Biology subjects

Khanduja, J. S.

Publications and source records attributed to Khanduja, J. S..

3 recordsLinked to original sources

bioRxiv2025

The Arabidopsis CYSTM α 5'UTR increases protein production from transgenes in plants and bacteria.

Achieving high levels of transgene expression is often crucial for the effective production of high value pharmaceutical proteins and bioactive compounds. Here, we show a 79-nucleotide sequence of the 5 UTR of the Arabidopsis thaliana cysteine-rich transmembrane module 1 (CYSTM1) significantly increases transient and stable transgene expression at the post-transcriptional level in multicellular plants, A. thaliana and Nicotiana benthamiana, in monocotyledon wheat germ extracts, and in the unicellular bacterium Escherichia coli by up to 7-fold. We also show the 79 nt CYSTM sequence has 50 % higher transgene expression than the broadly used Tobacco Mosaic Virus omega ({Omega}) sequence in both A. thaliana and N. benthamiana. Taken together, this study provides a short transgene expression enhancer for multicellular and unicellular organisms.

plant biology↗

bioRxiv2025

Discrete Subdomains Establish Epigenetic Diversity in Subtelomeric Heterochromatin

Subtelomeres are imperfect repeats adjacent to telomeres that are transcriptionally repressed by heterochromatin. Although essential for genome integrity, their repetitive nature has thwarted dissection of local heterochromatin assembly and maintenance mechanisms. By engineering Schizosaccharomyces pombe strains carrying fluorescent reporters at a single subtelomere, we uncovered distinct subdomains. These subdomains have different silencing requirements: Telomere-proximal regions rely on canonical shelterin- or RNAi-dependent nucleation pathways, whereas telomere-distal regions involve nucleosome remodelers, histone chaperones, and boundary-associated factors. Subdomains also exhibit discrete epigenetic states emerging both at homologous loci on different chromosome arms and along the same subtelomeric sequence. We document these epigenetic states using multi-generational live imaging and targeted perturbations. These analyses show that subtelomeric subdomains display position-specific, clonally variable silencing across a spectrum from robust to fragile epigenetic states. Interestingly, structural variants, common in subtelomeric sequences across eukaryotes, dictate local epigenetic stability. These findings reveal that subtelomeres, long recognized for their sequence variability, form a dynamic mosaic of coexisting epigenetic domains. This implies a wide range of gene-repressive regulatory logic at the chromosome ends, from environmental responsiveness to silencing stability.

genomics↗

bioRxiv2025

Protocol for the development and use of spike-in control for chromatin immunoprecipitation (ChIP) of chromatin-binding proteins

Chromatin immunoprecipitation (ChIP) assays provide quantitative information about the genomic localization of chromatin-binding proteins. However, their sensitivity is limited by several technical variables. To generate high-confidence datasets, in this protocol, we used the Saccharomyces cerevisiae chromatin as an exogenous spike-in control for the ChIP of two S. pombe heterochromatin-associated proteins. This permitted normalization of the ChIP signals based on immunoprecipitation efficiencies across samples. Here, we describe the steps for spike-in control preparation, validation, and its use in data normalization. For complete details on the use and execution of this protocol, please refer to Khanduja et al.1

molecular biology↗