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1 Journal of Life Science 2015 Vol. 25. No ~708 Histone Methylation Regulates Retinoic Acid-induced Hoxc Gene Expression in F9 EC Cells Hyehyun Min and Myoung Hee Kim* Department of Anatomy, Embryology Laboratory, Brain Korea 21 Plus project for Medical Science, Yonsei University College of Medicine, Seoul , Korea Received December 1, 2014 /Revised March 11, 2015 /Accepted March 12, 2015 Hox genes encode a highly conserved family of homeodomain-containing transcription factors controlling vertebrate pattern formation along the anteroposterior body axis during embryogenesis. Retinoic acid (RA) is a key morphogen in embryogenesis and a critical regulator of both adult and embryonic cellular activity. Specifically, RA regulates Hox gene expression in mouse- or human-derived embryonic carcinoma (EC) cells. Histone modification has been reported to play a pivotal role in the process of RA-induced gene expression and cell differentiation. As histone modification is thought to play an essential role in RA-induced Hox gene expression, we examined RA-induced initiation of collinear expression of Hox genes and the corresponding histone modifications in F9 murine embryonic teratocarcinoma (EC) cells. Hox expression patterns and histone modifications were analyzed by semiquantitative RT-PCR, RNA-sequencing, and chromatin immuno-precipitation (ChIP)-PCR analyses. The Hoxc4 gene (D0) was initiated earlier than the Hoxc5 to c10 genes (D3) upon RA treatment (day 0 [D0], day 1 [D1], and day 3 [D3]). The Hox nonexpressing D0 sample had a strong repressive marker, H3K27me3, than the D1 and D3 samples. In the D1 and D3 samples, reduced enrichment of the H3K27me3 marker was observed in the whole cluster. The active H3K4me3 marker was closely associated with the collinear expression of Hoxc genes. Thus, the Hoxc4 gene (D1) and all Hoxc genes (D3) expressed H3K4me3 upon transcription activation. In conclusion, these data indicated that removing H3K27me3 and acquiring H3K4me3 regulated RA-induced Hoxc gene collinearity in F9 cells. Key words : F9 EC cells, histone modification, Hoxc cluster, RA, retinoic acid ISSN (Print) ISSN (Online) DOI : - Note - 서 Hox 유전자는동물의초기배발생과정중시공간적으로 특이적인발현을하여전후축형태형성에중요한영향을끼 치는전사조절인자로알려져있다 [2]. 사람이나생쥐같은 고등동물의경우 39 개의 Hox 유전자가서로다른 4 개의염색 체에각각의 cluster 를이루어위치하고있으며 [9], 각 cluster 에서배아의전후축을따라 3 에서 5 방향으로 Hox 유전자가 순서대로위치하고있다 [17]. 