GATA simple sequence repeats function as enhancer blocker boundaries

Kumar, Ram P.; Krishnan, Jaya; Singh, Narendra Pratap; Singh, Lalji; Mishra, Rakesh K.

doi:10.1038/ncomms2872

Cited by 26 publications

(19 citation statements)

References 46 publications

(57 reference statements)

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“…This (GATA) n motif is reported to be extended on Y or W chromosomes of several vertebrates, including human, mouse and snakes, and invertebrates species [30–32]. Furthermore, (GATA) n motif (included in Bkm repeats with (GACA) n motifs) could be required for sex determination and differentiation as well as to participate in the higher order chromatin organization and function, particularly in the formation of heterochromatin [33–35]. …”

Section: Discussionmentioning

confidence: 99%

Comparative repeatome analysis on Triatoma infestans Andean and Non-Andean lineages, main vector of Chagas disease

et al. 2017

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Triatoma infestans is the most important Chagas disease vector in South America. Two main evolutionary lineages, named Andean and non-Andean, have been recognized by geographical distribution, phenetic and genetic characteristics. One of the main differences is the genomic size, varying over 30% in their haploid DNA content. Here we realize a genome wide analysis to compare the repetitive genome fraction (repeatome) between both lineages in order to identify the main repetitive DNA changes occurred during T. infestans differentiation process. RepeatExplorer analysis using Illumina reads showed that both lineages exhibit the same amount of non-repeat sequences, and that satellite DNA is by far the major component of repetitive DNA and the main responsible for the genome size differentiation between both lineages. We characterize 42 satellite DNA families, which are virtually all present in both lineages but with different amount in each lineage. Furthermore, chromosomal location of satellite DNA by fluorescence in situ hybridization showed that genomic variations in T. infestans are mainly due to satellite DNA families located on the heterochromatic regions. The results also show that many satDNA families are located on the euchromatic regions of the chromosomes.

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Section: Discussionmentioning

confidence: 99%

Comparative repeatome analysis on Triatoma infestans Andean and Non-Andean lineages, main vector of Chagas disease

et al. 2017

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“…The mtND1 200 bp PCR fragment was purified after PCR using 32 P dATP. For gel shift, radiolabeled DNA was incubated with mTSC extract for 30 min in 25 mm HEPES ( pH 7.6), 100 mm NaCl, 1 mm DTT, 0.1 mm PMSF, 10% glycerol, 10 μg tRNA and 0.5 μg poly(dI.dC) at room temperature following a previously described protocol (Kumar et al, 2013). For super-shift, equal amounts of TEAD4 antibody or IgG were included in the incubation mix.…”

Section: Electrophoretic Mobility Shift Assaymentioning

confidence: 99%

Regulation of energy metabolism during early mammalian development: TEAD4 controls mitochondrial transcription

et al. 2018

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Early mammalian development is crucially dependent on the establishment of oxidative energy metabolism within the trophectoderm (TE) lineage. Unlike the inner cell mass, TE cells enhance ATP production via mitochondrial oxidative phosphorylation (OXPHOS) and this metabolic preference is essential for blastocyst maturation. However, molecular mechanisms that regulate establishment of oxidative energy metabolism in TE cells are incompletely understood. Here, we show that conserved transcription factor TEAD4, which is essential for pre-implantation mammalian development, regulates this process by promoting mitochondrial transcription. In developing mouse TE and TE-derived trophoblast stem cells (TSCs), TEAD4 localizes to mitochondria, binds to mitochondrial DNA (mtDNA) and facilitates its transcription by recruiting mitochondrial RNA polymerase (POLRMT). Loss of TEAD4 impairs recruitment of POLRMT, resulting in reduced expression of mtDNA-encoded electron transport chain components, thereby inhibiting oxidative energy metabolism. Our studies identify a novel TEAD4-dependent molecular mechanism that regulates energy metabolism in the TE lineage to ensure mammalian development.

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“…Microsatellites appear to be the important components of insulators [52], silencers [45,53] and enhancers [54]. In the Drosophila GATA simple sequence, the repeats function as enhancer blocker boundaries [55].…”

Section: Dna Secondary Structurementioning

confidence: 99%

Structural and functional significance of microsatellites

2016

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Here we review literature data on impact of microsatellite repeats on DNA and chromatin structure and the results of studies on association between the length of microsatellite repeats and predisposition to pathologies. The DNA secondary structure is modified in microsatellite sites, the repeats favour formation of Z-DNA, hairpins, triplexes and quadruplexes. The chromatin structure and chromatin loop organization are also modified in microsatellite sites. The data of association studies are classified according to the localization of the microsatellite: in the gene promoter, in exon 1 part coding the signal sequence, in the gene introns, coding area s and 3'-UTRs.

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GATA simple sequence repeats function as enhancer blocker boundaries

Cited by 26 publications

References 46 publications

Comparative repeatome analysis on Triatoma infestans Andean and Non-Andean lineages, main vector of Chagas disease

Comparative repeatome analysis on Triatoma infestans Andean and Non-Andean lineages, main vector of Chagas disease

Regulation of energy metabolism during early mammalian development: TEAD4 controls mitochondrial transcription

Structural and functional significance of microsatellites

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