Identification of Novel Functional Elements in the Human Genome

Zheng, Liduan; Euskirchen, Ghia; Rinn, John L.; Martone, Rebecca; Bertone, Paul; Hartman, Stephen E.; Royce, Thomas; Nelson, K. E.; Sayward, Fred; Luscombe, Nicholas M.; Yang, Joan; Li, J L; Miller, Perry L.; Urban, Alexander; Gerstein, Mark; Weissman, Sherman M.; Snyder, M

doi:10.1101/sqb.2003.68.317

Cited by 2 publications

(2 citation statements)

References 13 publications

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“…Several studies have estimated that ∼10% of the nonrepeat sequences of the genome appear to be transcribed, polyadenylated, spliced in a high proportion of transcripts, and transported into the cytosol (Kapranov et al 2002;Lian et al 2003;Martone et al 2003;Rinn et al 2003;Yelin et al 2003;Cheng et al 2005). Considering the annotated transcripts present in RefSeq and GENCODE (Harrow et al 2006) databases, as well as all ESTs recorded in dbEST, more than half of the detected transcribed sequences are not observed to align with these annotated transcripts (The ENCODE Project Consortium 2007; Kapranov et al 2007a).…”

Section: Prevalence Of Tufs In Nonprotein-coding Regions Of Genomesmentioning

confidence: 99%

Origin of phenotypes: Genes and transcripts

Gingeras¹

2007

Genome Res.

181

152

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While the concept of a gene has been helpful in defining the relationship of a portion of a genome to a phenotype, this traditional term may not be as useful as it once was. Currently, “gene” has come to refer principally to a genomic region producing a polyadenylated mRNA that encodes a protein. However, the recent emergence of a large collection of unannotated transcripts with apparently little protein coding capacity, collectively called transcripts of unknown function (TUFs), has begun to blur the physical boundaries and genomic organization of genic regions with noncoding transcripts often overlapping protein-coding genes on the same (sense) and opposite strand (antisense). Moreover, they are often located in intergenic regions, making the genic portions of the human genome an interleaved network of both annotated polyadenylated and nonpolyadenylated transcripts, including splice variants with novel 5′ ends extending hundreds of kilobases. This complex transcriptional organization and other recently observed features of genomes argue for the reconsideration of the term “gene” and suggests that transcripts may be used to define the operational unit of a genome.

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Section: Prevalence Of Tufs In Nonprotein-coding Regions Of Genomesmentioning

confidence: 99%

Origin of phenotypes: Genes and transcripts

Gingeras¹

2007

Genome Res.

181

152

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show abstract

“…This is of relevance because there is mounting evidence that a tremendous amount of unknown RNA is evidently expressed from the human genome at a much greater amount than what was previously anticipated. [7][8][9][10][11] The biological role of this RNA is still being investigated, but there is much that appears to be non-coding in nature. These newly identified RNAs could have regulatory capacity, however, and perform some of the functions described here.…”

Section: Non-coding Rnamentioning

confidence: 99%

MicroRNA Modulation of RNA-Binding Protein Regulatory Elements

George¹,

Tenenbaum²

2006

RNA Biology

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Identification of Novel Functional Elements in the Human Genome

Cited by 2 publications

References 13 publications

Origin of phenotypes: Genes and transcripts

Origin of phenotypes: Genes and transcripts

MicroRNA Modulation of RNA-Binding Protein Regulatory Elements

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