Shamimuzzaman et al. 2018 (PRJNA277363)

General Details

Title Ribosome profiling reveals changes in translational status of soybean transcripts during immature cotyledon development
Organism
Number of Samples 10
Release Date 2015/03/05 00:00
Sequencing Types
Protocol Details

Study Links

Repository Details

SRA SRP055880
ENA SRP055880
GEO
BioProject PRJNA277363

Publication

Title
Authors Shamimuzzaman M,Vodkin L
Journal PloS one
Publication Date 2018
Abstract To understand translational capacity on a genome-wide scale across three developmental stages of immature soybean seed cotyledons, ribosome profiling was performed in combination with RNA sequencing and cluster analysis. Transcripts representing 216 unique genes demonstrated a higher level of translational activity in at least one stage by exhibiting higher translational efficiencies (TEs) in which there were relatively more ribosome footprint sequence reads mapping to the transcript than were present in the control total RNA sample. The majority of these transcripts were more translationally active at the early stage of seed development and included 12 unique serine or cysteine proteases and 16 2S albumin and low molecular weight cysteine-rich proteins that may serve as substrates for turnover and mobilization early in seed development. It would appear that the serine proteases and 2S albumins play a vital role in the early stages. In contrast, our investigation of profiles of 19 genes encoding high abundance seed storage proteins, such as glycinins, beta-conglycinins, lectin, and Kunitz trypsin inhibitors, showed that they all had similar patterns in which the TE values started at low levels and increased approximately 2 to 6-fold during development. The highest levels of these seed protein transcripts were found at the mid-developmental stage, whereas the highest ribosome footprint levels of only up to 1.6 TE were found at the late developmental stage. These experimental findings suggest that the major seed storage protein coding genes are primarily regulated at the transcriptional level during normal soybean cotyledon development. Finally, our analyses also identified a total of 370 unique gene models that showed very low TE values including over 48 genes encoding ribosomal family proteins and 95 gene models that are related to energy and photosynthetic functions, many of which have homology to the chloroplast genome. Additionally, we showed that genes of the chloroplast were relatively translationally inactive during seed development.
PMC PMC5865733
PMID 29570733
DOI
Run Accession Study Accession Scientific Name Cell Line Library Type Treatment GWIPS-viz Trips-Viz Reads BAM BigWig (F) BigWig (R)
SRR1840399 PRJNA277363 Glycine max Ribo-Seq
SRR1840401 PRJNA277363 Glycine max Ribo-Seq
SRR1840403 PRJNA277363 Glycine max Ribo-Seq
SRR1840405 PRJNA277363 Glycine max Ribo-Seq
SRR1840407 PRJNA277363 Glycine max Ribo-Seq
SRR1840409 PRJNA277363 Glycine max Ribo-Seq
SRR1840411 PRJNA277363 Glycine max Ribo-Seq
SRR1840413 PRJNA277363 Glycine max Ribo-Seq
SRR1840415 PRJNA277363 Glycine max Ribo-Seq
SRR1840417 PRJNA277363 Glycine max Ribo-Seq
Run Accession Study Accession Scientific Name Cell Line Library Type Treatment GWIPS-viz Trips-Viz Reads BAM BigWig (F) BigWig (R)

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