TY - JOUR T1 - DDX24 is required for muscle fiber organization and the suppression of wound-induced Wnt activity necessary for pole re-establishment during planarian regeneration. JF - Dev Biol Y1 - 2022 A1 - Sarkar, Souradeep R A1 - Dubey, Vinay Kumar A1 - Jahagirdar, Anusha A1 - Lakshmanan, Vairavan A1 - Haroon, Mohamed Mohamed A1 - Sowndarya, Sai A1 - Sowdhamini, Ramanathan A1 - Palakodeti, Dasaradhi AB -

Planarians have a remarkable ability to undergo whole-body regeneration. Successful regeneration outcome is determined by processes like polarity establishment at the wound site, which is followed by pole (organizer) specification. Interestingly, these determinants are almost exclusively expressed by muscles in these animals. However, the molecular toolkit that enables the functional versatility of planarian muscles remains poorly understood. Here we report that SMED_DDX24, a D-E-A-D Box RNA helicase, is necessary for planarian survival and regeneration. We found that DDX24 is enriched in muscles and its knockdown disrupts muscle fiber organization. This leads to defective pole specification, which in turn results in misregulation of many positional control genes specifically during regeneration. ddx24 RNAi also upregulates wound-induced Wnt signalling. Suppressing this ectopic Wnt activity rescues the knockdown phenotype by enabling better anterior pole regeneration. To summarize, our work highlights the role of an RNA helicase in muscle fiber organization, and modulating amputation-induced wnt levels, both of which seem critical for pole re-organization, thereby regulating whole-body regeneration.

VL - 488 ER - TY - JOUR T1 - S. mediterranea ETS-1 regulates the function of cathepsin-positive cells and the epidermal lineage landscape via basement membrane remodeling. JF - J Cell Sci Y1 - 2022 A1 - Dubey, Vinay Kumar A1 - Sarkar, Souradeep R A1 - Lakshmanan, Vairavan A1 - Dalmeida, Rimple A1 - Gulyani, Akash A1 - Palakodeti, Dasaradhi KW - Animals KW - Basement Membrane KW - Cathepsins KW - Cell Differentiation KW - Epidermis KW - Humans KW - Matrix Metalloproteinases KW - Mediterranea KW - Planarians KW - Transcription Factors AB -

Extracellular matrix (ECM) is an important component of stem cell niche. Remodeling of ECM mediated by ECM regulators, such as matrix metalloproteinases (MMPs) plays a vital role in stem cell function. However, the mechanisms that modulate the function of ECM regulators in the stem cell niche are understudied. Here, we explored the role of the transcription factor (TF) ETS-1, which is expressed in the cathepsin-positive cell population, in regulating the expression of the ECM regulator, mt-mmpA, thereby modulating basement membrane thickness. In planarians, the basement membrane around the gut/inner parenchyma is thought to act as a niche for pluripotent stem cells. It has been shown that the early epidermal progenitors migrate outwards from this region and progressively differentiate to maintain the terminal epidermis. Our data shows that thickening of the basement membrane in the absence of ets-1 results in defective migration of stem cell progeny. Furthermore, the absence of ets-1 leads to a defective epidermal progenitor landscape, despite its lack of expression in those cell types. Together, our results demonstrate the active role of ECM remodeling in regulating tissue homeostasis and regeneration in the planarian Schmidtea mediterranea. This article has an associated First Person interview with one of the co-first authors of the paper.

VL - 135 IS - 20 ER - TY - JOUR T1 - Comprehensive annotation and characterization of planarian tRNA and tRNA-derived fragments (tRFs). JF - RNA Y1 - 2021 A1 - Lakshmanan, Vairavan A1 - T N, Sujith A1 - Bansal, Dhiru A1 - Padubidri, Shivaprasad V A1 - Palakodeti, Dasaradhi A1 - Krishna, Srikar AB -

