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

PubWeight™: 0.84‹?›

🔗 View Article (PMC 3334603)

Published in Genome Biol on November 23, 2011

Authors

Rajesh Pandey1, Amit K Mandal, Vineet Jha, Mitali Mukerji

Author Affiliations

1: Genomics and Molecular Medicine, Institute of Genomics and Integrative Biology, Council of Scientific and Industrial Research (CSIR-IGIB), Delhi- India.

Articles cited by this

Initial sequencing and analysis of the human genome. Nature (2001) 212.86

The human genome browser at UCSC. Genome Res (2002) 168.23

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc (2009) 137.99

Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics (2003) 100.88

WebLogo: a sequence logo generator. Genome Res (2004) 59.58

Long non-coding RNAs: insights into functions. Nat Rev Genet (2009) 19.61

Mobile elements create structural variation: analysis of a complete human genome. Genome Res (2009) 7.06

Non-coding RNAs: regulators of disease. J Pathol (2010) 5.12

Heat shock factors: integrators of cell stress, development and lifespan. Nat Rev Mol Cell Biol (2010) 4.63

Human cathelicidin antimicrobial peptide (CAMP) gene is a direct target of the vitamin D receptor and is strongly up-regulated in myeloid cells by 1,25-dihydroxyvitamin D3. FASEB J (2005) 4.36

Human Alu RNA is a modular transacting repressor of mRNA transcription during heat shock. Mol Cell (2008) 4.24

In search of antisense. Trends Biochem Sci (2004) 3.93

Over 20% of human transcripts might form sense-antisense pairs. Nucleic Acids Res (2004) 3.45

The relationship between non-protein-coding DNA and eukaryotic complexity. Bioessays (2007) 3.41

The expanding RNA polymerase III transcriptome. Trends Genet (2007) 3.07

Complete genomic sequence and analysis of 117 kb of human DNA containing the gene BRCA1. Genome Res (1996) 2.91

Close association of RNA polymerase II and many transcription factors with Pol III genes. Proc Natl Acad Sci U S A (2010) 2.90

Long non-coding RNAs in nervous system function and disease. Brain Res (2010) 2.53

Comparative analysis of transposed element insertion within human and mouse genomes reveals Alu's unique role in shaping the human transcriptome. Genome Biol (2007) 2.35

Alu elements as regulators of gene expression. Nucleic Acids Res (2006) 2.31

Cell stress and translational inhibitors transiently increase the abundance of mammalian SINE transcripts. Nucleic Acids Res (1995) 2.28

Analysis of copy number variants and segmental duplications in the human genome: Evidence for a change in the process of formation in recent evolutionary history. Genome Res (2008) 2.17

Genomic binding profiles of functionally distinct RNA polymerase III transcription complexes in human cells. Nat Struct Mol Biol (2010) 2.15

Pol II and its associated epigenetic marks are present at Pol III-transcribed noncoding RNA genes. Nat Struct Mol Biol (2010) 1.93

An Alu element in the myeloperoxidase promoter contains a composite SP1-thyroid hormone-retinoic acid response element. J Biol Chem (1996) 1.92

Alu elements contain many binding sites for transcription factors and may play a role in regulation of developmental processes. BMC Genomics (2006) 1.80

Physiological stresses increase mouse short interspersed element (SINE) RNA expression in vivo. Gene (1999) 1.79

Identification of a new subclass of Alu DNA repeats which can function as estrogen receptor-dependent transcriptional enhancers. J Biol Chem (1995) 1.78

Alu repeat analysis in the complete human genome: trends and variations with respect to genomic composition. Bioinformatics (2004) 1.77

B2 RNA and Alu RNA repress transcription by disrupting contacts between RNA polymerase II and promoter DNA within assembled complexes. Proc Natl Acad Sci U S A (2009) 1.65

Alu repeat discovery and characterization within human genomes. Genome Res (2010) 1.62

Purification and characterization of transcription factor IIIC2. J Biol Chem (1989) 1.54

