Biology subjects

Saini, H.

Publications and source records attributed to Saini, H..

6 recordsLinked to original sources

bioRxiv2026

Genetic compensation in β-actin mutants occurs independently of mutations that destabilize β-actin mRNA

Proper maintenance of gene expression in response to mutations or environmental fluctuations is critical for cell development and survival. Recently, a novel genetic compensation mechanism was described wherein mutant mRNA decay triggers increased transcription of paralogous genes. This effect was reported for several genes, including {beta}-actin (Actb) in mouse embryonic stem cells, where Actb mRNA with a premature termination codon enhances transcription of its paralog, {gamma}-actin (Actg1), and partially rescues cytoskeletal defects. Here we show that, in both mouse and human embryonic stem cells, mutations in the ACTB gene, regardless of mutant mRNA expression, trigger genetic compensation. Furthermore, transgenic expression of mutant ACTB mRNA with a premature stop codon fails to induce genetic compensation. Depletion of the SRF or MRTF-A transcription factors, which are known to increase ACTB transcription in response to low ACTB protein levels, diminishes the genetic compensation response in ACTB mutants. These results suggest that genetic compensation in ACTB mutants is primarily mediated by a transcriptional feedback loop via SRF/MRTF-A, independent of the expression or degradation of mutant ACTB mRNA.

molecular biology↗

bioRxiv2024

Arv1 interacts with and regulates the first step of GPI biosynthesis in Candida albicans

The ubiquitous ARV1 gene shows significant functional conservation across eukaryotes. In humans, it is implicated in early onset epileptic encephalopathy. Evidence suggests that the phenotypes manifested in affected patients are probably due to the deficiency in expression of cell surface GPI anchored proteins. S. cerevisiae Arv1 is proposed to be the elusive GPI flippase that delivers the GPI intermediate from the cytoplasmic face to the luminal side of the ER for further elaboration by the first mannosyltransferase of the pathway. Human and fungal ARV1 complement S. cerevisiae ARV1. Overexpressing some of the GPI-N-acetylglucosamine transferase (GPI-GnT) subunits rescues the null strain of S. cerevisiae ARV1. In mammals and in T. brucei Arv1 co-immunoprecipitates with one or more subunits of the GPI-GnT. Based on these reports we hypothesized a cross-talk for ARV1 with the GPI biosynthetic pathway in the human pathogenic fungus, C. albicans. Using super resolution radial fluctuation (SRRF) analysis for co-localization, co-immunoprecipitation assays, and acceptor-photobleaching Forster resonance energy transfer (FRET) studies, we show that C. albicans Arv1 physically interacts with the GPI-GnT. It also transcriptionally regulates the expression of the GPI-GnT genes to control the GPI biosynthetic pathway via its very first step. Overexpression of one of the GPI-GnT subunits, CaGpi19, in C. albicans ARV1 null strain rescues its cold-sensitive growth, azole sensitivity, cell wall phenotype and GPI-GnT activity. Thus, our results suggest extensive interactions between Arv1 and GPI biosynthesis in C. albicans.

microbiology↗

bioRxiv2023

Requirements for establishment and epigenetic stability of mammalian heterochromatin

Heterochromatic domains of DNA account for a large fraction of mammalian genomes and play critical roles in silencing transposons and genes, but the mechanisms that establish and maintain these domains are not fully understood. Here we use an inducible heterochromatin formation system combined with a CRISPR-based genetic screen to investigate the requirements for the establishment and maintenance of heterochromatin in mouse embryonic stem cells (mESCs). We show that DNA sequence-independent and histone H3 lysine 9 methylation (H3K9me)-dependent heterochromatin can be inherited for a limited number of cell divisions in mESCs but becomes stable upon differentiation. We provide evidence that the increased stability of heterochromatin in differentiated cells results from the downregulation of one or more enzymes that erase H3K9me and DNA methylation. Moreover, we show that in addition to components of the H3K9 and DNA methylation pathways, heterochromatin maintenance requires DHX9 and other RNA processing proteins. DHX9 is an RNA/DNA helicase with previously described roles in preventing genomic instability resulting from transcription-associated replication stress. We found that deletion of DHX9 results in defective heterochromatin inheritance and is associated with increased transcription of major satellite repeats, accumulation of R-loops, and loss of H3K9me. Our findings define the requirements for the establishment and epigenetic inheritance of mammalian heterochromatin and suggest that R-loops and replication stress lead to epigenetic instability.

developmental biology↗

bioRxiv2022

Pseudogenes limit the identification of novel common transcripts generated by their parent genes

The human genome contains numerous duplicated regions, such as parent-pseudogene pairs, causing sequencing reads to align equally well to either gene. The extent to which this ambiguity complicates transcriptomic analyses is currently unknown. This is concerning as many parent genes have been linked to disease, including GBA1, causally linked to both Parkinsons and Gaucher disease. We find that most of the short sequencing reads that map to GBA1, also map to its pseudogene, GBAP1. Using long-read RNA-sequencing in human brain, where all reads mapped uniquely, we demonstrate significant differences in expression compared to short-read data. We identify novel transcripts from both GBA1 and GBAP1, including protein-coding transcripts that are translated in vitro and detected in proteomic data, but that lack GCase activity. By combining long-read with single-nuclear RNA-sequencing to analyse brain-relevant cell types we demonstrate that transcript expression varies by brain region with cell-type-selectivity. Taken together, these results suggest a non-lysosomal function for both GBA1 and GBAP1 in brain. Finally, we demonstrate that inaccuracies in annotation are widespread among parent genes, with implications for many human diseases.

genetics↗

bioRxiv2021

Leveraging omic features with F3UTER enables identification of unannotated 3'UTRs for synaptic genes

There is growing evidence for the importance of 3 untranslated region (3UTR) dependent regulatory processes. However, our current human 3UTR catalogue is incomplete. Here, we developed a machine learning-based framework, leveraging both genomic and tissue-specific transcriptomic features to predict previously unannotated 3UTRs. We identify unannotated 3UTRs associated with 1,513 genes across 39 human tissues, with the greatest abundance found in brain. These unannotated 3UTRs were significantly enriched for RNA binding protein (RBP) motifs and exhibited high human lineage-specificity. We found that brain-specific unannotated 3UTRs were enriched for the binding motifs of important neuronal RBPs such as TARDBP and RBFOX1, and their associated genes were involved in synaptic function and brain- related disorders. Our data is shared through an online resource F3UTER (https://astx.shinyapps.io/F3UTER/). Overall, our data improves 3UTR annotation and provides novel insights into the mRNA-RBP interactome in the human brain, with implications for our understanding of neurological and neurodevelopmental diseases.

bioinformatics↗

bioRxiv2019

Free circular introns with an unusual branchpoint in neuronal projections

The polarized structure of axons and dendrites in neuronal cells depends in part on RNA localization. Previous studies have looked at which polyadenylated RNAs are enriched in neuronal projections or at synapses, but less is known about the distribution of non-adenylated RNAs. By physically dissecting projections from cell bodies of primary rat hippocampal neurons and sequencing total RNA, we found an unexpected set of free circular introns with a non-canonical branchpoint enriched in neuronal projections. These introns appear to be tailless lariats that escape debranching. They lack ribosome occupancy, sequence conservation, and known localization signals, and their function, if any, is not known. Nonetheless, their enrichment in projections has important implications for our understanding of the mechanisms by which RNAs reach distal compartments of asymmetric cells.

cell biology↗