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Related Concept Videos

RNA Splicing01:32

RNA Splicing

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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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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.
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MicroRNAs01:22

MicroRNAs

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MicroRNA (miRNA) are short, regulatory RNA transcribed from introns (non-coding regions of a gene) or intergenic regions (stretches of DNA present between genes). Several processing steps are required to form biologically active, mature miRNA. The initial transcript, called primary miRNA (pri-mRNA), base-pairs with itself, forming a stem-loop structure. Within the nucleus, an endonuclease enzyme, called Drosha, shortens the stem-loop structure into hairpin-shaped pre-miRNA. After the pre-miRNA...
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Riboswitches01:56

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Riboswitches are non-coding mRNA domains that regulate the transcription and translation of downstream genes without the help of proteins. Riboswitches bind directly to a metabolite and can form unique stem-loop or hairpin structures in response to the amount of the metabolite present. They have two distinct regions – a metabolite-binding aptamer and an expression platform.
The aptamer has high specificity for a particular metabolite which allows riboswitches to specifically regulate...
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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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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.
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Updated: Sep 11, 2025

Engineering Artificial Factors to Specifically Manipulate Alternative Splicing in Human Cells
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Dysregulated Alternative Splicing in Breast Cancer Subtypes of RIF1 and Other Transcripts.

Emma Parker1, Laura Akintche1, Alexandra Pyatnitskaya1

  • 1Chromosome & Cellular Dynamics Section, Institute of Medical Sciences, University of Aberdeen, Aberdeen AB25 2ZD, UK.

International Journal of Molecular Sciences
|August 14, 2025
PubMed
Summary
This summary is machine-generated.

Rap1 Interacting Factor 1 (RIF1) gene expression and splicing are altered in various cancers. Specific RIF1 splicing patterns in breast cancer subtypes correlate with clinical outcomes, highlighting its role in genome instability and cancer progression.

Keywords:
RNA splicingTCGAbreast cancer

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Area of Science:

  • Molecular Biology
  • Cancer Research
  • Genomics

Background:

  • Genome instability is a key feature of cancer, often caused by DNA replication and repair defects.
  • Rap1 Interacting Factor 1 (RIF1) is vital for maintaining genome stability and is implicated in cancer development.
  • RIF1 exists as two splice variants, RIF1-Long and RIF1-Short, with differing roles in cellular response to replication stress.

Purpose of the Study:

  • To investigate differential expression and splicing of RIF1 in cancer cell lines under replication stress.
  • To analyze RIF1 expression and splicing patterns in human tumors using The Cancer Genome Atlas (TCGA) data.
  • To explore the clinical significance of RIF1 splicing variants in different cancer subtypes, particularly breast cancer.

Main Methods:

  • Analysis of RIF1 expression and splicing in cancer cell lines after induced replication stress.
  • Bioinformatic analysis of matched normal and tumor data from TCGA for RIF1 expression and exon usage.
  • Correlation of RIF1 splicing patterns with clinical outcomes in various breast cancer subtypes (LumA, LumB, HER2E, Basal).

Main Results:

  • Overall RIF1 expression is altered in several cancer types, notably increased in colon and lung cancers.
  • Distinct RIF1 splicing patterns were observed, especially in breast cancer subtypes.
  • Exclusion of RIF1 Exon 31, favoring RIF1-Short, was prevalent in LumA, LumB, and HER2E breast cancers, correlating with poorer outcomes.
  • Breast cancer subtypes showed a tendency for short exon exclusion, suggesting length-dependent splicing dysregulation.
  • Basal breast cancer exhibited exon exclusion but lacked a short-exon bias, with inconsistent Exon 31 exclusion.

Conclusions:

  • RIF1 expression and splicing are dysregulated in cancer, contributing to genome instability.
  • Specific RIF1 splicing patterns, particularly Exon 31 exclusion in certain breast cancer subtypes, are associated with adverse clinical outcomes.
  • The differential splicing of RIF1 variants may represent a novel therapeutic target for specific cancer types.