A major challenge in biology is to understand how complex gene expression patterns are encoded in the genome. While transcriptional enhancers have been studied extensively, few transcriptional ...silencers have been identified, and they remain poorly understood. Here, we used a novel strategy to screen hundreds of sequences for tissue-specific silencer activity in whole Drosophila embryos. Almost all of the transcriptional silencers that we identified were also active enhancers in other cellular contexts. These elements are bound by more transcription factors than non-silencers. A subset of these silencers forms long-range contacts with promoters. Deletion of a silencer caused derepression of its target gene. Our results challenge the common practice of treating enhancers and silencers as separate classes of regulatory elements and suggest the possibility that thousands or more bifunctional CRMs remain to be discovered in Drosophila and 104–105 in humans.
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•Silencers are bifunctional and can act as enhancers in other cellular contexts•A subset of silencers forms long-range contacts to promoters•Deletion of a silencer by genome editing caused derepression of its target gene•Results suggest that thousands of bifunctional elements in flies remain to be discovered
Gisselbrecht et al. performed a screen in developing Drosophila embryos for genomic sequences that can act as transcriptional silencers. They report that nearly all silencers are enhancers in other tissues or at other developmental stages. Their silencers fall into two classes, one of which forms physical chromosomal contacts with promoters.
This study investigates the sound insulation capabilities of two electromagnetic induction membranes controlled by shunt circuits in the duct sound field. The real and imaginary parts of the ...diaphragm acoustic impedance can be precisely decoupled and regulated through the operational amplifiers and adjustable resistors in the shunt circuits. The parameter indicators ΓH(B2l2/(2MmRδ2)) and ΓL(B2l2Cm/(2Rδ2)) are also presented to evaluate the adjustable performance of the diaphragm and the side sound insulation performance. Finally, the performance of a duct sound insulation system composed of two electromagnetic units was demonstrated through theory and experiments. The maximum sound insulation level was 17.4 dB with a pair of units.
Regeneration involves gene expression changes explained in part by context-dependent recruitment of transcriptional activators to distal enhancers. Silencers that engage repressive transcriptional ...complexes are less studied than enhancers and more technically challenging to validate, but they potentially have profound biological importance for regeneration. Here, we identified candidate silencers through a screening process that examined the ability of DNA sequences to limit injury-induced gene expression in larval zebrafish after fin amputation. A short sequence (s1) on chromosome 5 near several genes that reduce expression during adult fin regeneration could suppress promoter activity in stable transgenic lines and diminish nearby gene expression in knockin lines. High-resolution analysis of chromatin organization identified physical associations of s1 with gene promoters occurring preferentially during fin regeneration, and genomic deletion of s1 elevated the expression of these genes after fin amputation. Our study provides methods to identify “tissue regeneration silencer elements” (TRSEs) with the potential to reduce unnecessary or deleterious gene expression during regeneration.
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•A larval screen identifies candidate silencers during zebrafish fin regeneration•s1 contains sequences essential to repress expression from nearby genes•s1 makes physical contacts with genes that reduce expression during fin regeneration•s1 is essential for regeneration-associated reductions in expression of nearby genes
Ando et al. report a screen in zebrafish to identify sequences that repress gene expression during tissue regeneration and find an element with silencing activity that physically contacts nearby genes and tempers their RNA levels during regeneration. The investigation of silencers can illustrate how regeneration programs are controlled in animals.
Silencers are regulatory DNA elements that reduce transcription from their target promoters; they are the repressive counterparts of enhancers. Although discovered decades ago, and despite evidence ...of their importance in development and disease, silencers have been much less studied than enhancers. Recently, however, a series of papers have reported systematic studies of silencers in various model systems. Silencers are often bifunctional regulatory elements that can also act as enhancers, depending on cellular context, and are enriched for expression quantitative trait loci (eQTLs) and disease-associated variants. There is not yet evidence of a ‘silencer chromatin signature’, in the distribution of histone modifications or associated proteins, that is common to all silencers; instead, silencers may fall into various subclasses, acting by distinct (and possibly overlapping) mechanisms.
Silencers are less well-studied than enhancers, but a recent spate of papers has begun to systematically explore these repressive regulatory elements.Silencers are important for precise control of gene expression and are enriched for disease-associated regulatory variants.Most newly discovered silencers are bifunctional regulatory elements that also act as enhancers in other contexts. The traditional distinction between enhancers and silencers may be an oversimplification.Silencers appear to act by a variety of mechanisms, and may fall into various functionally distinct subclasses. This complicates the search for a predictive chromatin signature that would enable the rapid identification of silencers from high-throughput data.Understanding silencer function will be key to predicting the regulatory impact of genomic variation.
cis-Regulatory communication is crucial in mammalian development and is thought to be restricted by the spatial partitioning of the genome in topologically associating domains (TADs). Here, we ...discovered that the Xist locus is regulated by sequences in the neighboring TAD. In particular, the promoter of the noncoding RNA Linx (LinxP) acts as a long-range silencer and influences the choice of X chromosome to be inactivated. This is independent of Linx transcription and independent of any effect on Tsix, the antisense regulator of Xist that shares the same TAD as Linx. Unlike Tsix, LinxP is well conserved across mammals, suggesting an ancestral mechanism for random monoallelic Xist regulation. When introduced in the same TAD as Xist, LinxP switches from a silencer to an enhancer. Our study uncovers an unsuspected regulatory axis for X chromosome inactivation and a class of cis-regulatory effects that may exploit TAD partitioning to modulate developmental decisions.
