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Related Concept Videos

Alternative RNA Splicing02:18

Alternative RNA Splicing

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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...
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RNA Splicing01:32

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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...
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RNA-seq03:21

RNA-seq

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RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
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Chromatin Structure Regulates pre-mRNA Processing02:41

Chromatin Structure Regulates pre-mRNA Processing

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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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Leaky Scanning02:28

Leaky Scanning

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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...
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Updated: Jan 13, 2026

Using RNA-sequencing to Detect Novel Splice Variants Related to Drug Resistance in In Vitro Cancer Models
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Long-Read Sequencing Reveals Cell- and State-Specific Alternative Splicing in 293T and A549 Cell Transcriptomes.

Xin Li1,2, Hanyun Que2,3, Zhaoyu Liu2

  • 1Institute for Chinese Medicine Frontier Interdisciplinary Science and Technology, Shaanxi University of Chinese Medicine, Xianyang 712046, China.

International Journal of Molecular Sciences
|January 10, 2026
PubMed
Summary

Alternative splicing (AS) is crucial for cell identity. This study used long-read sequencing to reveal cell-specific AS changes in kidney and lung cancer cells, uncovering novel isoforms and distinct cellular responses.

Keywords:
293TA549FLAIRRNA-seqSQANTI3differentially expressed genes (DEGs)genes with differential transcript usage (gDTUs)

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Area of Science:

  • Molecular Biology
  • Genomics
  • Transcriptomics

Background:

  • Alternative splicing (AS) generates transcriptomic diversity, influencing cellular identity.
  • Cell-type-specific AS, especially in response to receptor signaling, is not fully understood in common cell lines like 293T and A549.
  • Understanding AS dynamics is key to interpreting cellular function and disease states.

Purpose of the Study:

  • To characterize cell-type-specific alternative splicing dynamics in 293T and A549 cells under basal and stimulated conditions.
  • To investigate the impact of G protein-coupled receptor (GPCR) overexpression on transcriptomic complexity and splicing patterns.
  • To evaluate the utility of integrating long-read sequencing with bioinformatic tools for comprehensive AS analysis.

Main Methods:

  • Integrated Oxford Nanopore long-read sequencing with BGI short-read sequencing.
  • Profiled transcriptomes of 293T and A549 cells under basal and GPCR-overexpressing conditions (ADORA3 in 293T, P2RY12 in A549).
  • Performed full-length isoform analysis using FLAIR and SQANTI3.

Main Results:

  • Discovered extensive transcriptomic complexity, with 18.02% novel isoforms in 293T and 19.52% in A549 cells.
  • Observed a stable transcriptome in 293T cells, enriched in splicing-related pathways.
  • Identified broader transcriptional remodeling in A549 cells associated with tumorigenic processes.

Conclusions:

  • 293T cells are a suitable model for studying splicing regulation due to their stable transcriptome.
  • A549 cells provide a relevant model for exploring tumor-associated transcriptome dynamics.
  • Integrating long-read sequencing with FLAIR/SQANTI3 is valuable for dissecting cell-state-specific AS regulation.