Research

Genome organization and cancer resistance

Aug 21 , 2021

The rodents of hystricomorpha and sciuromorpha suborders exhibit remarkably lower incidence of cancer. The underlying genetic basis remains obscure. We report a convergent evolutionary split of human 3p21.31, a locus hosting a large number of tumour-suppressor genes (TSGs) and frequently deleted in several tumour types, in hystrico- and sciuromorphs. Analysis of 34 vertebrate genomes revealed that the synteny of 3p21.31 cluster is functionally and evolutionarily constrained in most placental mammals, but exhibit large genomic interruptions independently in hystricomorphs and sciuromorphs, owing to relaxation of underlying constraints. Hystrico- and sciuromorphs, therefore, escape from pro-tumorigenic co-deletion of several TSGs in cis. The split 3p21.31 sub-clusters gained proximity to proto-oncogene clusters from elsewhere, which might further nullify pro-tumorigenic impact of copy number variations due to co-deletion or co-amplification of genes with opposing effects. The split of 3p21.31 locus coincided with the accelerated rate of its gene expression and the body mass evolution of ancestral hystrico- and sciuromorphs. The genes near breakpoints were associated with the traits specific to hystrico- and sciuromorphs, implying adaptive significance. We conclude that the convergently evolved chromosomal interruptions of evolutionarily constrained 3p21.31 cluster might have impacted evolution of cancer resistance, body mass variation and ecological adaptations in hystrico- and sciuromorphs.

Genome architecture and mono-allelic expression

Aug 21 , 2020

Mammalian genomes exhibit widespread mono-allelic expression of autosomal genes. However, the mechanistic insight that allows specific expression of one allele remains enigmatic. Here, we present evidence that the linear and the three dimensional architecture of the genome ascribes the appropriate framework that guides the mono-allelic expression of genes. We show that: 1) mono-allelically expressed genes are positioned in clusters that are insulated from bi-allelically expressed genes through CTCF mediated chromatin loops; 2) evolutionary and cell-type specific gain and loss of mono-allelic expression coincide respectively with the gain and loss of chromatin insulator sites; 3) dosage of mono-allelically expressed genes is more sensitive to loss of chromatin insulation associated with CTCF depletion as compared to bi-allelically expressed genes; 4) distinct susceptibility of mono- and bi-allelically expressed genes to CTCF depletion can be attributed to distinct functional roles of CTCF around these genes. Altogether, our observations highlight a general topological framework for the mono-allelic expression of genes, wherein the alleles are insulated from the spatial interference of chromatin and transcriptional states from neighbouring bi-allelic domains via CTCF mediated chromatin loops. The study also suggests that 3D genome organization might have evolved under the constraint to mitigate the fluctuations in the dosage of mono-allelically expressed genes, which otherwise are dosage sensitive.

"Position-effect" work is out in Genetics

Apr 19 , 2019

Did position-effect guide the evolutionary dynamics of developmental gene expression? Conserved noncoding elements (CNEs) have significant regulatory influence on their neighbouring genes. Loss of synteny to CNEs through genomic rearrangements can, therefore, impact the transcriptional states of the cognate genes. Yet, the evolutionary implications of such chromosomal position effects have not been studied. Through genome-wide analysis of CNEs and the cognate genes of representative species from 5 different mammalian orders, we observed significant loss of synteny to CNEs in rat lineage. The CNEs and genes losing synteny had significant association with the fetal, but not the post-natal, brain development as assessed through ontology terms, developmental gene expression, chromatin marks and genetic mutations. The loss of synteny correlated with the independent evolutionary loss of fetus-specific upregulation of genes in rat brain. DNA-breakpoints implicated in brain abnormalities of germ-line origin had significant representation between CNE and the gene that exhibited loss of synteny, signifying the underlying developmental tolerance of genomic rearrangements that had allowed the evolutionary splits of CNEs and the cognate genes in rodent lineage. These observations highlighted the non-trivial impact of chromosomal position-effect in shaping the evolutionary dynamics of mammalian brain development and might explain loss of brain traits, like cerebral folding of cortex, in rodent lineage.

Best poster award to Meenakshi from PLoS Genetics

Dec 20 , 2016

Meenakshi Bagadia from our group was awarded PloS Genetics Best Poster award in the  international conference on chromosome stability held on Dec. 15-18 , 2016 at IISER-TVM. She presented her work on "Chromosomal position effect in the evolution of mammalian gene expression". Congratulations !

