References
Adachi N and
Lieber MR
(2002)
Bidirectional gene organization: a common architectural feature of the human genome.
Cell
109:
807–809.
Andrianaki A,
Siapati EK,
Hirata RK,
Russell DW and
Vassilopoulos G
(2010)
Dual transgene expression by foamy virus vectors carrying an endogenous bidirectional promoter.
Gene Therapy
17:
380–388.
Anno Y‐N,
Myslinski E,
Ngondo‐Mbongo RP et al.
(2011)
Genome‐wide evidence for an essential role of the human Staf/ZNF143 transcription factor in bidirectional transcription.
Nucleic Acids Research
39:
3116–3127.
Antoniou M,
Harland L,
Mustoe T et al.
(2003)
Transgenes encompassing dual‐promoter CpG islands from the human TBP and HNRPA2B1 loci are resistant to heterochromatin‐mediated silencing.
Genomics
82:
269–279.
Batada NN,
Urrutia AO and
Hurst LD
(2007)
Chromatin remodelling is a major source of coexpression of linked genes in yeast.
Trends in Genetics
23:
480–484.
Burbelo PD,
Martin GR and
Yamada Y
(1988)
Alpha 1(IV) and alpha 2(IV) collagen genes are regulated by a bidirectional promoter and a shared enhancer.
Proceedings of the National Academy of Sciences of the USA
85:
9679–9682.
Chen PY,
Chang WS,
Chou RH et al.
(2007)
Two non‐homologous brain diseases‐related genes, SERPINI1 and PDCD10, are tightly linked by an asymmetric bidirectional promoter in an evolutionarily conserved manner.
BMC Molecular Biology
8:
2.
Chen Y‐Q,
Yu H,
Li Y‐X and
Li Y‐Y
(2010)
Sorting out inherent features of head‐to‐head gene pairs by evolutionary conservation.
BMC Bioinformatics
11(suppl. 11):
S16.
Collins PJ,
Kobayashi Y,
Nguyen L,
Trinklein ND and
Myers RM
(2007)
The ets‐related transcription factor GABP directs bidirectional transcription.
PLoS Genetics
3:
2247–2255.
Davila Lopez M,
Martinez Guerra JJ and
Samuelsson T
(2010)
Analysis of gene order conservation in eukaryotes identifies transcriptionally and functionally linked genes.
PLoS One
5:
e10654.
Deyneko IV,
Kalybaeva YM,
Kel AE and
Bloecker H
(2010)
Human–chimpanzee promoter comparisons: Property‐conserved evolution?
Genomics
96:
129–133.
Didych DA,
Shamsutdinov MF,
Smirnov NA et al.
(2013)
Human PSENEN and U2AF1L4 genes are concertedly regulated by a genuine bidirectional promoter.
Gene
515:
34–41.
Fablet M,
Bueno M,
Potrzebowski L and
Kaessmann H
(2009)
Evolutionary origin and functions of retrogene introns.
Molecular Biology and Evolution
26:
2147–2156.
Franck E,
Hulsen T,
Huynen MA et al.
(2008)
Evolution of closely linked gene pairs in vertebrate genomes.
Molecular Biology and Evolution
25:
1909–1921.
Garcia SAB and
Nagai MA
(2011)
Transcriptional regulation of bidirectional gene pairs by 17‐beta‐estradiol in MCF‐7 breast cancer cells.
Brazilian Journal of Medical and Biological Research
44:
112–122.
Gaston K and
Fried M
(1994)
YY1 is involved in the regulation of the bi‐directional promoter of the Surf‐1 and Surf‐2 genes.
FEBS Letters
347:
289–294.
Gotea V,
Petrykowska HM and
Elnitski L
(2013)
Bidirectional promoters as important drivers for the emergence of species‐specific transcripts.
PLoS One
8:
e57323.
Gotea V,
Visel A,
Westlund JM et al.
(2010)
Homotypic clusters of transcription factor binding sites are a key component of human promoters and enhancers.
Genome Research
20:
565–577.
Guarguaglini G,
Battistoni A,
Pittoggi C et al.
