Dynamics of Setdb1 expression in early mouse development

Cho, Sunwha,Park, Jung Sun,Kwon, Sujin,Kang, Yong-Kook Elsevier 2012 Gene expression patterns Vol.12 No.5

<P><B>Highlights</B></P><P>► We monitored Setdb1 expression during early mouse development. ► Setdb1 signals emerge as dots associated with the perinucleolar rims in zygotes. ► From 2-cell stage on, Setdb1 signals diffusely exist in the nucleus. ► In blastocyst and outgrowth, Setdb1 signals are found condensed foci. ► The varying expression patterns mean its involvement in diverse biological processes.</P> <P><B>Abstract</B></P><P>Setdb1/Eset, a histone lysine methyltransferase, is recruited by various transcription factors to modify local chromatin. The observation that <I>Setdb1</I>-null blastocysts fail to produce epiblast-lineage cells suggests a role for Setdb1 in generating mouse embryonic stem cells (mESCs). When examined in mouse zygotes, Setdb1 proteins appeared as dots at perinucleolar rims of pronuclei, with the dot-shaped signals more prominent in male pronuclei. Setdb1 signals were observed diffusely in the nucleus from the two-cell stage onward and, by the blastocyst, took a punctate form, away from nucleolus. Such varying expression patterns suggest its involvement in diverse biological processes at preimplantation stage. Setdb1 appeared in Oct4-positive cells of inner-cell-mass origin but not in trophectoderm-lineage cells in blastocyst outgrowths. Setdb1 co-immunoprecipitated with Oct4 in mESCs, and Setdb1 expression was markedly reduced upon retinoic acid-induced differentiation. These observations suggest that Setdb1 has an important role in maintaining the self-renewal of mESCs through collaboration with Oct4.</P>

암종양유전자 SETDB1과 FosB 발현에 대한 p53의 음성 조절기작

윤현지(Hyeon Ji Yun),나한흠(Han-Heom Na),김근철(Keun-Cheol Kim) 한국생명과학회 2020 생명과학회지 Vol.30 No.12

암세포에 항암제를 처리하게 되면, 세포증식, 이동성 또는 약물 내성과 관련된 많은 유전자들의 발현 변화가 발생하며, 유전자 발현 변화는 상호간의 조절 네트워크에 의해 밀접하게 연결될 수도 있다고 추측된다. 본 연구에서 p53 유전자 유무가 다른 A549와 H1299 인간 폐암세포에 독소루비신을 처리하면, 원종양유전자인 FosB의 발현은 증가하지만, 원종양유전자인 SETDB1의 발현은 감소하지만, 단백질 발현의 양적인 차이가 발생한다는 사실을 알 수 있었다. TF motif binding 분석 프로그램을 이용하여 SETDB1과 FosB 프로모터지역에서의 p53단백질의 결합가능성을 분석한 결과, SETDB1의 경우 18부위, FosB의 경우 21 부위의 p53 결합부위를 예측할 수 있었다. SETDB1과 FosB 프로모터의 subcloning하여 luciferase 분석을 수행한 결과, p53은 SETDB1과 FosB을 음성적으로 조절한다는 사실을 알 수 있었다. 또한, H1299 세포에 p53의 과발현은 SETDB1 과 FosB의 발현을 감소시킬 수 있음을 RT-PCR, western blot, qPCR, 면역염색 실험을 통해 확인하였다. 이러한 결과를 종합하여 본다면, p53에 의한 SETDB1과 FosB 유전자 발현 조절은 항암제 처리과정에서 나타나는 암세포의 사멸과 생존에 대한 기능적 조절 네트워크로 사료된다. Treatment with anticancer drugs changes the expression of multiple genes related to cell proliferation, migration, and drug resistance. These changes in gene expression may be connected to regulatory networks for each other. This study showed that doxorubicin treatment induces the expression of oncogenic FosB and decreases the expression of oncogenic SETDB1 in A549 and H1299 human lung cancer cells, which are different in tumor suppressor p53 status. However, a small difference was detected in the quantitative expression of those proteins in the two kinds of cells. To examine the potential regulation of SETDB1 and FosB by p53, we predicted putative p53 binding sites on the genomic DNA of SETDB1 and FosB using a TF motif binding search program. These putative p53 binding sites were identified as 18 sites in the promoter regions of SETDB1 and 21 sites in the genomic DNA of FosB. A luciferase assay confirmed that p53 negatively regulated the promoter activities of SETDB1 and FosB. Furthermore, the results of RT-PCR, western blot, qPCR, and immunostaining experiments indicated that the transfection of exogenous p53 decreases the expression of SETDB1 and FosB in H1299 cells. This indicates that p53 negatively regulates the expression of SETDB1 and FosB at the transcriptional level. Collectively, the downregulation of SETDB1 and FosB by p53 may provide functional networks for apoptosis and for the survival of cancer cells during anticancer drug treatment.