tRNA-derived fragments (tRFs) have recently gained a lot of scientific interest due to their diverse regulatory roles in several cellular processes. However, their function in dynamic biological process such as development and regeneration remains unexplored. Here, we show that tRFs are dynamically expressed during planarian regeneration suggesting a possible role for these small RNAs in the regulation of regeneration. In order to characterise planarian tRFs, we first annotated 457 tRNAs in S.mediterranea combining two tRNA prediction algorithms. Annotation of tRNAs facilitated the identification of three main species of tRFs in planarians - the shorter tRF-5s and itRFs, and the abundantly expressed 5'-tsRNAs. Spatial profiling of tRFs in sequential transverse sections of planarians revealed diverse expression patterns of these small RNAs, including those that are enriched in the head and pharyngeal regions. Expression analysis of these tRF species revealed dynamic expression of these small RNAs over the course of regeneration suggesting an important role in planarian anterior and posterior regeneration. Finally, we show that 5'-tsRNA in planaria interact with all three SMEDWI proteins and an involvement of Ago1 in the processing of itRFs. In summary, our findings implicate a novel role for tRFs in planarian regeneration, highlighting their importance in regulating complex systemic processes. Our study adds to the catalogue of post-transcriptional regulatory systems in planarian, providing valuable insights on the biogenesis and the function of tRFs in neoblasts and planarian regeneration.

ER - TY - JOUR T1 - Discovery of a body-wide photosensory array that matures in an adult-like animal and mediates eye-brain-independent movement and arousal. JF - Proc Natl Acad Sci U S A Y1 - 2021 A1 - Shettigar, Nishan A1 - Chakravarthy, Anirudh A1 - Umashankar, Suchitta A1 - Lakshmanan, Vairavan A1 - Palakodeti, Dasaradhi A1 - Gulyani, Akash AB -

The ability to respond to light has profoundly shaped life. Animals with eyes overwhelmingly rely on their visual circuits for mediating light-induced coordinated movements. Building on previously reported behaviors, we report the discovery of an organized, eye-independent (extraocular), body-wide photosensory framework that allows even a head-removed animal to move like an intact animal. Despite possessing sensitive cerebral eyes and a centralized brain that controls most behaviors, head-removed planarians show acute, coordinated ultraviolet-A (UV-A) aversive phototaxis. We find this eye-brain-independent phototaxis is mediated by two noncanonical rhabdomeric opsins, the first known function for this newly classified opsin-clade. We uncover a unique array of dual-opsin-expressing photoreceptor cells that line the periphery of animal body, are proximal to a body-wide nerve net, and mediate UV-A phototaxis by engaging multiple modes of locomotion. Unlike embryonically developing cerebral eyes that are functional when animals hatch, the body-wide photosensory array matures postembryonically in "adult-like animals." Notably, apart from head-removed phototaxis, the body-wide, extraocular sensory organization also impacts physiology of intact animals. Low-dose UV-A, but not visible light (ocular-stimulus), is able to arouse intact worms that have naturally cycled to an inactive/rest-like state. This wavelength selective, low-light arousal of resting animals is noncanonical-opsin dependent but eye independent. Our discovery of an autonomous, multifunctional, late-maturing, organized body-wide photosensory system establishes a paradigm in sensory biology and evolution of light sensing.

VL - 118 IS - 20 ER - TY - JOUR T1 - Glycomic and glycotranscriptomic profiling of mucin-type O-glycans in planarian Schmidtea mediterranea. JF - Glycobiology Y1 - 2021 A1 - Subramanian, Sabarinath Peruvemba A1 - Lakshmanan, Vairavan A1 - Palakodeti, Dasaradhi A1 - Subramanian, Ramaswamy AB -

