Top 3 Biorxiv Papers Today in Genomics


2.0 Mikeys
#1. LincRNA sequences are biased to counteract their translation
Anneke Brümmer, René Dreos, Ana C Marques, Sven Bergmann
Long intergenic non-coding RNAs (lincRNAs) account for a large fraction of transcribed loci in the human genome. While many lincRNAs are retained in the cell nucleus, preventing their association with ribosomes, binding of cytosolic lincRNAs to ribosomes has been observed, but rarely results in translation. This raises the question of how translation of short open reading frames (ORFs) within cytosolic lincRNAs is hindered. Here, we investigate the content of nucleotide triplets in lincRNA putative ORFs (i.e. 'codons') and its potential impact on ribosome binding and translation. We find that lincRNA and mRNA ORFs have distinct codon frequencies, that are well conserved between human and mouse. In lincRNAs, codon frequencies are less correlated with the corresponding tRNA abundance measures than in mRNAs. This correlation is weaker for cytoplasmic lincRNAs and lowest for those without experimental evidence for ribosome binding. Our results suggest that putative lincRNA codons are a substrate of evolutionary forces modulating them...
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prashbio: RT @biorxiv_genomic: LincRNA sequences are biased to counteract their translation https://t.co/d4BquR8cjp #biorxiv_genomic
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Authors: 4
Total Words: 9504
Unqiue Words: 2313

1.997 Mikeys
#2. Population genomic SNPs from epigenetic RADs: gaining genetic and epigenetic data from a single established next-generation sequencing approach
Marco Crotti, Colin Adams, Kathryn R Elmer
Epigenetics is increasingly recognised as an important molecular mechanism underlying phenotypic variation. To study DNA methylation in ecological and evolutionary contexts, epiRADseq is a cost-effective next-generation sequencing technique based on reduced representation sequencing of genomic regions surrounding non-/methylated sites. EpiRADseq for genome-wide methylation abundance and ddRADseq for genome-wide SNP genotyping follow very similar library and sequencing protocols, but to date these two types of dataset have been handled separately. Here we test the performance of using epiRADseq data to generate SNPs for population genomic analyses. We tested the robustness of using epiRADseq data for population genomics with two independent datasets: a newly generated single-end dataset for the European whitefish Coregonus lavaretus, and a re-analysis of publicly available, previously published paired-end data on corals. Using standard bioinformatic pipelines with a reference genome and without (i.e. de novo catalogue loci), we...
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Authors: 3
Total Words: 9712
Unqiue Words: 2924

1.997 Mikeys
#3. PuMA: a papillomavirus genome annotation tool
Josh Sayre Pace, Kenneth Youens-Clark, Cordell Justin Freeman, Bonnie L Hurwitz, Koenraad Van Doorslaer
High-throughput sequencing technologies provide unprecedented power to identify novel viruses from a wide variety of (environmental) samples. The field of 'viral metagenomics' has dramatically expanded our understanding of viral diversity. Viral metagenomic approaches imply that many novel viruses will not be described by researchers who are experts on the genomic organization of that virus. There is a need to develop analytical approaches to reconstruct, annotate, and classify viral genomes. We have developed the papillomavirus annotation tool (PuMA) to provide researchers with a convenient and reproducible method to annotate novel papillomaviruses. PuMA provides an accessible method for automated papillomavirus genome annotation. PuMA currently has a 98% accuracy when benchmarked against the 481 reference genomes in the papillomavirus episteme (PaVE). Finally, PuMA was used to annotate 168 newly isolated papillomaviruses, and successfully annotated 1424 viral features. To demonstrate its general applicability, we developed a...
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Authors: 5
Total Words: 2712
Unqiue Words: 1139

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