생물정보 프로그램을 활용한 SETDB1 유전자 프로모터 클로닝

노희정(Hee-Jung Noh),김근철(Keun-Cheol Kim) 한국생명과학회 2014 생명과학회지 Vol.24 No.1

진핵세포의 유전자 발현은 genomic DNA 부위의 프로모터라고 불리우는 지역에 전사인자와 RNA 중합효소가 자리하면서 시작되는 기작이다. 유전자 내의 프로모터를 동정하는 여러종류의 실험 방법들이 있지만, 많은 시간과 노동력이 요구되어진다. 본 연구에서는 Ensembl, NCBI, CpG plot 등과 같은 생물정보학 관련 프로그램들을 활용하여 SETDB1 유전자의 프로모터를 동정하여 클로닝하고자 하였다. PCR 증폭을 수행한 후 얻은 약 2 kb DNA 조각을 SETDB1-P1이라 명명하였으며, PCR 산물은 TA 벡터로 클로닝 후 확인하였으며, 이를 다시 제한 효소 절단을 통하여 pGL3-luc 벡터로 클로닝하였다. 클로닝된 pGL3-SETDB1-P1-luc 플라스미드를 H1299 폐암세포주에 transfection 시킨 후 여러 가지 항암제를 처리하였을 때, taxol, 5-FU, doxorubicin 처리군에서 SETDB1 프로모터 활성이 감소하는 것을 확인하였다. 이러한 결과는 웨스턴 블롯 및 RT-PCR 실험을 통해 항암제 처리 후 SETDB1 유전자 발현이 조절됨을 확인하였다. 그러므로 bioinformatics 프로그램을 통한 프로모터 동정 및 클로닝 방법을 다른 유전자들에도 적용시킨다면, 유전자 발현 연구에 매우 유용할 것으로 사료된다. Eukaryotic gene expression is an important process, which is initiated by several transcription factors and RNA polymerases that occupy the promoter region of genomic DNA. Although there are many experiments to identify the promoter region in a gene, it is time and labor consuming to finalize it. In this study, we utilized bioinformatic programs, including Ensembl, NCBI, and CpG plots, to identify the cloning promoter region in SETDB1 genomic DNA. We performed PCR amplification to obtain the SETDB1 promoter on an approximately 2 kb region upstream from the TSS named SETDB1-P1. The PCR product was ligated with TA cloning vectors, and we confirmed the insert size using restriction enzyme digestion. Sequentially, the insert was subcloned into a pGL3-luc vector to produce pGL3-SETDB1- P1-luc and then confirmed by DNA sequencing. We also obtained a fragmented PCR product called P2 and P3 and performed a luciferase assay using pGL3-SETDB1-P1-luc transfection. We found that several anticancer drugs, including taxol, 4-FU, and doxorubicin, decreased the promoter activity of SETDB1. We obtained consistent data on the regulation of SETDB1 gene expression after anticancer drug treatment using Western blot analysis and RT-PCR. Our results suggest that promoter cloning of the human SETDB1 gene utilizing bioinformatics is a very useful and timesaving approach to study gene expression.

