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Related Concept Videos

Cis-regulatory Sequences02:02

Cis-regulatory Sequences

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Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
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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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The gene expression in cells is regulated at different stages: (i) transcription, (ii) RNA processing, (iii) RNA localization, and (iv) translation. Transcriptional regulation is mediated by regulatory proteins such as transcription factors, activators, or repressors—these control gene expression by initiating or inhibiting the transcription of genes. Once a precursor or pre-mRNA is produced, it undergoes post-transcriptional modification, including 5' capping, splicing, and the...
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Regulation of Expression Occurs at Multiple Steps02:24

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Master Transcription Regulators02:23

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Master transcription regulators are regulatory proteins that are predominantly responsible for regulating the expression of multiple genes. Often these genes work in concert to drive a  complex process. Activation of a master transcription regulator can lead to a cascade of transcriptional activation necessary for that outcome. These regulators can directly bind to the regulatory sequences of the various genes involved, or they can indirectly regulate transcription by binding to regulatory...
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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.
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Updated: Jul 9, 2025

High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture 4C-seq
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MAE-seq refines regulatory elements across the genome.

Xiusheng Zhu1, Qitong Huang1,2, Lei Huang1

  • 1Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China.

Nucleic Acids Research
|December 1, 2023
PubMed
Summary
This summary is machine-generated.

We developed MAE-seq to identify functional regulatory elements (REs) at 25-bp resolution. This method precisely maps enhancers, revealing novel elements and improving genome annotation for gene regulation studies.

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Area of Science:

  • Genomics and Molecular Biology
  • Epigenetics and Gene Regulation

Background:

  • Precise cell fate determination requires accurate identification of regulatory elements (REs) and their interactions with genes.
  • Current methods for defining REs lack resolution, leading to sequence redundancy and ambiguity in genomic context.

Purpose of the Study:

  • To develop and validate a high-resolution method for experimentally identifying functional REs at a 25-bp scale.
  • To characterize novel enhancers and their roles in gene regulation across different cell types.

Main Methods:

  • MAE-seq (Massive Active Enhancers by Sequencing) was developed to identify functional REs at 25-bp resolution.
  • MAE-seq was applied to mouse embryonic stem cells (mESCs), C2C12, and HEK 293T cells, analyzing trillions of DNA fragments and billions of cells.
  • High-resolution Hi-C data and CRISPR-Cas9 technology were integrated for functional validation.

Main Results:

  • MAE-seq identified hundreds of thousands of 25-bp enhancers in the studied cell types, with 626,879 in mESCs.
  • A significant portion (33.85%) of identified enhancers were novel, lacking prior epigenetic modification.
  • These 25-bp elements function as units, regulating gene expression similarly to larger elements, and enabling precise annotation of super enhancers.
  • Over 55% of novel elements showed distal interactions with target genes, with functional validation confirming their role in gene expression and cell proliferation.

Conclusions:

  • MAE-seq provides unprecedented resolution for identifying and annotating functional regulatory elements.
  • The method reveals novel enhancers and their regulatory roles, advancing our understanding of genome organization and gene control.
  • This approach enhances genome annotation precision and opens new avenues for exploring the genomic landscape and its regulatory mechanisms.