Diverse splicing patterns of exonized Alu elements in human tissues. PLoS Genet (2008) 1.52

Useful 'junk': Alu RNAs in the human transcriptome. Cell Mol Life Sci (2007) 1.50

Nonrandom distribution of alu elements in genes of various functional categories: insight from analysis of human chromosomes 21 and 22. Mol Biol Evol (2003) 1.42

Genomic gems: SINE RNAs regulate mRNA production. Curr Opin Genet Dev (2010) 1.39

Human cis natural antisense transcripts initiated by transposable elements. Trends Genet (2008) 1.35

Nuclear translocated Ehrlichia chaffeensis ankyrin protein interacts with a specific adenine-rich motif of host promoter and intronic Alu elements. Infect Immun (2009) 1.32

The consensus sequence of a major Alu subfamily contains a functional retinoic acid response element. Proc Natl Acad Sci U S A (1995) 1.31

RNA polymerase III transcription repressed by Rb through its interactions with TFIIIB and TFIIIC2. J Biol Chem (1997) 1.31

Competitive and cooperative functioning of the anterior and posterior promoter elements of an Alu family repeat. Mol Cell Biol (1986) 1.27

Widespread Alu repeat-driven expansion of consensus DR2 retinoic acid response elements during primate evolution. BMC Genomics (2007) 1.27

Impact of Alu repeats on the evolution of human p53 binding sites. Biol Direct (2011) 1.25

The role of transposable elements in the regulation of IFN-lambda1 gene expression. Proc Natl Acad Sci U S A (2009) 1.24

Repetitive elements in the 5' untranslated region of a human zinc-finger gene modulate transcription and translation efficiency. Genomics (2001) 1.23

Exaptation of an ancient Alu short interspersed element provides a highly conserved vitamin D-mediated innate immune response in humans and primates. BMC Genomics (2009) 1.22

Methylation and deamination of CpGs generate p53-binding sites on a genomic scale. Trends Genet (2008) 1.17

Genome-wide analysis of antisense transcription with Affymetrix exon array. BMC Genomics (2008) 1.17

Alu sequences in undifferentiated human embryonic stem cells display high levels of A-to-I RNA editing. PLoS One (2010) 1.15

Evolution and distribution of RNA polymerase II regulatory sites from RNA polymerase III dependant mobile Alu elements. BMC Evol Biol (2004) 1.15

Epigenetic control of retrotransposon expression in human embryonic stem cells. Mol Cell Biol (2010) 1.14

Evidence for large diversity in the human transcriptome created by Alu RNA editing. Nucleic Acids Res (2009) 1.12

Alu repeats increase local recombination rates. BMC Genomics (2009) 1.11

Mining SAGE data allows large-scale, sensitive screening of antisense transcript expression. Nucleic Acids Res (2004) 1.06

Evolutionary rates and patterns for human transcription factor binding sites derived from repetitive DNA. BMC Genomics (2008) 1.02

Clusters of regulatory signals for RNA polymerase II transcription associated with Alu family repeats and CpG islands in human promoters. Genomics (2004) 1.00

Alu and b1 repeats have been selectively retained in the upstream and intronic regions of genes of specific functional classes. PLoS Comput Biol (2009) 0.99

Activation of RNA polymerase III transcription of human Alu elements by herpes simplex virus. Virology (1994) 0.98

A novel protein isoform of the multicopy human NAIP gene derives from intragenic Alu SINE promoters. PLoS One (2009) 0.98

Evolution of the repertoire of nuclear receptor binding sites in genomes. Mol Cell Endocrinol (2010) 0.97

Association of some potential hormone response elements in human genes with the Alu family repeats. Gene (1999) 0.94

Genome-wide chromatin remodeling modulates the Alu heat shock response. Gene (2001) 0.94

Evidence for common short natural trans sense-antisense pairing between transcripts from protein coding genes. Genome Biol (2008) 0.94

