Biology subjects

Amador, R.

Publications and source records attributed to Amador, R..

4 recordsLinked to original sources

bioRxiv2024

Expression dynamics of long non-coding RNAs during imaginal disc development and regeneration in Drosophila

The discovery of functional long non-coding RNAs (lncRNAs) changed their initial concept as transcriptional noise. LncRNAs have been found to participate in the regulation of multiple biological processes, including chromatin structure, gene expression, splicing, and mRNA degradation and translation. However, functional studies of lncRNAs are hindered by the usual lack of phenotypes upon deletion or inhibition. Here, we used Drosophila imaginal discs as a model system to identify lncRNAs involved in development and regeneration. We examined a subset of lncRNAs expressed in the wing, leg, and eye disc development. Additionally, we analyzed transcriptomic data from regenerating wing discs to profile the expression pattern of lncRNAs during tissue repair. We focused on the lncRNA CR40469, which is upregulated during regeneration. We generated CR40469 mutant flies that developed normally but showed impaired wing regeneration upon the induction of cell death. The ability of these mutants to regenerate was restored by the ectopic expression of CR40469. Furthermore, we found that the lncRNA CR34335 has a high degree of sequence similarity with CR40469 and can partially compensate for its function during regeneration in the absence of CR40469. Our findings point to a potential role of the lncRNA CR40469 in trans during the response to damage in the wing imaginal disc.

developmental biology↗

bioRxiv2023

Integration of transcription regulation and functional genomic data reveals lncRNA SNHG6's role in hematopoietic differentiation and leukemia

BackgroundLong non-coding RNAs (lncRNAs) are pivotal players in cellular processes, and their unique cell-type specific expression patterns make them attractive biomarkers and therapeutic targets. Yet, the functional roles of most lncRNAs remain enigmatic. To address the need to identify new druggable lncRNAs, we developed a comprehensive approach integrating transcription factor binding data with other genetic features to generate a machine learning model, which we have called INFLAMeR (Identifying Novel Functional LncRNAs with Advanced Machine Learning Resources). MethodsINFLAMeR was trained on high-throughput CRISPR interference (CRISPRi) screens across seven cell lines, and the algorithm was based on 71 genetic features. To validate the predictions, we selected candidate lncRNAs in the K562 leukemia cell line and determined the effect of their knockdown on cell proliferation and chemotherapy drug resistance. We further performed transcriptomic analysis for candidate genes. Based on these findings, we assessed the lncRNA Small Nucleolar RNA Host Gene 6 (SNHG6) for its role in myeloid differentiation by incubation with Phorbol 12-myristate 13-acetate (PMA) to induce megakaryocyte differentiation, or with hemin to induce erythrocyte differentiation. ResultsThe INFLAMeR model successfully reconstituted CRISPRi screening data and predicted functional lncRNAs that were previously overlooked. Intensive cell-based and transcriptomic validation of nearly fifty genes in K562 revealed cell type-specific functionality for 85% of the predicted lncRNAs. Our cell-based and transcriptomic analyses predicted a role for SNHG6 in hematopoiesis and leukemia. Consistent with its predicted role in hematopoietic differentiation, SNHG6 transcription is regulated by hematopoiesis-associated transcription factors. Knockdown of SNHG6 reduced the proliferation of leukemia cells and sensitized them to differentiation. Treatment of K562 leukemic cells with hemin and PMA, respectively, demonstrated that SNHG6 inhibits red blood cell differentiation but strongly promotes megakaryocyte differentiation. Despite SNHG6 transcripts showing strong cytoplasmic enrichment, SNHG6 regulates the expression of hematopoietic genes such as PPBP (Pro-Platelet Basic Protein) and PF4 (Platelet Factor 4). ConclusionsOur approach not only improved the identification and characterization of functional lncRNAs through genomic approaches in a cell type-specific manner, but also identified new lncRNAs with a role in hematopoiesis and leukemia. Such approaches cab be used to identify new targets for precision therapy.

