Research summary
Genome-scale transcriptome analysis was used to show that approximately three-quarters of the human genome can be transcribed and to catalogue RNAs across subcellular compartments, refining the picture of eukaryotic RNA output [1]. The GENCODE consortium annotation effort produced reference gene sets containing 20,687 protein-coding and 9,640 long noncoding RNA loci with 33,977 coding transcripts absent from UCSC and RefSeq [2], and was later extended into a continuously updated reference for both human and mouse genomes through 15 years of combined manual annotation, computational pipelines, and experimental validation [3]. As part of the ENCODE Project, regions of transcription, transcription factor binding, chromatin structure, and histone modification were mapped systematically, assigning biochemical activity to 80% of the genome and identifying candidate regulatory elements physically linked to expressed genes [4]. Structural-variant analysis of 2,504 human genomes from 26 populations integrated eight balanced and unbalanced variant classes phased onto haplotype blocks, revealing population-stratified gene-intersecting variants and naturally occurring homozygous knockouts that mark dispensable human genes [5]. The RNA-Seq method was introduced and applied to yeast to demonstrate that 74.5% of the nonrepetitive genome is transcribed, confirming known introns, identifying alternative initiation codons, and quantifying upstream open reading frames [6]. Together the studies establish reference annotations, expand the inventory of regulatory elements, and apply high-throughput sequencing to define both common and structural genetic variation across humans.
Recent publications
- RNA-Seq: a revolutionary tool for transcriptomicsDOI
- Landscape of transcription in human cellsDOI
- GENCODE: The reference human genome annotation for The ENCODE ProjectDOI
- Functional profiling of the Saccharomyces cerevisiae genomeDOI
- GENCODE reference annotation for the human and mouse genomesDOI
- The Molecular Taxonomy of Primary Prostate CancerDOI
- Global landscape of protein complexes in the yeast Saccharomyces cerevisiaeDOI
- An integrated encyclopedia of DNA elements in the human genome
- An integrated map of structural variation in 2,504 human genomesDOI
- The Transcriptional Landscape of the Yeast Genome Defined by RNA SequencingDOI
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External profiles
- ORCID: https://orcid.org/0000-0002-9746-3719
- OpenAlex: openalex.org
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