Phylogenetic Shadowing of Primate Sequences to Find Functional Regions of the Human Genome

Boffelli, Dario; McAuliffe, Jon; Ovcharenko, Dmitriy; Lewis, Keith D.; Ovcharenko, Ivan; Pachter, Lior; Rubin, Edward M.

doi:10.1126/science.1081331

Cited by 458 publications

(415 citation statements)

References 13 publications

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“…Boffelli et al (25) have shown recently that phylogenetic shadowing of primate sequences that includes sequence from as few as four to six primates in addition to humans is sufficient for the identification of functional elements in the human genome, many of which are likely to be missed by human-mouse comparisons. Consistent with these observations, our previous analysis of TNF-␣ sequences in the primate lineage demonstrated that such an approach is a powerful tool for the identification of candidate regions important for gene regulation.…”

Section: Discussionmentioning

confidence: 99%

T Cell-Specific Expression of the Human TNF-α Gene Involves a Functional and Highly Conserved Chromatin Signature in Intron 3

Barthel

Goldfeld

2003

The Journal of Immunology

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Using a phylogenetic approach, we identified highly conserved sequences within intron 3 of the human TNF-α gene. These sequences form cell type-specific DNase I hypersensitivity sites and display cell type-specific DNA-protein contacts in in vivo genomic footprints. Consistent with these results, intron 3 confers specific activity upon a TNF-α reporter gene in Jurkat T cells, but not THP-1 monocytic cells. Thus, using a combinatorial approach of phylogenetic analysis, DNase I hypersensitivity analysis, in vivo footprinting, and transfection analysis, we demonstrate that intronic regulatory elements are involved in the cell type-specific regulation of TNF-α gene expression.

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Section: Discussionmentioning

confidence: 99%

T Cell-Specific Expression of the Human TNF-α Gene Involves a Functional and Highly Conserved Chromatin Signature in Intron 3

Barthel

Goldfeld

2003

The Journal of Immunology

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“…This has been accomplished through comparison of the human genome with the genomes of a wide-range of species from primates to fish [1][2][3][4]. The underlying success of this strategy is based on comparing sufficiently divergent genomes to distinguish neutral versus functionally constrained sequence elements [5,6].…”

Section: Introductionmentioning

confidence: 99%

In vivo characterization of a vertebrate ultraconserved enhancer

et al. 2005

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Genomic sequence comparisons between human, mouse and pufferfish (Takifugu rubripes (Fugu)) have revealed a set of extremely conserved noncoding sequences. While this high degree of sequence conservation suggests severe evolutionary constraint and predicts a lack of tolerance to change in order to retain in vivo functionality, such elements have been minimally explored experimentally. In this study, we describe the in-depth characterization of an ancient conserved enhancer, Dc2 located near the dachshund gene, which displays a human-Fugu identity of 84% over 424 basepairs (bp). In addition to this large overall conservation, we find that Dc2 is characterized by the presence of a large block of sequence (144 bp) that is completely identical between human, mouse, chicken, zebrafish and Fugu. Through the testing of reporter vector constructs in transgenic mice, we observed that the 424 bp Dc2 conserved element is necessary and sufficient for brain tissue enhancer activity. In vivo analyses also revealed that the 144 bp 100% conserved sequence is necessary, but not sufficient, to replicate Dc2 enhancer function. However, the introduction of two separate 16 bp insertions into the highly conserved enhancer core did not cause any detectable modification of its in vivo activity. Our observations indicate that the 144 bp 100% conserved element is tolerant of change at least at the resolution of this transgenic mouse assay and suggest that purifying selection on Dc2 sequence might not be as strong as we predicted or that some unknown property also constrains this highly conserved enhancer sequence. Thank you for your letter of February 15 th and for the reviewers' comments on our manuscript entitled "In Vivo Characterization of a Vertebrate Ultra-conserved Enhancer", by Poulin et al. We have addressed the reviewers' concerns in a revised manuscript, which we are resubmitting for your consideration.Our detailed response is as follows:Reviewer #21. Abstract -last sentence should read: "tolerant of change at least AT the resolution…"We have changed this typo. 2.Introduction paragraph four (page 4), first sentence. Statement "which is involved in embryonic development" is too vague. Please state, briefly, the function of DACH.We have added an introduction description of DACHs known function and reference to its Drosophila homolog. 3.Introduction paragraph four (page 4). When first introducing Dc2, please define it as a conserved, functional element at DACH (i.e., since the Dc nomenclature was not used previously in the text).We have made this change. 4.Introduction paragraph four (page 4). Please provide a reference for the statement "known degeneracy of the sequences recognized by transcription factors".We have added a reference. 5.Results paragraph one (page 5), first sentence. Please restate the locus (DACH) at which Dc2 resides.We have made this change. 6.Results "Refinement of the Minimal Necessary Dc2 Enhancer". Authors state that the 424 bp fragment drives expression pattern in transgenics that is "indistingu...

