使用 RiboTaper/ORFquant 进行全基因组范围内活跃翻译的开放阅读框的分析。

Genome-Wide Analysis of Actively Translated Open Reading Frames Using RiboTaper/ORFquant.

机构信息

IRI Life Sciences, Institute of Biology, Humboldt-Universität zu Berlin, Berlin, Germany.

Max Delbruck Centre for Molecular Medicine in the Helmholtz Association, Berlin Institute for Medical Systems Biology, Berlin, Germany.

出版信息

Methods Mol Biol. 2021;2252:331-346. doi: 10.1007/978-1-0716-1150-0_16.

DOI:10.1007/978-1-0716-1150-0_16

PMID:33765284

Abstract

Ribosome profiling, or Ribo-seq, provides precise information about the position of actively translating ribosomes. It can be used to identify open reading frames (ORFs) that are translated in a given sample. The RiboTaper pipeline, and the ORFquant R package, leverages the periodic distribution of such ribosomes along the ORF to perform a statistically robust test for translation which is insensitive to aperiodic noise and provides a statistically robust measure of translation. In addition to accounting for complex loci with overlapping ORFs, ORFquant is also able to use Ribo-seq as a tool for distinguishing actively translated transcripts from non-translated ones, within a given gene locus.

摘要

核糖体图谱分析（ribosome profiling，或 Ribo-seq）提供了关于活跃翻译核糖体位置的精确信息。它可用于鉴定在给定样本中被翻译的开放阅读框（open reading frames，ORFs）。RiboTaper 分析流程和 ORFquant R 包利用核糖体在 ORF 上的这种周期性分布，对翻译进行稳健的统计检验，该检验对非周期性噪声不敏感，并提供翻译的稳健统计度量。除了对具有重叠 ORFs 的复杂基因座进行计算外，ORFquant 还能够将 Ribo-seq 用作工具，在给定基因座内，将活跃翻译的转录本与非翻译的转录本区分开来。