purifying Selection ◽  
Full Length ◽  
Ltr Retrotransposons ◽  
Sequencing Data ◽  
Genomic Shock ◽  
Solo Ltrs ◽  
Wide Range ◽  
Long Read

Hybridization is thought to reactivate transposable elements (TEs) that were efficiently suppressed in the genomes of the parental hosts. Here, we provide evidence for this 'genomic shock hypothesis' in the fission yeast Schizosaccharomyces pombe. The species is characterized by divergence of two ancestral lineages (Sp and Sk) which have experienced recent, likely human induced, hybridization. We used long-read sequencing data to assemble genomes of 37 samples derived from 31 S. pombe strains spanning a wide range of ancestral admixture proportions. A comprehensive TE inventory revealed exclusive presence of long terminal repeat (LTR) retrotransposons. In-depth sequence analyses of active full-length elements, as well as solo-LTRs, revealed a complex history of homologous recombination. Population genetic analyses of syntenic sequences placed insertion of many solo-LTRs prior to the split of the Sp and Sk lineages. Most full-length elements were inserted more recently after hybridization. With the exception of a single full-length element with signs of positive selection, both solo-LTRs, and in particular, full-length elements carried signatures of purifying selection indicating effective removal by the host. Consistent with reactivation upon hybridization, the number of full-length LTR retrotransposons, varying extensively from zero to 87 among strains, significantly increased with the degree of genomic admixture. This study gives a detailed account of global TE diversity in S. pombe, documents complex recombination histories within TE elements and provides evidence for the ‘genomic shock hypothesis’ with implications for the role of TEs in adaptation and speciation.

scholarly journals Reactivation of transposable elements following hybridization in fission yeast

2021 ◽  
Author(s):  
Sergio Tusso ◽  
Fang Suo ◽  
Yue Liang ◽  
Li-Lin Du ◽  
Jochen B.W Wolf
Keyword(s):  
Transposable Elements ◽  
Fission Yeast ◽  
Purifying Selection ◽  
Full Length ◽  
Ltr Retrotransposons ◽  
Sequencing Data ◽  
Genomic Shock ◽  
Solo Ltrs ◽  
Wide Range ◽  
Long Read

Hybridization is thought to reactivate transposable elements (TEs) that were efficiently suppressed in the genomes of the parental hosts. Here, we provide evidence for this 'genomic shock hypothesis' in the fission yeast Schizosaccharomyces pombe. The species is characterized by divergence of two ancestral lineages (Sp and Sk) which have experienced recent, likely human induced, hybridization. We used long-read sequencing data to assemble genomes of 37 samples derived from 31 S. pombe strains spanning a wide range of ancestral admixture proportions. A comprehensive TE inventory revealed exclusive presence of long terminal repeat (LTR) retrotransposons. In-depth sequence analyses of active full-length elements, as well as solo-LTRs, revealed a complex history of homologous recombination. Population genetic analyses of syntenic sequences placed insertion of many solo-LTRs prior to the split of the Sp and Sk lineages. Most full-length elements were inserted more recently after hybridization. With the exception of a single full-length element with signs of positive selection, both solo-LTRs, and in particular, full-length elements carried signatures of purifying selection indicating effective removal by the host. Consistent with reactivation upon hybridization, the number of full-length LTR retrotransposons, varying extensively from zero to 87 among strains, significantly increased with the degree of genomic admixture. This study provides a detailed account of global TE diversity in S. pombe, documents complex recombination histories within TE elements and provides first evidence for the 'genomic shock hypothesis' in fungi with implications for the role of TEs in adaptation and speciation.

Detection and sequence analysis of an imperfect stem-loop structure in cis activating gene element from SV40PolyA

2011 ◽  
Vol 33 (4) ◽  
pp. 337-346
Author(s):  
Hong-Gang WANG ◽  
Huan MA ◽  
Zhu LI ◽  
Bin ZHANG ◽  
Xiang-Yang JING ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Loop Structure ◽  
Stem Loop ◽  
Stem Loop Structure ◽  
In Cis ◽  
Gene Element

scholarly journals Differential Morpho-Physiological and Transcriptomic Responses to Heat Stress in Two Blueberry Species

2021 ◽  
Vol 22 (5) ◽  
pp. 2481
Author(s):  
Jodi Callwood ◽  
Kalpalatha Melmaiee ◽  
Krishnanand P. Kulkarni ◽  
Amaranatha R. Vennapusa ◽  
Diarra Aicha ◽  
...  
Keyword(s):  
Heat Stress ◽  
Molecular Mechanisms ◽  
Stomatal Closure ◽  
Enrichment Analysis ◽  
Leaf Size ◽  
Vaccinium Corymbosum ◽  
Climatic Conditions ◽  
Differentially Expressed ◽  
Transcriptomic Changes ◽  
Go Terms