O-Glycans on cell surfaces play important roles in cell-cell, cell-matrix, and receptor-ligand interaction. Therefore, glycan-based interactions are important for tissue regeneration and homeostasis. Free-living flatworm Schmidtea mediterranea, because of its robust regenerative potential, is of great interest in the field of stem cell biology and tissue regeneration. Nevertheless, information on the composition and structure of O-glycans in planaria is unknown. Using mass spectrometry and in silico approaches, we characterized the glycome and the related transcriptome of mucin-type O-glycans of planarian S. mediterranea. Mucin-type O-glycans were composed of multiple isomeric, methylated, and unusually extended mono- and di-substituted O-GalNAc structures. Extensions made of hexoses and 3-O methyl hexoses were the glycoforms observed. From glycotranscriptomic analysis, sixty genes belonging to five distinct enzyme classes were identified to be involved in mucin-type O-glycan biosynthesis. These genes shared homology with those in other invertebrate systems. While a majority of the genes involved in mucin-type O-glycan biosynthesis was highly expressed during organogenesis and in differentiated cells, a few select genes in each enzyme class were specifically enriched during early embryogenesis. Our results indicate a unique temporal and spatial role for mucin-type O-glycans during embryogenesis and organogenesis and in adulthood. In summary, this is the first report on O-glycans in planaria. This study expands the structural and biosynthetic possibilities in cellular glycosylation in the invertebrate glycome and provides a framework towards understanding the biological role of mucin-type O-glycans in tissue regeneration using planarians.

ER - TY - JOUR T1 - Mechanical instability of adherens junctions overrides intrinsic quiescence of hair follicle stem cells. JF - Dev Cell Y1 - 2021 A1 - Biswas, Ritusree A1 - Banerjee, Avinanda A1 - Lembo, Sergio A1 - Zhao, Zhihai A1 - Lakshmanan, Vairavan A1 - Lim, Ryan A1 - Le, Shimin A1 - Nakasaki, Manando A1 - Kutyavin, Vassily A1 - Wright, Graham A1 - Palakodeti, Dasaradhi A1 - Ross, Robert S A1 - Jamora, Colin A1 - Vasioukhin, Valeri A1 - Jie, Yan A1 - Raghavan, Srikala AB -

Vinculin, a mechanotransducer associated with both adherens junctions (AJs) and focal adhesions (FAs), plays a central role in force transmission through cell-cell and cell-substratum contacts. We generated the conditional knockout (cKO) of vinculin in murine skin that results in the loss of bulge stem cell (BuSC) quiescence and promotes continual cycling of the hair follicles. Surprisingly, we find that the AJs in vinculin cKO cells are mechanically weak and impaired in force generation despite increased junctional expression of E-cadherin and α-catenin. Mechanistically, we demonstrate that vinculin functions by keeping α-catenin in a stretched/open conformation, which in turn regulates the retention of YAP1, another potent mechanotransducer and regulator of cell proliferation, at the AJs. Altogether, our data provide mechanistic insights into the hitherto-unexplored regulatory link between the mechanical stability of cell junctions and contact-inhibition-mediated maintenance of BuSC quiescence.

VL - 56 IS - 6 ER - TY - JOUR T1 - Mitochondrial state determines functionally divergent stem cell population in planaria. JF - Stem Cell Reports Y1 - 2021 A1 - Mohamed Haroon, Mohamed A1 - Lakshmanan, Vairavan A1 - Sarkar, Souradeep R A1 - Lei, Kai A1 - Vemula, Praveen Kumar A1 - Palakodeti, Dasaradhi AB -

Mitochondrial state changes were shown to be critical for stem cell function. However, variation in the mitochondrial content in stem cells and the implication, if any, on differentiation is poorly understood. Here, using cellular and molecular studies, we show that the planarian pluripotent stem cells (PSCs) have low mitochondrial mass compared with their progenitors. Transplantation experiments provided functional validation that neoblasts with low mitochondrial mass are the true PSCs. Further, the mitochondrial mass correlated with OxPhos and inhibiting the transition to OxPhos dependent metabolism in cultured cells resulted in higher PSCs. In summary, we show that low mitochondrial mass is a hallmark of PSCs in planaria and provide a mechanism to isolate live, functionally active, PSCs from different cell cycle stages (G0/G1 and S, G2/M). Our study demonstrates that the change in mitochondrial metabolism, a feature of PSCs is conserved in planaria and highlights its role in organismal regeneration.

