About
Kannanganattu V. Prasanth is a Professor in the Department of Cell and Developmental Biology at the University of Illinois. His research focuses on the regulation of gene expression and RNA biology, with a particular emphasis on long noncoding RNAs (lncRNAs) and their roles in nuclear domain structure and breast cancer progression. Prasanth's laboratory investigates how lncRNAs localized within nuclear domains control gene expression, especially during cancer progression, using cellular and molecular biological approaches. His work has elucidated the functions of several lncRNAs in mammalian cells and their involvement in cancer, with ongoing studies dissecting the mechanisms by which lncRNAs regulate gene expression through modulation of nuclear domains and chromatin structure, cell cycle regulation, and cancer metastasis. A significant focus of Prasanth's research is on nuclear domain-enriched lncRNAs such as MALAT1, a highly conserved nuclear speckle-enriched lncRNA implicated in cancer progression and metastasis. His laboratory demonstrated MALAT1's role in alternative splicing of pre-mRNAs and the organization of splicing factors within nuclear speckles, contributing to understanding the molecular basis of MALAT1's physiological and pathological functions. Additionally, his group studies cell cycle-regulated lncRNAs that influence cell proliferation and cancer progression by regulating protein-coding genes and signaling pathways such as HIPPO. Prasanth's research also extends to characterizing lncRNAs deregulated in triple-negative breast cancer, identifying numerous lncRNAs with aberrant expression during cancer progression and exploring their functional roles in tumor biology. Prasanth earned his M.Sc. from the Vector Control Research Center in Pondicherry, India, and his Ph.D. from the Cytogenetics Laboratory at Banaras Hindu University, Varanasi, India. He completed postdoctoral training at Cold Spring Harbor Laboratory in New York. His laboratory's long-term goal is to unravel the molecular mechanisms by which lncRNAs regulate gene expression and contribute to cancer progression, aiming to develop lncRNA-focused therapeutic strategies. His work has significantly advanced the understanding of lncRNA biology, nuclear domain organization, and their implications in cancer.
Research topics
- Biology
- Cell biology
- Genetics
- Cancer research
- Molecular biology
- Biochemistry
Selected publications
bioRxiv (Cold Spring Harbor Laboratory) · 2026-02-20
articleOpen accessCorrespondingAbstract Intron retention (IR) is increasingly recognized as a feature of long noncoding RNAs (lncRNAs), yet the mechanisms that shape IR in lncRNAs and the functional consequences of this process remain largely unexplored. To investigate how IR contributes to lncRNA regulation, we performed a genome-wide screen to identify factors controlling IR in the lncRNA PURPL . This approach uncovered a prominent role for U2AF2, which promotes retention of a specific intron in PURPL through a weak polypyrimidine tract. IR of this intron drives nuclear enrichment of PURPL and enhances cell proliferation, revealing biological relevance. Transcriptome-wide analyses showed that although U2AF2 broadly supports canonical splicing consistent with its well-established function in promoting splicing, it also facilitates IR within a distinct subset of RNAs, including the nuclear speckle–associated lncRNA MALAT1 . Loss of U2AF2 disrupts MALAT1 speckle localization and using MALAT1 knockout cells reconstituted with wild-type or intron deleted variants, we identified a single intron critical for MALAT1 ’s speckle localization. Deletion of this intron from endogenous MALAT1 impaired speckle localization and reduced cell migration, phenocopying the loss of MALAT1 . Together, these findings reveal IR as a key regulatory mechanism governing lncRNA localization and function and uncover an unexpected role for U2AF2 in promoting IR within specific lncRNA contexts.
Molecular Cell · 2026-03-01 · 2 citations
articleOpen accessSenior authorBPS2025 - Nuclear speckle proteins undergo intrinsic and RNA-dependent microphase separation
Biophysical Journal · 2025-02-01
articleBPS2025 - Nuclear speckle proteins undergo intrinsic and RNA-dependent microphase separation
Biophysical Journal · 2025-02-01
articleNuclear speckle proteins form intrinsic and <i>MALAT1</i> -dependent microphases
bioRxiv (Cold Spring Harbor Laboratory) · 2025-02-27 · 11 citations
preprintOpen accessSummary Nuclear speckles are enriched in serine / arginine rich splicing factors (SRSFs), such as SRSF1. Splicing factors and proteins such as TDP-43 concentrate into distinct speckle territories to enable pre-mRNA processing. We have discovered that SRSFs and TDP-43 are block copolymers and the protein-specific interplay of inter-block repulsions and attractions drives spontaneous microphase separation. This gives rise to size-limited, ordered assemblies, that are 30 – 45 nm in diameter. Depending on the protein, each microphase comprises several tens to hundreds of molecules. The sub-micron scale territories observed in cells are shown to be clusters of microphases. The regulatory lncRNA MALAT1 binds preferentially to SRSF1 microphases to enhance microphase separation and alter microphase structures. Microphase separation enables the concentration of finite numbers of splicing factors into assemblies with distinct nanoscale structures that can be modulated by MALAT1 . Our findings provide a structural framework for the functional organization of splicing factors.
