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Whole chromosome elimination and chromosome terminus elimination both contribute to somatic differentiation in Taiwanese hagfish Paramyxine sheni

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Abstract

Chromosome elimination is a process in which some chromatins are discarded from the presumptive somatic cells during early embryogenesis. Eliminated chromatins in hagfish generally consist of repetitive sequences, and they are highly heterochromatinized in germ cells. In this study, we characterized four novel eliminated DNA families, EEPs1–4, from the Taiwanese hagfish Paramyxine sheni. Sequences of these four elements occupied 20–27% of eliminated DNA in total, and each family was arranged mainly in tandem in the germline genome with high copy numbers. Although most of these elements were eliminated, a minor fraction remained in somatic cells. Some eliminated DNA families are shared as eliminated sequences between Eptatretidae and Myxinidae. Fluorescence in situ hybridization (FISH) of these elements showed that not only heterochromatic chromosomes but also both ends of euchromatic chromosomes in germ cells are absent in somatic cells of P. sheni. It strongly suggests that chromosome terminus elimination, in addition to whole chromosome elimination, contributes to somatic chromosome differentiation. Telomere-FISH further showed that chromosome fragmentation and the subsequent de novo addition of telomeric repeats are the likely mechanisms underlying chromosome terminus elimination. These characteristics make it indispensable to study the evolution and mechanisms underlying chromosome elimination in hagfish.

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Abbreviations

Cbs:

Chromosome breakage sequence

CBRs:

Chromosomal breakage regions

DAPI:

4′,6-diamidino-2-phenylindole

DIG:

Digoxigenin

EEEb:

Eliminated element of Eptatretus burgeri

EEEc:

Eliminated element of Eptatretus cirrhatus

EEEo:

Eliminated element of Eptatretus okinoseanus

EEPa:

Eliminated element of Paramyxine atami

EEPs:

Eliminated element of Paramyxine sheni

FISH:

Fluorescence in situ hybridization

FITC:

Fluorescein isothiocyanate

ORF:

Open-reading frame

PI:

Propidium iodide

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Acknowledgments

We are grateful to Mr. Chien-Hsien Kuo and Dr. Li-Lian Liu of the Institute of Marine Biology, National Sun Yat-sen University, Kaohsiung, Taiwan; to Prof. J.-O. Strömberg and the staff of the Kristineberg Marine Biological Station, as well as to Dr. S. Nilsson of the University of Göteborg, Sweden; Dr. W. Davison and Mr. J. van Berkel of the Kaikoura Marine Station, University of Canterbury, New Zealand; Mr. Y. Ono and coworkers at Ono Suisan Ltd., Onahama, Japan; and the staff of the Misaki Marine Biological Station, the University of Tokyo, Japan, for supplying experimental materials. We thank Dr. Mika Fujiwara for useful discussions. This work was supported in part by Nukada Grants-in-Aid for the promotion of scientific research from Toho University, and special grant to S. Kubota in support of advanced scientific projects at the Faculty of Science, Toho University.

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Authors and Affiliations

  1. Department of Biology, Faculty of Science, Toho University, Miyama 2-2-1, Funabashi, Chiba, 274-8510, Japan

    Noriko F. Kojima, Shuichi Kobayakawa, Naoki Higashide, Chiemi Hamanaka, Ayumi Nitta, Ikuyo Koeda, Toru Yamaguchi, Motoharu Shichiri, Sei-ichi Kohno & Souichirou Kubota

  2. Genetic Information Research Institute, 1925 Landings Drive, Mountain View, CA, 94043, USA

    Kenji K. Kojima

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  1. Noriko F. Kojima
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Correspondence to Souichirou Kubota.

Additional information

Communicated by Hans J. Lipps

Electronic supplementary material

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Supplementary material S1

Summary of chromosome elimination in hagfishes (DOC 55 kb)

Supplementary material S2

The consensus nucleotide sequence (top) and 34 sequences of EEPs1 family, isolated from the “SmaI fragment”. The consensus sequence was deduced from the 34 repeating units from ten insert sequences in individual clones, designated pUPSS-1, -4, -5, -10, -12, -14, -16, -18, -20, and -21. Dots (.) represent nucleotides identical to those in the consensus sequence at the top. Base substitutions are indicated by the respective bases. Dashes (-) represent alignment gaps. Y indicates C or T. The SmaI and internal HhaI recognition sites are underlined. Box indicates the region in which 16 bp of the palindrome sequence is conserved with 75–87.5% sequence identity. In some unit of each SmaI fragment, palindrome sequences can be extended to almost the complete unit. Arrows denote the inverted repeats. Monomers of EEPs1 were closely related to each other, and the average divergence was 11.6%. The sequence data of pUPSS-12 are available in DDBJ/EMBL/GenBank under accession number AB219575. (JPEG 266 kb)

