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

  • Yen-Hua Huang
  • Shu-Fen Peng
  • Yao-Pin Lin
  • Ya-Ming ChengEmail author
Original Article

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.

Keywords

B chromosome microRNA small RNA sequencing maize B-10L translocation 

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

Notes

Funding information

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).

Supplementary material

10577_2019_9620_MOESM1_ESM.xlsx (13 kb)
ESM 1 (XLSX 13 kb)

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Copyright information

© Springer Nature B.V. 2019

Authors and Affiliations

  1. 1.Department of AgronomyNational Chung Hsing UniversityTaichungTaiwan
  2. 2.Department of Medical ResearchChina Medical University HospitalTaichungTaiwan
  3. 3.Agricultural Biotechnology Research CenterAcademia SinicaTaipeiTaiwan

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