Integrated genomic analysis reveals key features of long undecoded transcript isoform-based gene repression

Amy Tresenrider,Kaitlin Morse,Victoria Jorgensen,Minghao Chia,Hanna Liao,Folkert Jacobus Van Werven,Elçin Ünal

doi:10.1016/j.molcel.2021.03.013

Abstract

SummaryLong undecoded transcript isoforms (LUTIs) represent a class of non-canonical mRNAs that downregulate gene expression through the combined act of transcriptional and translational repression. While single gene studies revealed important aspects of LUTI-based repression, how these features affect gene regulation on a global scale is unknown. Using transcript leader and direct RNA sequencing, here, we identify 74 LUTI candidates that are specifically induced in meiotic prophase. Translational repression of these candidates appears to be ubiquitous and is dependent on upstream open reading frames. However, LUTI-based transcriptional repression is variable. In only 50% of the cases, LUTI transcription causes downregulation of the protein-coding transcript isoform. Higher LUTI expression, enrichment of histone 3 lysine 36 trimethylation, and changes in nucleosome position are the strongest predictors of LUTI-based transcriptional repression. We conclude that LUTIs downregulate gene expression in a manner that integrates translational repression, chromatin state changes, and the magnitude of LUTI expression.

Highlights

Gene expression programs determine cellular identity, form, and function through extensive regulation
Transcript leader and nanopore sequencing identifies 74 potential Long undecoded transcript isoforms (LUTIs) in meiotic prophase To determine the prominent features of LUTI-based repression, we sought to identify meiotic mRNAs with 50 extensions (Figure 1B)
The second technique, nanopore sequencing, confirmed the instances in which transcription start sites (TSSs) identified by transcript leader sequencing (TL-seq) produced transcripts that elongate across an entire coding sequence (CDS) (Figure S1; Garalde et al, 2018)

Summary

Introduction

Gene expression programs determine cellular identity, form, and function through extensive regulation. Key regulators of such programs include transcription factors (TFs), which initiate cascades of gene expression that drive changes in cellular state. A key TF complex, Ime1-Ume, activates the distal NDC80 promoter (P2) to induce a 50-extended mRNA isoform (Figure 1A). This transcript cannot be translated into a functional protein because the upstream open reading frames (uORFs) in its 50 leader inhibit the translation of the coding sequence (CDS). Reliance of the LUTI-based repression of NDC80 on Ime1-Ume couples gene activation and repression events to a common TF

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