Computational tools to unmask transposable elements
P Goerner-Potvin, G Bourque - Nature Reviews Genetics, 2018 - nature.com
A substantial proportion of the genome of many species is derived from transposable
elements (TEs). Moreover, through various self-copying mechanisms, TEs continue to …
elements (TEs). Moreover, through various self-copying mechanisms, TEs continue to …
Principles and innovative technologies for decrypting noncoding RNAs: from discovery and functional prediction to clinical application
YM Sun, YQ Chen - Journal of hematology & oncology, 2020 - Springer
Noncoding RNAs (ncRNAs) are a large segment of the transcriptome that do not have
apparent protein-coding roles, but they have been verified to play important roles in diverse …
apparent protein-coding roles, but they have been verified to play important roles in diverse …
TEtranscripts: a package for including transposable elements in differential expression analysis of RNA-seq datasets
Y **, OH Tam, E Paniagua, M Hammell - Bioinformatics, 2015 - academic.oup.com
Motivation: Most RNA-seq data analysis software packages are not designed to handle the
complexities involved in properly apportioning short sequencing reads to highly repetitive …
complexities involved in properly apportioning short sequencing reads to highly repetitive …
piRNA-guided transposon cleavage initiates Zucchini-dependent, phased piRNA production
PIWI-interacting RNAs (piRNAs) protect the animal germ line by silencing transposons.
Primary piRNAs, generated from transcripts of genomic transposon “junkyards”(piRNA …
Primary piRNAs, generated from transcripts of genomic transposon “junkyards”(piRNA …
Relaxed targeting rules help PIWI proteins silence transposons
I Gainetdinov, J Vega-Badillo, K Cecchini, A Bagci… - Nature, 2023 - nature.com
In eukaryotes, small RNA guides, such as small interfering RNAs and microRNAs, direct
AGO-clade Argonaute proteins to regulate gene expression and defend the genome against …
AGO-clade Argonaute proteins to regulate gene expression and defend the genome against …
A single mechanism of biogenesis, initiated and directed by PIWI proteins, explains piRNA production in most animals
In animals, PIWI-interacting RNAs (piRNAs) guide PIWI proteins to silence transposons and
regulate gene expression. The mechanisms for making piRNAs have been proposed to …
regulate gene expression. The mechanisms for making piRNAs have been proposed to …
Elimination of PCR duplicates in RNA-seq and small RNA-seq using unique molecular identifiers
Background RNA-seq and small RNA-seq are powerful, quantitative tools to study gene
regulation and function. Common high-throughput sequencing methods rely on polymerase …
regulation and function. Common high-throughput sequencing methods rely on polymerase …
[HTML][HTML] Large Drosophila germline piRNA clusters are evolutionarily labile and dispensable for transposon regulation
PIWI proteins and their guiding Piwi-interacting small RNAs (piRNAs) are crucial for fertility
and transposon defense in the animal germline. In most species, the majority of piRNAs are …
and transposon defense in the animal germline. In most species, the majority of piRNAs are …
The evolutionarily conserved piRNA-producing locus pi6 is required for male mouse fertility
Abstract Pachytene PIWI-interacting RNAs (piRNAs), which comprise> 80% of small RNAs
in the adult mouse testis, have been proposed to bind and regulate target RNAs like …
in the adult mouse testis, have been proposed to bind and regulate target RNAs like …
Single-molecule long-read sequencing reveals a conserved intact long RNA profile in sperm
Sperm contributes diverse RNAs to the zygote. While sperm small RNAs have been shown
to impact offspring phenotypes, our knowledge of the sperm transcriptome, especially the …
to impact offspring phenotypes, our knowledge of the sperm transcriptome, especially the …