%0 Journal Article %J iScience %D 2018 %T FMRP Interacts with C/D Box snoRNA in the Nucleus and Regulates Ribosomal RNA Methylation. %A D'Souza, Michelle Ninochka %A Gowda, Naveen Kumar Chandappa %A Tiwari, Vishal %A Babu, Rosana Ottakandathil %A Anand, Praveen %A Dastidar, Sudhriti Ghosh %A Singh, Randhir %A James, Owen G %A Selvaraj, Bhuvaneish %A Pal, Rakhi %A Ramesh, Arati %A Chattarji, Sumantra %A Chandran, Siddharthan %A Gulyani, Akash %A Palakodeti, Dasaradhi %A Muddashetty, Ravi S %X

FMRP is an RNA-binding protein that is known to localize in the cytoplasm and in the nucleus. Here, we have identified an interaction of FMRP with a specific set of C/D box snoRNAs in the nucleus. C/D box snoRNAs guide 2'O methylations of ribosomal RNA (rRNA) on defined sites, and this modification regulates rRNA folding and assembly of ribosomes. 2'O methylation of rRNA is partial on several sites in human embryonic stem cells, which results in ribosomes with differential methylation patterns. FMRP-snoRNA interaction affects rRNA methylation on several of these sites, and in the absence of FMRP, differential methylation pattern of rRNA is significantly altered. We found that FMRP recognizes ribosomes carrying specific methylation patterns on rRNA and the recognition of methylation pattern by FMRP may potentially determine the translation status of its target mRNAs. Thus, FMRP integrates its function in the nucleus and in the cytoplasm.

%B iScience %V 9 %P 399-411 %8 2018 Nov 30 %G eng %R 10.1016/j.isci.2018.11.007 %0 Journal Article %J G3 (Bethesda) %D 2016 %T Genome-Wide Analysis of Polyadenylation Events in Schmidtea mediterranea. %A Lakshmanan, Vairavan %A Bansal, Dhiru %A Kulkarni, Jahnavi %A Poduval, Deepak %A Krishna, Srikar %A Sasidharan, Vidyanand %A Anand, Praveen %A Seshasayee, Aswin %A Palakodeti, Dasaradhi %K 3' Untranslated Regions %K Animals %K Computational Biology %K Genome, Helminth %K Genome-Wide Association Study %K High-Throughput Nucleotide Sequencing %K MicroRNAs %K Molecular Sequence Annotation %K Platyhelminths %K Poly A %K Polyadenylation %K Reproducibility of Results %K RNA Interference %K RNA Processing, Post-Transcriptional %K RNA, Messenger %X

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.

%B G3 (Bethesda) %V 6 %P 3035-3048 %8 2016 10 13 %G eng %N 10 %R 10.1534/g3.116.031120