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Related Concept Videos

Alternative RNA Splicing

Alternative RNA Splicing

Alternative RNA Splicing

Alternative RNA Splicing

Alternative RNA splicing is the regulated splicing of exons and introns to produce different mature mRNAs from a single pre-mRNA. Unlike in constitutive splicing where a single gene produces a single type of mRNA, alternative splicing allows an organism to produce multiple proteins from a single gene and plays an important role in protein diversity.
There are five types of alternative RNA splicing that vary in the ways the pre-mRNA segments are removed or retained in the mature mRNA. The first...

RNA Splicing

RNA Splicing

Splicing is the process by which eukaryotic RNA is edited before its translation into protein. The RNA strand transcribed from eukaryotic DNA is called the primary transcript. The primary transcripts that become mRNAs are called precursor messenger RNAs (pre-mRNAs). Eukaryotic pre-mRNA contains alternating sequences of exons and introns. Exons are nucleotide sequences that code for proteins, whereas introns are the non-coding regions. In RNA splicing, introns are removed and exons are bonded...

Pre-mRNA Processing: RNA Splicing

Pre-mRNA Processing: RNA Splicing

Chromatin Structure and RNA Splicing

Chromatin Structure and RNA Splicing

Chromatin Structure Regulates pre-mRNA Processing

Chromatin Structure Regulates pre-mRNA Processing

In eukaryotic cells, nascent mRNA transcripts need to undergo many post-transcriptional modifications to reach the cell cytoplasm and translate into functional proteins. For a long time, transcription and pre-mRNA processing were considered two independent events that occur sequentially in the cell. However, it has now been well established that transcription and pre-mRNA processing are two simultaneous processes that are precisely regulated inside the cell.
The chromatin structure, especially...

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Related Experiment Video

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Using RNA-sequencing to Detect Novel Splice Variants Related to Drug Resistance in In Vitro Cancer Models

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Published on: December 9, 2016

Microfluidic isoform sequencing shows widespread splicing coordination in the human transcriptome.

Hagen Tilgner¹, Fereshteh Jahanbani², Ishaan Gupta¹

¹Brain and Mind Research Institute, Weill Cornell Medicine, New York, New York 10021, USA.

Genome Research

|December 3, 2017

Summary

Sparse isoform sequencing (spISO-seq) offers a cost-effective method to analyze 10-100 million RNA molecules. This approach enhances understanding of transcriptome complexity and splicing coordination in human biology and disease.

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Area of Science:

Molecular Biology
Genomics
Bioinformatics

Background:

Transcriptome complexity is vital for understanding human biology and disease.
Existing long-read RNA sequencing methods have limitations in input amount and amplification bias.
Assessing splicing coordination requires high-depth transcriptomic analysis.

Purpose of the Study:

To introduce a novel, cost-effective droplet-based method for deep RNA sequencing.
To analyze transcriptome complexity and identify splicing coordination events.
To overcome limitations of current long-read sequencing technologies.

Main Methods:

Developed sparse isoform sequencing (spISO-seq), a droplet-based method sequencing 10-200 molecules per partition.
Sequenced 10-100 million RNA molecules with minimal input cDNA (<1 ng) and reduced amplification bias.
Analyzed splicing coordination across protein-coding and noncoding genes.

Main Results:

spISO-seq enables deep analysis of transcriptome complexity with reduced cost and bias.
Confirmed known splicing coordination (e.g., BIN1) and discovered new cases (e.g., MAPT).
Found extensive splicing coordination in protein-coding genes (23.5%-59.3%), particularly involving internal exons, and identified new coordination types.

Conclusions:

Splicing coordination plays a significant role in shaping proteins and may facilitate protein complex formation.
spISO-seq provides a powerful and accessible tool for comprehensive transcriptome analysis.
The findings highlight the necessity of long-read transcriptomics for understanding gene regulation.