genetics↗

bioRxiv2022

Heme-induced genes facilitate endosymbiont (Sodalis glossinidius) colonization of the tsetse fly (Glossina morsitans) midgut

Tsetse flies (Glossina spp.) feed exclusively on vertebrate blood. After a blood meal, the enteric endosymbiont Sodalis glossinidius is exposed to various environmental stressors including high levels of heme. To investigate how S. glossinidius morsitans (Sgm, the Sodalis subspecies that resides within the gut of G. morsitans) tolerates the heme-induced oxidative environment of tsetses midgut, we used RNAseq to identify bacterial genes that are differentially expressed in cells cultured in high versus lower heme environments. Our analysis identified 436 genes that were significantly differentially expressed (> or < 2-fold) in the presence of high heme [219 heme-induced genes (HIGs) and 217 heme-repressed genes (HRGs)]. HIGs were enriched in Gene Ontology (GO) terms related to regulation of a variety of biological functions, including gene expression and metabolic processes. We observed that 11 out of 13 Sgm genes that were heme regulated in vitro were similarly regulated in bacteria that resided within tsetses midgut 24 hr (high heme environment) and 96 hr (low heme environment) after the flies had consumed a blood meal. We used intron mutagenesis to make insertion mutations in 12 Sgm HIGs and observed no significant change in growth in vitro in any of the mutant strains in high versus low heme conditions. However, Sgm strains that carried mutations in genes encoding a putative undefined phosphotransferase sugar (PTS) system component (SG2427), fucose transporter (SG0182), bacterioferritin (SG2280), and a DNA-binding protein (SGP1-0002) presented growth and/or survival defects in tsetse midguts as compared to normal Sgm. These findings suggest that the uptake up of sugars and storage of iron represent strategies that Sgm employs to successfully reside within the high heme environment of its tsetse hosts midgut. Our results are of epidemiological relevance, as many hematophagous arthropods house gut-associated bacteria that mediate their hosts competency as a vector of disease-causing pathogens. Author summaryTsetse flies feed exclusively on vertebrate blood. This nutrient source contains large quantities of heme, which can be toxic to the flys associated microorganisms. We investigated the genetic mechanisms that underlie the ability of the bacterial endosymbiont, Sodalis glossinidius, to successfully reside within tsetses heme-rich midgut. Exposure of cultured S. glossinidius to high levels of heme induced changes in the expression of genes that encode proteins involved in transcription, replication and repair of DNA, inorganic ion transport, and carbohydrate transport and metabolism processes. Changes in the expression of several of these same S. glossinidius genes also occurred within tsetses midgut following exposure to a blood meal. S. glossinidius genetically engineered to present mutations in several of these heme regulated genes were unable to successfully colonize tsetses gut. Our results provide insight into how bacteria that live in the gut of blood feeding arthropods mitigate the toxic effects of excessive heme. This information is of epidemiological relevance, as many of these bacteria influence their hosts ability to transmit disease pathogens that cause disease in humans and domesticated animals.

microbiology↗

bioRxiv2021

Day-night and seasonal variation of human gene expression across tissues

Circadian and circannual cycles trigger physiological changes whose reflection on human transcriptomes remains largely uncharted. We used the time and season of death of 932 individuals from GTEx to jointly investigate transcriptomic changes associated with those cycles across multiple tissues. Overall, most variation across tissues during day-night and among seasons was unique to each cycle. Although all tissues remodeled their transcriptomes, brain and gonadal tissues exhibited the highest seasonality, whereas those in the thoracic cavity showed stronger day-night regulation. Core clock genes displayed marked day-night differences across multiple tissues, which were largely conserved in baboon and mouse, but adapted to their nocturnal or diurnal habits. Seasonal variation of expression affected multiple pathways and it was enriched among genes associated with the immune response, consistent with the seasonality of viral infections. Furthermore, they unveiled cytoarchitectural changes in brain regions. Altogether, our results provide the first combined atlas of how transcriptomes from human tissues adapt to major cycling environmental conditions.

genomics↗