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Table 1 High-throughput profiling of nuclear microRNAs

From: Nuclear functions of mammalian MicroRNAs in gene regulation, immunity and cancer

Cell line

Method

Result

Year

L6 rat myoblast

(nucleolus)

Microarray

One third of the detected miRNAs exhibited nucleolar expression at least as high as those observed in the cytoplasm

2009 [26]

In situ hybridization

MiR-351, miR-494, miR-664, miR-1, miR-206 are concentrated in the nucleolus

MiR-199a-3p, miR-21, miR-125a-5p, and let-7a are more concentrated in the nucleoplasm and cytoplasm

RT-qPCR

MiR-351, miR-1, miR-206, miR-21 are concentrated in the nucleolus

MiR-494, miR-664 are more concentrated in the nucleoplasm and cytoplasm

Human nasopharyngeal carcinoma (NPC) 5-8F cell line

Deep sequencing

Among 339 nuclear and 324 cytoplasmic miRNAs, 300 of them overlap

2010 [27]

HCT116 human colorectal carcinoma cell

Microarray

The overall average of nuclear ratio of miRNAs is 0.471 ± 0.15

2010 [28]

RT-PCR

MiR-16, miR-19b, miR-200b, miR-222, miR-29b, miR-29c are highly expressed in the nucleus

Northern blot

MiR-19b, miR-195 are highly expressed in the nucleus

Human monocytic leukemia cell line (THP-1)

Deep sequencing

MiR-16, miR-15b and miR-374b are all over 2-fold enriched in the nucleus;

Nuclear/cytoplasmic ratios of 16 microRNAs are over 1.

2010 [134]

Northern blot

MiR-15 (both a and b) and miR-16 are over 2-fold enriched in the nucleus

C57BL/6 J mouse liver cell

Microarray

MiR-709, miR-805, miR-690 and miR-122 are enriched in the nucleus

2012 [49]

RT-qPCR

MiR-709, miR-690 and miR-30e are highly expressed in the nucleus

The human breast cancer cell MDA-MB-231

High-throughput sequencing

Almost one-fifth of nuclear small RNAs are annotated as piRNAs

2012 [31]

The human breast cancer cell line MCF-7(noninvasive breast cancer cells), MDA-MB-231(invasive breast cancer cell) and the human mammary epithelial cell line MCF-10A (normal breast cells)

Microarray

Nuclear/cytoplasmic ratios of numerous miRNAs vary considerably across different cell lines

Rat primary cortical neuron

Microarray

87 (32.6%) miRNAs are dominant in the cytoplasm, while only (1.5%) miR-133b*, miR-365*, miR-328a* and miR-92a are in the nucleus

2013 [29]

Deep sequencing

MiR-143 and miR-126* are enriched in the nucleus

Northern blot

MiR-25, miR-92a, miR-27a, miR-92b are highly expressed in the nucleus

MiR-138, miR-19b are highly expressed in the cytoplasm

RT-qPCR

MiR-25 and miR-92a are highly expressed in the nucleus

Fluorescence in situ hybridization

MiR-25, miR-92 are highly expressed in the nucleus

MiR-9 is highly expressed in the cytoplasm

HeLa cell

(nucleolus)

RT-qPCR array

11 miRNAs are highly expressed in the nucleolus

2013 [30]

HeLa cell, lung cancer cell H1299, liver cancer cell Huh7, RPE cells, human adult fibroblast AG06858 and primary mouse adult fibroblast (nucleolus)

In situ Hybridization

MiR191, miR-484, miR-574-3p and miR-193b are highly expressed in the nucleolus

Four murine myeloid cell lines (LSK, promyelocyte, myelocyte and granulocyte)

RT-qPCR array

Nuclear/cytoplasmic ratios of miR-706, miR-467a*, miR-709, miR-690, miR-135a* (now miR-135a-1-3p) and miR-142-3p are over 0.1 in one or more cell lines;

Nuclear/cytoplasmic ratios of miR-706 and miR-467a* (now miR-467a-3p) are over 1 in promyelocytes;

2014 [32]

Individual RT-qPCR

MiR-706, miR-709 and miR-690 are enriched in the nucleus;

MiR-467a* is enriched only in the nucleus of LSK and promyelocyte