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BOX elements modulate gene expression in Streptococcus pneumoniae: impact on the fine-tuning of competence development
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Knutsen E Johnsborg O Quentin Y Claverys JP Håvarstein LS 《Journal of bacteriology》2006,188(23):8307-8312
More than 100 BOX elements are randomly distributed in intergenic regions of the pneumococcal genome. Here we demonstrate that these elements can affect expression of neighboring genes and present evidence that they are mobile. Together, our findings show that BOX elements enhance genetic diversity and genomic plasticity in Streptococcus pneumoniae. 相似文献
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Yezhang Zhu Jiali Yu Jiahui Gu Chaoran Xue Long Zhang Jiekai Chen Li Shen 《Nucleic acids research》2021,49(21):12167
The 3D genome organization is crucial for gene regulation. Although recent studies have revealed a uniquely relaxed genome conformation in totipotent early blastomeres of both fertilized and cloned embryos, how weakened higher-order chromatin structure is functionally linked to totipotency acquisition remains elusive. Using low-input Hi-C, ATAC-seq and ChIP-seq, we systematically examined the dynamics of 3D genome and epigenome during pluripotent to totipotent-like state transition in mouse embryonic stem cells (ESCs). The spontaneously converted 2-cell-embryo-like cells (2CLCs) exhibited more relaxed chromatin architecture compared to ESCs, including global weakening of both enhancer-promoter interactions and TAD insulation. While the former correlated with inactivation of ESC enhancers and down-regulation of pluripotent genes, the latter might facilitate contacts between the putative new enhancers arising in 2CLCs and neighboring 2C genes. Importantly, disruption of chromatin organization by depleting CTCF or the cohesin complex promoted the ESC to 2CLC transition. Our results thus establish a critical role of 3D genome organization in totipotency acquisition. 相似文献
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In eukaryotes, neighboring genes can be packaged together in specific chromatin structures that ensure their coordinated expression. Examples of such multi-gene chromatin domains are well-documented, but a global view of the chromatin organization of eukaryotic genomes is lacking. To systematically identify multi-gene chromatin domains, we constructed a compendium of genome-scale binding maps for a broad panel of chromatin-associated proteins in Drosophila melanogaster. Next, we computationally analyzed this compendium for evidence of multi-gene chromatin domains using a novel statistical segmentation algorithm. We find that at least 50% of all fly genes are organized into chromatin domains, which often consist of dozens of genes. The domains are characterized by various known and novel combinations of chromatin proteins. The genes in many of the domains are coregulated during development and tend to have similar biological functions. Furthermore, during evolution fewer chromosomal rearrangements occur inside chromatin domains than outside domains. Our results indicate that a substantial portion of the Drosophila genome is packaged into functionally coherent, multi-gene chromatin domains. This has broad mechanistic implications for gene regulation and genome evolution. 相似文献
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Pervasive gene expression responses to a fluctuating diet in Drosophila melanogaster: The importance of measuring multiple traits to decouple potential mediators of life span and reproduction
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Jelle Zandveld Joost van den Heuvel Maarten Mulder Paul M. Brakefield Thomas B. L. Kirkwood Daryl P. Shanley Bas J. Zwaan 《Evolution; international journal of organic evolution》2017,71(11):2572-2583
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Georges St. Laurent Yuri Vyatkin Denis Antonets Maxim Ri Yao Qi Olga Saik Dmitry Shtokalo Michiel?J.L. de?Hoon Hideya Kawaji Masayoshi Itoh Timo Lassmann Erik Arner Alistair R.R. Forrest The FANTOM consortium Estelle Nicolas Timothy A. McCaffrey Piero Carninci Yoshihide Hayashizaki Claes Wahlestedt Philipp Kapranov 《Nucleic acids research》2016,44(7):3233-3252
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