Biology subjects

Batish, M.

Publications and source records attributed to Batish, M..

8 recordsLinked to original sources

bioRxiv2026

Reduced LANCL1-AS1 in old human skeletal muscle diminishes mitochondrial activity, shortens mt-mRNA poly(A) tails, and suppresses myogenesis

Regeneration of skeletal muscle preserves muscle mass and function, which decline with age. Here, we sought to identify long noncoding (lnc)RNAs involved in skeletal muscle myogenesis and potentially relevant to muscle aging. Cross-sectional analysis of skeletal muscle transcriptomes from healthy 22-through 89-year-old individuals revealed lncRNA LANCL1-AS1 among the top declining transcripts. Conversely, LANCL1-AS1 increased robustly during skeletal myogenesis and promoted myogenic differentiation in culture. Affinity pulldown by ChIRP followed by mass spectrometry revealed that LANCL1-AS1 associated with the mitochondrial protein LRPPRC, enhancing the formation of the chaperone complex LRPPRC-SLIRP, which maintains longer poly(A) tails of mitochondrial (mt-)mRNAs and stabilizes mt-mRNAs. Importantly, while myoblasts from old rhesus monkey muscle expressed lower levels of LANCL1-AS1 and mt-mRNAs, and displayed lower mitochondrial activity than young monkey myoblasts, overexpressing LANCL1-AS1 in old myoblasts restored mitochondrial activity and myogenesis. We propose that the age-associated reduction in LANCL1-AS1 contributes to impaired mitochondrial function and reduced myogenic capacity in aging skeletal muscle.

molecular biology↗

bioRxiv2025

EVRCEPT: EV RNA Cargo Enrichment Prediction Tool to predict enrichment of RNA into Extracellular Vesicles

Extracellular vesicles (EVs) are small membrane-bound vesicles that are released by most cells. EVs have been shown to transport molecules including proteins and various types of RNAs between cells of even different types. Furthermore, EV RNAs are shown to modulate gene expression in physiological and pathological conditions in recipient cells which can be utilized in therapeutics by engineering cells to enrich RNA of interest in EVs. However, how specific RNA species are enriched in EVs is a long-standing question in the field. Here, we used sequence features of RNAs to predict its enrichment in EVs. These features include length, nucleotide and dinucleotide frequencies, secondary structure information, number of exons, coding probability for non-coding RNAs as well as RNA binding protein (RBP) motifs. The model achieved a performance (AU-ROC: 90%, 77%) for circRNAs and mRNAs, respectively. Here, we present a web tool called, EV RNA Cargo Enrichment Prediction Tool (EVRCEPT), that allows users to predict likelihood of input RNA to be enriched into EVs. This tool will also provide the list of RBPs that are likely to interact with the input RNA and works with both linear and circular RNAs. This webtool, which is freely accessible at https://euler.dbi.udel.edu/evrcept, will help understand extracellular RNA transport and guide the design of therapeutic RNAs to maximize their incorporation in EVs towards targeted personalized medicine.

bioinformatics↗

bioRxiv2025

Structural Insights into Allosteric Regulation of GdpP: A Conformationally Dynamic Phosphodiesterase

The phosphodiesterase GdpP is a central regulator of the bacterial second messenger c-di-AMP and a key driver of antibiotic resistance in pathogenic Firmicutes. GdpP integrates environmental signals through its sensory PAS domain to control its C-terminal catalytic domain activity, but the molecular basis for this allosteric communication has remained unknown due to the lack of structural data for the complete cytosolic region. Here, we present the first Cryo-EM structures of the cytosolic region of Streptococcus mutans GdpP (SmGdpP74) in multiple conformational states, revealing a sophisticated tetrameric architecture that enables asymmetric catalytic regulation. Our structural and functional analyses demonstrate that SmGdpP74 operates through substrate-induced conformational transition, with the DHHA1 domain interface serving as the primary determinant of asymmetric catalysis. The non-canonical GGDEF domain functions as a tetrameric scaffolding hub that positions the DHH-DHHA1 catalytic domains, representing the first detailed example of a GGDEF domain repurposed to stabilize heterologous catalytic domains. We identify a flexible GGDEF-DHH linker as a critical coupling element that transmits conformational signals between domains, with the conserved KRSR motif acting as a molecular switch for heme-mediated inhibition. Additionally, the flexibility of this linker is essential for the enzymes catalytic activity. Based on these findings, we propose a comprehensive mechanistic model where SmGdpP74 integrates substrate availability with conformational changes for efficient hydrolysis and allosteric control of its enzymatic activity through the PAS domain. These structural insights provide a foundation for rational drug design targeting allosteric regulatory mechanisms in GdpP, potentially offering new approaches to combat antibiotic resistance in pathogenic Firmicutes.

