Genome indexing by histone H3 variants in a single-celled species
Each cell in a multi-cellular organism carries the same genomic content but not all genes are expressed in every cell of the same organism. Multiple mechanisms have been shown to be involved in converting a genome into several lineage-specific “epigenomes”. One of the provocative hypotheses is many similar forms of histone proteins, popularly known as variant histones, may play a crucial role in this process. Among the four core histones, histone H3 variants have been shown to be important in indexing mammalian genomes in transcriptionally active or silenced domains. A centromere-specific histone H3 variant, CENP-A, present in centromeres of most known organisms, is a classic example of how a specialized function can be defined on a eukaryotic chromosome by a histone H3 variant. Most unicellular organisms,such as popular model yeasts,Saccharomyces cerevisiae or Schizosaccharomycespombe,do not need to undergo cellular differentiation. Thus, these organisms have CENP-A but lack variants of canonical histone H3. Interestingly, we discovered presence of both CENP-A and variants of canonical histone H3 in the genomes of a group of single-celled organisms of the CTG clade. I will discuss our results on how CENP-A and other histone H3 variants bar code the genome of a dreaded human pathogen Candida albicans in functionally distinct domains.
Sept 19, 2016
Dr. Jyotsna Dhawan, CSIR Center for Cellular & Molecular Biology, Hyderabad, & Institute for Stem Cell Biology & Regenerative Medicine, Bangalore
Local Host: Siddhartha S. Jana
Venue & Time: C V Raman Hall, Sept 19, 2016
Quiescence and stem cell function-how does a dormant cell contribute to tissue repair?
Abstract: Adult stem cells persist within tissues in a quiescent state (G0), and when activated by damage, contribute to regeneration. Growing evidence supports the view that G0 is a balanced or poised state where both the cell cycle and tissue-specific programs are held in check by active mechanisms. We have used a comparative approach to understanding quiescence, contrasting G0 to terminal differentiation, another mitotically inactive state, where distinct molecular mechanisms drive a tissue-specific program. Using skeletal muscle cells as a model, we find that in G0 myoblasts but not in differentiated myotubes, chromatin mechanisms ensure that repressed cell cycle genes are poised for activation. Genome-wide analysis of RNA polymerase II location and activity supports the emerging picture that polymerase stalling also contributes to maintenance of the poised state. Combined with analysis of gene activation in G1, our findings suggest that these transcriptional control mechanisms impact cell cycle exit and re-entry from quiescence. I will provide a brief introduction to stem cells and then discuss our interest in the quiescent or dormant state of the adult stem cell in tissues that are capable of robust regeneration such as skeletal muscle.
Nov 7, 2016
Dr. Satyajit Rath, National Institute of Immunology, New Delhi, India
Source and consequences of biological diversity: lessons from the immune system
The immune system shows enormous variation, both between individual cells and between individual organisms. Within organisms, quantitative variation in cellular activation in the immune system can have diverse consequences, resulting in heterogeneity in activation and survival as well as in effector programming and function of cells. Between organisms, diversity in immune responses can provide species-survival advantages. I will use our data from a couple of different areas to explain our interest in the sources and consequences of immune heterogeneity. While examining relationships between lymphocyte heterogeneity and functionality, we have found that apparently unimodally distributed heterogeneity among T lymphocytes, which we simplistically expected to be due to intrinsic noise, is not only correlated with major functional variation but is modulated by extrinsic microenvironmental cues in vivo. Further, our results from related investigations suggest that heterogeneity in responding T cell populations is also likely to be a determinant of the familiar dose-response relationships in T cell responses. Finally, I will connect these mouse data-based ideas of heterogeneity to some field evidence in order to illustrate how measurement of heterogeneity can lead to interesting insights into both developmental and functional inter-individual variations in the human immune system.
Fine Tuning Gene Expression in Physiology and Pathophysiology: Implications in Therapeutics
The highly ordered nucleoprotein structure in the eukaryotic nuclei is referred as chromatin. Though DNA sequence is the template for gene expression, the fine tuning of this process is mediated by the epigenetic machinery. Broadly, epigenetics refers to the modification of DNA, and the proteins that help organize the eukaryotic DNA. The protein component of chromatin undergoes several reversible post-translational modifications such as acetylation, methylation, phosphorylation etc., which occur on specific amino acid residues. We have found that lysine acetylation and arginine methylation of histones are essential for regulating the synthesis of mRNA as well as microRNA with functional consequences. The acetylation of proteins assisting transcription activation has also been found to be essential for the activation of gene expression.