(1997)
Expression of the murine RanBP1 and Htf9‐c genes is regulated from a shared bidirectional promoter during cell cycle progression.
Biochemical Journal
325:
277–286.
Hansen JJ,
Bross P,
Westergaard M et al.
(2003)
Genomic structure of the human mitochondrial chaperonin genes: HSP60 and HSP10 are localised head to head on chromosome 2 separated by a bidirectional promoter.
Human Genetics
112:
71–77.
Huang CC and
Chang WS
(2009)
Cooperation between NRF‐2 and YY‐1 transcription factors is essential for triggering the expression of the PREPL‐C2ORF34 bidirectional gene pair.
BMC Molecular Biology
10:
67.
Kalitsis P and
Saffery R
(2009)
Inherent promoter bidirectionality facilitates maintenance of sequence integrity and transcription of parasitic DNA in mammalian genomes.
BMC Genomics
10:
498.
Koyanagi KO,
Hagiwara M,
Itoh T,
Gojobori T and
Imanishi T
(2005)
Comparative genomics of bidirectional gene pairs and its implications for the evolution of a transcriptional regulation system.
Gene
353:
169–176.
Kruglyak S and
Tang H
(2000)
Regulation of adjacent yeast genes.
Trends in Genetics
16:
109–111.
Lee B‐K,
Bhinge AA and
Iyer VR
(2011)
Wide‐ranging functions of E2F4 in transcriptional activation and repression revealed by genome‐wide analysis.
Nucleic Acids Research
39:
3558–3573.
Lengronne A,
Katou Y,
Mori S et al.
(2004)
Cohesin relocation from sites of chromosomal loading to places of convergent transcription.
Nature
430:
573–578.
Lercher MJ,
Blumenthal T and
Hurst LD
(2003)
Coexpression of neighboring genes in Caenorhabditis elegans is mostly due to operons and duplicate genes.
Genome Research
13:
238–243.
Lercher MJ,
Urrutia AO and
Hurst LD
(2002)
Clustering of housekeeping genes provides a unified model of gene order in the human genome.
Nature Genetics
31:
180–183.
Li YY,
Yu H,
Guo ZM et al.
(2006)
Systematic analysis of head‐to‐head gene organization: evolutionary conservation and potential biological relevance.
PLoS Computational Biology
2:
e74.
Lin JM,
Collins PJ,
Trinklein ND et al.
(2007)
Transcription factor binding and modified histones in human bidirectional promoters.
Genome Research
17:
818–827.
Liu B,
Chen J and
Shen B
(2011)
Genome‐wide analysis of the transcription factor binding preference of human bi‐directional promoters and functional annotation of related gene pairs.
BMC Systems Biology
5(suppl. 1):
S2.
Okazaki Y,
Furuno M,
Kasukawa T et al.
(2002)
Analysis of the mouse transcriptome based on functional annotation of 60,770 full‐length cDNAs.
Nature
420:
563–573.
Piontkivska H,
Yang MQ,
Larkin DM et al.
(2009)
Cross‐species mapping of bidirectional promoters enables prediction of unannotated 5′ UTRs and identification of species‐specific transcripts.
BMC Genomics
10:
189.
Rada‐Iglesias A,
Ameur A,
Kapranov P et al.
(2008)
Whole‐genome maps of USA and USF2 binding and histone H3 acetylation reveal new aspects of promoter structure and candidate genes for common human disorders.
Genome Research
18:
380–392.
Sandelin A,
Carninci P,
Lenhard B et al.
(2007)
Mammalian RNA polymerase II core promoters: insights from genome‐wide studies.
Nature Reviews Genetics
8:
424–436.
Schuettengruber B,
Doetzlhofer A,
Kroboth K,
Wintersberger E and
Seiser C
(2003)
Alternate activation of two divergently transcribed mouse genes from a bidirectional promoter is linked to changes in histone modification.
Journal of Biological Chemistry
278:
1784–1793.
Shearwin KE,
Callen BP and
Egan JB
(2005)
Transcriptional interference – a crash course.
Trends in Genetics
21:
339–345.