발생과정중 Hox 유전자들이 순차적으로발현된다는것이보고되어있으며 [14], 이는 3 쪽에위치한유전자들이 5 쪽에위치한유전자보다더머리쪽 (anterior) 에서발현하며, 시기적으로도먼저발현한다는것을 뜻한다. 이러한 Hox 유전자의위치특이적이고순차적인발현 은배아의형태형성에있어매우중요한역할을하지만, 이에 *Corresponding author *Tel : , Fax : * mhkim1@yuhs.ac This is an Open-Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License ( which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. 론 대한정확한기작은아직많은것이밝혀져있지않다. Hox 유전자의순차적인발현은다양한조절인자들에의해일어나고, 그발현이유지된다. Retinoic acid (RA) [18], FGF 신호 [16], Cdx 단백질 [25], polycomb group (PcG) 과 trithorax group (TrxG) [19] 이중요한조절인자로알려져있다. 이중 RA는비타민 A의유도체로배아와중추신경계의발달에관여하며상피조직의성장과분화를조절하는중요한형태형성인자 (morphogen) 이다 [4, 22]. 또한배자의발생과정중세포수명등다양한생물학적기능을조절하는중요한역할을한다 [13]. 특히, RA에의해 Hox 유전자들의발현이유도되고, 배자의전후축형성에중요한역할한다는것이보고되어있지만 [1, 5, 23] 그에대한자세한기작은잘알려져있지않다. Hox 유전자의특이적인발현은크로마틴구조변형 [12] 과히스톤변이 [19, 20] 와같은정교한후성유전학적기작을통해조절된다고도알려져있다. 특히히스톤변이는세포의분화과정중매우중요한역할을한다고알려져있으며, 히스톤의특정아미노산잔기의메틸화, 아세틸화등을통해 Hox 유전자의발현양상이변화된다고보고된바있다 [11]. 최근의보고에따르면형태조절인자인 RA를처리하여유전자전사를유도한 F9 생쥐배아기형암종 (embryonic teratocarcinoma, EC) 세포에서발현에따라유전자좌위에다양한히스톤변이가표지
2 704 생명과학회지 2015, Vol. 25. No. 6 되어있으며, 크로마틴구조의변형이일어나기도한다 [6, 10, 12]. 본연구에서는 retinoic acid (RA) 에의해유도된 Hoxc 유전자의순차적인발현이유전자좌위의특정히스톤변이에의해일어나는것인지를밝히기위해, F9 EC 세포에날짜별로레티노산 (RA) 을처리한후 RT-PCR, RNA-sequencing, ChIP assay 등의분자생물 후성유전학적기법을이용하여실험을진행하였다. 재료및방법 세포배양본실험에사용된 F9 배아암종 (EC) 세포는 10% heat-inactivated fetal bovine serum (FBS, WelGENE Inc., Daegu, Korea) 과 100 ug/ml penicillin-streptomycin (WelGENE Inc.) 을첨가한 Dulbecco s Modified Eagles Medium (DMEM, WelGENE Inc.) 배지를이용하여 37, 5% CO 2 조건에서배양하였다. 세포는 M 레티노산 (Retinoic acid (RA), Sigma- Aldrich, St Louis, MO, USA) 을배지에첨가하여분화를유도하였고, 시약처리후 1일째부터 3일째까지의세포를수집하였다. 시약을처리하지않은세포는대조군으로이용하였다. RNA의분리적정조건에서배양된세포들의 RNA를분리하기위해 Trizol reagent (Invitrogen, Carlsbad, CA, USA) 를이용하였다. 세포가담긴 plate의배지를제거한후 PBS로세척해준뒤, 세포당 1 ul의 Trizol을첨가하여세포를분쇄시켰다. 얼음에서약 5분간보관한뒤회사에서제공한방법에따라 RNA를분리하고농도를측정하였다. 1 ug의 RNA로 Im- Prom-ll TM Reverse Transcriptase (Promega, Madison, WI, USA) 를사용하여 cdna를제작하였다. Reverse transcription-polymerase chain reaction (RT-PCR) 및 RNA sequencing 합성한 cdna를주형으로한 PCR은 Taq DNA polymerase (Bioneer, Daejeon, Korea) 를이용하여수행하였고, 모든 PCR primer는이전의논문과동일하게사용하였다 [15]. PCR 반응산물을 1% agarose를이용하여분리한뒤, 발현의차이를비교하였다. 유전자발현정도를정량적으로분석하기위해 Multi Gauge V3.0 software (Fuji, Tokyo, Japan) 를이용하였다. 