Biology subjects

Rajachandran, S.

Publications and source records attributed to Rajachandran, S..

4 recordsLinked to original sources

bioRxiv2026

Extrachromosomal Circular DNA Function as Mobile Elements to Alter the Mammalian Germline Genome

The viability of any species including the human requires that the germline genome is kept stable as it is transmitted across generations by the germ cells. Failure to safeguard the genome integrity and stability would lead to inherited diseases and infertility. Thus, a better understanding of the mechanisms that alter the germline genome is crucial to ensure human health and our continuation as a species. Here, we show that the extrachromosomal circular DNA (eccDNA) in the mouse and human male germline represents a new mechanism in altering the mammalian germline genome. To enable the tracking of germline eccDNA in vivo, we established a novel mouse model that allows the generation of a reporter eccDNA in a cell type-specific manner. Using this mouse model, we showed that eccDNA formed in the developing male germ cells can integrate into the germline genome. Using eccDNA-containing sperm for in vitro fertilization led to the eccDNA sequence being inherited by the embryos. By analyzing a large cohort of long-read whole genome sequencing data, we showed that eccDNA-mediated germline genome insertions represent an important source of human genome structural variations. Finally, by leveraging human sperm samples, we found that diabetes induces an increase in sperm eccDNA quantity, which is mediated at least in part through poly (ADP-ribose) polymerases. Together, our results provide new insights into how the mammalian germline genome can be altered, with important implications for human health and genome evolution.

developmental biology↗

bioRxiv2026

ECHOS enables spatial epigenome profiling at subcellular resolution

Biological structures and the epigenome are intertwined. For example, complex tissues are often the combined products of various groups of spatially patterned cell types with distinct epigenetic states. Furthermore, chromatin at various subnuclear locations within a cell often differ in their epigenetic properties. Thus, a systematic understanding of the relationship between the epigenome and its spatial distribution across biological scales would inform tissue and cellular functions as well as gene regulatory mechanisms. Yet, spatially resolved epigenome profiling--particularly at subcellular resolution--remains technically challenging. Here, we present Epigenetic CUT&Tag via High-resolution Optical Selection (ECHOS), a platform that combines high-resolution imaging and high-throughput sequencing to enable precise, spatially targeted epigenetic profiling across biological scales. At the cellular scale, ECHOS generates high-quality DNA-binding protein and histone modification datasets that show strong concordances with datasets from ChIP-seq and CUT&Tag experiments. Further optimization of ECHOS (ECHOS+) enables the characterization of the histone modification landscape of chromatin at the sub-micron resolution. Using ECHOS+, we revealed distinct gene regulatory logics at different layers of human ectocervical epithelium. We also showed that micronuclei--small nucleus-like structures formed by mitotic errors--exhibited a different epigenetic state from the same chromosome regions on the intact nuclei. Finally, we found that human aging altered the epigenetic state of the inactive X chromosome located in a subcellular nuclear structure called the Barr body, which may contribute to genes escaping X chromosome inactivation during female aging. Together, ECHOS and ECHOS+ represent a scalable and generalizable framework for spatial epigenomic analyses, with broad potential applications in various domains of biology.

genetics↗

bioRxiv2024

Subcellular Level Spatial Transcriptomics with PHOTON

The subcellular localization of RNA is closely linked to its function. Many RNA species are partitioned into organelles and other subcellular compartments for storage, processing, translation, or degradation. Thus, capturing the subcellular spatial distribution of RNA would directly contribute to the understanding of RNA functions and regulation. Here, we present PHOTON (Photoselection of Transcriptome over Nanoscale), a method which combines high resolution imaging with high throughput sequencing to achieve spatial transcriptome profiling at subcellular resolution. We demonstrate PHOTON as a versatile tool to accurately capture the transcriptome of target cell types in situ at the tissue level such as granulosa cells in the ovary, as well as RNA content within subcellular compartments such as the nucleolus and the stress granule. Using PHOTON, we also reveal the functional role of m6A modification on mRNA partitioning into stress granules. These results collectively demonstrate that PHOTON is a flexible and generalizable platform for understanding subcellular molecular dynamics through the transcriptomic lens.

genomics↗

bioRxiv2024

Functional and Clinical Implications of Extrachromosomal Circular DNA in the Human Germline

Extrachromosomal circular DNA (eccDNA) originates from linear chromosomal DNA and can be found in various human cell types including the male germline. However, the functional effects and biogenesis mechanisms of the eccDNA in the human male germline are not well understood. Here, we developed a sequencing approach to extract eccDNA sequence information and the paired transcriptome information from the same cells. By applying this approach to human samples, we found evidence of transcriptional activities of germline eccDNAs. We also showed that patients with chronic diseases such as hypertension and diabetes had a significantly higher number of eccDNAs in the sperm than their healthy counterparts. This was, at least partly, due to an increased apoptosis signaling in the germline. Analysis of single cell RNA sequencing data of spermatogenic cells from diabetic patients vs. healthy individuals suggested that a dysregulation in the expression levels of multiple poly (ADP-ribose) polymerases may contribute to the increased amount of germline eccDNAs in diseased patients. In addition, we identified a potential horizontal transfer mechanism through which healthy sperm can take up eccDNAs from their surrounding microenvironment. Together, our results suggest that eccDNA may have functional effects on the germline, and it may serve as a non-invasive clinical biomarker for human health.

genomics↗