3D organization of genome might have guided the dynamics of gene order evolution

Mar 02 , 2016

In eukaryotes, genes are non-randomly organized into short gene-dense regions or 'gene-clusters' interspersed by long gene-poor regions. How these gene-clusters have evolved is not entirely clear. Gene duplication may not account for all the gene-clusters since the genes in most of the clusters do not exhibit significant sequence similarity. In this study, using genome-wide datasets from budding yeast, fruit-fly and human, we show that: i) long-range evolutionary repositioning of genes strongly associate with their spatial proximity in the nucleus; ii) presence of evolutionary DNA break-points at involved loci hints at their susceptibility to undergo long-range genomic rearrangements; iii) correlated epigenetic and transcriptional states of engaged genes highlight the underlying evolutionary constraints. The significance of observation i, ii & iii are particularly stronger for the instances of inferred evolutionary gain, as compared to loss, of linear gene-clustering. These observations suggest that the long-range genomic rearrangements guided through 3D genome organization might have contributed to the evolution of gene order. We further hypothesize that the evolution of linear gene-clusters in eukaryotic genomes might have been mediated through spatial interactions among distant loci in order to optimize co-ordinated regulation of genes. We model this hypothesis through a heuristic model of gene-order evolution.

Co-replication, not necessarily co-expression, constrains yeast genome in 3D

Jan 21 , 2016

The underlying functional constraints that shape the three-dimensional organization of eukaryotic genome are not entirely clear. Through comprehensive multivariate analyses of genome-wide datasets, we show that cis and trans interactions in yeast genome have significantly distinct functional associations. In particular, (i) the transinteractions are constrained by coordinated replication and co-varying mutation rates of early replicating domains through interactions among early origins, while cis interactions are constrained by coordination of late replication through interactions among late origins; (ii) cis and transinteractions exhibit differential preference for nucleosome occupancy; (iii)cis interactions are also constrained by the essentiality and co-fitness of interacting genes. Essential gene clusters associate with high average interaction frequency, relatively short-range interactions of low variance, and exhibit less fluctuations in chromatin conformation, marking a physically restrained state of engaged loci that, we suggest, is important to mitigate the epigenetic errors by restricting the spatial mobility of loci. Indeed, the genes with lower expression noise associate with relatively short-range interactions of lower variance and exhibit relatively higher average interaction frequency, a property that is conserved acrossEscherichia coli, yeast, and mESCs. Altogether, our observations highlight the coordination of replication and the minimization of expression noise, not necessarily co-expression of genes, as potent evolutionary constraints shaping the spatial organization of yeast genome.

DNA-binding baits in intrinsically disordered regions

Feb 10 , 2014

Despite recent advances, it is yet not clear how intrinsically disordered regions in proteins recognize their targets without any defined structures. Short linear motifs had been proposed to mediate molecular recognition by disordered regions; however, the underlying structural prerequisite remains elusive. Moreover, the role of short linear motifs in DNA recognition has not been studied. We report a repertoire of short evolutionarily Conserved Recognition Elements (CoREs) in long intrinsically disordered regions, which have very distinct amino-acid propensities from those of known motifs, and exhibit a strong tendency to retain their three-dimensional conformations compared to adjacent regions. The majority of CoREs directly interact with the DNA in the available 3D structures, which is further supported by literature evidence, analyses of ΔΔG values of DNA-binding energies and threading-based prediction of DNA binding potential. CoREs were enriched in cancer-associated missense mutations, further strengthening their functional nature. Significant enrichment of glycines in CoREs and the preference of glycyl ϕ-Ψ values within the left-handed bridge range in the l-disallowed region of the Ramachandran plot suggest that Gly-to-nonGly mutations within CoREs might alter the backbone conformation and consequently the function, a hypothesis that we reconciled using available mutation data. We conclude that CoREs might serve as bait for DNA recognition by long disordered regions and that certain mutations in these peptides can disrupt their DNA binding potential and consequently the protein function. We further hypothesize that the preferred conformations of CoREs and of glycyl residues therein might play an important role in DNA binding. The highly ordered nature of CoREs hints at a therapeutic strategy to inhibit malicious molecular interactions using small molecules mimicking CoRE conformations.

