Cruciform Formable Sequences within Pou5f1 Enhancer Are Indispensable for Mouse ES Cell Integrity.

Published on Mar 26, 2021in International Journal of Molecular Sciences4.556
· DOI :10.3390/IJMS22073399
Yu Yamamoto , Osamu Miura31
Estimated H-index: 31
+ 0 AuthorsTakashi Ohyama17
Estimated H-index: 17
DNA can adopt various structures besides the B-form. Among them, cruciform structures are formed on inverted repeat (IR) sequences. While cruciform formable IRs (CFIRs) are sometimes found in regulatory regions of transcription, their function in transcription remains elusive, especially in eukaryotes. We found a cluster of CFIRs within the mouse Pou5f1 enhancer. Here, we demonstrate that this cluster or some member(s) plays an active role in the transcriptional regulation of not only Pou5f1, but also Sox2, Nanog, Klf4 and Esrrb. To clarify in vivo function of the cluster, we performed genome editing using mouse ES cells, in which each of the CFIRs was altered to the corresponding mirror repeat sequence. The alterations reduced the level of the Pou5f1 transcript in the genome-edited cell lines, and elevated those of Sox2, Nanog, Klf4 and Esrrb. Furthermore, transcription of non-coding RNAs (ncRNAs) within the enhancer was also upregulated in the genome-edited cell lines, in a similar manner to Sox2, Nanog, Klf4 and Esrrb. These ncRNAs are hypothesized to control the expression of these four pluripotency genes. The CFIRs present in the Pou5f1 enhancer seem to be important to maintain the integrity of ES cells.
Metal cations are associated with many biological processes. The effects of these cations on nucleic acids and chromatin were extensively studied in the early stages of nucleic acid and chromatin research. The results revealed that some monovalent and divalent metal cations, including Mg2+, profoundly affect the conformations and stabilities of nucleic acids, the folding of chromatin fibers, and the extent of chromosome condensation. Apart from these effects, there have only been a few reports o...
6 CitationsSource
#1Osamu Miura (Waseda University)H-Index: 2
#2Toshihiro Ogake (Waseda University)H-Index: 1
Last. Takashi Ohyama (Waseda University)H-Index: 17
view all 5 authors...
DNA sequences that read the same from 5′ to 3′ in either strand are called inverted repeat sequences or simply IRs. They are found throughout a wide variety of genomes, from prokaryotes to eukaryotes. Despite extensive research, their in vivo functions, if any, remain unclear. Using Saccharomyces cerevisiae, we performed genome-wide analyses for the distribution, occurrence frequency, sequence characteristics and relevance to chromatin structure, for the IRs that reportedly have a cruciform-form...
2 CitationsSource
#1San-Gang Wu (Fujian Medical University)H-Index: 4
#2Wen-Wen Zhang (SYSU: Sun Yat-sen University)H-Index: 10
Last. Zhen-Yu He (SYSU: Sun Yat-sen University)H-Index: 17
view all 7 authors...
Introduction: To assess the role of the 21-gene recurrence score (RS) assay on decision-making of postoperative radiotherapy (RT) following breast-conserving surgery (BCS) in elderly women with early-stage breast cancer. Methods: The 21-gene RS for elderly (≥65 years) women with stage T1–2N0M0 estrogen receptor-positive breast cancer who underwent BCS from 2004 to 2015 was obtained from the Surveillance, Epidemiology, and End Results program. We estimated the association of 21-gene RS and adjuva...
183 CitationsSource
#1Noa Gil (Weizmann Institute of Science)H-Index: 7
#2Igor Ulitsky (Weizmann Institute of Science)H-Index: 39
Summary Active enhancers in mammals produce enhancer RNAs (eRNAs) that are bidirectionally transcribed, unspliced, and unstable. Enhancer regions are also enriched with long noncoding RNA (lncRNA) transcripts, which are typically spliced and substantially more stable. In order to explore the relationship between these two classes of RNAs, we analyzed DNase hypersensitive sites with evidence of bidirectional transcription, which we termed eRNA-producing centers (EPCs). EPCs found very close to tr...