molecular biology↗

bioRxiv2024

Defining the parameters for sorting of different RNA cargo into Extracellular vesicles

Extracellular vesicles (EVs) are small particles that are released by cells and mediate cell-cell communication by transferring bioactive molecules. RNA cargo of EVs, including coding and non-coding RNAs, can change the behavior of recipient cells, affecting processes like gene expression, proliferation, and apoptosis. Circular RNAs (CircRNA) are a newly appreciated class of regulatory RNAs that are stable, resistant to degradation and have been shown to be enriched in EVs. They play key roles in gene regulation and are also emerging as promising biomarkers for disease diagnosis. While microRNAs (miRNAs) are the most well studied RNA cargo of EVs, very little is known about the mechanisms of enrichment of circRNAs as well as long linear RNAs. Here, we take a comprehensive genome-wide approach to investigate the role of GC%, size, exon count, structuredness and coding potential, in the sorting and enrichment of circular and long linear RNAs into EVs. We found that size and structuredness had a significant role in enriching RNAs into EVs which was consistent across all classes of RNAs. Furthermore, we found that structuredness could explain the relative enrichment of circRNAs over their linear counterparts. These results were validated on existing public databases of circular and linear RNAs in EVs. By identifying and analyzing these factors, we aim to better understand the complex mechanisms behind EV-mediated RNA transfer and its impact on cell communication in both health and disease. This mechanistic understanding of RNA enrichment in EVs is crucial for engineering EVs with selective RNA cargo.

cell biology↗

bioRxiv2024

Simultaneous protein and RNA analysis in single extracellular vesicles, including viruses: SPIRFISH

Interest in using nanoparticles for delivery of therapeutic RNA has been steadily growing, provoking a need to precisely understand their structure and contents. Single-particle and single-molecule analysis techniques provide snapshots of single biological nanoparticles, including viruses, liposomes, and extracellular vesicles (EVs). While existing methods primarily focus on protein detection, RNA delivery is becoming increasingly prevalent. A method to simultaneously detect protein and internal RNA in the same particle would reveal variability in size, structure, and RNA packaging efficiency, enabling optimization of nanoparticle delivery. Here, we introduce SPIRFISH, a high-throughput method for single-particle protein and RNA analysis, combining single particle interferometric reflectance imaging sensor (SP-IRIS) with single-molecule fluorescence in-situ hybridization (smFISH). Using SPIRFISH, we detect HIV-1 envelope protein and genomic RNA within single infectious virions, allowing resolution against EV background and noninfectious virions. We further show that SPIRFISH can be used to detect specific RNA within EVs. SPIRFISH should enable single particle analysis of a broad class of RNA-containing nanoparticles. Teaser: A new single particle analysis technique simultaneously detects specific RNA and protein in biological nanoparticles.

molecular biology↗

bioRxiv2023

RNA landscapes of brain tissue and brain tissue-derived extracellular vesicles in simian immunodeficiency virus (SIV) infection and SIV-related central nervous system pathology