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•The Tsix-TAD regulates not only Tsix but also Xist, in part via LinxP•LinxP influences choice making during random XCI by regulating Xist expression in cis•Linx transcription affects local topology but is not necessary for Xist regulation•LinxP is conserved in sequence and synteny across placental mammals
Galupa et al. uncover elements important for Xist regulation in its neighboring TAD and reveal that these elements can influence gene regulation both within and between topological domains. These findings, in a context where dynamic, developmental expression is necessary, challenge current models for TAD-based gene-regulatory landscapes.
Microorganisms produce a wealth of structurally diverse specialized metabolites with a remarkable range of biological activities and a wide variety of applications in medicine and agriculture, such ...as the treatment of infectious diseases and cancer, and the prevention of crop damage. Genomics has revealed that many microorganisms have far greater potential to produce specialized metabolites than was thought from classic bioactivity screens; however, realizing this potential has been hampered by the fact that many specialized metabolite biosynthetic gene clusters (BGCs) are not expressed in laboratory cultures. In this Review, we discuss the strategies that have been developed in bacteria and fungi to identify and induce the expression of such silent BGCs, and we briefly summarize methods for the isolation and structural characterization of their metabolic products.
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Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SBMB, SIK, UILJ, UKNU, UL, UM, UPUK
Oct4, Sox2, Klf4, and cMyc (OSKM) reprogram somatic cells to pluripotency. To gain a mechanistic understanding of their function, we mapped OSKM-binding, stage-specific transcription factors (TFs), ...and chromatin states in discrete reprogramming stages and performed loss- and gain-of-function experiments. We found that OSK predominantly bind active somatic enhancers early in reprogramming and immediately initiate their inactivation genome-wide by inducing the redistribution of somatic TFs away from somatic enhancers to sites elsewhere engaged by OSK, recruiting Hdac1, and repressing the somatic TF Fra1. Pluripotency enhancer selection is a stepwise process that also begins early in reprogramming through collaborative binding of OSK at sites with high OSK-motif density. Most pluripotency enhancers are selected later in the process and require OS and other pluripotency TFs. Somatic and pluripotency TFs modulate reprogramming efficiency when overexpressed by altering OSK targeting, somatic-enhancer inactivation, and pluripotency enhancer selection. Together, our data indicate that collaborative interactions among OSK and with stage-specific TFs direct both somatic-enhancer inactivation and pluripotency-enhancer selection to drive reprogramming.
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•Genome-wide annotation of cis-regulatory elements at four reprogramming stages•Somatic enhancer silencing is initiated through several OSK-induced mechanisms•Stepwise pluripotency enhancer selection is dependent on collaborative TF binding•Stage-specific TFs influence OSK occupancy and enhancer selection
Oct4, Sox2, and Klf4 work collaboratively with the help of other transcription factors to change the enhancer landscape during reprogramming.
In the human genome, two short open reading frames (ORFs) separated by a transcriptional silencer and a small intervening sequence stem from the gene
. The two ORFs show different translational ...characteristics, and they also show divergent patterns of evolutionary development. The studies presented here describe the evolution of the components of
. One ORF consists of an ultra-conserved 68 amino acid (aa) sequence, whose origins can be traced beyond the evolutionary age of divergence of the elephant shark, ~462 MYA. The silencer also has ancient origins, but it has a complex and divergent pattern of evolutionary formation, as it overlaps both at the 68 aa ORF and the intervening sequence. The other ORF consists of 107 aa. It develops during primate evolution but is found to originate de novo from an ancestral non-coding genomic region with root origins within the Afrothere clade of placental mammals, whose evolutionary age of divergence is ~99 MYA. The formation of the complete 107 aa ORF during primate evolution is outlined, whereby sequence development is found to occur through biased mutations, with disruptive random mutations that also occur but lead to a dead-end. The 107 aa ORF is of particular significance, as there is evidence to suggest it is a protein that may function in human brain development. Its evolutionary formation presents a view of a human-specific ORF and its linked silencer that were predetermined in non-primate ancestral species. The genomic position of the silencer offers interesting possibilities for the regulation of transcription of the 107 aa ORF. A hypothesis is presented with respect to possible spatiotemporal expression of the 107 aa ORF in embryonic tissues.
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