각각의시료에서추출한 RNA의 sequencing (RNA-seq (exon analysis)) 은포항공대생명과학과노태영교수님실험실에서진행하였다. In silico data 분석 RNA-seq의결과는 UCSC genome browser ( 에서 Genome browser의 custom track에 law data를 upload한뒤대조군과실험군의 Hoxc 유전자발현양상을분석하고그래프화하였다. Chromatin immunoprecipitation (ChIP) assay 각각의시료에서 Hoxc 좌위의히스톤변이를관찰하기위해 ChIP assay를수행하였다. F9 세포는 Formaldehyde (final 1%) 를첨가한 serum-free DMEM (WelGENE Inc.) 배지로교체하고실온에서 15분간반응시켰다. 2.5 M glycine을첨가하여반응을종료한후 12,000 rpm, 4 에서 5분간원심분리시킨다음 PBS로세척하였다. 세척후 1% SDS, 10 mm EDTA, 50 mm Tris (ph 8.0) 가함유된 SDS lysis buffer 750 ul를첨가하여얼음에서 10분간세포를파괴하였다. 용해시킨세포는 Vibracell TM sonicator (VCX130, Sonics & Materials Inc., Newton, CT, USA) 를이용하여 (30 times, pulse on 10 sec, pulse off 30 sec, Amplitude 30%) chromatin DNA 단편이 500-1,000 bp가되도록절단하였다. 절단된 DNA sample에 salmon sperm DNA/protein A/G agarose beads (Santa Cruz, CA, USA) 와 1 ug의 H3K4me3, H3K27me3 항체 (Abcam, Cambridge, UK) 를첨가하여 4 에서 16시간이상반응시켰다. 다음날, wash buffer로세척한뒤 elution buffer 를첨가하여 15분동안실온에서반응시켰다. 4,000 rpm에서 5분간원심분리하고얻어진상등액에 RNase A를첨가하고 65 에서 5시간이상반응시킨뒤 PCR purification kit (COSMO Genetech, Seoul, Korea) 로 DNA를정제하였다. ChIP-PCR ChIP assay를통해얻은 chromatin DNA를주형으로하여 PCR을수행하였으며, PCR primer와조건은이전의논문 [15] 과동일하게사용하였다. 반응산물은 1.5% agarose를이용하여분리한뒤, 각시료간의히스톤변이의차이를비교하였다. 결과및고찰 F9 배아암종 (embryonic carcinoma, EC) 세포에서 RA 에의한 Hoxc 유전자의순차적인발현변화레티노산 (RA) 에의한 Hoxc 유전자의순차적인발현변화를관찰하기위해생쥐 F9 EC 세포에 M 의 RA를 3일간처리했다. RA를처리하지않은 day0 (D0), RA를 1일처리한 day1 (D1) 과 RA를 3일간처리한 day3 (D3), 각각세가지의 RNA 시료를이용하여 RT-PCR을수행하였다 (Fig. 1A). RT- PCR 결과, D0는 Hoxc 유전자들의발현이일어나지않았고 D1의경우 Hoxc4만발현이유도되었으며, D3에서는 Hoxc4부터 -c10의발현이관찰되었다. Hoxc13은 D0에서부터이미발현하고있으며 D3에서는그발현이증가하는것을볼수있었다. Fig. 1B는 agarose gel에 loading한 PCR 결과물을 β-actin
3 Journal of Life Science 2015, Vol. 25. No A B Fig. 1. Expression pattern of Hoxc cluster genes following Retinoic acid (RA) treatment in F9 EC cells by RT-PCR. Mouse F9 EC cells were cultured with RA for 3 days. Total RNAs were isolated each day from Day 0 (D0), Day 1 (D1) and Day 3 (D3), and then (A) RT-PCR was performed with each Hoxc primers. β-actin was used as a positive control for amplifiable cdna. (B) The RT-PCR results were normalized using the β-actin signal. The data are representative of the three replicate experiments. 값으로나누어정량적으로분석하여그래프화한결과로, D0 와비교하여 D1과 D3에서 Hoxc 유전자의발현이앞에서부터차례대로증가하는것을확인할수있었다. 이결과들을종합해보면 F9 EC 세포에 RA를처리하여유도된 Hoxc 유전자의발현은시간에따라순차적으로일어난다는것을알수있으며, 이는이전의결과와동일하다 [12, 13]. RNA-seq을이용한 Hoxc 유전자의발현변화관찰레티노산 (RA) 에의한 Hoxc 유전자발현의변화를 semiquantitative RT-PCR로관찰한뒤, 이를 genome-wide하게분석하기위해 RNA-sequencing을수행하였다. 