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Related Concept Videos

Multi-species Conserved Sequences02:51

Multi-species Conserved Sequences

Next-generation sequencing technologies have created large genomic databases of a variety of animals and plants. Ever since the human genome project was completed, scientists studied the genome of primates, mammals, and other phylogenetically distant living beings. Such large-scale  studies have provided new insights into the evolutionary relationship between organisms.
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved DNA...
Cis-regulatory Sequences02:02

Cis-regulatory Sequences

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...
Cis-regulatory Sequences02:02

Cis-regulatory Sequences

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...
lncRNA - Long Non-coding RNAs02:39

lncRNA - Long Non-coding RNAs

In humans, more than 80% of the genome gets transcribed. However, only around 2% of the genome codes for proteins. The remaining part produces non-coding RNAs which includes ribosomal RNAs, transfer RNAs, telomerase RNAs, and regulatory RNAs, among other types. A large number of regulatory non-coding RNAs have been classified into two groups depending upon their length – small non-coding RNAs, such as microRNA, which are less than 200 nucleotides in length, and long non-coding RNA (lncRNA)...
lncRNA - Long Non-coding RNAs02:39

lncRNA - Long Non-coding RNAs

In humans, more than 80% of the genome gets transcribed. However, only around 2% of the genome codes for proteins. The remaining part produces non-coding RNAs which includes ribosomal RNAs, transfer RNAs, telomerase RNAs, and regulatory RNAs, among other types. A large number of regulatory non-coding RNAs have been classified into two groups depending upon their length – small non-coding RNAs, such as microRNA, which are less than 200 nucleotides in length, and long non-coding RNA (lncRNA)...
Comparing Copy Number Variations and SNPs02:26

Comparing Copy Number Variations and SNPs

Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...

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mRNA Interactome Capture from Plant Protoplasts
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Published on: July 28, 2017

Conserved noncoding sequences (CNSs) in higher plants.

Michael Freeling1, Shabarinath Subramaniam

  • 1Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA. freeling@nature.berkeley.edu

Current Opinion in Plant Biology
|March 3, 2009
PubMed
Summary
This summary is machine-generated.

Plant conserved noncoding sequences (CNSs) function in gene regulation, often near genes encoding transcription factors. Some CNSs, termed Bigfoot genes, have long phylogenetic footprints and may involve novel DNA-templated protein assembly mechanisms.

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Last Updated: Jun 25, 2026

mRNA Interactome Capture from Plant Protoplasts
12:29

mRNA Interactome Capture from Plant Protoplasts

Published on: July 28, 2017

Isolation and Transcriptome Analysis of Plant Cell Types
08:53

Isolation and Transcriptome Analysis of Plant Cell Types

Published on: April 7, 2023

Laser-Capture Microdissection RNA-Sequencing for Spatial and Temporal Tissue-Specific Gene Expression Analysis in Plants
08:33

Laser-Capture Microdissection RNA-Sequencing for Spatial and Temporal Tissue-Specific Gene Expression Analysis in Plants

Published on: August 5, 2020

Area of Science:

  • Plant molecular biology
  • Genomics
  • Evolutionary biology

Background:

  • Conserved noncoding sequences (CNSs) are functional elements in plant genomes.
  • Plant CNSs exhibit lower conservation levels compared to vertebrate ultraconserved noncoding sequences.
  • CNSs are frequently located near genes and are enriched for regulatory elements.

Purpose of the Study:

  • To investigate the characteristics and potential functions of plant conserved noncoding sequences (CNSs).
  • To explore the association of CNSs with specific gene types, such as transcription factors.
  • To examine the phenomenon of 'Bigfoot genes' characterized by long phylogenetic footprints.

Main Methods:

  • Comparative genomics to identify conserved noncoding sequences across plant species.
  • Analysis of CNS distribution relative to gene locations and functions.
  • Investigating transcribed CNSs for short peptide products.
  • Bioinformatic analysis of 'Bigfoot genes' and their associated regulatory elements.

Main Results:

  • Plant CNSs are functionally validated phylogenetic footprints, often clustered around regulatory genes.
  • Genes encoding transcription factors or responding to stimuli are particularly CNS-rich.
  • A subset of CNSs, termed 'Bigfoot genes,' exhibit extended phylogenetic footprints.
  • Some transcribed CNSs may produce short peptides for regulatory control.

Conclusions:

  • Plant CNSs play crucial roles in gene regulation, particularly for transcription factor genes.
  • The 'Bigfoot gene' phenomenon suggests unique evolutionary pressures and regulatory mechanisms.
  • A novel 'DNA-templated protein assembly' model is proposed to explain the function of Bigfoot gene CNSs.