Setdb1 Associates with Promyelocytic Leukemia Protein (PML) in Early Mouse Development

Sunwha Cho,Jung Sun Park,Yong-Kook Kang 한국동물생명공학회(구 한국동물번식학회) 2011 발생공학 국제심포지엄 및 학술대회 Vol.2011 No.1

Covalent modifications of histone tails have fundamental roles in chromatin structure and transcriptional activity of a target locus. One of such modifications, Methylation at Lysine 9 of histone H3 (H3-K9) causes several epigenetic phenomena including heterochromatin formation, transcriptional regulation and DNA methylation. Setdb1, H3-K9 specific histone methyltransferase, functions in gene silencing, heterochromatin formation and essential role for early development. Here, we demonstrate that Setdb1 associates with promyelocytic leukemia (Pml) protein from the early stage of mouse development and is a constitutive member of PML nuclear bodies (PML-NBs) that have been linked to many cellular processes such as apoptosis, DNA damage responses, and transcriptional regulation. Immunostaining of mouse blastocyst showed that Setdb1 and Pml signals were scattered in nucleus as a few speckles and microinjected Pmlmyc signals colocalize with Setdb1 signals. This colocalization was observed in mEF and the punctate signals of Setdb1 were observed to be present in every nucleus of mEFs and dividing cells with condensed chromosomes. Arsenic treatment, which induces Pml degradation, also caused Setdb1 signals to disappear. Setdb1 knockdown resulted in disassembly of PML-NBs and immunoprecipitation results demonstrated physical interactions between Setdb1 and Pml. These data suggest that Setdb1 was associated in PML-NB and Setdb1 has important function in maintenance of PML-NB structure.

SETDB1 genomic DNA 를 표적하는 TALEN construct 제작 및 분석

노희정(Hee-Jung Noh),강윤성(Yoonsung Kang),김근철(Keun-Cheol Kim) 한국생명과학회 2014 생명과학회지 Vol.24 No.12

TALEN은 특정유전자를 표적 하여 knock-out 시킬 수 있는 새로운 개념의 유전자 클로닝 방법이다. TALEN 플라스미드에는 DNA binding 도메인과 Fok1 절단효소 기능이 융합되어 있기 때문에, genomic DNA 의 어느 부위라도 결합할 수 있고, 표적 염기서열을 절단하여 유전자 돌연변이를 유도할 수 있다. 본 연구에서 우리는 SETDB1 HMTase 유전자의 단백질 개시코돈과 프로모터 -25 upstream 부위를 표적 하는 두 종의 TALEN constructs 를 제작하였다. 이를 위하여 두 단계의 클로닝이 진행되었다. 첫 번째는 모듈벡터에서 pFUS배열벡터로 표적서열을 옮겨 콜로니 PCR을 통해 smear밴드와 Esp1 제한 효소를 이용하여 약 1 kb의 insert가 들어 있음을 확인하였다. 두 번째는 배열 벡터로부터 TALEN 발현벡터로 옮기는 과정을 진행하였으며, 염기서열분석을 통해 확인하였다. 그 결과 최초의 고안된 모듈벡터 서열들이 약 100 bp 간격으로 배열되어 있음을 확인하였다. 제작된 TALEN-DBEX2 construct는 transfection을 통해 SETDB1의 발현이 사라지는 것을 확인하였고, T7E1 분석을 통하여 표적부위에서 돌연변이가 발생하였음을 추정할 수 있었다. 한편, TALEN-DBPR25 transfection을 통하여서도 SETDB1의 발현이 감소하는 현상을 확인 하였다. DBEX2, DBPR25를 이입시킨 HeLa 세포에서 세포 형태가 길어지는 현상을 관찰할 수 있었다. 그러므로 단백질 개시코돈 또는 -25 upstream을 표적 하는 TALEN knock-out 방법은 SETDB1 유전자의 기능연구에 매우 유용하다고 사료된다. TALEN is a newly developed gene engineering method to knock out specific genes. It contains a DNA binding domain and a Fok1 nuclease domain in the TALEN plasmid. Therefore, the engineered TALEN construct can bind to any region of genomic DNA and cut the target nucleotide, thereby inducing mutation. In this study, we constructed two TALEN constructs targeted to a protein initiation codon (DBEX2) or the 25th upstream region (DBPR25) to enable mRNA synthesis of SETDB1 HMTase. We performed the TALEN cloning in two steps. The first step was from module vectors to pFUS array vectors. We confirmed successful cloning with a colony PCR experiment and Esp31 restriction enzyme digestion, which resulted in a smear band and a 1 Kb insert band, respectively The second step of the cloning was from a pFUS array vector to a mammalian TALEN expression vector. The engineered TALEN construct was sequenced with specific primers in an expression vector. As expected, a specific array from the module vectors was shown in the sequencing analysis. The specific module sequences were regularly arrayed in every 100 bp, and SETDB1 expression totally disappeared in the TALEN-DBEX2 transfection. PCR amplification targeting of DBEX2 was performed, and the PCR product was digested with a T7E1 restriction enzyme. The expression of SETDB1 was down-regulated in the TALEN-DBPR25 transfection. Morphological changes were also observed in the two TALEN constructs with transfected HeLa cells. These results suggest that the engineered TALEN constructs in two strategic approaches are very useful to knock-out of the SETDB1 gene and to study gene function.

