Generally repressed by epigenetic mechanisms, retrotransposons represent around 40% of the murine genome. At the Agouti viable yellow (Avy) locus, an endogenous retrovirus (ERV) of the intracisternal ...A particle (IAP) class retrotransposed upstream of the agouti coat-color locus, providing an alternative promoter that is variably DNA methylated in genetically identical individuals. This results in variable expressivity of coat color that is inherited transgenerationally. Here, a systematic genome-wide screen identifies multiple C57BL/6J murine IAPs with Avy epigenetic properties. Each exhibits a stable methylation state within an individual but varies between individuals. Only in rare instances do they act as promoters controlling adjacent gene expression. Their methylation state is locus-specific within an individual, and their flanking regions are enriched for CTCF. Variably methylated IAPs are reprogrammed after fertilization and re-established as variable loci in the next generation, indicating reconstruction of metastable epigenetic states and challenging the generalizability of non-genetic inheritance at these regions.
Display omitted
•Repertoire of variably methylated repeat elements defined in inbred mice•VM-IAPs are flanked by CTCF binding sites, and very few act as promoters•Methylation variability is re-established from one generation to the next•Memory of parental methylation state is an exception rather than the rule
A genome-wide interrogation of variably methylated endogenous retroviruses shows common reprogramming of methylation states after fertilization, challenging the paradigm of transgenerational non-genetic inheritance at such loci.
Transcription factors bind DNA in specific sequence contexts. In addition to distinguishing one nucleobase from another, some transcription factors can distinguish between unmodified and modified ...bases. Current models of transcription factor binding tend not to take DNA modifications into account, while the recent few that do often have limitations. This makes a comprehensive and accurate profiling of transcription factor affinities difficult.
Here, we develop methods to identify transcription factor binding sites in modified DNA. Our models expand the standard A/C/G/T DNA alphabet to include cytosine modifications. We develop Cytomod to create modified genomic sequences and we also enhance the MEME Suite, adding the capacity to handle custom alphabets. We adapt the well-established position weight matrix (PWM) model of transcription factor binding affinity to this expanded DNA alphabet. Using these methods, we identify modification-sensitive transcription factor binding motifs. We confirm established binding preferences, such as the preference of ZFP57 and C/EBPβ for methylated motifs and the preference of c-Myc for unmethylated E-box motifs.
Using known binding preferences to tune model parameters, we discover novel modified motifs for a wide array of transcription factors. Finally, we validate our binding preference predictions for OCT4 using cleavage under targets and release using nuclease (CUT&RUN) experiments across conventional, methylation-, and hydroxymethylation-enriched sequences. Our approach readily extends to other DNA modifications. As more genome-wide single-base resolution modification data becomes available, we expect that our method will yield insights into altered transcription factor binding affinities across many different modifications.
Inner mitochondrial membrane fusion and cristae shape depend on optic atrophy protein 1, OPA1. Mutations in
lead to autosomal dominant optic atrophy (ADOA), an important cause of inherited blindness. ...The Guanosin Triphosphatase (GTPase) and GTPase effector domains (GEDs) of OPA1 are essential for mitochondrial fusion; yet, their specific roles remain elusive. Intriguingly, patients carrying
GTPase mutations have a higher risk of developing more severe multisystemic symptoms in addition to optic atrophy, suggesting pathogenic contributions for the GTPase and GED domains, respectively. We studied
GTPase and GED mutations to understand their domain-specific contribution to protein function by analyzing patient-derived cells and gain-of-function paradigms. Mitochondria from
GTPase (c.870+5G>A and c.889C>T) and GED (c.2713C>T and c.2818+5G>A) mutants display distinct aberrant cristae ultrastructure. While all OPA1 mutants inhibited mitochondrial fusion, some GTPase mutants resulted in elongated mitochondria, suggesting fission inhibition. We show that the GED is dispensable for fusion and OPA1 oligomer formation but necessary for GTPase activity. Finally, splicing defect mutants displayed a posttranslational haploinsufficiency-like phenotype but retained domain-specific dysfunctions. Thus, OPA1 domain-specific mutants result in distinct impairments in mitochondrial dynamics, providing insight into OPA1 function and its contribution to ADOA pathogenesis and severity.
