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Related Concept Videos

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. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
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Ribosome Profiling

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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
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Related Experiment Video

Updated: Sep 13, 2025

A Rapid High-throughput Method for Mapping Ribonucleoproteins RNPs on Human pre-mRNA
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Enhancing transcriptome mapping with rapid PRO-seq profiling of nascent RNA.

Pradeep Kumar Reddy Cingaram1, Felipe Beckedorff1, Jingyin Yue1

  • 1University of Miami Miller School of Medicine, Sylvester Comprehensive Cancer Center, Department of Human Genetics, 1501 NW 10(th) Avenue, Miami, FL 33136, USA.

Molecular Cell
|July 25, 2025
PubMed
Summary

Rapid PRO-seq (rPRO-seq) streamlines transcriptome mapping to under 12 hours, requiring minimal cells. This new method aids in understanding gene regulation and neurodevelopmental disorders.

Keywords:
INTS11Integrator complexRNA polymerase IIenhancer RNAhematopoietic progenitor cellsnascent transcriptionneurodevelopmental genesrapid PRO-seqtranscriptional elongationtranscriptional pausing

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Area of Science:

  • Molecular Biology
  • Genomics
  • Transcriptomics

Background:

  • Precision nuclear run-on (PRO) sequencing (PRO-seq) maps transcriptomes at nucleotide resolution.
  • Current PRO-seq protocols are lengthy, complex, and require substantial starting material.

Purpose of the Study:

  • To develop a rapid and efficient PRO-seq protocol (rPRO-seq).
  • To overcome limitations of the standard PRO-seq method, including time, technical difficulty, and sample input.

Main Methods:

  • Development of rapid PRO-seq (rPRO-seq).
  • Application of rPRO-seq to mouse hematopoietic progenitor cells (mHPCs) and mouse neurons.
  • Utilizing acute depletion of INTS11 in neuronal cells.

Main Results:

  • rPRO-seq enables efficient transcriptome mapping in approximately 12 hours.
  • The protocol increases ligation efficiency, eliminates adapter dimers, and minimizes sample loss and RNA degradation.
  • rPRO-seq requires as few as 5,000 cells for transcriptome mapping.
  • Demonstrated the role of INTS11 in regulating genes associated with neurodevelopmental disorders.

Conclusions:

  • rPRO-seq significantly advances nascent transcript analysis.
  • This method is valuable for generating patient-specific, genome-wide transcription profiles with minimal sample input.
  • rPRO-seq facilitates the study of gene regulation in various cell types, including those relevant to neurodevelopmental disorders.