이전단계의실험과동일하게생쥐 F9 EC 세포에 5x10-7 M 의 RA를 3일간처리하였다. RA를처리하지않은 D0 ( 대조군 ) 와 RA를 3일간처리한 D3 ( 실험군 ), 각각의 RNA 시료를이용하여 RNA-sequencing을수행하였다. RNA-sequencing 데이터를 UCSC genome browser에 upload하여분석한결과, RT-PCR 결과와동일하게 D0에서는 Hoxc 유전자의발현이거의일어나지않았고, D3에서는 Hoxc4 부터 -c10까지발현되어있는것을관찰할수있었다 (Fig. 2). 또한 Hoxa, -b, -d cluster 유전자의발현도 D0와비교하여 D3에서증가하는것을관찰하였다 (data not shown). 이와같이 F9 EC 세포에 RA를처리하여유전자의전사정도를 genome-wide하게분석을한결과, Hox 유전자는 RA에의해발현이유도되며이는 4개의 Hox 유전자집합체 (Hoxa, -b, -c, -d cluster) 모두에게영향을끼치는것을알수있었다. Hoxc 유전자의순차적인발현과히스톤변이와의관계 Hoxc 유전자의순차적인발현변화가크로마틴구조의리모델링과관련되어있다는이전의보고 [12] 와더불어 Hoxc 유전자의발현과히스톤변이와는어떤상관관계가있는지알아보기위해히스톤표지항체로 ChIP assay를수행하였다. RA를날짜별로처리한 D0, D1, D3 세포에서크로마틴을분리하고, 전사발현시히스톤에표지되는마커인 H34me3 (histone H3 lysine 4 tri-methylation) 과전사억제시히스톤에표지되는마커인 H3K27me3 (histone H3 lysine 27 trimethylation) 항체를첨가하여반응시켰다. 반응후얻어낸각각의크로마틴시료로 ChIP-PCR을수행하였다 (Fig. 3). D0의경우전사억제마커인 H3K27me3이모든 Hoxc 좌위에서관찰되었고, 전사발현마커인 H3K4me3은관찰되지않았다. D1 에서는모든 H3K27me3 변이가사라지고발현중인 Hoxc4에
4 706 생명과학회지 2015, Vol. 25. No. 6 Fig. 2. Expression profiles of Hoxc genes following RA treatment in F9 EC cells by RNA-sequencing (RNA-seq). Total RNAs were isolated each day from D0 and D3 (D0: control cells with no RA treatment). These RNA-seq data were illustrated using UCSC genome browser. Reference genes are depicted at the lower in blue (Hoxc genes). Sequential expression pattern of Hoxc cluster genes in RA-untreated (D0) and treated (D3) samples. 대한 H3K4me3 변이의표지만관찰되었다. D3에는 D1과마찬가지로 H3K27me3 변이가관찰되지않았고모든 Hoxc 좌위에서 H3K4me3 변이가표지된것을확인할수있었다. Hoxc11 과 Hoxc12의경우 D3에서발현하지않음에도불구하고 H3K4me3 변이가관찰되고있는데, 이는 Hoxc11과 Hoxc12 유전자는히스톤변이만으로는발현이시작될수없어다른전사인자단백질이필요한것으로유추할수있다. 최근발표된논문에서 Hoxc11, -c12 유전자가 posterior Hoxc 유전자의 upstream regulator의영향을받아조절된다는보고 [7] 가되어있어단순히히스톤표지의변이만으로는설명할수없는발 현기작이따로존재할것으로보인다. Hoxc13 유전자는 D0에서부터이미발현되고있으며, 이는 RA 처리에의해증가된다 (Fig. 1). 이데이터는 1997년에발표된실험결과와유사한것으로 [3], 이논문의 human EC 세포또한 RA를처리하기전부터 HOXC13이이미발현하고있으며 RA처리후약간의발현증가를보이는것이관찰되었다. 이처럼다른 Hoxc 유전자들의순차적인발현과관계없이 Hoxc13 유전자가따로발현하는것은 EC 세포의특징으로보인다. Hoxc13의경우히스톤변이가유전자의발현양상과동일하게움직이지않는것도관찰되었는데 (Fig. 3), Hoxc11, -c12와마찬가지로히스톤표지 Fig. 3. Histone H3 modifications at Hoxc loci in mouse F9 EC cells. ChIP assays were performed with the indicated histone antibodies on cross-linked chromatin samples from the Day 0, Day 1 and Day 3 samples. Immunoprecipitated and input DNAs were amplified by PCR using region specific primers. The data show the results of one experiment of at least three independent experiments giving comparable results.