Breast cancer is one of the leading causes of woman deaths worldwide, being a major public health problem. It has been reported that the expression of the RNA-editing enzyme Adenosine Deaminase ...Acting on RNAs 1 (ADAR1) is upregulated in breast cancer, predicting poor prognosis in patients. A few reports in literature examine ADAR1 and long non-coding RNAs (lncRNAs) interplay in cancer and suggest key roles in cancer-related pathways. This study aimed to investigate whether ADAR1 could alter the expression levels of lncRNAs and explore how those changes are related to breast cancer biology.
ADAR1 overexpression and knockdown studies were performed in breast cancer cell lines to analyze the effects over lncRNAs expression. Guilt-by-Association correlation analysis of the TCGA-BRCA cohort was performed to predict the function of the lncRNA LINC00944.
Here, we show that LINC00944 is responsive to ADAR1 up- and downregulation in breast cancer cells. We found that LINC00944 expression has a strong relationship with immune signaling pathways. Further assessment of the TCGA-BRCA cohort showed that LINC00944 expression was positively correlated to tumor-infiltrating T lymphocytes and pro-apoptotic markers. Moreover, we found that LINC00944 expression was correlated to the age at diagnosis, tumor size, and estrogen and progesterone receptor expression. Finally, we show that low expression of LINC00944 is correlated to poor prognosis in breast cancer patients.
Our study provides further evidence of the effect of ADAR1 over lncRNA expression levels, and on the participation of LINC00944 in breast cancer, suggesting to further investigate its potential role as prognostic biomarker.
Display omitted
The understanding of host-microbial partnerships has become a hot topic during the last decade as it has been shown that associated microbiota play critical roles in the host physiological functions ...and susceptibility to diseases. Moreover, the microbiome may contribute to host resilience to environmental stressors. The sea anemone Aiptasia is a good laboratory model system to study corals and their microbial symbiosis. In this regard, studying its bacterial microbiota provides a better understanding of cnidarian metaorganisms as a whole. Here, we investigated the bacterial communities of different Aiptasia host-symbiont combinations under long-term heat stress in laboratory conditions. Following a 16S rRNA gene sequencing approach we were able to detect significant differences in the bacterial composition and structure of Aiptasia reared at different temperatures. A higher number of taxa (i.e., species richness), and consequently increased α-diversity and β-dispersion, were observed in the microbiomes of heat-stressed individuals across all host strains and experimental batches. Our findings are in line with the recently proposed Anna Karenina principle (AKP) for animal microbiomes, which states that dysbiotic or stressed organisms have a more variable and unstable microbiome than healthy ones. Microbial interactions affect the fitness and survival of their hosts, thus exploring the AKP effect on animal microbiomes is important to understand host resilience. Our data contributes to the current knowledge of the Aiptasia holobiont and to the growing field of study of host-associated microbiomes.
The use of photovoltaic systems for clean electrical energy has increased. However, due to their low efficiency, researchers have looked for ways to increase their effectiveness and improve their ...efficiency. The Maximum Power Point Tracking (MPPT) inverters allow us to maximize the extraction of as much energy as possible from PV panels, and they require algorithms to extract the Maximum Power Point (MPP). Several intelligent algorithms show acceptable performance; however, few consider using Artificial Neural Networks (ANN). These have the advantage of giving a fast and accurate tracking of the MPP. The controller effectiveness depends on the algorithm used in the hidden layer and how well the neural network has been trained. Articles over the last six years were studied. A review of different papers, reports, and other documents using ANN for MPPT control is presented. The algorithms are based on ANN or in a hybrid combination with FL or a metaheuristic algorithm. ANN MPPT algorithms deliver an average performance of 98% in uniform conditions, exhibit a faster convergence speed, and have fewer oscillations around the MPP, according to this research.