ALU-ring elements in the primate genomes. Genetica (2005) 0.94

Effects of Alu elements on global nucleosome positioning in the human genome. BMC Genomics (2010) 0.91

Genomic analysis reveals a novel nuclear factor-κB (NF-κB)-binding site in Alu-repetitive elements. J Biol Chem (2011) 0.90

Further characterization of thyroid hormone response elements in the human type 1 iodothyronine deiodinase gene. Endocrinology (1998) 0.89

Mechanism of down-regulation of RNA polymerase III-transcribed non-coding RNA genes in macrophages by Leishmania. J Biol Chem (2010) 0.89

Increased level of polymerase III transcribed Alu RNA in hepatocellular carcinoma tissue. Mol Carcinog (2005) 0.88

Down-regulation of 7SL RNA expression and impairment of vesicular protein transport pathways by Leishmania infection of macrophages. J Biol Chem (2005) 0.88

ALU repeats in promoters are position-dependent co-response elements (coRE) that enhance or repress transcription by dimeric and monomeric progesterone receptors. Mol Endocrinol (2009) 0.88

From 'JUNK' to just unexplored noncoding knowledge: the case of transcribed Alus. Brief Funct Genomics (2011) 0.85

The human myeloperoxidase gene is regulated by LXR and PPARalpha ligands. Biochem Biophys Res Commun (2006) 0.83

Alu elements in human growth hormone receptor gene 5' untranslated region exons. J Mol Endocrinol (2001) 0.82

Articles by these authors

Mapping human genetic diversity in Asia. Science (2009) 7.40

Whole genome expression and biochemical correlates of extreme constitutional types defined in Ayurveda. J Transl Med (2008) 2.55

Genome-wide prediction of G4 DNA as regulatory motifs: role in Escherichia coli global regulation. Genome Res (2006) 2.12

Alu repeat analysis in the complete human genome: trends and variations with respect to genomic composition. Bioinformatics (2004) 1.77

EGLN1 involvement in high-altitude adaptation revealed through genetic analysis of extreme constitution types defined in Ayurveda. Proc Natl Acad Sci U S A (2010) 1.74

Brain death--think twice before labeling a patient. Am J Emerg Med (2011) 1.65

Nonrandom distribution of alu elements in genes of various functional categories: insight from analysis of human chromosomes 21 and 22. Mol Biol Evol (2003) 1.42

SNPs in stress-responsive rice genes: validation, genotyping, functional relevance and population structure. BMC Genomics (2012) 1.18

Evolution and distribution of RNA polymerase II regulatory sites from RNA polymerase III dependant mobile Alu elements. BMC Evol Biol (2004) 1.15

Complex patterns of genomic admixture within southern Africa. PLoS Genet (2013) 1.12

Identification of optimum sequencing depth especially for de novo genome assembly of small genomes using next generation sequencing data. PLoS One (2013) 1.04

Differential serum cytokine levels are associated with cytokine gene polymorphisms in north Indians with active pulmonary tuberculosis. Infect Genet Evol (2011) 0.99

Post-zygotic de novo trinucleotide repeat expansion at spinocerebellar ataxia type 7 locus: evidence from an Indian family. J Hum Genet (2005) 0.99

Hypoxia response in asthma: differential modulation on inflammation and epithelial injury. Am J Respir Cell Mol Biol (2012) 0.98

Ayurgenomics: a new way of threading molecular variability for stratified medicine. ACS Chem Biol (2011) 0.96

ALU-ring elements in the primate genomes. Genetica (2005) 0.94

MLC1 gene is associated with schizophrenia and bipolar disorder in Southern India. Biol Psychiatry (2005) 0.93

MtSNPscore: a combined evidence approach for assessing cumulative impact of mitochondrial variations in disease. BMC Bioinformatics (2009) 0.90

Complex phenotypes in an Indian family with homozygous SCA2 mutations. Ann Neurol (2004) 0.88

Deletion of the APOBEC3B gene strongly impacts susceptibility to falciparum malaria. Infect Genet Evol (2011) 0.88

