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Related Concept Videos

Regulation of Expression at Multiple Steps01:23

Regulation of Expression at Multiple Steps

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 addition of a...
Regulation of Expression Occurs at Multiple Steps02:24

Regulation of Expression Occurs at Multiple Steps

Gene expression can be regulated at almost every step from gene to protein. Transcription is the step that is most commonly regulated. This involves the binding of proteins to short regulatory sequences on the DNA. This association can either promote or inhibit the transcription of a gene associated with the respective sequence.
Transcription results in the generation of precursor (pre-mRNA) that consists of both exons and introns, which needs further processing before being translated to a...
Regulation of Expression Occurs at Multiple Steps02:24

Regulation of Expression Occurs at Multiple Steps

Gene expression can be regulated at almost every step from gene to protein. Transcription is the step that is most commonly regulated. This involves the binding of proteins to short regulatory sequences on the DNA. This association can either promote or inhibit the transcription of a gene associated with the respective sequence.
Transcription results in the generation of precursor (pre-mRNA) that consists of both exons and introns, which needs further processing before being translated to a...
Structure of a Gene01:30

Structure of a Gene

A gene is the fundamental unit of heredity. Every individual has two copies of each gene, one inherited from each parent. Although most people contain the same genes, there is a small fraction that is slightly different amongst people. A gene with a small difference in its sequence of DNA bases forms different alleles, contributing to different phenotypes.
However, only 1% of the DNA is composed of genes that encode proteins; the rest, 99% is non-coding DNA. This non-coding DNA performs...
What is Gene Expression?01:36

What is Gene Expression?

A gene is a stretch of DNA that serves as the blueprint for functional RNAs and proteins. Since DNA is comprised  of nucleotides and proteins are comprised of amino acids, a mediator is required to convert the information encoded in DNA into proteins. This mediator is the messenger RNA (mRNA). mRNA copies the blueprint from DNA by a process called transcription. In eukaryotes, transcription occurs in the nucleus by complementary base-pairing with the DNA template. The mRNA is then processed and...
What is Gene Expression?01:42

What is Gene Expression?

Overview
Gene expression is the process in which DNA directs the synthesis of functional products, that is, proteins. Cells can regulate gene expression at various stages. It allows organisms to generate different cell types and enables cells to adapt to internal and external factors.
Genetic Information Flows from DNA to RNA to Protein
A gene is a stretch of DNA that serves as the blueprint for functional RNAs and proteins. Since DNA is made up of nucleotides and proteins consist of amino...

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Updated: Jun 19, 2026

Describing a Transcription Factor Dependent Regulation of the MicroRNA Transcriptome
07:23

Describing a Transcription Factor Dependent Regulation of the MicroRNA Transcriptome

Published on: June 15, 2016

The Topological Regulatory Logic of noncoding RNA-mediated gene expression.

Thomas R Gingeras1

  • 1Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA gingeras@cshl.edu.

Genome Research
|June 17, 2026
PubMed
Summary

A new Topological Regulatory Logic (TRL) framework explains how long non-coding RNAs (lncRNAs) coordinate gene regulation. This model links lncRNA genomic topology to their broad regulatory scope and functions across biological scales.

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Last Updated: Jun 19, 2026

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Published on: March 7, 2018

Area of Science:

  • Genomics
  • Molecular Biology
  • Epigenetics

Background:

  • Long non-coding RNAs (lncRNAs) have diverse functions, but how they achieve coordinated gene regulation from local to genome-wide scales remains unclear.
  • Existing models do not link lncRNA genomic arrangements (antisense, intronic, etc.) to their regulatory scope or reconcile local cis effects with long-range trans communication.
  • Pervasive transcription generates numerous lncRNAs with varied genomic contexts, necessitating a unifying framework.

Purpose of the Study:

  • To propose a Topological Regulatory Logic (TRL) framework for understanding lncRNA function.
  • To explain how genomic topology and molecular mechanisms contribute to coordinated gene regulation by lncRNAs.
  • To reconcile local cis and long-range trans regulatory effects of lncRNAs.

Main Methods:

  • Conceptual framework development based on genomic topology and mechanistic layers.
  • Integration of linear genomic sequence and 3D nuclear organization principles.
  • Analysis of lncRNA configurations including overlap, divergence, intronic embedding, and subnuclear localization.

Main Results:

  • The TRL framework organizes lncRNA functions within a five-tier hierarchy and seven mechanistic layers.
  • Genomic topology defines regulatory opportunity and coordinative capacity, while molecular mechanisms determine effect magnitude and direction.
  • lncRNA topology enables genome-wide coordination through spatial coupling, kinetic buffering, and architectural memory, complementing protein-based regulation.

Conclusions:

  • The TRL framework provides a conceptual model for understanding how pervasive transcription by lncRNAs drives coordinated genome regulation.
  • Genomic topology is a key determinant of lncRNA regulatory scope and function across biological scales.
  • This framework unifies diverse lncRNA functions under principles of spatial coupling, kinetic buffering, and architectural memory.