|
1
|
Percharde M, Lin CJ, Yin Y, Guan J,
Peixoto GA, Bulut-Karslioglu A, Biechele S, Huang B, Shen X and
Ramalho-Santos M: A LINE1-nucleolin partnership regulates early
development and ESC identity. Cell. 174:391–405.e19. 2018.
View Article : Google Scholar : PubMed/NCBI
|
|
2
|
Milioto V, Perelman PL, Paglia L, Biltueva
L, Roelke M and Dumas F: Mapping retrotransposon LINE-1 sequences
into two cebidae species and homo sapiens genomes and a short
review on primates. Genes (Basel). 13:17422022. View Article : Google Scholar : PubMed/NCBI
|
|
3
|
Otsu M and Kawai G: Distinct RNA
recognition mechanisms in closely related LINEs from zebrafish.
Nucleosides Nucleotides Nucleic Acids. 38:294–304. 2019. View Article : Google Scholar : PubMed/NCBI
|
|
4
|
Wang F, Chamani IJ, Luo D, Chan K, Navarro
PA and Keefe DL: Inhibition of LINE-1 retrotransposition represses
telomere reprogramming during mouse 2-cell embryo development. J
Assist Reprod Genet. 38:3145–3153. 2021. View Article : Google Scholar : PubMed/NCBI
|
|
5
|
Tiwari B, Jones AE, Caillet CJ, Das S,
Royer SK and Abrams JM: p53 directly represses human LINE1
transposons. Genes Dev. 34:1439–1451. 2020. View Article : Google Scholar : PubMed/NCBI
|
|
6
|
Kajikawa M, Sugano T, Sakurai R and Okada
N: Low dependency of retrotransposition on the ORF1 protein of the
zebrafish LINE, ZfL2-1. Gene. 499:41–47. 2012. View Article : Google Scholar : PubMed/NCBI
|
|
7
|
Peterson CL and Hansen JC: Chicken
erythrocyte histone octamer preparation. CSH Protoc.
2008:pdb.prot51122008.PubMed/NCBI
|
|
8
|
Wehbi SS and Zu Dohna H: A comparative
analysis of L1 retrotransposition activities in human genomes
suggests an ongoing increase in L1 number despite an evolutionary
trend towards lower activity. Mob DNA. 12:262021. View Article : Google Scholar : PubMed/NCBI
|
|
9
|
Garcia-Cañadas M, Sanchez-Luque FJ,
Sanchez L, Rojas J and Garcia Perez JL: LINE-1 retrotransposition
assays in embryonic stem cells. Methods Mol Biol. 2607:257–309.
2023. View Article : Google Scholar
|
|
10
|
Chang NC, Rovira Q, Wells J, Feschotte C
and Vaquerizas JM: Zebrafish transposable elements show extensive
diversification in age, genomic distribution, and developmental
expression. Genome Res. 32:1408–1423. 2022. View Article : Google Scholar : PubMed/NCBI
|
|
11
|
Kohlrausch FB, Berteli TS, Wang F, Navarro
PA and Keefe DL: Control of LINE-1 expression maintains genome
integrity in germline and early embryo development. Reprod Sci.
29:328–340. 2022. View Article : Google Scholar
|
|
12
|
Lee HJ, Hou Y, Maeng JH, Shah NM, Chen Y,
Lawson HA, Yang H, Yue F and Wang T: Epigenomic analysis reveals
prevalent contribution of transposable elements to cis-regulatory
elements, tissue-specific expression, and alternative promoters in
zebrafish. Genome Res. 32:1424–1436. 2022. View Article : Google Scholar : PubMed/NCBI
|
|
13
|
Liang X, Hu Y, Feng S, Zhang S, Zhang Y
and Sun C: Heavy chain (LvH) and light chain (LvL) of lipovitellin
(Lv) of zebrafish can both bind to bacteria and enhance
phagocytosis. Dev Comp Immunol. 63:47–55. 2016. View Article : Google Scholar : PubMed/NCBI
|
|
14
|
Romero S, Laino A, Molina G, Cunningham M
and Garcia CF: Embryonic and post-embryonic development of the
spider Polybetes pythagoricus (Sparassidae): A biochemical point of
view. An Acad Bras Cienc. 94:e202101592022. View Article : Google Scholar : PubMed/NCBI
|
|
15
|
Li H and Zhang S: Functions of
vitellogenin in eggs. Results Probl Cell Differ. 63:389–401. 2017.