Blueberries (Vaccinium spp.) are highly vulnerable to changing climatic conditions, especially increasing temperatures. To gain insight into mechanisms underpinning the response to heat stress, two blueberry species were subjected to heat stress for 6 and 9 h at 45 °C, and leaf samples were used to study the morpho-physiological and transcriptomic changes. As compared with Vaccinium corymbosum, Vaccinium darrowii exhibited thermal stress adaptation features such as small leaf size, parallel leaf orientation, waxy leaf coating, increased stomatal surface area, and stomatal closure. RNAseq analysis yielded ~135 million reads and identified 8305 differentially expressed genes (DEGs) during heat stress against the control samples. In V. corymbosum, 2861 and 4565 genes were differentially expressed at 6 and 9 h of heat stress, whereas in V. darrowii, 2516 and 3072 DEGs were differentially expressed at 6 and 9 h, respectively. Among the pathways, the protein processing in the endoplasmic reticulum (ER) was the highly enriched pathway in both the species: however, certain metabolic, fatty acid, photosynthesis-related, peroxisomal, and circadian rhythm pathways were enriched differently among the species. KEGG enrichment analysis of the DEGs revealed important biosynthesis and metabolic pathways crucial in response to heat stress. The GO terms enriched in both the species under heat stress were similar, but more DEGs were enriched for GO terms in V. darrowii than the V. corymbosum. Together, these results elucidate the differential response of morpho-physiological and molecular mechanisms used by both the blueberry species under heat stress, and help in understanding the complex mechanisms involved in heat stress tolerance.

scholarly journals PacBio full-length transcriptome of wild apple (Malus sieversii) provides insights into canker disease dynamic response

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Xiaojie Liu ◽  
Xiaoshuang Li ◽  
Xuejing Wen ◽  
Yan Zhang ◽  
Yu Ding ◽  
...  
Keyword(s):  
Dynamic Response ◽  
Early Response ◽  
Full Length ◽  
Differentially Expressed ◽  
Late Response ◽  
Response Mechanism ◽  
Necrotrophic Pathogen ◽  
Canker Disease ◽  
Malus Sieversii ◽  
Highly Correlated

Abstract Background Valsa canker is a serious disease in the stem of Malus sieversii, caused by Valsa mali. However, little is known about the global response mechanism in M. sieversii to V. mali infection. Results Phytohormone jasmonic acid (JA) and salicylic acid (SA) profiles and transcriptome analysis were used to elaborate on the dynamic response mechanism. We determined that the JA was initially produced to respond to the necrotrophic pathogen V. mali infection at the early response stage, then get synergistically transduced with SA to respond at the late response stage. Furthermore, we adopted Pacific Biosciences (PacBio) full-length sequencing to identify differentially expressed transcripts (DETs) during the canker response stage. We obtained 52,538 full-length transcripts, of which 8139 were DETs. Total 1336 lncRNAs, 23,737 alternative polyadenylation (APA) sites and 3780 putative transcription factors (TFs) were identified. Additionally, functional annotation analysis of DETs indicated that the wild apple response to the infection of V. mali involves plant-pathogen interaction, plant hormone signal transduction, flavonoid biosynthesis, and phenylpropanoid biosynthesis. The co-expression network of the differentially expressed TFs revealed 264 candidate TF transcripts. Among these candidates, the WRKY family was the most abundant. The MsWRKY7 and MsWRKY33 were highly correlated at the early response stage, and MsWRKY6, MsWRKY7, MsWRKY19, MsWRKY33, MsWRKY40, MsWRKY45, MsWRKY51, MsWRKY61, MsWRKY75 were highly correlated at the late stage. Conclusions The full-length transcriptomic analysis revealed a series of immune responsive events in M. sieversii in response to V. mali infection. The phytohormone signal pathway regulatory played an important role in the response stage. Additionally, the enriched disease resistance pathways and differentially expressed TFs dynamics collectively contributed to the immune response. This study provides valuable insights into a dynamic response in M. sieversii upon the necrotrophic pathogen V. mali infection, facilitates understanding of response mechanisms to canker disease for apple, and provides supports in the identification of potential resistance genes in M. sieversii.

scholarly journals The relationship between the mTOR signaling pathway and ovarian aging in peak-phase and late-phase laying hens