Dynamics of Setdb1 Expression in Early Mouse Development

Sunwha Cho,Jung Sun Park,Sujin Kwon,Yong-Kook Kang 한국동물번식학회 2012 Reproductive & Developmental Biology(Supplement) Vol.36 No.2s

Setdb1/Eset, a histone lysine methyltransferase, is recruited by various transcription factors to modify local chromatin. The observation that Setdb1-null blastocysts fail to produce epiblast-lineage cells suggests a role for Setdb1 in generating mouse embryonic stem cells (mESCs). When examined in mouse zygotes, Setdb1 proteins appeared as dots at perinucleolar rims of pronuclei, with the dot-shaped signals more prominent in male pronuclei. Setdb1 signals were observed diffusely in the nucleus from the two-cell stage onward and, by the blastocyst, took a punctate form, away from nucleolus. Such varying expression patterns suggest its involvement in diverse biological processes at preimplantation stage. Setdb1 appeared in Oct4-positive cells of inner-cell-mass origin but not in trophectoderm-lineage cells in blastocyst outgrowths. Setdb1 co- immunoprecipitated with Oct4 in mESCs, and Setdb1 expression was markedly reduced upon retinoic acid- induced differentiation. These observations suggest that Setdb1 has an important role in maintaining the self-renewal of mESCs through collaboration with Oct4.

Setdb1 Is Required for Myogenic Differentiation of C2C12 Myoblast Cells via Maintenance of MyoD Expression

송영준,최장현,이한솔 한국분자세포생물학회 2015 Molecules and cells Vol.38 No.4

Setdb1, an H3-K9 specific histone methyltransferase, is associated with transcriptional silencing of euchromatic genes through chromatin modification. Functions of Setdb1 during development have been extensively studied in embryonic and mesenchymal stem cells as well as neurogenic progenitor cells. But the role of Sedtdb1 in myogenic differentiation remains unknown. In this study, we report that Setdb1 is required for myogenic potential of C2C12 myoblast cells through maintaining the expressions of MyoD and muscle-specific genes. We find that reduced Setdb1 expression in C2C12 myoblast cells severely delayed differentiation of C2C12 myoblast cells, whereas exogenous Setdb1 expression had little effect on. Gene expression profiling analysis using oligonucleotide microarray and RNA-Seq technologies demonstrated that depletion of Setdb1 results in downregulation of MyoD as well as the components of muscle fiber in proliferating C2C12 cells. In addition, exogenous expression of MyoD reversed transcriptional repression of MyoD promoter-driven luciferase reporter by Setdb1 shRNA and rescued myogenic differentiation of C2C12 myoblast cells depleted of endogenous Setdb1. Taken together, these results provide new insights into how levels of key myogenic regulators are maintained prior to induction of differentiation.

