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Impact of Alu repeats on the evolution of human p53 binding sites.

Cui F, Sirotin MV, Zhurkin VB.

Biol Direct. 2011 Jan 6;6:2. doi: 10.1186/1745-6150-6-2.


Clusters of regulatory signals for RNA polymerase II transcription associated with Alu family repeats and CpG islands in human promoters.

Oei SL, Babich VS, Kazakov VI, Usmanova NM, Kropotov AV, Tomilin NV.

Genomics. 2004 May;83(5):873-82.


Association of some potential hormone response elements in human genes with the Alu family repeats.

Babich V, Aksenov N, Alexeenko V, Oei SL, Buchlow G, Tomilin N.

Gene. 1999 Nov 1;239(2):341-9.


Interactions of chromatin context, binding site sequence content, and sequence evolution in stress-induced p53 occupancy and transactivation.

Su D, Wang X, Campbell MR, Song L, Safi A, Crawford GE, Bell DA.

PLoS Genet. 2015 Jan 8;11(1):e1004885. doi: 10.1371/journal.pgen.1004885. eCollection 2015 Jan.


Phylogenetic affinities of tarsier in the context of primate Alu repeats.

Zietkiewicz E, Richer C, Labuda D.

Mol Phylogenet Evol. 1999 Feb;11(1):77-83.


Noncanonical DNA motifs as transactivation targets by wild type and mutant p53.

Jordan JJ, Menendez D, Inga A, Noureddine M, Bell DA, Resnick MA.

PLoS Genet. 2008 Jun 27;4(6):e1000104. doi: 10.1371/journal.pgen.1000104. Erratum in: PLoS Genet. 2008 Nov;4(11) PLoS Genet. 2008 Jul;4(7). doi: 10.1371/annotation/13bc83be-2345-401d-b953-f1886e9fbdff. Nourredine, Maher [corrected to Noureddine, Maher]; Bell, Douglas [corrected to Bell, Douglas A].


Nuclear receptor HNF4α binding sequences are widespread in Alu repeats.

Bolotin E, Chellappa K, Hwang-Verslues W, Schnabl JM, Yang C, Sladek FM.

BMC Genomics. 2011 Nov 15;12:560. doi: 10.1186/1471-2164-12-560.


Whole-genome analysis of Alu repeat elements reveals complex evolutionary history.

Price AL, Eskin E, Pevzner PA.

Genome Res. 2004 Nov;14(11):2245-52.


Enrichment analysis of Alu elements with different spatial chromatin proximity in the human genome.

Gu Z, Jin K, Crabbe MJ, Zhang Y, Liu X, Huang Y, Hua M, Nan P, Zhang Z, Zhong Y.

Protein Cell. 2016 Apr;7(4):250-66. doi: 10.1007/s13238-015-0240-7. Epub 2016 Feb 10.


Shuffling of genes within low-copy repeats on 22q11 (LCR22) by Alu-mediated recombination events during evolution.

Babcock M, Pavlicek A, Spiteri E, Kashork CD, Ioshikhes I, Shaffer LG, Jurka J, Morrow BE.

Genome Res. 2003 Dec;13(12):2519-32.


Comparative analysis of Alu repeats in primate genomes.

Liu GE, Alkan C, Jiang L, Zhao S, Eichler EE.

Genome Res. 2009 May;19(5):876-85. doi: 10.1101/gr.083972.108.


Whole-genome cartography of p53 response elements ranked on transactivation potential.

Tebaldi T, Zaccara S, Alessandrini F, Bisio A, Ciribilli Y, Inga A.

BMC Genomics. 2015 Jun 17;16:464. doi: 10.1186/s12864-015-1643-9.


Enrichment for histone H3 lysine 9 methylation at Alu repeats in human cells.

Kondo Y, Issa JP.

J Biol Chem. 2003 Jul 25;278(30):27658-62. Epub 2003 Apr 30.


SATB1-binding sequences and Alu-like motifs define a unique chromatin context in the vicinity of human immunodeficiency virus type 1 integration sites.

Kumar PP, Mehta S, Purbey PK, Notani D, Jayani RS, Purohit HJ, Raje DV, Ravi DS, Bhonde RR, Mitra D, Galande S.

J Virol. 2007 Jun;81(11):5617-27. Epub 2007 Mar 21.


Heat shock factor binding in Alu repeats expands its involvement in stress through an antisense mechanism.

Pandey R, Mandal AK, Jha V, Mukerji M.

Genome Biol. 2011 Nov 23;12(11):R117. doi: 10.1186/gb-2011-12-11-r117.


DHX9 suppresses RNA processing defects originating from the Alu invasion of the human genome.

Aktaş T, Avşar Ilık İ, Maticzka D, Bhardwaj V, Pessoa Rodrigues C, Mittler G, Manke T, Backofen R, Akhtar A.

Nature. 2017 Apr 6;544(7648):115-119. doi: 10.1038/nature21715. Epub 2017 Mar 29.


A fish-specific transposable element shapes the repertoire of p53 target genes in zebrafish.

Micale L, Loviglio MN, Manzoni M, Fusco C, Augello B, Migliavacca E, Cotugno G, Monti E, Borsani G, Reymond A, Merla G.

PLoS One. 2012;7(10):e46642. doi: 10.1371/journal.pone.0046642. Epub 2012 Oct 31.


From 'JUNK' to just unexplored noncoding knowledge: the case of transcribed Alus.

Pandey R, Mukerji M.

Brief Funct Genomics. 2011 Sep;10(5):294-311. doi: 10.1093/bfgp/elr029. Review.


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