Analytical Chemistry · 2025-09-09 · 1 citations
articleOpen accessInfrared (IR) spectroscopic imaging combines the molecular specificity of vibrational spectroscopy with imaging capabilities of microscopy, potentially allowing for simultaneous quantitative observations of drugs and cellular response. However, accurately quantifying drug concentration within changing cells is complicated by the overlap between exogenous molecules’ and native cellular spectra. Here, we address this challenge by developing a derivative of the widely used chemotherapeutic doxorubicin as a spectral bioprobe (DOX-IR) using a strongly absorbing metal–carbonyl moiety [(Cp)Fe(CO)2]. The developed protocol for synthesis is validated by complete spectral characterization of DOX-IR, and an IR calibration curve is obtained for the two distinguishable peaks within the biosilent spectral region. The strong absorbance allowed cellular uptake of DOX-IR to be quantified using routinely available IR microscopes without any modifications. The capability to quantify drug compounds in a nondestructive and high-throughput manner using IR spectroscopic imaging provides straightforward analysis without perturbing the sample.
Handbooks of Crop Diversity : Conservation and Use of Plant Genetic Resources · 2025-01-01
book-chapter1st authorCorrespondingeLife · 2024-07-01
preprintOpen accessAbstract The IncRNA Malat1 was initially believed to be dispensable for physiology due to the lack of observable phenotypes in Malat1 knockout (KO) mice. However, our study challenges this conclusion. We found that both Malat1 KO and conditional KO mice in the osteoblast lineage exhibit significant osteoporosis. Mechanistically, Malat1 acts as an intrinsic regulator in osteoblasts to promote osteogenesis. Interestingly, Malat1 does not directly affect osteoclastogenesis but inhibits osteoclastogenesis in a non-autonomous manner in vivo via integrating crosstalk between multiple cell types, including osteoblasts, osteoclasts and chondrocytes. Our findings substantiate the existence of a novel remodeling network in which Malat1 serves as a central regulator by binding to β-catenin and functioning through the β-catenin-OPG/Jagged1 pathway in osteoblasts and chondrocytes. In pathological conditions, Malat1 significantly promotes bone regeneration in fracture healing. Bone homeostasis and regeneration are crucial to well-being. Our discoveries establish a previous unrecognized paradigm model of Malat1 function in the skeletal system, providing novel mechanistic insights into how a lncRNA integrates cellular crosstalk and molecular networks to fine tune tissue homeostasis, remodeling and repair.
eLife · 2024-12-13
preprintOpen accessAbstract The IncRNA Malat1 was initially believed to be dispensable for physiology due to the lack of observable phenotypes in Malat1 knockout (KO) mice. However, our study challenges this conclusion. We found that both Malat1 KO and conditional KO mice in the osteoblast lineage exhibit significant osteoporosis. Mechanistically, Malat1 acts as an intrinsic regulator in osteoblasts to promote osteogenesis. Interestingly, Malat1 does not directly affect osteoclastogenesis but inhibits osteoclastogenesis in a non-autonomous manner in vivo via integrating crosstalk between multiple cell types, including osteoblasts, osteoclasts and chondrocytes. Our findings substantiate the existence of a novel remodeling network in which Malatl serves as a central regulator by binding to β-catenin and functioning through the β-catenin-OPG/Jagged1 pathway in osteoblasts and chondrocytes. In pathological conditions, Malat1 significantly promotes bone regeneration in fracture healing. Bone homeostasis and regeneration are crucial to well-being. Our discoveries establish a previous unrecognized paradigm model of Malat1 function in the skeletal system, providing novel mechanistic insights into how a lncRNA integrates cellular crosstalk and molecular networks to fine tune tissue homeostasis, remodeling and repair.
Research Square · 2024-10-11 · 1 citations
preprintOpen access
Frequent coauthors
- 129 shared
Shinichi Nakagawa
Osaka University
- 115 shared
Ruge Chen
Hospital for Special Surgery
- 113 shared
Baohong Zhao
Hospital for Special Surgery
- 113 shared
Yongli Qin
Hospital for Special Surgery
- 111 shared
William M. Ricci
Hospital for Special Surgery
- 107 shared
Cheng Xu
Jianghan University
- 107 shared
Zhonghao Deng
Nanfang Hospital
- 107 shared
Mahmoud Elguindy
Neurological Surgery
Education
- 2007
post doctoral fellowship
Cold Spring Harbor Laboratory
- 2000
Ph.D., Cytogenetics laboratory
Banaras Hindu University
Awards & honors
- EAGER NSF award
- Research Scholar, American Cancer Society
- Cancer Center at Illinois seed grants
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