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Related Concept Videos

Lampbrush Chromosomes01:51

Lampbrush Chromosomes

In 1882, Flemming observed lampbrush chromosomes (LBC) in salamander eggs. Later in 1892, Rückert observed LBCs in shark egg cells and coined the term "lampbrush chromosomes" because they looked like brushes used to clean kerosene lamps.
LBCs are made up of two pairs of conjugating homologous chromatids. Each chromatid consists of alternatively positioned regions of condensed-inactive chromatin and loosely placed-active side loops, which can be contracted and extended. The loops resemble the...
Histone Variants at the Centromere02:30

Histone Variants at the Centromere

Histone variants are the histone proteins with structural and sequence variations. These variants may be regarded as “mutant” forms that replace their canonical histone counterparts in the nucleosomes. Specific post-translational modifications on the histone variants enable further chromatin complexity and regulate tissue-specific gene expression. The most common histone variants are from histone H2A, H2B, and linker histone H1 families. However, several variants of histone H3 variants are also...
Non-LTR Retrotransposons03:18

Non-LTR Retrotransposons

As the name suggests, non-LTR retrotransposons lack the long terminal repeats characteristic of the LTR retrotransposons. Additionally, both LTR and non-LTR retrotransposons use distinct mechanisms of mobilization. Non-LTR retrotransposons are further divided into two classes - Long interspersed nuclear elements (LINEs) and short interspersed nuclear elements (SINEs), both of which occur abundantly in most mammals, including humans. Some of the active non-LTR retrotransposons in humans are L1...
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...
Mouse Models of Cancer Study02:43

Mouse Models of Cancer Study

Mice have long served as models for studying human biology and pathology because of their phylogenetic and physiological similarity with humans. They are also easy to maintain and breed in the laboratory, and hence, many inbred strains are now available for research. Studies on mice have contributed immeasurably to our understanding of cancer biology.
The development of transgenic, knockout, and knock-in mice has led to an exponential increase in their use as model organisms in research,...
Heterochromatin02:38

Heterochromatin

The extent of chromatin compaction can be studied by staining chromatin using specific DNA binding dyes. Under the microscope, the dense-compacted regions that take up more dye are called heterochromatin. Heterochromatin is further classified into two forms – constitutive heterochromatin and facultative heterochromatin.
Constitutive heterochromatin: It is a highly compact region of chromatin that is mostly concentrated in the centromere and telomere. Unlike euchromatin, the amino acid at 9th...

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Robust 3D DNA FISH Using Directly Labeled Probes
12:16

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Published on: August 15, 2013

Complex Loci in human and mouse genomes.

Pär G Engström1, Harukazu Suzuki, Noriko Ninomiya

  • 1Computational Biology Unit, Bergen Center for Computational Science, University of Bergen, Bergen, Norway.

Plos Genetics
|May 10, 2006
PubMed
Summary
This summary is machine-generated.

Mammalian genomes contain numerous complex gene loci, often with antisense arrangements and bidirectional promoters. These loci show coordinated gene expression but frequently feature non-conserved structures, suggesting functional importance beyond sequence.

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Area of Science:

  • Genomics
  • Gene Regulation
  • Evolutionary Biology

Background:

  • Mammalian genomes possess a significant number of complex loci, characterized by genes in antisense orientation or bidirectional promoters.
  • These complex loci involve shared transcribed regions and bidirectional core promoters, influencing gene organization.

Purpose of the Study:

  • To investigate the prevalence, functional implications, and evolutionary history of mammalian complex loci.
  • To characterize cis-antisense pairs, bidirectional promoters, and multi-gene chains within human and mouse genomes.

Main Methods:

  • Identification and characterization of transcriptional units (TUs), cis-antisense pairs, bidirectional promoters, and gene chains in mouse and human genomes.
  • Comparative analysis of gene arrangements and conservation between species.
  • Microarray analysis to assess coordinate gene expression in mouse tissues.
  • Case study on homeotic loci to examine transcript function.

Main Results:

  • Identified thousands of cis-antisense pairs, bidirectional promoters, and gene chains in both human and mouse.
  • Found that 25% of TUs are in cis-antisense pairs, with only 17% conserved between species, indicating high species specificity.
  • Observed a higher probability of coordinate expression for genes within these complex loci compared to random gene pairs.
  • Noted extensive transcription of nonconserved sequences in homeotic loci, suggesting functional importance of transcript presence.

Conclusions:

  • Complex loci are widespread in mammalian genomes, housing many nonconserved gene structures and lineage-specific exonification events.
  • These arrangements may exert cis-regulatory effects on member genes.
  • The functional significance of these complex loci may lie in their regulation and structure rather than conserved sequence.