Chromatin loops orchestrate co-transcriptional splicing

June 26, 2013

In collaboration with ENCODE colleagues, we showed that DNase-hypersensitive sites in the exonic regions of genes col-localize to promoters and enhancers through long-range chromatin interactions. The study presents a mechanistic basis of co-transcriptional splicing wherein exons collide with each other and to regulatory elements by excluding the intronic regions into loops. This might ensure the close proximity of spliced exons to assemble the final transcripts. Interestingly, the association is particularly true for the exons which are alternatively spliced suggesting the role of 3D chromatin folding in transcriptional complexity of tissue-specific splice variants.

Systems organization of transcription associated chromatin

Oct 26, 2012

It is becoming increasingly clear that genes are not autonomous transcriptional units; instead, they physically interact with one another to coordinate transcriptional regulation. Using a network approach, Sandhu and colleagues have unravelled an evolutionarily constrained systems organization of transcription-associated chromatin in the human genome. Their article published in Cell Reports present a suggestion at the chromatin level as to how disease-associated mutations evolve and how key cellular genes escape genetic and transcriptional errors.

An integrated encyclopedia of DNA elements in the human genome

Sept. 5, 2012The Encyclopedia of DNA Elements (ENCODE) project systematically mapped genome-wide profiles of transcription, TF binding sites, histone modifications and higher order chromatin architecture in a grand fashion. The project enabled functional annotation of >80% of the genome and nailed down the fact that non-coding regions in the genome are not the junk. Sandhu and colleagues participated in mapping transcription associated long-range chromatin interactions in the genome. The work suggested an extensive physical and regulatory cross-talk among genes and their regulatory elements, which abandons the common presumption of localized control of gene expression.

Minimization of expression noise might have shaped the evolution of three dimensional genome organization

May 1, 2012

There is a possibility that the greater diversity in chromatin interactions of a genomic locus could contribute to stochastic variation in its gene expression. In a recent article in Nucleus, Sandhu showed that genomic regions with nucleosome depletion, abundant and rapid nascent transcription and with essential gene clusters exhibit relatively fewer trans chromatin interactions in the nucleus, while the genes with greater noise showed high mobility in the nuclear space, as predicted from their disproportionally large number of interactions in the cell-population.  Sandhu hypothesized that the three dimensional organization of eukaryotic genomes might have evolved under a selective pressure to minimize the expression noise of essential gene clusters in the nucleus. 

Wide-spread promoter-to-promoter physical interactions in the human genome

Jan. 20, 2012

In a path breaking study, Li, Ruan, Aurbach, Sandhu [equal contributors] et al unraveled that the human genome exhibits wide-spread promoter-to-promoter physical inteactions in the nuclear space. The gene engaged through promoter-promoter not only showed correlated expression profiles, but also showed potential to trans-regulate each other.  Interestingly, promoters with certain enhancer-like chromatin states, could funciton as enhancer and epigenetic errors at such promoters influences the activity of other interacting promoter also.  The observations abadon the traditional view of transcription and blurs the definitions of regulatory elements. The study appeared in Cell 2012, Jan 20; 148 (1-2): 84-98.  The article was ranked among the hottest articles published in Cell and was also reviewed by Faculty 1000. 

Protein-disorder in networks and network-disorder in proteins

Feb, 2012

As a part of  LINK group, we proposed several hypotheses pertaining to structure, function and dynamics  of disordered proteins.  In particular Sandhu proposed the influence of disordered proteins on other higher order networks in the nucleus. Dynamic perturbations in the bottom level network of protein structure can propagate to other interdependent higher order networks, like networks of protein-protein, protein-DNA and DNA-DNA interactions. Therefore, the errors in the protein stability and dynamics could also perturb the higher order networks in a pleiotropic manner.  

Sex-biased non-coding RNAs from regions escaping X-inactivation

July, 2010

In collboratoin with Bjorn Reinius, a swedish pal of mine, we showed that  sexually dimorphic gene expression in mouse is dispersed  among distinct parts of the brain. The sex-biased expression commono to most parts of the brain is generally restricted to the sex chromosomes. Importantly, we identified novel sex-biased non-coding RNAs being transcribed from the regions escaping the X-inactivation. We put forward a proposal that the non-coding transcripts might have some role in mediated the escape of their neighboring genes from X-inactivation.  Expression of  non-coding tanscripts might i) modulate the chromatin state of neighboring coding genes, or, ii) mediate the sub-nuclear localization of escapee domains to transcriptionally active comparrments, or ii) function as boundary elements to limit the leaking of neighboring repressive chromatin to the escapee loci.