5 Journal of Life Science 2015, Vol. 25. No 의변이만으로는설명할수없는후성유전학적발현기작 [8, 24] 이있을것으로예상된다. 또한, Hoxc11-c13 유전자발현과관계없이전체가동일한히스톤마커 (D0:H3K27me3, D1:no enrichment (Hoxc4 제외 ), D3:H3K4me3) 로표지되어있는것을볼수있는데, 이는 Hoxc 좌위전체에서히스톤변이가일어나지만 posterior Hoxc 유전자 (Hoxc11-c13) 의경우 anterior Hoxc 유전자 (Hoxc4-c10) 와다른기작으로발현이시작되며, 특히 EC 세포에서순차적인발현과관계없이따로독특하게움직이는 Hoxc13의발현은특이적인경로가있을것으로추측된다. 이과정을밝히기위해서는추가적으로심도있는연구가필요할것으로보인다. 이상의결과와이전에보고된결과 [12] 를통해 F9 EC 세포에서 Hoxc 유전자들이발현하지않을때 (D0) 는크로마틴뭉침현상과함께전사억제마커인 H3K27me3이표지되어있으며, RA를처리하여 Hoxc 유전자들이발현할때 (D1, D3) 는크로마틴풀림현상과함께 H3K27me3 변이가사라지고, H3K4me3 변이는유전자발현에따라표지되어있는것을알수있다. 결론적으로 F9 EC 세포에서 RA에의해유도된 Hoxc 유전자가시간에따라순차적으로발현하게되는것은 Hoxc 좌위의히스톤메틸화가중요한후성유전학적기작의하나로작용하여일어나는것으로사료된다. 감사의글 본연구는한국연구재단 (2013R1A1A ) 및연세대학교의과대학 ( ) 의연구비지원을받았습니다. References 1. Boncinelli, E., Simeone, A., Acampora, D. and Mavilio, F HOX gene activation by retinoic acid. Trends Genet. 7, Favier, B. and Dolle, P Developmental functions of mammalian Hox genes. Mol. Hum. Reprod. 3, Flagiello, D, Gibaud A, Dutrillaux, B, Poupon, M. F. and Malfoy, B Distinct patterns of all-trans retinoic acid dependent expression of HOXB and HOXC homeogenes in human embryonal and small-cell lung carcinoma cell lines. FEBS Lett. 415, Gillespie, R. F. and Gudas, L. J Retinoid regulated association of transcriptional co-regulators and the polycomb group protein SUZ12 with the retinoic acid response elements of Hoxa1, RARbeta (2), and Cyp26A1 in F9 embryonal carcinoma cells. J. Mol. Biol. 372, Kashyap, V., Gudas, L. J., Brenet, F., Funk, P., Viale, A. and Scandura, J. M Epigenomic reorganization of the clustered Hox genes in embryonic stem cells induced by retinoic acid. J. Biol. Chem. 286, Kashyap, V., Laursen, K. B., Brenet, F., Viale, A. J., Scandura, J. M. and Gudas, L. J RARgamma is essential for retinoic acid induced chromatin remodeling and transcriptional activation in embryonic stem cells. J. Cell Sci. 126, Kong, K. A., Lee, J. Y., Oh, J. H., Lee, Y. and Kim, M. H Akt1 mediates the posterior Hoxc gene expression through epigenetic modifications in mouse embryonic fibroblasts. Biochim. Biophys. Acta 1839, Kouzarides, T Chromatin modifications and their function. Cell 128, Krumlauf, R Evolution of the vertebrate Hox homeobox genes. Bioessays 14, Laursen, K. B., Wong, P. M. and Gudas, L. J Epigenetic regulation by RARalpha maintains ligand-independent transcriptional activity. Nucleic Acids Res. 40, Lee, E. R., Murdoch, F. E. and Fritsch, M. K High histone acetylation and decreased polycomb repressive complex 2 member levels regulate gene specific transcriptional changes during early embryonic stem cell differentiation induced by retinoic acid. Stem Cells 25, Lee, J. Y., Min, H., Wang, X., Khan, A. A. and Kim, M. H Chromatin organization and transcriptional activation of Hox genes. Anat. Cell. Biol. 43, Lee, Y., Lee, J. Y. and Kim, M. H PI3K/Akt pathway regulates retinoic acid-induced Hox gene expression in F9 cells. Dev. Growth. Differ. 