Cold Spring Harb Symp Quant Biol. 2006;71:111-6.

Novel transcribed regions in the human genome.

Rozowsky J, Wu J, Lian Z, Nagalakshmi U, Korbel JO, Kapranov P, Zheng D, Dyke S, Newburger P, Miller P, Gingeras TR, Weissman S, Gerstein M, Snyder M.

Source

Molecular Biophysics & Biochemistry Department, Yale University, New Haven, Connecticut 06520, USA.

Abstract

We have used genomic tiling arrays to identify transcribed regions throughout the human genome. Analysis of the mapping results of RNA isolated from five cell/tissue types, NB4 cells, NB4 cells treated with retinoic acid (RA), NB4 cells treated with 12-O-tetradecanoylphorbol-13 acetate (TPA), neutrophils, and placenta, throughout the ENCODE region reveals a large number of novel transcribed regions. Interestingly, neutrophils exhibit a great deal of novel expression in several intronic regions. Comparison of the hybridization results of NB4 cells treated with different stimuli relative to untreated cells reveals that many new regions are expressed upon cell differentiation. One such region is the Hox locus, which contains a large number of novel regions expressed in a number of cell types. Analysis of the trinucleotide composition of the novel transcribed regions reveals that it is similar to that of known exons. These results suggest that many of the novel transcribed regions may have a functional role.

PMID:: 17381286; [PubMed - indexed for MEDLINE]

Publication Types, MeSH Terms, Substances

Publication Types

Research Support, N.I.H., Extramural

MeSH Terms

Substances

LinkOut - more resources

Full Text Sources

HighWire Press - PDF

Other Literature Sources

COS Scholar Universe

Supplemental Content

Save items

Related citations in PubMed

Assessing the performance of different high-density tiling microarray strategies for mapping transcribed regions of the human genome. [Genome Res. 2007]
Assessing the performance of different high-density tiling microarray strategies for mapping transcribed regions of the human genome.
Emanuelsson O, Nagalakshmi U, Zheng D, Rozowsky JS, Urban AE, Du J, Lian Z, Stolc V, Weissman S, Snyder M, et al. Genome Res. 2007 Jun; 17(6):886-97. Epub 2006 Nov 21.
Global identification of human transcribed sequences with genome tiling arrays. [Science. 2004]
Global identification of human transcribed sequences with genome tiling arrays.
Bertone P, Stolc V, Royce TE, Rozowsky JS, Urban AE, Zhu X, Rinn JL, Tongprasit W, Samanta M, Weissman S, et al. Science. 2004 Dec 24; 306(5705):2242-6. Epub 2004 Nov 11.
Systematic analysis of transcribed loci in ENCODE regions using RACE sequencing reveals extensive transcription in the human genome. [Genome Biol. 2008]
Systematic analysis of transcribed loci in ENCODE regions using RACE sequencing reveals extensive transcription in the human genome.
Wu JQ, Du J, Rozowsky J, Zhang Z, Urban AE, Euskirchen G, Weissman S, Gerstein M, Snyder M. Genome Biol. 2008 Jan 3; 9(1):R3. Epub 2008 Jan 3.
Review In-depth query of large genomes using tiling arrays. [Methods Mol Biol. 2007]
Review In-depth query of large genomes using tiling arrays.
Samanta MP, Tongprasit W, Stolc V. Methods Mol Biol. 2007; 377:163-74.
Review Dark matter in the genome: evidence of widespread transcription detected by microarray tiling experiments. [Trends Genet. 2005]
Review Dark matter in the genome: evidence of widespread transcription detected by microarray tiling experiments.
Johnson JM, Edwards S, Shoemaker D, Schadt EE. Trends Genet. 2005 Feb; 21(2):93-102.

See reviews... See all...

Cited by 4 PubMed Central articles

Dynamic transcriptomes during neural differentiation of human embryonic stem cells revealed by short, long, and paired-end sequencing. [Proc Natl Acad Sci U S A. 2010]
Dynamic transcriptomes during neural differentiation of human embryonic stem cells revealed by short, long, and paired-end sequencing.
Wu JQ, Habegger L, Noisa P, Szekely A, Qiu C, Hutchison S, Raha D, Egholm M, Lin H, Weissman S, et al. Proc Natl Acad Sci U S A. 2010 Mar 16; 107(11):5254-9. Epub 2010 Mar 1.
A genomic analysis of RNA polymerase II modification and chromatin architecture related to 3' end RNA polyadenylation. [Genome Res. 2008]
A genomic analysis of RNA polymerase II modification and chromatin architecture related to 3' end RNA polyadenylation.
Lian Z, Karpikov A, Lian J, Mahajan MC, Hartman S, Gerstein M, Snyder M, Weissman SM. Genome Res. 2008 Aug; 18(8):1224-37. Epub 2008 May 16.
Systematic analysis of transcribed loci in ENCODE regions using RACE sequencing reveals extensive transcription in the human genome. [Genome Biol. 2008]
Systematic analysis of transcribed loci in ENCODE regions using RACE sequencing reveals extensive transcription in the human genome.
Wu JQ, Du J, Rozowsky J, Zhang Z, Urban AE, Euskirchen G, Weissman S, Gerstein M, Snyder M. Genome Biol. 2008 Jan 3; 9(1):R3. Epub 2008 Jan 3.

See all...

Related information

Related Citations
Calculated set of PubMed citations closely related to the selected article(s) retrieved using a word weight algorithm. Related articles are displayed in ranked order from most to least relevant, with the “linked from” citation displayed first.
Substance (MeSH Keyword)
PubChem chemical substance (submitted) records that are classified under the same Medical Subject Headings (MeSH) controlled vocabulary as the current articles.
Cited in PMC
Full-text articles in the PubMed Central Database that cite the current articles.

Recent activity

Clear Turn Off Turn On

Novel transcribed regions in the human genome.
Novel transcribed regions in the human genome.
Cold Spring Harb Symp Quant Biol. 2006 ;71:111-6.

PubMed
Affinity of different local anesthetic drugs and catecholamines for the contralu...
Affinity of different local anesthetic drugs and catecholamines for the contraluminal transport system for organic cations in proximal tubules of rat kidneys.
J Pharmacol Exp Ther. 1992 Feb ;260(2):734-41.

PubMed
TMACC: interpretable correlation descriptors for quantitative structure-activity...
TMACC: interpretable correlation descriptors for quantitative structure-activity relationships.
J Chem Inf Model. 2007 Mar-Apr ;47(2):626-34.

PubMed
[In vivo tracking of bone marrow mesenchymal stem cells labeled with superparama...
[In vivo tracking of bone marrow mesenchymal stem cells labeled with superparamagnetic iron oxide after cerebral ischemia in rats by magnetic resonance imaging].
Zhongguo Yi Xue Ke Xue Yuan Xue Bao. 2007 Feb ;29(1):73-7.

PubMed
Size of saccade and fixation duration of eye movements during reading: psychophy...
Size of saccade and fixation duration of eye movements during reading: psychophysics of Japanese text processing.
J Opt Soc Am A. 1992 Jan ;9(1):5-13.

PubMed

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

PubMed

Result Filters

Display Settings:

Send to: