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Leaky Scanning

Leaky Scanning

During most eukaryotic translation processes, the small 40S ribosome subunit scans an mRNA from its 5' end until it encounters the first start AUG codon. The large 60S ribosomal subunit then joins the smaller one to initiate protein synthesis. The location of the translation initiation is largely determined by the nucleotides near the start codon as there may be multiple translation initiation sites present on the mRNA. Marilyn Kozak discovered that the sequence RCCAUGG (where R...

Ribosome Profiling

Ribosome Profiling

Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique...

Initiation of Translation

Initiation of Translation

Initiating translation is complex because it involves multiple molecules. Initiator tRNA, ribosomal subunits, and eukaryotic initiation factors (eIFs) are all required to assemble on the initiation codon of mRNA. This process consists of several steps that are mediated by different eIFs.
First, the initiator tRNA must be selected from the pool of elongator tRNAs by eukaryotic initiation factor 2 (eIF2). The initiator tRNA (Met-tRNAi) has conserved sequence elements including modified bases at...

Non-LTR Retrotransposons

Non-LTR Retrotransposons

As the name suggests, non-LTR retrotransposons lack the long terminal repeats characteristic of the LTR retrotransposons. Additionally, both LTR and non-LTR retrotransposons use distinct mechanisms of mobilization. Non-LTR retrotransposons are further divided into two classes - Long interspersed nuclear elements (LINEs) and short interspersed nuclear elements (SINEs), both of which occur abundantly in most mammals, including humans. Some of the active non-LTR retrotransposons in humans are L1...

Ribosomal RNA Synthesis

Ribosomal RNA Synthesis

Ribosome synthesis is a highly complex and coordinated process involving more than 200 assembly factors. The synthesis and processing of ribosomal components occurs not only in the nucleolus but also in the nucleoplasm and the cytoplasm of eukaryotic cells.
Ribosome biogenesis begins with the synthesis of 5S and 45S pre-rRNAs by distinct RNA polymerases. The primary transcripts are extensively processed and modified before they are bound and folded by ribosomal proteins and assembly factors,...

pre-mRNA Processing

pre-mRNA Processing

In eukaryotic cells, transcripts made by RNA polymerase are modified and processed before exiting the nucleus. Unprocessed RNA is called precursor mRNA or pre-mRNA to distinguish it from mature mRNA.
Once about 20-40 ribonucleotides have been joined together by RNA polymerase, a group of enzymes adds a “cap” to the 5’ end of the growing transcript. In this process, a 5’ phosphate is replaced by modified guanosine that has a methyl group attached to it (7-Methyl...

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Related Experiment Video

Updated: May 9, 2025

De novo Identification of Actively Translated Open Reading Frames with Ribosome Profiling Data

De novo Identification of Actively Translated Open Reading Frames with Ribosome Profiling Data

Published on: February 18, 2022

Multiple human enhancer RNAs contain long translated open reading frames.

Pavel A Vlasov, Koichi Ogami, Elizabeth Valenzuela

Biorxiv : the Preprint Server for Biology

|May 5, 2025

Summary

This summary is machine-generated.

A surprising 12% of human enhancer RNAs (eRNAs) contain long open reading frames, producing stable proteins. These novel eRNA-derived proteins (eORFs) accumulate in cells and may play roles in nuclear processes.

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Last Updated: May 9, 2025

De novo Identification of Actively Translated Open Reading Frames with Ribosome Profiling Data

De novo Identification of Actively Translated Open Reading Frames with Ribosome Profiling Data

Published on: February 18, 2022

An Integrated Approach for Microprotein Identification and Sequence Analysis

An Integrated Approach for Microprotein Identification and Sequence Analysis

Published on: July 12, 2022

Cell Based Assays of SINEUP Non-coding RNAs That Can Specifically Enhance mRNA Translation

Cell Based Assays of SINEUP Non-coding RNAs That Can Specifically Enhance mRNA Translation

Published on: February 1, 2019

Area of Science:

Molecular Biology
Genomics
Biochemistry

Background:

Enhancer RNAs (eRNAs) are typically transiently transcribed and rapidly degraded.
Under specific conditions, noncoding RNAs, including eRNAs, can be stabilized and functional.

Purpose of the Study:

To investigate the translational potential of human intergenic eRNAs.
To characterize the proteins encoded by eRNAs and their cellular functions.

Main Methods:

Ribosome profiling to detect active translation.
Mass spectrometry (MS) to identify encoded proteins (eORFs).
Exogenous expression and subcellular localization studies of eORFs.

Main Results:

Approximately 12% of human intergenic eRNAs contain long open reading frames (>300 nts).
Many eRNAs are actively translated into stable proteins (eORFs) up to ~45 KDa.
These eORFs are highly basic, arginine-rich, and primarily localize to the nucleus, associating with chromatin.

Conclusions:

A subset of human eRNAs can function as messenger RNAs (mRNAs), encoding functional proteins.
These eRNA-derived proteins (eORFs) represent a newly discovered class of nuclear proteins with potential roles in gene regulation.
Some eORFs show evidence of recent de novo gene birth and human-specific evolution.