View Article : Google Scholar : PubMed/NCBI
|
|
16
|
Wang H, Sun W, Li Z, Wang X and Lv Z:
Identification and characterization of two critical sequences in
SV40PolyA that activate the green fluorescent protein reporter
gene. Genet Mol Biol. 34:396–405. 2011. View Article : Google Scholar : PubMed/NCBI
|
|
17
|
Dang Y, Wang F and Liu C: Real-time PCR
array to study the effects of chemicals on the growth
hormone/insulin-like growth factors (GH/IGFs) axis of zebrafish
embryos/larvae. Chemosphere. 207:365–376. 2018. View Article : Google Scholar : PubMed/NCBI
|
|
18
|
Dong M, Ding Y, Liu Y, Xu Z, Hong H, Sun
H, Huang X, Yu X and Chen Q: Molecular insights of
2,6-dichlorobenzoquinone-induced cytotoxicity in zebrafish embryo:
Activation of ROS-mediated cell cycle arrest and apoptosis. Environ
Toxicol. 38:694–700. 2023. View Article : Google Scholar
|
|
19
|
Holbech H, Andersen L, Petersen GI,
Korsgaard B, Pedersen KL and Bjerregaard P: Development of an ELISA
for vitellogenin in whole body homogenate of zebrafish (Danio
rerio). Comp Biochem Physiol C Toxicol Pharmacol. 130:119–131.
2001. View Article : Google Scholar : PubMed/NCBI
|
|
20
|
Li Z, Zhang S and Liu Q: Vitellogenin
functions as a multivalent pattern recognition receptor with an
opsonic activity. PLoS One. 3:e19402008. View Article : Google Scholar : PubMed/NCBI
|
|
21
|
Medina-Gali R, Belló-Pérez M, Ciordia S,
Mena MC, Coll J, Novoa B, Ortega-Villaizán MDM and Perez L: Plasma
proteomic analysis of zebrafish following spring viremia of carp
virus infection. Fish Shellfish Immunol. 86:892–899. 2019.
View Article : Google Scholar
|
|
22
|
Kielkopf CL, Bauer W and Urbatsch IL:
Sodium dodecyl sulfate-polyacrylamide gel electrophoresis of
proteins. Cold Spring Harb Protoc. 2021:pdb. prot1022282021.
View Article : Google Scholar
|
|
23
|
Stein A, Whitlock JP Jr and Bina M: Acidic
polypeptides can assemble both histones and chromatin in vitro at
physiological ionic strength. Proc Natl Acad Sci USA. 76:5000–5004.
1979. View Article : Google Scholar : PubMed/NCBI
|
|
24
|
Lusser A and Kadonaga JT: Strategies for
the reconstitution of chromatin. Nat Methods. 1:19–26. 2004.
View Article : Google Scholar
|
|
25
|
Athanikar JN, Badge RM and Moran JV: A
YY1-binding site is required for accurate human LINE-1
transcription initiation. Nucleic Acids Res. 32:3846–3855. 2004.
View Article : Google Scholar : PubMed/NCBI
|
|
26
|
You C, Ji D, Dai X and Wang Y: Effects of
Tet-mediated oxidation products of 5-methylcytosine on DNA
transcription in vitro and in mammalian cells. Sci Rep. 4:70522014.
View Article : Google Scholar : PubMed/NCBI
|
|
27
|
Purushothaman K, Das PP, Presslauer C, Lim
TK, Johansen SD, Lin Q and Babiak I: Proteomics analysis of early
developmental stages of zebrafish embryos. Int J Mol Sci.
20:63592019. View Article : Google Scholar : PubMed/NCBI
|
|
28
|
Ji N, Wu CG, Wang XD, Song ZX, Wu PY, Liu
X, Feng X, Zhang XM, Wang XF and Lv ZJ: Anti-aging effects of Alu
antisense RNA on human fibroblast senescence through the MEK-ERK
pathway mediated by KIF15. Curr Med Sci. 43:35–47. 2023. View Article : Google Scholar : PubMed/NCBI
|
|
29
|
Elshafie NO, Gribskov M, Lichti NI,
Sayedahmed EE, Childress MO and Dos Santos AP: miRNome expression
analysis in canine diffuse large B-cell lymphoma. Front Oncol.
13:12386132023. View Article : Google Scholar : PubMed/NCBI
|
|
30
|
Guo M, Yang F, Zhu L, Wang L, Li Z, Qi Z,
Fotopoulos V, Yu J and Zhou J: Loss of cold tolerance is conferred
by absence of the WRKY34 promoter fragment during tomato evolution.