IntroductionAntiretroviral treatment regimens can effectively control HIV replication and some aspects of disease progression. However, molecular events in end-organ diseases such as central nervous system (CNS) disease are not yet fully understood, and routine eradication of latent reservoirs is not yet in reach. Brain tissue-derived extracellular vesicles (bdEVs) act locally in the source tissue and may indicate molecular mechanisms in HIV CNS pathology. Regulatory RNAs from EVs have emerged as important participants in HIV disease pathogenesis. Using brain tissue and bdEVs from the simian immunodeficiency virus (SIV) model of HIV disease, we profiled messenger RNAs (mRNAs), microRNAs (miRNAs), and circular RNAs (circRNAs), seeking to identify possible networks of RNA interaction in SIV infection and neuroinflammation. MethodsPostmortem occipital cortex tissue were collected from pigtailed macaques: uninfected controls and SIV-infected subjects (acute phase and chronic phase with or without CNS pathology). bdEVs were separated and characterized in accordance with international consensus standards. RNAs from bdEVs and source tissue were used for sequencing and qPCR to detect mRNA, miRNA, and circRNA levels ResultsMultiple dysregulated bdEV RNAs, including mRNAs, miRNAs, and circRNAs, were identified in acute infection and chronic infection with pathology. Most dysregulated mRNAs in bdEVs reflected dysregulation in their source tissues. These mRNAs are disproportionately involved in inflammation and immune responses, especially interferon pathways. For miRNAs, qPCR assays confirmed differential abundance of miR-19a-3p, let-7a-5p, and miR-29a-3p (acute SIV infection), and miR- 146a-5p and miR-449a-5p (chronic with pathology) in bdEVs. In addition, target prediction suggested that several circRNAs that were differentially abundant in source tissue might be responsible for specific differences in small RNA levels in bdEVs during SIV infection. ConclusionsRNA profiling of bdEVs and source tissues reveals potential regulatory networks in SIV infection and SIV-related CNS pathology.

neuroscience↗

bioRxiv2021

24-nt phasiRNAs move from tapetal to meiotic cells in maize anthers

O_LIIn maize, 24-nt phased, secondary small interfering RNAs (phasiRNAs) are abundant in meiotic stage anthers, but their distribution and functions are not precisely known. C_LIO_LIUsing laser capture microdissection, we analyzed tapetal cells, meiocytes, and other somatic cells at several stages of anther development to establish the timing of 24-PHAS precursor transcripts and the 24-nt phasiRNA products. C_LIO_LIBy integrating RNA and small RNA profiling plus single-molecule and small RNA FISH (smFISH or sRNA-FISH) spatial detection, we demonstrate that the tapetum is the primary site of 24-PHAS precursor and Dcl5 transcripts and the resulting 24-nt phasiRNAs. Interestingly, 24-nt phasiRNAs accumulate in all cell types, with the highest levels in meiocytes, followed by tapetum. C_LIO_LIOur data support the conclusion that 24-nt phasiRNAs are mobile from tapetum to meiocytes and to other somatic cells. We discuss possible roles for 24-nt phasiRNAs in anther cell types. C_LI

plant biology↗

bioRxiv2018

Sex chromosome evolution via two genes

The origin of sex chromosomes has been hypothesized to involve the linkage of factors with antagonistic effects on male and female function. Garden asparagus (Asparagus officinalis L.) is an ideal species to test this hypothesis, as the X and Y chromosomes are cytologically homomorphic and recently evolved from an ancestral autosome pair in association with a shift from hermaphroditism to dioecy. Mutagenesis screens paired with singlemolecule fluorescence in situ hybridization (smFISH) directly implicate Y-specific genes that respectively suppress female organ development and are necessary for male gametophyte development. Comparison of contiguous X and Y chromosome shows that loss of recombination between the genes suppressing female function (SUPPRESSOR OF FEMALE FUNCTION, SOFF) and promoting male function (TAPETAL DEVELOPMENT AND FUNCTION 1, aspTDF1) is due to hemizygosity. We also experimentally demonstrate the function of aspTDF1. These finding provide direct evidence that sex chromosomes can evolve from autosomes via two sex determination genes: a dominant suppressor of femaleness and a promoter of maleness.\n\nOne Sentence SummarySex chromosomes can evolve from autosomes by mutations in two sex determination genes.

genetics↗