2021 ◽  
Vol 100 (1) ◽  
pp. 334-347
Author(s):  
Er-Ying Hao ◽  
De-He Wang ◽  
Yi-Fan Chen ◽  
Rong-Yan Zhou ◽  
Hui Chen ◽  
...  
Keyword(s):  
Signaling Pathway ◽  
Laying Hens ◽  
Late Phase ◽  
Mtor Signaling ◽  
Mtor Signaling Pathway ◽  
Ovarian Aging ◽  
The Relationship ◽  
Peak Phase

scholarly journals MITOCHONDRIAL DNA VARIANT C2639T IS AN APOE4 RESILIENCE FACTOR

2019 ◽  
Vol 3 (Supplement_1) ◽  
pp. S940-S940
Author(s):  
Brendan Miller ◽  
Su Jeong Kim ◽  
Junxiang Wan ◽  
Hemal H Mehta ◽  
Kelvin Yen ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Temporal Cortex ◽  
Genetic Network ◽  
Differentially Expressed ◽  
Wild Type ◽  
Sporadic Alzheimer’S Disease ◽  
Binding Partner ◽  
Apoe4 Allele ◽  
Cognitively Intact ◽  
The Relationship

Abstract The APOE4 allele is the greatest genetic risk factor for sporadic Alzheimer’s disease, yet select APOE4 carriers remain cognitively intact and become centenarians due to unclear reasons. In order to identify resilience genes for APOE4 carriers, we (1) sequenced whole mitochondrial DNA in a centenarian cohort, (2) searched for differentially expressed genes in the temporal cortex of APOE4 carriers, and (3) experimentally simulated the effects of a novel mitochondrial DNA variant that confers APOE4 resilience. The mitochondrial DNA variant, C2639T, is highly enriched in centenarians and APOE4 carriers, which changes the third amino acid of the mitochondrial-derived peptide humanin from proline to serine (humanin P3S). In addition, APOE4 carriers differentially expressed 127 genes in the humanin genetic network that map back to mitochondrial function. Therefore, we experimentally characterized the relationship between humanin, centenarian-enriched humanin P3S, and APOE. We found that humanin is a novel APOE binding partner, humanin P3S binds APOE nearly 15 times greater than wild type humanin, and humanin P3S modifies the APOE4 metabolic profile.

scholarly journals Slowing of brain atrophy with teriflunomide and delayed conversion to clinically definite MS

2020 ◽  
Vol 13 ◽  
pp. 175628642097075
Author(s):  
Robert Zivadinov ◽  
Michael G. Dwyer ◽  
Ellen Carl ◽  
Elizabeth M. Poole ◽  
Steve Cavalier ◽  
...  
Keyword(s):  
Gray Matter ◽  
Brain Volume ◽  
Clinically Isolated Syndrome ◽  
Phase Iii ◽  
Percent Reduction ◽  
Bottom Quartile ◽  
Core Study ◽  
Cortical Gray Matter ◽  
In Cis ◽  
The Relationship

Background: We explored the effect of teriflunomide on cortical gray matter (CGM) and whole brain (WB) atrophy in patients with clinically isolated syndrome (CIS) from the phase III TOPIC study and assessed the relationship between atrophy and risk of conversion to clinically definite MS (CDMS). Methods: Patients (per McDonald 2005 criteria) were randomized 1:1:1 to placebo, teriflunomide 7 mg, or teriflunomide 14 mg for ⩽108 weeks (core study). In the extension, teriflunomide-treated patients maintained their original dose; placebo-treated patients were re-randomized 1:1 to teriflunomide 7 mg or 14 mg. Brain volume was assessed during years 1–2. Results: Teriflunomide 14 mg significantly slowed annualized CGM and WB atrophy versus placebo during years 1–2 [percent reduction: month 12, 61.4% (CGM; p = 0.0359) and 28.6% (WB; p = 0.0286); month 24, 40.2% (CGM; p = 0.0416) and 43.0% (WB; p < 0.0001)]. For every 1% decrease in CGM or WB volume during years 1–2, risk of CDMS conversion increased by 14.5% ( p =  0.0004) and 47.3% ( p < 0.0001) during years 1–2, respectively, and 6.6% ( p =  0.0570) and 35.9% ( p = 0.0250) during years 1–5. In patients with the least (bottom quartile) versus most (top quartile) atrophy during years 1–2, risk of CDMS conversion was reduced by 58% (CGM; p = 0.0024) and 58% (WB; p = 0.0028) during years 1–2, and 42% (CGM; p = 0.0138) and 29% (WB; p = 0.1912) during years 1–5. Conclusion: These findings support the clinical relevance of CGM and WB atrophy and early intervention with teriflunomide in CIS.

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