Nat Commun. 15:66672024. View Article : Google Scholar : PubMed/NCBI
|
|
31
|
Wei W, Cheng B, Yang X, Chu X, He D, Qin
X, Zhang N, Zhao Y, Shi S, Cai Q, et al: Single-cell multiomics
analysis reveals cell/tissue-specific associations in bipolar
disorder. Transl Psychiatry. 14:3232024. View Article : Google Scholar : PubMed/NCBI
|
|
32
|
Langmead B and Salzberg SL: Fast
gapped-read alignment with Bowtie 2. Nat Methods. 9:357–359. 2012.
View Article : Google Scholar : PubMed/NCBI
|
|
33
|
Zhan Y, Yin A, Su X, Tang N, Zhang Z, Chen
Y, Wang W and Wang J: Interpreting the molecular mechanisms of
RBBP4/7 and their roles in human diseases (Review). Int J Mol Med.
53:482024. View Article : Google Scholar : PubMed/NCBI
|
|
34
|
Farhana R, Lei R, Pham K, Derrien V,
Cedeño J, Rodriquez V, Bernad S, Lima FF and Miksovska J: Globin X:
A highly stable intrinsically hexacoordinate globin. J Inorg
Biochem. 236:1119762022. View Article : Google Scholar : PubMed/NCBI
|
|
35
|
Li C, Tan XF, Lim TK, Lin Q and Gong Z:
Comprehensive and quantitative proteomic analyses of zebrafish
plasma reveals conserved protein profiles between genders and
between zebrafish and human. Sci Rep. 6:243292016. View Article : Google Scholar : PubMed/NCBI
|
|
36
|
Yilmaz O, Patinote A, Nguyen TV, Com E,
Lavigne R, Pineau C, Sullivan CV and Bobe J: Scrambled eggs:
Proteomic portraits and novel biomarkers of egg quality in
zebrafish (Danio rerio). PLoS One. 12:e01880842017. View Article : Google Scholar : PubMed/NCBI
|
|
37
|
Moyano TC, Gutiérrez RA and Alvarez JM:
Genomic footprinting analyses from DNase-seq data to construct gene
regulatory networks. Methods Mol Biol. 2328:25–46. 2021. View Article : Google Scholar : PubMed/NCBI
|
|
38
|
Carmignac V, Barberet J, Iranzo J, Quéré
R, Guilleman M, Bourc'his D and Fauque P: Effects of assisted
reproductive technologies on transposon regulation in the mouse
pre-implanted embryo. Hum Reprod. 34:612–622. 2019. View Article : Google Scholar : PubMed/NCBI
|
|
39
|
Navarro PA, Wang F, Pimentel R, Robinson
LG Jr, Berteli TS and Keefe DL: Zidovudine inhibits telomere
elongation, increases the transposable element LINE-1 copy number
and compromises mouse embryo development. Mol Biol Rep.
48:7767–7773. 2021. View Article : Google Scholar : PubMed/NCBI
|
|
40
|
Han JS and Boeke JD: A highly active
synthetic mammalian retrotransposon. Nature. 429:314–318. 2004.
View Article : Google Scholar : PubMed/NCBI
|
|
41
|
Zhang P, Ludwig AK, Hastert FD, Rausch C,
Lehmkuhl A, Hellmann I, Smets M, Leonhardt H and Cardoso MC: L1
retrotransposition is activated by Ten-eleven-translocation protein
1 and repressed by methyl-CpG binding proteins. Nucleus. 8:548–562.
2017. View Article : Google Scholar : PubMed/NCBI
|
|
42
|
Zhang S, Dong Y and Cui P: Vitellogenin is
an immunocompetent molecule for mother and offspring in fish. Fish
Shellfish Immunol. 46:710–715. 2015. View Article : Google Scholar : PubMed/NCBI
|
|
43
|
Veil M, Yampolsky LY, Grüning B and
Onichtchouk D: Pou5f3, SoxB1, and Nanog remodel chromatin on high
nucleosome affinity regions at zygotic genome activation. Genome
Res. 29:383–395. 2019. View Article : Google Scholar : PubMed/NCBI
|
|
44
|
Wang J, Zhang X, Shan R, Ma S, Tian H,
Wang W and Ru S: Lipovitellin as an antigen to improve the
precision of sandwich ELISA for quantifying zebrafish (Danio rerio)
vitellogenin. Comp Biochem Physiol C Toxicol Pharmacol.
