Cytoplasmic poly (A) binding protein (PABPC2) critically regulates epidermal maintenance and turnover in planarian <i>Schmidtea mediterranea</i>

Bansal, Dhiru; Kulkarni, Jahnavi; Nadahalli, Kavana; Lakshmanan, Vairavan; Krishna, Srikar; Sasidharan, Vidyanand; Geo, Jini; Dilipkumar, Shilpa; Pasricha, Renu; Gulyani, Akash; Raghavan, Srikala; Palakodeti, Dasaradhi

doi:10.1242/dev.152942

Cited by 14 publications

(13 citation statements)

References 66 publications

(92 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…This dataset was used to analyze the expression of different tRNA fragment species during planarian regeneration. As observed in salami sections, we obtained 2 to 5.4% of total reads (18)(19)(20)(21)(22)(23)(24)(25)(26)(27)(28)(29)(30)(31)(32)(33)(34)(35) mapping to tRNAs (Figure 4B and Table S7). Preliminary analysis revealed dynamic changes in the different species of tRFs in both anterior and posterior regeneration.…”

Section: Expression Of 5'-tsrna During Planarian Regenerationsupporting

confidence: 69%

“…These events are controlled by underlying gene regulatory networks that spatially and temporally control the expression of specific genes thus orchestrating a coordinated regeneration process (20,21). Planarians possess several gene regulatory programs that are critical for neoblast function and regeneration (17,20,(22)(23)(24)(25)(26). Small RNAs are one of the key regulators of gene expression.…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Comprehensive annotation and characterization of planarian tRNA and tRNA-derived fragments (tRFs)

Lakshmanan

Sujith

Bansal

et al. 2021

RNA

Self Cite

View full text Add to dashboard Cite

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.

show abstract

Section: Expression Of 5'-tsrna During Planarian Regenerationsupporting

confidence: 69%

Section: Introductionmentioning

confidence: 99%

Comprehensive annotation and characterization of planarian tRNA and tRNA-derived fragments (tRFs)

Lakshmanan

Sujith

Bansal

et al. 2021

RNA

Self Cite

View full text Add to dashboard Cite

show abstract

“…These events are controlled by underlying gene regulatory networks that spatially and temporally control the expression of specific genes thus orchestrating a coordinated regeneration process (13,14). Planarians possess several gene regulatory programs that are critical for neoblast function and regeneration (10,13,(15)(16)(17)(18)(19). Small RNAs are one of the key regulators of gene expression.…”

Section: Introductionmentioning

confidence: 99%

Comprehensive annotation and characterization of planarian tRNA and tRNA-derived fragments (tRFs)

Lakshmanan

Bansal

Sujith

et al. 2020

Preprint

Self Cite

View full text Add to dashboard Cite

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 identify and characterise a role for tRFs in planarian regeneration. We first annotated 457 tRNA loci in S.mediterranea combining two tRNA prediction programs. 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 while sequence analysis revealed a possible involvement of Dicers 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.

show abstract

“…Many RBPs show enriched expression in stem and/or progenitor cells, including homologs of the piRNA-binding protein PIWI ( Palakodeti et al, 2008 ; Reddien et al, 2005 ; Rouhana et al, 2014 ), the PUF family protein Pumilio ( Salvetti et al, 2005 ), the DEAD-box helicases Vasa and RCK/p54/Me31B ( Rouhana et al, 2010 ; Shibata et al, 1999 ; Wagner et al, 2012 ; Yoshida-Kashikawa et al, 2007 ), the translational regulators Bruno and MEX-3 ( Guo et al, 2006 ; Solana et al, 2016 ; Zhu et al, 2015 ), the dimethylarginine-associated factors Tudor and PRMT5 ( Rouhana et al, 2012 ; Solana et al, 2009 ), components of the snRNA-processing Integrator complex ( Schmidt et al, 2018 ), LSm splicing factors ( Fernandez-Taboada et al, 2010 ), and the deadenylating complex subunit CCR4-NOT ( Solana et al, 2013 ). Together with RBPs exhibiting constitutive expression, these factors help to orchestrate gene expression, cell fate specification, and differentiation ( Bansal et al, 2017 ; Krishna et al, 2019 ; Lakshmanan et al, 2016 ; Palakodeti et al, 2008 ; Reddien et al, 2005 ; Rouhana et al, 2010 ; Shibata et al, 2016 ; Solana et al, 2016 , 2013 ; Zhu et al, 2015 ).…”

Section: Introductionmentioning

confidence: 99%

The exon junction complex is required for stem and progenitor cell maintenance in planarians

Kimball

Powers

Dustin

et al. 2020

Developmental Biology

View full text Add to dashboard Cite

Named for its assembly near exon-exon junctions during pre-mRNA splicing, the exon junction complex (EJC) regulates multiple aspects of RNA biochemistry, including export of spliced mRNAs from the nucleus and translation. Transcriptome analyses have revealed broad EJC occupancy of spliced metazoan transcripts, yet inhibition of core subunits has been linked to surprisingly specific phenotypes and a growing number of studies support gene-specific regulatory roles. Here we report results from a classroom-based RNAi screen revealing the EJC is necessary for regeneration in the planarian flatworm Schmidtea mediterranea. RNAi animals rapidly lost the stem and progenitor cells that drive formation of new tissue during both regeneration and cell turnover, but exhibited normal amputation-induced changes in gene expression in differentiated tissues. Together with previous reports that partial loss of EJC function causes stem cell defects in Drosophila and mice, our observations implicate the EJC as a conserved, posttranscriptional regulator of gene expression in stem cell lineages. This work also highlights the combined educational and scientific impacts of discovery-based research in the undergraduate biology curriculum.

show abstract

Cytoplasmic poly (A) binding protein (PABPC2) critically regulates epidermal maintenance and turnover in planarian Schmidtea mediterranea

Cited by 14 publications

References 66 publications

Comprehensive annotation and characterization of planarian tRNA and tRNA-derived fragments (tRFs)

Comprehensive annotation and characterization of planarian tRNA and tRNA-derived fragments (tRFs)

Comprehensive annotation and characterization of planarian tRNA and tRNA-derived fragments (tRFs)

The exon junction complex is required for stem and progenitor cell maintenance in planarians

Contact Info

Product

Resources

About