Molecular model represents pieces of evidence, suggesting that LncRNA SOX2‐OT promotes AKT/ERK phosphorylation, as well as histone mark modifications (Activation H3K4me3/H3K27Ac versus Repression ...H3K9me3/H3K27me3) at GLI‐1 and SOX2‐OT gene promoter sequences (Likely SOX2) in a probable indirect manner (Dotted lines). Supporting that LncRNA SOX2‐OT is post‐translational and epigenetically involved in therapy resistance mechanisms, lung cancer malignancy, therapy resistance mechanisms, and clinical prognosis.
The involvement of LncRNA SOX2‐overlapping transcript (SOX2‐OT), SOX2, and GLI‐1 transcription factors in cancer has been well documented. Nonetheless, it is still unknown whether co‐expressed SOX2‐OT/SOX2 or SOX2‐OT/SOX2/GLI‐1 axes are epigenetically/transcriptionally involved in terms of resistance to oncology therapy and in poorer clinical outcomes for patients with lung cancer. We evaluated the role of SOX2‐OT/SOX2 and SOX2‐OT/SOX2/GLI‐1 axes using RT‐qPCR, western blot, immunofluorescence analyses, gene silencing, cellular cytotoxic, and ChIP‐qPCR assays on human cell lines, solid lung malignant tumors, and normal lung tissue. We detected that the SOX2‐OT/SOX2/GLI‐1 axis promotes resistance to tyrosine kinase inhibitor (TKI)‐erlotinib and cisplatin‐based therapy. Evidence from this study show that SOX2‐OT modulates the expression/activation of EGFR‐pathway members AKT/ERK. Further, both SOX2‐OT and GLI‐1 genes are epigenetically regulated at their promoter sequences, in an LncRNA SOX2‐OT‐dependent manner, mainly through modifying the enrichment of the activation histone mark H3K4me3/H3K27Ac, versus the repressive histone mark H3K9me3/H3K27me3. In addition, we identified that inhibition of SOX2‐OT and reduced expression of SOX2/GLI‐1 sensitizes lung cancer cells to EGFR/TKI‐erlotinib or cisplatin‐based treatment. Finally, we show that high co‐expression of SOX2‐OT/SOX2 transcripts and SOX2/GLI‐1 proteins appears to correlate with a poor clinical prognosis and lung malignant phenotype. Collectively, these results present evidence that LncRNA SOX2‐OT modulates an orchestrated resistance mechanism, promoting poor prognosis and human lung malignancy through genetic, epigenetic, and post‐translational mechanisms.
Single-cell RNA-seq has the potential to facilitate isoform quantification as the confounding factor of a mixed population of cells is eliminated. However, best practice for using existing ...quantification methods has not been established. We carry out a benchmark for five popular isoform quantification tools. Performance is generally good for simulated data based on SMARTer and SMART-seq2 data. The reduction in performance compared with bulk RNA-seq is small. An important biological insight comes from our analysis of real data which shows that genes that express two isoforms in bulk RNA-seq predominantly express one or neither isoform in individual cells.
RCOR1 is a known transcription repressor that recruits and positions LSD1 and HDAC1/2 on chromatin to erase histone methylation and acetylation. However, there is currently an incomplete ...understanding of RCOR1's range of localization and function. Here, we probe RCOR1's distribution on a genome-wide scale and unexpectedly find that RCOR1 is predominantly associated with transcriptionally active genes. Biochemical analysis reveals that RCOR1 associates with RNA Polymerase II (POL-II) during transcription and deacetylates its carboxy-terminal domain (CTD) at lysine 7. We provide evidence that this non-canonical RCOR1 activity is linked to dampening of POL-II productive elongation at actively transcribing genes. Thus, RCOR1 represses transcription in two ways-first, via a canonical mechanism by erasing transcriptionally permissive histone modifications through associating with HDACs and, second, via a non-canonical mechanism that deacetylates RNA POL-II's CTD to inhibit productive elongation. We conclude that RCOR1 is a transcription rheostat.
PDF