22 CitationsSource
#1E. Canon (Université Paris-Saclay)H-Index: 2
#2Luc Jouneau (Université Paris-Saclay)H-Index: 24
Last. Véronique DuranthonH-Index: 22
view all 12 authors...
: The POU5F1 gene encodes one of the 'core' transcription factors necessary to establish and maintain pluripotency in mammals. Its function depends on its precise level of expression, so its transcription has to be tightly regulated. To date, few conserved functional elements have been identified in its 5' regulatory region: a distal and a proximal enhancer, and a minimal promoter, epigenetic modifications of which interfere with POU5F1 expression and function in in vitro-derived cell lines. Als...
3 CitationsSource
#1Nathaniel D. Tippens (Cornell University)H-Index: 7
#2Anniina Vihervaara (Cornell University)H-Index: 10
Last. John T. Lis (Cornell University)H-Index: 91
view all 3 authors...
: Following the discovery of widespread enhancer transcription, enhancers and promoters have been found to be far more similar than previously thought. In this issue of Genes & Development, two studies (Henriques and colleagues [pp. 26-41] and Mikhaylichenko and colleagues [pp. 42-57]) shine new light on the transcriptional nature of promoters and enhancers in Drosophila Together, these studies support recent work in mammalian cells that indicates that most active enhancers drive local transcrip...
41 CitationsSource
#1Charles F. Spurlock (Vandy: Vanderbilt University)H-Index: 12
#2Guzel Shaginurova (Vandy: Vanderbilt University)H-Index: 6
Last. Thomas M. Aune (Vandy: Vanderbilt University)H-Index: 38
view all 8 authors...
We employed whole-genome RNA-sequencing to profile mRNAs and both annotated and novel long noncoding RNAs (lncRNAs) in human naive, central memory, and effector memory CD4 + T cells. Loci transcribing both lineage-specific annotated and novel lncRNA are adjacent to lineage-specific protein-coding genes in the genome. Lineage-specific novel lncRNA loci are transcribed from lineage-specific typical- and supertranscriptional enhancers and are not multiexonic, thus are more similar to enhancer RNAs....
19 CitationsSource
#1Daniel Bose (UPenn: University of Pennsylvania)H-Index: 12
#2Greg Donahue (UPenn: University of Pennsylvania)H-Index: 27
Last. Shelley L. Berger (UPenn: University of Pennsylvania)H-Index: 94
view all 6 authors...
CBP/p300 are transcription co-activators whose binding is a signature of enhancers, cis-regulatory elements that control patterns of gene expression in multicellular organisms. Active enhancers produce bi-directional enhancer RNAs (eRNAs) and display CBP/p300-dependent histone acetylation. Here, we demonstrate that CBP binds directly to RNAs in vivo and in vitro. RNAs bound to CBP in vivo include a large number of eRNAs. Using steady-state histone acetyltransferase (HAT) assays, we show that an ...
165 CitationsSource
#1Kazutoshi Takahashi (UCSF: University of California, San Francisco)H-Index: 45
#2Shinya Yamanaka (UCSF: University of California, San Francisco)H-Index: 101
This year marks the tenth anniversary of the generation of induced pluripotent stem cells (iPSCs) by transcription factor-mediated somatic cell reprogramming. Takahashi and Yamanaka portray the path towards this ground-breaking discovery and discuss how, since then, research has focused on understanding the mechanisms underlying iPSC generation and on translating such advances to the clinic.
393 CitationsSource
#1Kazuto Yoshimi (Kyoto University)H-Index: 11
#2Yayoi Kunihiro (Kyoto University)H-Index: 7
Last. Tomoji Mashimo (Kyoto University)H-Index: 30
view all 6 authors...
The CRISPR-Cas system is a powerful tool for generating genetically modified animals; however, targeted knock-in (KI) via homologous recombination remains difficult in zygotes. Here we show efficient gene KI in rats by combining CRISPR-Cas with single-stranded oligodeoxynucleotides (ssODNs). First, a 1-kb ssODN co-injected with guide RNA (gRNA) and Cas9 messenger RNA produce GFP-KI at the rat Thy1 locus. Then, two gRNAs with two 80-bp ssODNs direct efficient integration of a 5.5-kb CAG-GFP vecto...
200 CitationsSource
Cited By0