VL - 16 IS - 5 ER - TY - JOUR T1 - Modulation of β-catenin levels regulates cranial neural crest patterning and dispersal into first pharyngeal arch. JF - Dev Dyn Y1 - 2020 A1 - Javali, Alok A1 - Lakshmanan, Vairavan A1 - Palakodeti, Dasaradhi A1 - Sambasivan, Ramkumar AB -

BACKGROUND: Vertebrate cranial neural crest cells (CNCCs) are multipotent, proximal to the source CNCC form the cranial ganglia. Distally, in the pharyngeal arches, they give rise to the craniofacial skeleton and connective tissues. Fate choices are made as CNCC pattern into distinct destination compartments. In spite of this importance, the mechanism patterning CNCC is poorly defined.

RESULTS: Here, we report that a novel β-catenin-dependent regulation of N-Cadherin levels may drive CNCC patterning. In mouse embryos, at the first pharyngeal arch axial level, membrane β-catenin levels correlate with the extent of N-cadherin-mediated adhesion and thus suggest the presence of collective and dispersed states of CNCC. Using in vitro human neural crest model and chemical modulators of β-catenin levels, we show a requirement for down-modulating β-catenin for regulating N-cadherin levels and cell-cell adhesion. Similarly, in β-catenin gain-of-function mutant mouse embryos, CNCC fail to lower N-cadherin levels. This indicates a failure to reduce cell-cell adhesion, which may underlie the failure of mutant CNCC to populate first pharyngeal arch.

CONCLUSION: We suggest that β-catenin-mediated regulation of CNCC adhesion, a previously underappreciated mechanism, underlies the patterning of CNCC into fate-specific compartments.

ER - TY - JOUR T1 - Dynamic expression of tRNA-derived small RNAs define cellular states. JF - EMBO Rep Y1 - 2019 A1 - Krishna, Srikar A1 - Yim, Daniel Gr A1 - Lakshmanan, Vairavan A1 - Tirumalai, Varsha A1 - Koh, Judice Ly A1 - Park, Jung Eun A1 - Cheong, Jit Kong A1 - Low, Joo Leng A1 - Lim, Michelle Js A1 - Sze, Siu Kwan A1 - Shivaprasad, Padubidri A1 - Gulyani, Akash A1 - Raghavan, Srikala A1 - Palakodeti, Dasaradhi A1 - DasGupta, Ramanuj AB -

Transfer RNA (tRNA)-derived small RNAs (tsRNAs) have recently emerged as important regulators of protein translation and shown to have diverse biological functions. However, the underlying cellular and molecular mechanisms of tsRNA function in the context of dynamic cell-state transitions remain unclear. Expression analysis of tsRNAs in distinct heterologous cell and tissue models of stem vs. differentiated states revealed a differentiation-dependent enrichment of 5'-tsRNAs. We report the identification of a set of 5'-tsRNAs that is upregulated in differentiating mouse embryonic stem cells (mESCs). Notably, interactome studies with differentially enriched 5'-tsRNAs revealed a switch in their association with "effector" RNPs and "target" mRNAs in different cell states. We demonstrate that specific 5'-tsRNAs can preferentially interact with the RNA-binding protein, Igf2bp1, in the RA-induced differentiated state. This association influences the transcript stability and thereby translation of the pluripotency-promoting factor, c-Myc, thus providing a mechanistic basis for how 5'-tsRNAs can modulate stem cell states in mESCs. Together our study highlights the role of 5'-tsRNAs in defining distinct cell states.

VL - 20 IS - 7 ER - TY - JOUR T1 - KMT1 family methyltransferases regulate heterochromatin-nuclear periphery tethering via histone and non-histone protein methylation. JF - EMBO Rep Y1 - 2019 A1 - Rao, Radhika Arasala A1 - Ketkar, Alhad Ashok A1 - Kedia, Neelam A1 - Krishnamoorthy, Vignesh K A1 - Lakshmanan, Vairavan A1 - Kumar, Pankaj A1 - Mohanty, Abhishek A1 - Kumar, Shilpa Dilip A1 - Raja, Sufi O A1 - Gulyani, Akash A1 - Chaturvedi, Chandra Prakash A1 - Brand, Marjorie A1 - Palakodeti, Dasaradhi A1 - Rampalli, Shravanti AB -

