Biology subjects

Sivasubbu, S.

Publications and source records attributed to Sivasubbu, S..

28 records · Page 2Linked to original sources

bioRxiv2020

Genome and transcriptome analysis of the mealybug Maconellicoccus hirsutus: A model for genomic Imprinting

In mealybugs, transcriptional inactivation of the entire paternal genome in males, due to genomic imprinting, is closely correlated with sex determination. The sequencing, de-novo assembly and annotation of the mealybug, Maconellicoccus hirsutus genome and its comparison with Planococcus citri genome strengthened our gene identification. The expanded gene classes, in both genomes relate to the high pesticide and radiation resistance; the phenotypes correlating with increased gene copy number rather than the acquisition of novel genes. The complete repertoire of genes for epigenetic regulation and multiple copies of genes for the core members of polycomb and trithorax complexes and the canonical chromatin remodelling complexes are present in both the genomes. Phylogenetic analysis with Drosophila shows high conservation of most genes, while a few have diverged outside the functional domain. The proteins involved in mammalian X-chromosome inactivation are identified in mealybugs, thus demonstrating the evolutionary conservation of factors for facultative heterochromatization. The transcriptome analysis of adult male and female M.hirsutus indicates the expression of the epigenetic regulators and the differential expression of metabolic pathway genes and the genes for sexual dimorphism. The depletion of endosymbionts in males during development is reflected in the significantly lower expression of endosymbiont genes in them. Author summaryThe mealybug system offers a unique model for genomic imprinting and differential regulation of homologous chromosomes that pre-dates the discovery of dosage compensation of X chromosomes in female mammals. In the absence of robust genetics for mealybugs, we generated and analysed the genome and transcriptome profile as primary resources for effective exploration. The expanded gene classes in the mealybugs relate to their unique biology; the expansion of pesticide genes, trehalose transporter, SETMAR and retrotransposons correlate with pesticide, desiccation and radiation resistance, respectively. The similarity in the genomic profile of two species of mealybugs strengthens our gene prediction. All the known epigenetic modifiers and proteins of the primary complexes like the PRC1,2 and the trithorax are conserved in mealybugs, so also the homologues of mammalian proteins involved in X chromosome inactivation. The high copy number of genes for many partners in these complexes could facilitate the inactivation of a large part of the genome and raise the possibility of formation of additional non-canonical complexes for sex specific chromosome inactivation. In adult males and females, the status of epigenetic regulation is likely to be in a maintenance state; therefore, it is of interest to analyze the expression of epigenetic regulators during development.

genomics↗

bioRxiv2020

Genome-wide comparison of DNA methylation between life cycle stages of Drosophila melanogaster using high-throughput sequencing techniques.

Drosophila melanogaster undergoes holometabolous development, has very low levels of DNA methylation, and is known to possess a single known methyltransferase, dDNMT2. This study compares the DNA methylation patterns between the two life cycle stages of D. melanogaster using a combination of DNA immunoprecipitation and high throughput sequencing techniques. Our results indicate, a change in the chromosomal distribution of the sparse DNA methylation concerning genes and natural transposable elements between in the embryo and the adult stages of D. melanogaster. The differentially methylated regions localised on genes involved in the regulation of cell cycle processes of mitotic cell divisions and chromosomal segregation. dDNMT2 knockout flies exhibited altered patterns of DNA methylation. The observed differences in DNA methylation were in genes involved in cellular communication and cytoskeletal functions. The variation in DNA methylation between the two life cycle stages is indicative that it could have a role in regulatory processes during development and, dDNMT2 may have a role as a co-factor for the hitherto undiscovered DNA methyltransferase in D. melanogaster.