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“…LD analysis generally identifies more than 30,000 of candidate genes for a specific pathology and evidences the major risk alleles [139]. Although this analysis is very suggestive and likely gives a clear identification of potential candidate genes for a single pathology, as suggested for instance in cancer [21], it still in infancy because of the presence of many genes with modest effects [17]. Thus, many efforts are actually in progress in order to separate ''robust'' genes from ''modest'' genes.…”

Section: Zinc-hsp70 Gene Interactionmentioning

confidence: 98%

Zinc–gene interaction related to inflammatory/immune response in ageing

Mocchegiani

Malavolta

2008

Genes Nutr

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The pivotal role played by zinc-gene interaction in affecting some relevant cytokines (IL-6 and TNF-a) and heat shock proteins (HSP70-2) in ageing, successful ageing (nonagenarians) and the most common age-related diseases, such as atherosclerosis and infections, is now recognized. The polymorphisms of genes codifying proteins related to the inflammation are predictive on one hand in longevity, on the other hand they are associated with atherosclerosis or severe infections. Since the health lifespan has a strong genetic component, which in turn also affected by nutritional factors like zinc, the association of these polymorphisms with innate immune response, zinc ion bioavailability and Metallothioneins (MT) homeostasis is an useful tool to unravel the role played by zinc-gene interactions in longevity, especially due to the inability of MT in zinc release in ageing and chronic inflammation. In ageing, this last fact leads to depressed innate immune response for host defence. In contrast, in very old age the inflammation is lower with subsequent more zinc ion bioavailability, less MT gene expression and satisfactory innate immunity. Therefore, the zinc-gene (IL-6, TNF-a, Hsp70-2) interactions, via MT homeostasis, are crucial to achieve successful ageing. Human genes and longevityAgeing is a universal phenomenon that affects nearly all of animal species. According to Helfand and Rogina [69], ageing can be characterized as: (1) an inevitable consequence of being a multicellular organism; (2) associated with a random, passive decline in function; (3) leading to a global loss of homeostasis over time and (4) mortality increasing with ageing. Evolutionary studies on ageing have drawn the attention on the importance of the genetic mechanisms involved in somatic maintenance and repair that secure longevity [82]. Evidence from model organisms has indicated that subtle variation in the genes can dramatically influence lifespan. However, findings on potential candidate genetic mechanisms determining ageing and lifespan in model organisms are far to explain variations in human populations because phenotypes are critically dependent on the setting in which genes are expressed, while laboratory conditions and modern environments are markedly dissimilar [86]. Genetic analysis of human ageing is mainly approached by searching the genetic basis of susceptibility to major geriatric disorders or the allelic contributions to exceptionally long life span. It is just thanks to these last studies in centenarians populations that several candidate longevity genes or pathways including PON1 [19,130], IGF1/insulin pathway [84,120], elements of lipid metabolism [12], stress response [34] and inflammatory response have been identified [53].Genes related to inflammation and stress response, in particular the pro-inflammatory cytokines IL-1, IL-6, TNFalpha, the anti-inflammatory cytokine IL-10, the HSP70 chaperones and the regulators of trace elements homeostasis, metallothioneins (MT), seem particularly relevant taking into accoun...

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Phylogenetic Shadowing of Primate Sequences to Find Functional Regions of the Human Genome

Abstract: Materials and Methods 1. Generation of sequencing targets. Sequencing targets were amplified from genomic DNA using Platinum Taq HiFi (Invitrogen) following the manufacturer's recommendations, with primers

Cited by 458 publications

References 13 publications

T Cell-Specific Expression of the Human TNF-α Gene Involves a Functional and Highly Conserved Chromatin Signature in Intron 3

T Cell-Specific Expression of the Human TNF-α Gene Involves a Functional and Highly Conserved Chromatin Signature in Intron 3

In vivo characterization of a vertebrate ultraconserved enhancer

Zinc–gene interaction related to inflammatory/immune response in ageing

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