Setdb1 Is Required for Myogenic Differentiation of C2C12 Myoblast Cells via Maintenance of MyoD Expression

Song, Young Joon,Choi, Jang Hyun,Lee, Hansol Korean Society for Molecular and Cellular Biology 2015 Molecules and cells Vol.38 No.4

Setdb1, an H3-K9 specific histone methyltransferase, is associated with transcriptional silencing of euchromatic genes through chromatin modification. Functions of Setdb1 during development have been extensively studied in embryonic and mesenchymal stem cells as well as neurogenic progenitor cells. But the role of Sedtdb1 in myogenic differentiation remains unknown. In this study, we report that Setdb1 is required for myogenic potential of C2C12 myoblast cells through maintaining the expressions of MyoD and muscle-specific genes. We find that reduced Setdb1 expression in C2C12 myoblast cells severely delayed differentiation of C2C12 myoblast cells, whereas exogenous Setdb1 expression had little effect on. Gene expression profiling analysis using oligonucleotide microarray and RNA-Seq technologies demonstrated that depletion of Setdb1 results in downregulation of MyoD as well as the components of muscle fiber in proliferating C2C12 cells. In addition, exogenous expression of MyoD reversed transcriptional repression of MyoD promoter-driven luciferase reporter by Setdb1 shRNA and rescued myogenic differentiation of C2C12 myoblast cells depleted of endogenous Setdb1. Taken together, these results provide new insights into how levels of key myogenic regulators are maintained prior to induction of differentiation.

SETDB1 regulates SMAD7 expression for breast cancer metastasis

( Tae Young Ryu ),( Kwangho Kim ),( Seon-kyu Kim ),( Jung-hwa Oh ),( Jeong-ki Min ),( Cho-rok Jung ),( Mi-young Son ),( Dae-soo Kim ),( Hyun-soo Cho ) 생화학분자생물학회 2019 BMB Reports Vol.52 No.2

Breast cancer (BRC) is the most invasive cancer in women. Although the survival rate of BRC is gradually increasing due to improved screening systems, development of novel therapeutic targets for inhibition of BRC proliferation, metastasis and recurrence have been constantly needed. Thus, in this study, we identified overexpression of SETDB1 (SET Domain Bifurcated 1), a histone methyltransferase, in RNA-seq data of BRC derived from TCGA portal. In Gene Ontology (GO) analysis, cell migration-related GO terms were enriched, and we confirmed down-regulation of cell migration/invasion and alteration of EMT /MET markers after knockdown of SETDB1. Moreover, gene network analysis showed that SMAD7 expression is regulated by SETDB1 levels, indicating that up-regulation of SMAD7 by SETDB1 knockdown inhibited BRC metastasis. Therefore, development of SETDB1 inhibitors and functional studies may help develop more effective clinical guidelines for BRC treatment. [BMB Reports 2019; 52(2): 139-144]

BMB Reports : SETDB1 mediated FosB expression increases the cell proliferation rate during anticancer drug therapy

( Han Heom Na ),( Hee Jung Noh ),( Hyang Min Cheong ),( Yoonsung Kang ),( Keun Cheol Kim ) 생화학분자생물학회 2016 BMB Reports Vol.49 No.4

The efficacy of anticancer drugs depends on a variety of signaling pathways, which can be positively or negatively regulated. In this study, we show that SETDB1 HMTase is down-regulated at the transcriptional level by several anticancer drugs, due to its inherent instability. Using RNA sequence analysis, we identified FosB as being regulated by SETDB1 during anticancer drug therapy. FosB expression was increased by treatment with doxorubicin, taxol and siSETDB1. Moreover, FosB was associated with an increased rate of proliferation. Combinatory transfection of siFosB and siSETDB1 was slightly increased compared to transfection of siFosB. Furthermore, FosB was regulated by multiple kinase pathways. ChIP analysis showed that SETDB1 and H3K9me3 interact with a specific region of the FosB promoter. These results suggest that SETDB1- mediated FosB expression is a common molecular phenomenon, and might be a novel pathway responsible for the increase in cell proliferation that frequently occurs during anticancer drug therapy. [BMB Reports 2016; 49(4): 238-243]