Shu J,
Jelinek J,
Chang H et al.
(2006)
Silencing of bidirectional promoters by DNA methylation in tumorigenesis.
Cancer Research
66:
5077–5084.
Sugino RP and
Innan H
(2012)
Natural selection on gene order in the genome reorganization process after whole‐genome duplication of yeast.
Molecular Biology and Evolution
29:
71–79.
Takai D and
Jones PA
(2004)
Origins of bidirectional promoters: computational analyses of intergenic distance in the human genome.
Molecular Biology and Evolution
21:
463–467.
Trappe R,
Doenecke D and
Albig W
(1999)
The expression of human H2A–H2B histone gene pairs is regulated by multiple sequence elements in their joint promoters.
Biochimica et Biophysica Acta
1446:
341–351.
Trinklein ND,
Aldred SF,
Hartman SJ et al.
(2004)
An abundance of bidirectional promoters in the human genome.
Genome Research
14:
62–66.
Wei W,
Pelechano V,
Jarvelin AI and
Steinmetz LM
(2011)
Functional consequences of bidirectional promoters.
Trends in Genetics
27:
267–276.
Williams EJ and
Bowles DJ
(2004)
Coexpression of neighboring genes in the genome of Arabidopsis thaliana.
Genome Research
14:
1060–1067.
Woo YH and
Li W‐H
(2011)
Gene clustering pattern, promoter architecture, and gene expression stability in eukaryotic genomes.
Proceedings of the National Academy of Sciences of the USA
108:
3306–3311.
Xu C,
Chen J and
Shen B
(2012)
The preservation of bidirectional promoter architecture in eukaryotes: what is the driving force?
BMC Systems Biology
6(suppl. 1):
S21.
Yang L and
Yu J
(2009)
A comparative analysis of divergently‐paired genes (DPGs) among Drosophila and vertebrate genomes.
BMC Evolutionary Biology
9:
55.
Yang MQ and
Elnitski L
(2007a)
Diversity of core promoter elements comprising human bidirectional promoters.
BMC Genomics
9(suppl. 2):
S3.
Yang MQ and
Elnitski LL
(2007b)
Prediction‐based approaches to characterize bidirectional promoters in the mammalian genome.
BMC Genomics
9(suppl. 1):
S2.
Yang MQ,
Koehly LM and
Elnitski LL
(2007)
Comprehensive annotation of bidirectional promoters identifies co‐regulation among breast and ovarian cancer genes.
PLoS Computational Biology
3:
733–742.
Further Reading
ENCODE Project Consortium
(2012)
An integrated encyclopedia of DNA elements in the human genome.
Nature
489(7414):
57–74.
Hurst LD,
Pal C and
Lercher MJ
(2004)
The evolutionary dynamics of eukaryotic gene order.
Nature Reviews Genetics
5(4):
299–310.
Kapranov P,
Willingham AT and
Gingeras TR
(2007)
Genome‐wide transcription and the implications for genomic organization.
Nature Reviews Genetics
8(6):
413–423.
Lanctôt C,
Cheutin T,
Cremer M,
Cavalli G and
Cremer T
(2007)
Dynamic genome architecture in the nuclear space: regulation of gene expression in three dimensions.
Nature Reviews Genetics
8(2):
104–115.
Lawrence JG
(2002)
Shared strategies in gene organization among prokaryotes and eukaryotes.
Cell
110(4):
407–413.
Michalak P
(2008)
Coexpression, coregulation, and cofunctionality of neighboring genes in eukaryotic genomes.
Genomics
91(3):
243–248.
Wakano C,
Byun JS,
Di LJ and
Gardner K
(2012)
The dual lives of bidirectional promoters.
Biochimica et Biophysica Acta
1819(7):
688–693.
Wray GA,
Hahn MW,
Abouheif E et al.
(2003)
The evolution of transcriptional regulation in eukaryotes.
Molecular Biology and Evolution
20(9):
1377–1419.
Zhou VW,
Goren A and
Bernstein BE
(2010)
Charting histone modifications and the functional organization of mammalian genomes.
Nature Reviews Genetics
12(1):
7–18.
