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The maize B chromosome is capable of expressing microRNAs and altering the expression of microRNAs derived from A chromosomes

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Abstract

Supernumerary B chromosomes (Bs) are nonessential chromosomes that are considered genetically inert. However, the maize B carries control elements that direct its behavior, such as that of nondisjunction, during the second pollen mitosis, and affects normal A chromosomes during cell division. Recently, the maize B has been found to contain transcriptionally active sequences and to affect the transcription of genes on A chromosomes. To better understand the regulatory mechanisms underlying the maize B, we constructed two small RNA libraries from maize B73 inbred lines with and without Bs. The sequencing results revealed that 18 known microRNAs (miRNAs) were significantly differentially expressed in response to the presence of the B, and most target mRNAs were characterized as transcription factors. Moreover, three novel B-derived miRNAs were identified via stem-loop reverse transcriptase-polymerase chain reaction (RT-PCR)-based analysis, and all showed consistent B-specific expression in almost all analyzed inbred lines and in all tissue types, including leaves, roots, and pollen grains. By the use of B-10L translocations, the three B-derived miRNAs were mapped to specific B regions. The results from this study suggest that the maize B can express miRNAs and affect the expression of A-derived miRNAs, which could regulate the expression of A-located genes.

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Abbreviations

CBF:

CCAAT-binding factor

cDNA-AFLP:

Complementary DNA-amplified fragment length polymorphism

CK:

Centromeric knob

DCL:

Dicer-like

DE:

Distal euchromatin

DH:

Distal heterochromatin

DPE:

Distal portion of proximal euchromatin

hc-siRNA:

Heterochromatic small interfering RNA

miRNA:

MicroRNA

NAM:

No apical meristem

NAT-siRNA:

Natural antisense transcript small interfering RNA

NCBI:

National Center for Biotechnology Information

PE:

Proximal euchromatin

Phased siRNA:

Phased small interfering RNA

PPE:

Proximal portion of proximal euchromatin

RISC:

RNA-induced silencing complex

RT-PCR:

Reverse transcriptase-polymerase chain reaction

sRNA:

Small RNA

SRA:

Sequence read archive

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Funding

This work was supported by grants from the Ministry of Science and Technology of Taiwan (MOST 104-2311-B-005-012-MY3 and MOST 107-2311-B-005-003).

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Authors and Affiliations

  1. Department of Agronomy, National Chung Hsing University, 250 Kuo Kuang Road, Taichung, 402, Taiwan

    Yen-Hua Huang & Ya-Ming Cheng

  2. Department of Medical Research, China Medical University Hospital, Taichung, Taiwan

    Shu-Fen Peng

  3. Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan

    Yao-Pin Lin

Authors
  1. Yen-Hua Huang
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  2. Shu-Fen Peng
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  3. Yao-Pin Lin
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  4. Ya-Ming Cheng
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Correspondence to Ya-Ming Cheng.

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Huang, YH., Peng, SF., Lin, YP. et al. The maize B chromosome is capable of expressing microRNAs and altering the expression of microRNAs derived from A chromosomes. Chromosome Res 28, 129–138 (2020). https://doi.org/10.1007/s10577-019-09620-2

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  • DOI: https://doi.org/10.1007/s10577-019-09620-2

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