genomics↗

bioRxiv2019

Histone code dictates fate biasing of neural crest cells to melanocyte lineage

In the neural crest lineage, progressive fate-restriction and stem cell assignment are critical for both development and regeneration. While the fate-commitment events have distinct transcriptional footprints, fate-biasing is often transitory and metastable, and is thought to be moulded by epigenetic programs. Hence molecular basis of specification is difficult to define. In this study, we establish a role of a histone variant H2a.z.2 in specification of melanocyte lineage from multipotent neural crest cells. Silencing of H2a.z.2 reduces the number of melanocyte precursors in developing zebrafish embryos, and from mouse embryonic stem cells in vitro. We demonstrate that this histone variant occupies nucleosomes in the promoter of key melanocyte determinant Mitf, and enhances its induction. CRISPR-Cas9 based targeted mutagenesis of this gene in zebrafish drastically reduces adult melanocytes, as well as their regeneration. Thereby our study establishes a histone based specification code upstream to the core gene regulatory network in the neural crest lineage of melanocytes. This epigenetic code renders a poised state to the promoter of key determinant and enhances activation by external instructive signals thereby establishing melanocyte fate identity.

developmental biology↗

bioRxiv2019

A temporal map of gene expression pattern during zebrafish liver regeneration

Background & AimsZebrafish is increasingly being used to study liver injury and regeneration. However, very little is known about molecular players that respond to injury and participate in liver regeneration. Here we aim to generate a temporal map of gene expression changes at injury and during regeneration of the adult zebrafish liver.\n\nMethodsWe use a metronidazole-nitroreductase (MTZ-nfsb) based system to selectively ablate hepatocytes in adult zebrafish to create a model for liver injury and regeneration. Through RNA sequencing of liver samples at multiple time points we generate a comprehensive temporal map of gene expression changes during injury and regeneration.\n\nResultsGene expression reveals that soon after injury the immediate early transcription factor MYC induces a battery of genes that respond to the metronidazole-induced ROS by activating oxido-reductase pathways and apoptosis machinery. Upon injury, liver cells down regulate genes encoding complement proteins, bile acid and lipid biosynthesis pathway in a concerted manner. Midway through regeneration, we discover a spike of cholesterol biosynthesis and protein folding machinery genes suggesting an important role for these pathways in liver regeneration.\n\nConclusionsThe temporal transcriptomic map of liver regeneration would serve as a framework for further studies in understanding, and for screening for compounds that augment liver regeneration.\n\nGeneral significanceUsing a hepatocyte specific ablation of zebrafish liver, we create a model of adult liver regeneration. This model was used to generate a comprehensive transcriptomic map of gene expression trends during liver regeneration. This temporal map lays the groundwork to study important events in liver regeneration.\n\nHighlightsO_LIZebrafish is a valuable model for developing therapeutic strategies to augment liver regeneration\nC_LIO_LILiver regeneration in zebrafish is not well studied and pathways poorly understood\nC_LIO_LIWe develop a hepatocyte ablation model of liver injury and regeneration in adult zebrafish\nC_LIO_LIWe generate a comprehensive transcriptomic map of various stages of liver injury and regeneration\nC_LIO_LIWe discover a novel regulation of cholesterol biosynthesis pathways during liver regeneration\nC_LI\n\nGraphical abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=92 SRC=\"FIGDIR/small/677781v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (16K):\norg.highwire.dtl.DTLVardef@13a322corg.highwire.dtl.DTLVardef@1b40200org.highwire.dtl.DTLVardef@ef8f80org.highwire.dtl.DTLVardef@1b61e01_HPS_FORMAT_FIGEXP M_FIG C_FIG

genomics↗

bioRxiv2019

The Vertebrate Codex Gene Breaking Protein Trap Library For Genomic Discovery and Disease Modeling Applications

