Related Experiment Video
Updated: Jan 9, 2026
07:29
Characterization of In Vitro Differentiation of Human Primary Keratinocytes by RNA-Seq Analysis
Published on: May 16, 2020
6.6K
Genome annotations matter: characterizing Ensembl hg38 annotations from 2014 to 2023.
Madeline L Page1,2,3, Mark E Wadsworth1,2,3, Bernardo Aguzzoli Heberle1,2,3
1Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA.
BMC Genomics
|December 4, 2025
Summary
Accurate genome annotation is crucial for understanding biological complexity. Recent human Ensembl annotation updates reveal significant gains in identifying novel gene isoforms and their expression patterns, highlighting transcriptional complexity.
Area of Science:
- Genomics
- Transcriptomics
- Bioinformatics
Background:
- Accurate genome annotation is essential for RNA sequencing and understanding biological complexity.
- Annotations include gene/isoform locations, coding sequences, and metadata.
Purpose of the Study:
- To characterize changes in human Ensembl genome annotations from 2014 to 2023.
- To quantify the expression of newly annotated isoforms and assess their biological significance.
Main Methods:
- Analysis of Ensembl human genome annotation data from 2014-2023.
- Quantification of gene and isoform expression using GTEx tissue data for isoforms annotated between 2019-2023.
Main Results:
- Human Ensembl annotations generally increased, with fluctuations in specific years.
- Significant gains in identifying novel isoforms, with PCBP1-AS1 having the most annotated isoforms (296).
- Expression of new isoforms was detected in various tissues, often showing higher relative expression than previously known isoforms.
Conclusions:
- Genome annotation accuracy is vital for comprehending biological complexity.
- Recent annotation updates reveal significant transcriptional complexity previously overlooked.
Related Concept Videos
03:36Genome Annotation and Assembly
20.5K
The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
20.5K
03:00Next-generation Sequencing
97.6K
The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features....
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features....
97.6K
01:57Sanger Sequencing
772.9K
DNA sequencing is a fundamental technique that is routinely used in the biological sciences. This method can be applied to a range of questions at different scales - from the sequencing of a cloned DNA fragment or the study of a mutation in a gene up to whole-genome sequencing. However, despite the widespread use of sequencing today, it was not until 1977 that Fredrick Sanger and his collaborators developed the chain-termination method to decode DNA sequences. It relies on the separation of a...
772.9K
02:05Gene Evolution - Fast or Slow?
7.9K
The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
In contrast, regions which code...
In contrast, regions which code...
7.9K
02:54Evolutionary Relationships through Genome Comparisons
6.8K
Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
6.8K
01:05Maxam-Gilbert Sequencing
12.5K
In the same year as the discovery of the Sanger sequencing method, another group of scientists, Allan Maxam and Walter Gilbert, demonstrated their chemical-cleavage method for DNA sequencing. The Maxam-Gilbert method relies on using different chemicals that can cleave the DNA sequence at specific sites, the separation of resulting DNA fragments of variable size using electrophoresis, and deciphering the DNA sequence from the resulting gel bands.
Challenges of the Maxam-Gilbert Method
The...
Challenges of the Maxam-Gilbert Method
The...
12.5K