Euchromatic histone methyltransferases (EHMTs), members of the KMT1 family, methylate histone and non-histone proteins. Here, we uncover a novel role for EHMTs in regulating heterochromatin anchorage to the nuclear periphery (NP) via non-histone methylation. We show that EHMTs methylate and stabilize LaminB1 (LMNB1), which associates with the H3K9me2-marked peripheral heterochromatin. Loss of LMNB1 methylation or EHMTs abrogates heterochromatin anchorage at the NP We further demonstrate that the loss of EHMTs induces many hallmarks of aging including global reduction of H3K27methyl marks and altered nuclear morphology. Consistent with this, we observe a gradual depletion of EHMTs, which correlates with loss of methylated LMNB1 and peripheral heterochromatin in aging human fibroblasts. Restoration of EHMT expression reverts peripheral heterochromatin defects in aged cells. Collectively, our work elucidates a new mechanism by which EHMTs regulate heterochromatin domain organization and reveals their impact on fundamental changes associated with the intrinsic aging process.

ER - TY - JOUR T1 - Serotonin is essential for eye regeneration in planaria Schmidtea mediterranea. JF - FEBS Lett Y1 - 2019 A1 - Sarkar, Arunabha A1 - Mukundan, Namita A1 - Sowndarya, Sai A1 - Dubey, Vinay Kumar A1 - Babu, Rosana A1 - Lakshmanan, Vairavan A1 - Rangiah, Kannan A1 - Panicker, Mitradas M A1 - Palakodeti, Dasaradhi A1 - Subramanian, Sabarinath Peruvemba A1 - Ramaswamy, Subramanian AB -

Planaria is an ideal system to study factors involved in regeneration and tissue homeostasis. Little is known about the role of metabolites and small molecules in stem cell maintenance and lineage specification in planarians. Using liquid chromatography and mass spectrometry (LC-MS)-based quantitative metabolomics, we determined the relative levels of metabolites in stem cells, progenitors, and differentiated cells of the planarian Schmidtea mediterranea. Tryptophan and its metabolic product serotonin are significantly enriched in stem cells and progenitor population. Serotonin biosynthesis in these cells is brought about by a non-canonical enzyme, phenylalanine hydroxylase (PAH). Knockdown of Smed-pah leads to complete disappearance of eyes in regenerating planaria, while exogenous supply of serotonin and its precursor rescue the eyeless phenotype. Our results demonstrate a key role for serotonin in eye regeneration.

ER - TY - JOUR T1 - Stromal cells downregulate miR-23a-5p to activate protective autophagy in acute myeloid leukemia. JF - Cell Death Dis Y1 - 2019 A1 - Ganesan, Saravanan A1 - Palani, Hamenth Kumar A1 - Lakshmanan, Vairavan A1 - Balasundaram, Nithya A1 - Alex, Ansu Abu A1 - David, Sachin A1 - Venkatraman, Arvind A1 - Korula, Anu A1 - George, Biju A1 - Balasubramanian, Poonkuzhali A1 - Palakodeti, Dasaradhi A1 - Vyas, Neha A1 - Mathews, Vikram AB -

Complex molecular cross talk between stromal cells and the leukemic cells in bone marrow is known to contribute significantly towards drug-resistance. Here, we have identified the molecular events that lead to stromal cells mediated therapy-resistance in acute myeloid leukemia (AML). Our work demonstrates that stromal cells downregulate miR-23a-5p levels in leukemic cells to protect them from the chemotherapy induced apoptosis. Downregulation of miR-23a-5p in leukemic cells leads to upregulation of protective autophagy by targeting TLR2 expression. Further, autophagy inhibitors when used as adjuvants along with conventional drugs can improve drug sensitivity in vitro as well in vivo in a mouse model of leukemia. Our work also demonstrates that this mechanism of bone marrow stromal cell mediated regulation of miR-23a-5p levels and subsequent molecular events are relevant predominantly in myeloid leukemia. Our results illustrate the critical and dynamic role of the bone marrow microenvironment in modulating miRNA expression in leukemic cells which could contribute significantly to drug resistance and subsequent relapse, possibly through persistence of minimal residual disease in this environment.