The zebrafish is a powerful model to explore the molecular genetics and expression of the vertebrate genome. The gene break transposon (GBT) is a unique insertional mutagen that reports the expression of the tagged member of the proteome while generating Cre-revertible genetic alleles. This 1000+ locus collection represents novel codex expression data from the illuminated mRFP protein trap, with 36% and 87% of the cloned lines showcasing to our knowledge the first described expression of these genes at day 2 and day 4 of development, respectively. Analyses of 183 molecularly characterized loci indicate a rich mix of genes involved in diverse cellular processes from cell signaling to DNA repair. The mutagenicity of the GBT cassette is very high as assessed using both forward and reverse genetic approaches. Sampling over 150 lines for visible phenotypes after 5dpf shows a similar rate of discovery of embryonic phenotypes as ENU and retroviral mutagenesis. Furthermore, five cloned insertions were in loci with previously described phenotypes; embryos homozygous for each of the corresponding GBT alleles displayed strong loss of function phenotypes comparable to published mutants using other mutagenesis strategies (ryr1b, fras1, tnnt2a, edar and hmcn1). Using molecular assessment after positional cloning, to date nearly all alleles cause at least a 99+% knockdown of the tagged gene. Interestingly, over 35% of the cloned loci represent 68 mutants in zebrafish orthologs of human disease loci, including nervous, cardiovascular, endocrine, digestive, musculoskeletal, immune and integument systems. The GBT protein trapping system enabled the construction of a comprehensive protein codex including novel expression annotation, identifying new functional roles of the vertebrate genome and generating a diverse collection of potential models of human disease.

genomics↗

bioRxiv2019

Investigating Coronary Artery Disease methylome through targeted bisulfite sequencing

BackgroundGene environment interactions leading to epigenetic alterations play pivotal role in the pathogenesis of Coronary Artery Disease (CAD). Altered DNA methylation is one such epigenetic factor that could lead to altered disease etiology. In this study, we comprehensively identified methylation sites in several genes that have been previously associated with young CAD patients.\n\nMethodsThe study population consisted of 42 healthy controls and 33 young CAD patients (age group < 50 years). We performed targeted bisulfite sequencing of promoter as well as genic regions of several genes in various pathways like cholesterol synthesis and metabolism, endothelial dysfunction, apoptosis, which are implicated in the development of CAD.\n\nResultsWe observed that the genes like GALNT2, HMGCR were hypermethylated in the promoter whereas LDLR gene promoter was hypomethylated indicating that intracellular LDL uptake was higher in CAD patients. Although APOA1 did not show significant change in methylation but APOC3 and APOA5 showed variation in methylation in promoter and exonic regions. Glucokinase (GCK) and endothelial nitric oxide synthase 3 (NOS3) were hyper methylated in the promoter. Genes involved in apoptosis (BAX/BCL2/AKT2) and inflammation (PHACTR1/LCK) also showed differential methylation between controls and CAD patients.\n\nConclusionsThis study is unique because it highlights important gene methylation alterations which might predict the risk of young CAD in Indian population. Large scale studies in different populations would be important for validating our findings and understanding the epigenetic events associated with CAD.

genomics↗

bioRxiv2019

pH controlled histone acetylation amplifies melanocyte differentiation program downstream of MITF

Tanning response and melanocyte differentiation are mediated by the central transcription factor MITF. Enigmatically, these involve rapid and selective induction of melanocyte maturation genes, while concomitantly maintaining the expression of other effectors. In this study using cell-based and zebrafish model systems, we elucidate a pH mediated feed-forward mechanism of epigenetic regulation that enables selective amplification of melanocyte maturation program. We demonstrate that MITF activation directly elevates the expression of Carbonic Anhydrase 14 (Ca14) enzyme. Nuclear localized Ca14 increases the intracellular pH, resulting in the activation of histone acetyl transferase activity of p300/CBP. In turn enhanced H3K27 histone acetylation marks of select differentiation genes facilitates their amplified expression by MITF. CRISPR-mediated targeted missense mutation of CA14 in zebrafish results in immature acidic melanocytes with decreased pigmentation, establishing the centrality of this mechanism in rapidly activating melanocyte differentiation. Thereby we reveal a novel epigenetic control through pH modulation that reinforces a deterministic cell fate by altering chromatin dynamics.