In pathophysiological conditions such as cancer, AIDS and in neurodegenerative disorders, homeostasis is affected, and the state of these modifications also undergoes alteration. Hence, enzymes responsible for these modifications could be target for new generation epigenetic therapeutics. We have discovered a few small molecules which specifically target these enzymes and eventually suppress tumor growth, viral multiplication in AIDS and enhance cognate brain function in a model of neurodegeneration. Besides therapeutic implications, these efforts significantly contribute to our understanding of fundamental disease biology.
Feb 6, 2017
Prof. B J Rao, TIFR, Mumbai
Venue & Time: C V Raman Hall, 6th Feb, 2017 at 4:00 PM
Local biochemical problems and non-local solutions in biological designs: some of our recent take-homes
It is a recurring theme that local biochemical reactions often require large-scale systemic non-local changes in cells and tissues, the design of which is not easily intuitive. We explore this theme using DNA Damage Response (DDR) paradigm in normal human cells and Drosophila. We uncover that damaged chromosomes traverse large distances reversibly to repair damaged DNA. Damaged replication forks collapse if the repair remains persistently active where the repair has inbuilt non-local design to attenuate itself. Interestingly, un-repaired dying cells seem to trigger changes across large distances in the tissue-field to provoke additional cellular proliferation, “compensating for death and thereby renewing life”. I illustrate these with examples and argue that most of these biological regulations are based on the “system as a whole” rather than “the parts thereof” based regulation.
Molecular Insights into Meiotic Chromosome Synapsis from Single Molecule Analysis
In humans, defects in meiotic chromosome synapsis and segregation results in aneuploidy leading to miscarriages and genetic disorders. Aneuploidy occurs with much higher probability for the female counterpart, and increases dramatically with age. An evolutionarily conserved meiosis-specific proteinaceous structure, the synaptonemal complex (SC), is required for normal synapsis of meiotic chromosomes. However, very little is known about the biochemical properties of SC components or the mechanisms underlying their roles in meiotic chromosome synapsis and recombination. Structural and functional analysis of Saccharomyces cerevisiae Hop1, a key structural component of SC, has begun to reveal important insights into its function in the synapsis of meiotic chromosomes. Toward this end, we showed that Hop1 is a structure-specific DNA-binding protein, displays higher binding affinity for G-quadruplex DNA and the Holliday junction, and causes structural distortion of the latter at the core of the junction. Using atomic force microscopy and magnetic tweezers techniques, we discovered that Hop1 exhibits the ability to bridge non-contiguous DNA segments into intramolecular stem-loop structures in which the DNA segments are fully synapsed within the filamentous protein stems. Additional evidence suggested that Hop1 folds DNA into rigid protein-DNA filaments and higher-order nucleoprotein structures. Importantly, Hop1 promotes robust intra- and intermolecular synapsis between double-stranded DNA molecules, suggesting that juxtaposition of DNA sequences may assist in strand exchange between homologs by recombination-associated proteins. Furthermore, evidence from in vitro and in vivo studies disclosed the existence of G-quadruplex and i-motif structures at meiosis-specific recombination hot spots. Taken together, these studies support the notion that understanding of meiotic chromosome synapsis and recombination must consider protein binding interactions in conjunction with DNA structural motifs at meiosis-specific recombination hotspots.
Feb 20, 2017
Prof. Dipankar Chatterjee, MBU, IISc., Bangalore
Venue & Time: C V Raman Hall at 3-30 PM to 5-00 PM
Second Messengers (p)ppGppand Cyclic di-GMP mediated regulation of Cell Shape, Cell Division and Antibiotic Sensitivity in Mycobacterium smegmatis
Quorum Sensing, a cell to cell communication phenomenon, is involved in modulating the social behavior of bacteria. Nucleotide based second messengers like (p)ppGpp and c-di-GMP are known to regulate such communication in mycobacteria. (p)ppGpp is synthesized by bacteria to face any kind of stress; while the signalling nucleotide c-di-GMP is synthesized principally to switch from motile (planktonic) to sessile (biofilm) life style. We investigated the effect of disrupting (p)ppGpp and c-di-GMP signalling on the antibiotic sensitivity in M. smegmatis. Using Phenotype Microarray (PM) technology, the growth of Δreland ΔdcpAknock out strains was compared to those of the wild-type and respective complemented strains in 240 different antimicrobials. It was found that the knockout mutants displayed enhanced survival in the presence of multiple antibiotics. The PM data was corroborated by the independent determination of minimum inhibitory concentrations of seven different antibiotics. Microscopy analyses revealed that the Δrel and ΔdcpA strains are elongated, multinucleate and multiseptate in M. smegmatis. The higher levels of (p)ppGpp and c-di-GMP caused M. Smegmatisassume coccoid morphology. The overproduction of (p)ppGpp and c-di-GMP, achieved through overexpression of Rel and DcpA proteins, encased the overexpression strains relOE and dcpAOE in a biofilm like matrix.