Spectrum of large copy number variations in 26 diverse Indian populations: potential involvement in phenotypic diversity. Hum Genet (2011) 0.87

Origin and instability of GAA repeats: insights from Alu elements. J Biomol Struct Dyn (2002) 0.87

SCA 1, SCA 2 & SCA 3/MJD mutations in ataxia syndromes in southern India. Indian J Med Res (2007) 0.86

Founder haplotype for Machado-Joseph disease in the Indian population: novel insights from history and polymorphism studies. Arch Neurol (2005) 0.85

Recent admixture in an Indian population of African ancestry. Am J Hum Genet (2011) 0.85

IGVBrowser--a genomic variation resource from diverse Indian populations. Database (Oxford) (2010) 0.85

From diversity to delivery: the case of the Indian Genome Variation initiative. Nat Rev Genet (2008) 0.85

From 'JUNK' to just unexplored noncoding knowledge: the case of transcribed Alus. Brief Funct Genomics (2011) 0.85

Transcriptome-wide expansion of non-coding regulatory switches: evidence from co-occurrence of Alu exonization, antisense and editing. Nucleic Acids Res (2013) 0.84

SMARCA2 and THAP11: potential candidates for polyglutamine disorders as evidenced from polymorphism and protein-folding simulation studies. J Hum Genet (2004) 0.84

Non-random genomic divergence in repetitive sequences of human and chimpanzee in genes of different functional categories. Mol Genet Genomics (2007) 0.83

Synthesis of the C3-C18 fragment of amphidinolides G and H. Org Lett (2007) 0.83

Discovery of imidazo[1,2-a]pyrazine-based Aurora kinase inhibitors. Bioorg Med Chem Lett (2010) 0.83

Flocculating property of extracellular polymeric substances produced by a biofilm-forming bacterium Acinetobacter junii BB1A. Appl Biochem Biotechnol (2012) 0.81

Insights into the mutational history and prevalence of SCA1 in the Indian population through anchored polymorphisms. Hum Genet (2005) 0.81

Utilizing linkage disequilibrium information from Indian Genome Variation Database for mapping mutations: SCA12 case study. J Genet (2009) 0.80

A genome-wide search for non-UGT1A1 markers associated with unconjugated bilirubin level reveals significant association with a polymorphic marker near a gene of the nucleoporin family. Ann Hum Genet (2011) 0.80

Spinocerebellar ataxia 7 (SCA7) in Indian population: predilection of ATXN7-CAG expansion mutation in an ethnic population. Indian J Med Res (2015) 0.79

SCA-LSVD: a repeat-oriented locus-specific variation database for genotype to phenotype correlations in spinocerebellar ataxias. Hum Mutat (2009) 0.78

North and South Indian populations share a common ancestral origin of Friedreich's ataxia but vary in age of GAA repeat expansion. Ann Hum Genet (2010) 0.76

Stereocontrol in organic synthesis using silicon-containing compounds. Studies directed towards the synthesis of ebelactone A. Org Biomol Chem (2004) 0.75

Finding Alu in primate genomes with AF-1. Bioinformation (2009) 0.75

Enzymatic hydrolyzed feather peptide, a welcoming drug for multiple-antibiotic-resistant Staphylococcus aureus: structural analysis and characterization. Appl Biochem Biotechnol (2015) 0.75

Bioisosteric approach to the discovery of imidazo[1,2-a]pyrazines as potent Aurora kinase inhibitors. Bioorg Med Chem Lett (2010) 0.75

Guidelines for Diagnosis and Management of Bronchial Asthma: Joint Recommendations of National College of Chest Physicians (India) and Indian Chest Society. Indian J Chest Dis Allied Sci (2015) 0.75

Infantile onset spinocerebellar ataxia 2 (SCA2): a clinical report with review of previous cases. J Child Neurol (2013) 0.75

Discovery of orally bioavailable imidazo[1,2-a]pyrazine-based Aurora kinase inhibitors. Bioorg Med Chem Lett (2010) 0.75