cell biology↗

bioRxiv2018

Identification of novel circadian transcripts in the zebrafish retina

High fecundity, transparent embryos for monitoring the rapid development of organs and the availability of a well-annotated genome has made zebrafish a model organism of choice for developmental biology and neurobiology. This vertebrate model, a favourite in chronobiology studies, shows striking circadian rhythmicity in behaviour. Here, we identify novel genes in the zebrafish genome, which shows their expression in the zebrafish retina. We further resolve the expression pattern over time and assign specific novel transcripts to the retinal cell type, predominantly in the inner nuclear layer. Using chemical ablation and free run experiments we segregate the transcripts that are rhythmic when entrained by light from those that show sustained oscillations in the absence of external cues. The transcripts reported here with rigorous annotation and specific functions in circadian biology provide the groundwork for functional characterisation of novel players in the zebrafish retinal clock.

neuroscience↗

bioRxiv2017

Insights into regeneration from the genome, transcriptome and metagenome analysis of Eisenia fetida

Earthworms show a wide spectrum of regenerative potential with certain species like Eisenia fetida capable of regenerating more than two-thirds of their body while other closely related species, such as Paranais litoralis seem to have lost this ability. Earthworms belong to the phylum annelida, in which the genomes of the marine oligochaete Capitella telata, and the freshwater leech Helobdella robusta have been sequenced and studied. The terrestrial annelids, in spite of their ecological relevance and unique biochemical repertoire, are represented by a single rough genome draft of Eisenia fetida (North American isolate), which suggested that extensive duplications have led to a large number of HOX genes in this annelid. Herein, we report the draft genome sequence of Eisenia fetida (Indian isolate), a terrestrial redworm widely used for vermicomposting assembled using short reads and mate-pair reads. An in-depth analysis of the miRNome of the worm, showed that many miRNA gene families have also undergone extensive duplications. Genes for several important proteins such as sialidases and neurotrophins were identified by RNA sequencing of tissue samples. We also used de novo assembled RNA-Seq data to identify genes that are differentially expressed during regeneration, both in the newly regenerating cells and in the adjacent tissue. Sox4, a master regulator of TGF-beta induced epithelial-mesenchymal transition was induced in the newly regenerated tissue. The regeneration of the ventral nerve cord was also accompanied by the induction of nerve growth factor and neurofilament genes. The metagenome of the worm, characterized using 16S rRNA sequencing, revealed the identity of several bacterial species that reside in the nephridia of the worm. Comparison of the bodywall and cocoon metagenomes showed exclusion of hereditary symbionts in the regenerated tissue. In summary, we present extensive genome, transcriptome and metagenome data to establish the transcriptome and metagenome dynamics during regeneration.

genomics↗

bioRxiv2017

Aminoglycoside Antibiotics Perturb Physiologically Important MicroRNA Contributing To Drug Toxicity

miRNAs are key non-protein coding regulators of gene expression in various pathophysiological conditions. Targeting miRNA with small molecules offer an unconventional approach, where clinically active compounds with RNA binding activity can be tested for their ability to modulate miRNA levels and thus for drug repositioning. Aminoglycoside antibiotics are highly effective microbicidal RNA binding molecules that bind to prokaryotic rRNA secondary structures. Here, we report that specific subsets of miRNA can be modulated by aminoglycosides. However, ototoxicity (cochlear and vestibular) and nephrotoxicity of multiple origins resulting from prolonged use are a well-known disadvantage of aminoglycosides. Mature non-coding RNAs and their precursors can present off-target sites, by forming secondary structures that resemble ribosomal RNA, thus providing an additional molecular basis for the toxicity of aminoglycosides. Using in vitro, in cellulae and physiological responses, we provide evidence for the direct functional perturbation of the miR- 96 cluster leading to selective cell death in neuromasts- the zebrafish equivalent of cochlear hair cells, by Streptomycin, a prototype aminoglycoside antibiotic, thus contributing to the observed ototoxicity. Our observations, collectively underscore the importance of re- evaluating RNA binding drugs for their off-targeting effects in the context of miRNA and other functional non-coding RNA.

cell biology↗