185-186:87–93. 2016. View Article : Google Scholar : PubMed/NCBI
|
|
45
|
Thompson JR and Banaszak LJ: Lipid-protein
interactions in lipovitellin. Biochemistry. 41:9398–9409. 2002.
View Article : Google Scholar : PubMed/NCBI
|
|
46
|
Ramos KS, Bojang P and Bowers E: Role of
long interspersed nuclear element-1 in the regulation of chromatin
landscapes and genome dynamics. Exp Biol Med (Maywood).
246:2082–2097. 2021. View Article : Google Scholar : PubMed/NCBI
|
|
47
|
Tian T, Wang L, Shen Y, Zhang B, Finnell
RH and Ren A: Hypomethylation of GRHL3 gene is associated with the
occurrence of neural tube defects. Epigenomics. 10:891–901. 2018.
View Article : Google Scholar : PubMed/NCBI
|
|
48
|
Desai K, Spikings E and Zhang T: Effect of
chilling on sox2, sox3 and sox19a gene expression in zebrafish
(Danio rerio) embryos. Cryobiology. 63:96–103. 2011. View Article : Google Scholar : PubMed/NCBI
|
|
49
|
Fang F, Chen D, Basharat AR, Poulos W,
Wang Q, Cibelli JB, Liu X and Sun L: Quantitative proteomics
reveals the dynamic proteome landscape of zebrafish embryos during
the maternal-to-zygotic transition. iScience. 27:1099442024.
View Article : Google Scholar : PubMed/NCBI
|
|
50
|
Lindeman LC, Winata CL, Aanes H, Mathavan
S, Alestrom P and Collas P: Chromatin states of
developmentally-regulated genes revealed by DNA and histone
methylation patterns in zebrafish embryos. Int J Dev Biol.
54:803–813. 2010. View Article : Google Scholar : PubMed/NCBI
|
|
51
|
Sokolova M and Vartiainen MK: Chromatin
immunoprecipitation experiments from Drosophila ovaries. Methods
Mol Biol. 2626:335–351. 2023. View Article : Google Scholar : PubMed/NCBI
|
|
52
|
Popchock AR, Larson JD, Dubrulle J, Asbury
CL and Biggins S: Direct observation of coordinated assembly of
individual native centromeric nucleosomes. EMBO J. 42:e1145342023.
View Article : Google Scholar : PubMed/NCBI
|
|
53
|
Pallarès-Albanell J, Ortega-Flores L,
Senar-Serra T, Ruiz A, Abril JF, Rossello M and Almudi I: Gene
regulatory dynamics during the development of a paleopteran insect,
the mayfly Cloeon dipterum. bioRxiv. May 17–2024.Epub ahead of
print.
|
|
54
|
Muto Y, Wilson PC, Ledru N, Wu H, Dimke H,
Waikar SS and Humphreys BD: Single cell transcriptional and
chromatin accessibility profiling redefine cellular heterogeneity
in the adult human kidney. Nat Commun. 12:21902021. View Article : Google Scholar : PubMed/NCBI
|
|
55
|
Jiang Z and Zhang B: On the role of
transcription in positioning nucleosomes. PLoS Comput Biol.
17:e10085562021. View Article : Google Scholar : PubMed/NCBI
|
|
56
|
Zhao M, Wang Z, Yung S and Lu Q:
Epigenetic dynamics in immunity and autoimmunity. Int J Biochem
Cell Biol. 67:65–74. 2015. View Article : Google Scholar : PubMed/NCBI
|
|
57
|
Hocher A, Laursen SP, Radford P, Tyson J,
Lambert C, Stevens KM, Montoya A, Shliaha PV, Picardeau M, Sockett
RE, et al: Histones with an unconventional DNA-binding mode in
vitro are major chromatin constituents in the bacterium
Bdellovibrio bacteriovorus. Nat Microbiol. 8:2006–2019. 2023.
View Article : Google Scholar : PubMed/NCBI
|
|
58
|
Wang SH, Liu L, Bao KY, Zhang YF, Wang WW,
Du S, Jia NE, Suo S, Cai J, Guo JF and Lv G: EZH2 contributes to
anoikis resistance and promotes epithelial ovarian cancer
peritoneal metastasis by regulating m6A. Curr Med Sci. 43:794–802.
2023. View Article : Google Scholar : PubMed/NCBI
|
|
59
|
Guo H, Zhu P, Yan L, Li R, Hu B, Lian Y,
Yan J, Ren X, Lin S, Li J, et al: The DNA methylation landscape of
human early embryos. Nature. 511:606–610. 2014. View Article : Google Scholar : PubMed/NCBI
|