VL - 10 IS - 10 ER - TY - JOUR T1 - Cytoplasmic poly (A)-binding protein critically regulates epidermal maintenance and turnover in the planarian . JF - Development Y1 - 2017 A1 - Bansal, Dhiru A1 - Kulkarni, Jahnavi A1 - Nadahalli, Kavana A1 - Lakshmanan, Vairavan A1 - Krishna, Srikar A1 - Sasidharan, Vidyanand A1 - Geo, Jini A1 - Dilipkumar, Shilpa A1 - Pasricha, Renu A1 - Gulyani, Akash A1 - Raghavan, Srikala A1 - Palakodeti, Dasaradhi KW - Animals KW - Cell Lineage KW - Cell Proliferation KW - Cytoplasm KW - Epidermis KW - Epithelium KW - Extracellular Matrix KW - Gene Knockdown Techniques KW - Homeostasis KW - Models, Biological KW - Planarians KW - Poly(A)-Binding Protein I KW - Regeneration KW - RNA, Messenger KW - Wound Healing AB -

Identifying key cellular events that facilitate stem cell function and tissue organization is crucial for understanding the process of regeneration. Planarians are powerful model system to study regeneration and stem cell (neoblast) function. Here, using planaria, we show that the initial events of regeneration, such as epithelialization and epidermal organization are critically regulated by a novel cytoplasmic poly A-binding protein, SMED-PABPC2. Knockdown leads to defects in epidermal lineage specification, disorganization of epidermis and ECM, and deregulated wound healing, resulting in the selective failure of neoblast proliferation near the wound region. Polysome profiling suggests that epidermal lineage transcripts, including , are translationally regulated by SMED-PABPC2 Together, our results uncover a novel role for SMED-PABPC2 in the maintenance of epidermal and ECM integrity, critical for wound healing and subsequent processes for regeneration.

VL - 144 IS - 17 ER - TY - JOUR T1 - The miR-124 family of microRNAs is crucial for regeneration of the brain and visual system in the planarian Schmidtea mediterranea JF - Development Y1 - 2017 A1 - Sasidharan, Vidyanand A1 - Marepally, Srujan A1 - Elliott, Sarah A. A1 - Baid, Srishti A1 - Lakshmanan, Vairavan A1 - Nayyar, Nishtha A1 - Bansal, Dhiru A1 - Sánchez Alvarado, Alejandro A1 - Vemula, Praveen Kumar A1 - Palakodeti, Dasaradhi AB -

Brain regeneration in planarians is mediated by precise spatiotemporal control of gene expression and is crucial for multiple aspects of neurogenesis. However, the mechanisms underpinning the gene regulation essential for brain regeneration are largely unknown. Here, we investigated the role of the miR-124 family of microRNAs in planarian brain regeneration. The miR-124 family (miR-124) is highly conserved in animals and regulates neurogenesis by facilitating neural differentiation, yet its role in neural wiring and brain organization is not known. We developed a novel method for delivering anti-miRs using liposomes for the functional knockdown of microRNAs. Smed-miR-124 knockdown revealed a key role for these microRNAs in neuronal organization during planarian brain regeneration. Our results also demonstrated an essential role for miR-124 in the generation of eye progenitors. Additionally, miR-124 regulates Smed-slit-1, which encodes an axon guidance protein, either by targeting slit-1 mRNA or, potentially, by modulating the canonical Notch pathway. Together, our results reveal a role for miR-124 in regulating the regeneration of a functional brain and visual system.

