From clonal diversity to transposon derived long noncoding RNA in trematode Himasthla elongata parthenogenetic generations We investigated clonal diversity of parthenogenetic larvae, cercaria, with a simplified AFLP (SAFLP, Amplified fragment length polymorphism) method and explored the nature of diverse zones from electrophoretic patterns. LINE retroelements prevail in fragments analized. One of them was aligned to the spacer region in ORF2 of the CR1like (LINE class) transposon and named CR1renegade (CR1rng). CR1renegade exists in two types of transcripts: the long ones, containing reverse transcriptase and other domains, and the short ones, containing CR1rng solely. Probes of CR1 reverse transcriptase (CR1RT) and CR1rng yielded strikingly different pictures in FISH physical mapping despite being fragments of CR1 transposons. The CR1RT probe demonstrated dispersed signal distribution throughout the nuclei and all chromosomes while CR1rng localized preferentially to the heterochromatic regions. We suppose that CR1rng transcripts are related to lncRNA regulatory network.

Ribosomal inframe mistranslation of stop codons in multiple open reading frames of specific human long noncoding RNAs. One of the major discoveries of the early postgenomic era, as embodied by the gene catalogs of the FANTOM and ENCODE (Encyclopedia of DNA Elements) consortia, is that twothirds of human genes do not encode known proteins. Those 40,000 nonproteincoding (noncoding RNA) human genes (www.gencodegenes.org) remain poorly understood. Long noncoding RNA (lncRNA) genes are the most numerous category of human ncRNA genes. Hundreds of lncRNAs have recentlydiscovered functions and are now understood to be fundamental nuclear and cytoplasmic, epigenetic and posttranscriptional, positive and negative regulators of gene expression in normal cellular functions and in a wide range of human diseases. However, the functions, if any, of the vast majority of lncRNAs remain obscure. Significantly, an unconventional role for their transcripts as unexpected defacto messenger RNAs has not been formally excluded. Ribosome profiling (Riboseq) predicts translational potential; nonetheless, without independent evidence of proteins matching lncRNA open reading frames (ORFs), ribosome binding does not prove translation. We were the first to massspectrometrically document translation of specific lncRNAs in human cells (https:genome.cshlp.orgcontent2291646.long). We have now performed a global search for lncRNA translation in human MCF7 breast cancer cells, integrating strandspecific RNAseq, Riboseq, and deep mass spectrometry of trypsindigested u003c15kDa fractions postUHPLC (Orbitrap MSMS) in biological quadruplicates by two independent core facilities. We excluded knownprotein matches. UCSC Genome Browserassisted manual annotation of imperfect (trypticdigestpeptides)to(lncRNAthreeframe translations) alignments initially revealed three peptides hypothetically explicable by xe2x80x9cstoptononstopxe2x80x9d in frame replacement of stop codons by amino acids in two ORFs of the lncRNA MMP24AS1. To search for this phenomenon genomewide, we designed and implemented an unprecedented computational pipeline, matching trypticdigest spectra to wildcardinsteadofstop versions of repeatmasked, sixframe, wholegenome translations. Along with singleton stoptononstop events affecting four other lncRNAs, we identified 24 additional peptides with stoptononstop inframe substitutions from multiple MMP24AS1 lncRNA ORFs. Only UAG and UGA, but not UAA, stop codons were affected. All MMP24AS1matching spectra met the same significance thresholds as highconfidence knownprotein signatures. Targeted resequencing of MMP24AS1 genomic DNA and cDNA from the same samples did not reveal any mutations, polymorphisms, or sequencingdetectable RNA editing. We have therefore discovered an apparent genespecific violation of the genetic code. It highlights the importance of matching peptides to wholegenome, not knowngenesonly, ORFs in massspectrometry workflows, and suggests a new mechanism enhancing the combinatorial complexity of the proteome.