56, McGinnis, W. and Krumlauf, R Homeobox genes and axial patterning. Cell 68, Min, H., Lee, J. Y. and Kim, M. H Structural dynamics and epigenetic modifications of Hoxc loci along the anteroposterior body axis in developing mouse embryos. Int. J. Biol. Sci. 8, Partanen, J., Schwartz, L. and Rossant, J Opposite phenotypes of hypomorphic and Y766 phosphorylation site mutations reveal a function for Fgfr1 in anteroposterior patterning of mouse embryos. Genes Dev. 12, Pearson, J. C., Lemons, D. and McGinnis, W Modulating Hox gene functions during animal body patterning. Nat. Rev. Genet. 6, Simeone, A., Acampora, D., Arcioni, L., Andrews, P. W., Boncinelli, E. and Mavilio, F Sequential activation of HOX2 homeobox genes by retinoic acid in human embryonal carcinoma cells. Nature 346, Soshnikova, N. and Duboule, D Epigenetic regulation of Hox gene activation: the waltz of methyls. Bioessays 30, Soshnikova, N. and Duboule, D Epigenetic temporal control of mouse Hox genes in vivo. Science 324, Soshnikova, N. and Duboule, D Epigenetic regulation of vertebrate Hox genes: a dynamic equilibrium. Epigenetics 4, Soprano, D. R., Teets, B. W. and Soprano, K. J Role of retinoic acid in the differentiation of embryonal carcinoma and embryonic stem cells. Vitam. Horm. 75, Stornaiuolo, A., Acampora, D., Pannese, M., D'Esposito, M., Morelli, F., Migliaccio, E., Rambaldi, M., Faiella, A., Nigro, V., Simeone, A. and et al Human HOX genes are dif-
6 708 생명과학회지 2015, Vol. 25. No. 6 ferentially activated by retinoic acid in embryonal carcinoma cells according to their position within the four loci. Cell Differ. Dev. 31, Strahl, B. D. and Allis, C. D The language of covalent histone modifications. Nature 403, Young, T. and Deschamps, J Hox, Cdx, and anteroposterior patterning in the mouse embryo. Curr. Top. Dev. Biol. 88, 초록 :F9 EC 세포에서레티노산에의해유도되는 Hoxc 유전자의발현에히스톤메틸화가미치는영향 민혜현 김명희 * ( 연세대학교의과대학해부학교실발생학실험실 ) Hox 유전자는호메오도메인을포함한전사인자로써, 발생과정중전후축을따라몸의형태형성을조절하는역할을한다. 레티노산 (RA) 은발생과정에서필수적인형태형성인자이며세포의특성을결정하는데중요한조절자이다. 특히, RA 는생쥐나인간으로부터만들어진배아암종 (EC) 세포에서 Hox 유전자의발현을조절한다고밝혀져있다. 또한 RA 에의한세포분화와유전자조절과정에히스톤변이가중요한역할을하는것으로보고되어있다. 히스톤변이가 RA 에의해유도되는 Hox 유전자의발현에특이적인역할을할것으로유추되기때문에, 이연구의목적은 F9 생쥐배아기형암종세포에서 RA 에의해유도되는 Hoxc 유전자의순차적인발현이히스톤변이에의해일어나는것인지를조사하는것이다. Hox 유전자의발현양상과히스톤변이는 semi-quantitative RT-PCR, RNA-sequencing 과 chromatin immuno-precipitation (ChIP)-PCR 기법을이용하여관찰하였다. RA 처리후 (0 일 (D0), 1 일 (D1), 3 일 (D3)), Hoxc4 유전자의발현 (D1) 은 Hoxc5 부터 c10 유전자 (D3) 보다먼저시작되었다. Hox 가발현하지않는 D0 샘플은전사억제마커인 H3K27me3 이모든 Hoxc 좌위에강하게표지되어있었으나 D1 과 D3 샘플에서는모든좌위의 H3K27me3 표지가확연히줄어들어있었다. 전사발현마커인 H3K4me3 가 Hoxc 유전자의순차적인발현과더연관성이있는것으로보이는데 D1 에서 Hoxc4 발현과함께 H3K4me3 이표지되어있었고, D3 에서는 Hoxc 유전자발현과함께모든좌위에서 H3K4me3 마커가존재했기때문이다. 모든결과를종합해보았을때 F9 세포에서 RA 에의해유도된 Hoxc 유전자의순차적인발현은 Hoxc 좌위에서 H3K27me3 가사라지고, H3K4me3 가표지되는히스톤메틸화의변이에의해결정되는것으로사료된다.
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