High resolution image (TIFF 2,312 kb)

Supplementary material S3

The consensus nucleotide sequence (top) and 11 sequences of EEPs2 family, isolated from the AluI fragment. The consensus sequence was deduced from the 11 insert sequences in individual clones, designated pUPSA-11, -12, -13, -27, -46, -63, -68, -72, -76, -98, and -99. The AluI and internal Sau 3AI sites were underlined. Arrows denote the direct repeats, each pair sharing more than 77% nucleotide identity. A short sequence motif (positions 71 to 101 in the consensus sequence) showing similarity with the partial sequence of EEPs3 is underlined. Monomers of EEPs2 were closely related to each other, and the average divergence was 2.0%. The sequence data of pUPSA-72 are available in DDBJ/EMBL/GenBank under accession number AB219576. The other notations correspond to those in Supplementary material S2. (JPEG 320 kb)

High resolution image (TIFF 3,729 kb)

Supplementary material S4

The consensus nucleotide sequence (top) and 24 sequences of the “Hinf-a” family (EEPs3), isolated from the HinfI fragment. The consensus sequence was deduced from the 19 sequences in individual clones, designated pUPSH-2, -4, -5, -6, -7, -8, -10, -11, -12, -13, -15, -16, -19, -20, -28, -33, -36, -40, and -44. The HinfI recognition sites are underlined, and the three pairs of short direct repeats are denoted by arrows. Each pair of direct repeat shared more than 75% nucleotide identity. Monomers were closely related to one another, and the divergence was 2.5%. The sequence data of pUPSH-13 are available in DDBJ/EMBL/GenBank under accession number AB219577. The other notations correspond to those in Supplementary material S2. (JPEG 188 kb)

High resolution image (TIFF 1,963 kb)

Supplementary material S5

The consensus nucleotide sequence (top) and 24 sequences of the “Hinf-b” family (EEPs4), isolated from the HinfI fragment. The consensus sequence was deduced from the 28 repeating units from seven insert sequences in individual clones, designated pUPsH-3, -9, -14, -22, -31, -32, and -38. The average sequence divergence of the 15-bp units was 5.2%. The sequence data of pUPSH-31 are available in DDBJ/EMBL/GenBank under accession number AB219578. The other notations correspond to those in Supplementary material S2. (JPEG 158 kb)

High resolution image (TIFF 1,198 kb)

Supplementary material S6

FISH for metaphase chromosomes in primary spermatocytes of P. sheni. FISH signals were detected with DIG-rhodamine (red), while chromatin was counterstained with DAPI (blue). In a and c, only DAPI signals are shown, while in b and d, both DAPI and FISH signals are shown. The FISH probes were pUPSS-14 (EEPs1) for b and pUPSH-13 (EEPs3) for d (Supplementary materials S2 and S4). Asterisks indicate bivalent presumptive somatic chromosomes. Germline-specific chromosomes are smaller than presumptive somatic chromosomes and preferentially show the peripheral distribution. Most of the microchromosomes had accumulated EEPs3 and were strongly stained with DAPI. (JPEG 105 kb)

High resolution image (EPS 6,420 kb)

Supplementary material S7

Localization of the telomeric TTAGGG repeats. Metaphase chromosomes in a spermatogonia, b primary spermatocytes, and c somatic cells of P. sheni after FISH with telomeric repeats [TTAGGG]n as a probe. Hybridization signals of DIG-labeled probes were detected with anti-DIG-fluorescein (yellow). Chromatin was counterstained with PI (red). Bar represents 10 μm. (JPEG 85 kb)

High resolution image (EPS 3,776 kb)

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Kojima, N.F., Kojima, K.K., Kobayakawa, S. et al. Whole chromosome elimination and chromosome terminus elimination both contribute to somatic differentiation in Taiwanese hagfish Paramyxine sheni . Chromosome Res 18, 383–400 (2010). https://doi.org/10.1007/s10577-010-9122-2

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