TY - JOUR T1 - FMRP Interacts with C/D Box snoRNA in the Nucleus and Regulates Ribosomal RNA Methylation. JF - iScience Y1 - 2018 A1 - D'Souza, Michelle Ninochka A1 - Gowda, Naveen Kumar Chandappa A1 - Tiwari, Vishal A1 - Babu, Rosana Ottakandathil A1 - Anand, Praveen A1 - Dastidar, Sudhriti Ghosh A1 - Singh, Randhir A1 - James, Owen G A1 - Selvaraj, Bhuvaneish A1 - Pal, Rakhi A1 - Ramesh, Arati A1 - Chattarji, Sumantra A1 - Chandran, Siddharthan A1 - Gulyani, Akash A1 - Palakodeti, Dasaradhi A1 - Muddashetty, Ravi S AB -

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.

VL - 9 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 -