VL - 144 UR - http://dev.biologists.org/content/144/18/3211 ER - TY - JOUR T1 - Genome-Wide Analysis of Polyadenylation Events in Schmidtea mediterranea. JF - G3 (Bethesda) Y1 - 2016 A1 - Lakshmanan, Vairavan A1 - Bansal, Dhiru A1 - Kulkarni, Jahnavi A1 - Poduval, Deepak A1 - Krishna, Srikar A1 - Sasidharan, Vidyanand A1 - Anand, Praveen A1 - Seshasayee, Aswin A1 - Palakodeti, Dasaradhi KW - 3' Untranslated Regions KW - Animals KW - Computational Biology KW - Genome, Helminth KW - Genome-Wide Association Study KW - High-Throughput Nucleotide Sequencing KW - MicroRNAs KW - Molecular Sequence Annotation KW - Platyhelminths KW - Poly A KW - Polyadenylation KW - Reproducibility of Results KW - RNA Interference KW - RNA Processing, Post-Transcriptional KW - RNA, Messenger AB -

In eukaryotes, 3' untranslated regions (UTRs) play important roles in regulating posttranscriptional gene expression. The 3'UTR is defined by regulated cleavage/polyadenylation of the pre-mRNA. The advent of next-generation sequencing technology has now enabled us to identify these events on a genome-wide scale. In this study, we used poly(A)-position profiling by sequencing (3P-Seq) to capture all poly(A) sites across the genome of the freshwater planarian, Schmidtea mediterranea, an ideal model system for exploring the process of regeneration and stem cell function. We identified the 3'UTRs for ∼14,000 transcripts and thus improved the existing gene annotations. We found 97 transcripts, which are polyadenylated within an internal exon, resulting in the shrinking of the ORF and loss of a predicted protein domain. Around 40% of the transcripts in planaria were alternatively polyadenylated (ApA), resulting either in an altered 3'UTR or a change in coding sequence. We identified specific ApA transcript isoforms that were subjected to miRNA mediated gene regulation using degradome sequencing. In this study, we also confirmed a tissue-specific expression pattern for alternate polyadenylated transcripts. The insights from this study highlight the potential role of ApA in regulating the gene expression essential for planarian regeneration.

VL - 6 IS - 10 ER - TY - JOUR T1 - A quantitative metabolomics peek into planarian regeneration. JF - Analyst Y1 - 2015 A1 - Natarajan, Nivedita A1 - Ramakrishnan, Padma A1 - Lakshmanan, Vairavan A1 - Palakodeti, Dasaradhi A1 - Rangiah, Kannan KW - Animals KW - Calibration KW - Chromatography, High Pressure Liquid KW - Limit of Detection KW - Metabolomics KW - Planarians KW - Reference Standards KW - Regeneration KW - Reproduction, Asexual KW - Species Specificity KW - Tandem Mass Spectrometry AB -

The fresh water planarian species Schmidtea mediterranea is an emerging stem cell model because of its capability to regenerate a whole animal from a small piece of tissue. It is one of the best model systems to address the basic mechanisms essential for regeneration. Here, we are interested in studying the roles of various amines, thiols and nucleotides in planarian regeneration, stem cell function and growth. We developed mass spectrometry based quantitative methods and validated the differential enrichment of 35 amines, 7 thiol metabolites and 4 nucleotides from both intact and regenerating planarians. Among the amines, alanine in sexual and asparagine in asexual are the highest (>1000 ng/mg) in the intact planarians. The levels of thiols such as cysteine and GSH are 651 and 1107 ng mg(-1) in planarians. Among the nucleotides, the level of cGMP is the lowest (0.03 ng mg(-1)) and the level of AMP is the highest (187 ng mg(-1)) in both of the planarian strains. We also noticed increasing levels of amines in both anterior and posterior regenerating planarians. The blastema from day 3 regenerating planarians also showed higher amounts of many amines. Interestingly, the thiol (cysteine and GSH) levels are well maintained during planarian regeneration. This suggests an inherent and effective mechanism to control induced oxidative stress because of the robust regeneration and stem cell proliferation. Like in intact planarians, the level of cGMP is also very low in regenerating planarians. Surprisingly, the levels of amines and thiols in head regenerating blastemas are ∼3 times higher compared to those for tail regenerating blastemas. Thus our results strongly indicate the potential roles of amines, thiols and nucleotides in planarian regeneration.

VL - 140 IS - 10 ER -