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Evolution of the human-specific microRNA miR-941.

ABSTRACT: MicroRNA-mediated gene regulation is important in many physiological processes. Here we explore the roles of a microRNA, miR-941, in human evolution. We find that miR-941 emerged de novo in the human lineage, between six and one million years ago, from an evolutionarily volatile tandem repeat sequence. Its copy-number remains polymorphic in humans and shows a trend for decreasing copy-number with migration out of Africa. Emergence of miR-941 was accompanied by accelerated loss of miR-941-binding sites, presumably to escape regulation. We further show that miR-941 is highly expressed in pluripotent cells, repressed upon differentiation and preferentially targets genes in hedgehog- and insulin-signalling pathways, thus suggesting roles in cellular differentiation. Human-specific effects of miR-941 regulation are detectable in the brain and affect genes involved in neurotransmitter signalling. Taken together, these results implicate miR-941 in human evolution, and provide an example of rapid regulatory evolution in the human linage.

SUBMITTER: Hu HY

PROVIDER: S-EPMC3493648 | biostudies-literature | 2012

REPOSITORIES: biostudies-literature

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Evolution of the human-specific microRNA miR-941.

Hu Hai Yang HY He Liu L Fominykh Kseniya K Yan Zheng Z Guo Song S Zhang Xiaoyu X Taylor Martin S MS Tang Lin L Li Jie J Liu Jianmei J Wang Wen W Yu Haijing H Khaitovich Philipp P

Nature communications 20120101

MicroRNA-mediated gene regulation is important in many physiological processes. Here we explore the roles of a microRNA, miR-941, in human evolution. We find that miR-941 emerged de novo in the human lineage, between six and one million years ago, from an evolutionarily volatile tandem repeat sequence. Its copy-number remains polymorphic in humans and shows a trend for decreasing copy-number with migration out of Africa. Emergence of miR-941 was accompanied by accelerated loss of miR-941-binding ...[more]

PMID: 23093182

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Project description:miRNA-mediated gene expression silencing has previously been shown to be important for a variety of physiological and pathological processes. Here, we have explored the role of one bona fide human-specific miRNA (miR-941) in evolution of the human-specific expression and function. Using combination of high-throughput sequencing (GSE26545), miRNA transfection and large-scale PCR of various human populations, we have shown that emergence and rapid expansion of miR-941 might take place on the human evolutionary linage between six and one million years ago. Functionally, miR-941 could be associated with hedgehog and insulin signaling pathways, and thus might potentially play a role in evolution of human longevity. Human-specific effects of miR-941 regulation are detectable in human brain and affect genes involved in neurotransmitter signaling. Furthermore, emergence of miR-941 on the human evolutionary linage was accompanied by the accelerated loss of its binding sites. Taken together, these results strongly implicate the contribution of miR-941 in evolution of the human-specific phenotype. Ago2 Immunoprecipitation (Ago2-IP) experiments after miR-941 overexpression were conducted in 293T cell line. Briefly, All transfections were performed using human 293T cells cultured in 6-well tissue culture plates. Lipofectamine 2000 (Invitrogen) was used for a Synthetic miR-941 or a scrambled oligo transfection, at 30 nmol/l each (final concentration) per 1x106 cells/well of a 6-well plate using DharmaFECT (GE Healthcare). Total 5x106 cells were collected and subjected to Ago2 immunoprecipitation (Ago2-IP) using the RNA isolation kit Mouse Ago2 (Wako Chemicals) according to the manufacturer's instructions. For a negative control, immunoprecipitation was performed using nonimmune IgG beads prepared with the antibody immobilization bead kit (Wako Chemicals). The IP pull down RNA was used as template for an “in vitro” transcription reaction generating biotin-labeled antisense cRNA. The cRNA was analyzed on affymetrix Human Genome U133 Plus 2.0 arrays following the manufacturer’s instructions. R RMA package was used to quantify gene expression levels.

Project description:miRNA-mediated gene expression silencing has previously been shown to be important for a variety of physiological and pathological processes. Here, we have explored the role of one bona fide human-specific miRNA (miR-941) in evolution of the human-specific expression and function. Using combination of high-throughput sequencing (GSE26545), miRNA transfection and large-scale PCR of various human populations, we have shown that emergence and rapid expansion of miR-941 might take place on the human evolutionary linage between six and one million years ago. Functionally, miR-941 could be associated with hedgehog and insulin signaling pathways, and thus might potentially play a role in evolution of human longevity. Human-specific effects of miR-941 regulation are detectable in human brain and affect genes involved in neurotransmitter signaling. Furthermore, emergence of miR-941 on the human evolutionary linage was accompanied by the accelerated loss of its binding sites. Taken together, these results strongly implicate the contribution of miR-941 in evolution of the human-specific phenotype. miRNA transfection experiments were conducted in 6 cell lines: two human derived kidney cell lines (HEK and 293T), one human skin fibroblast cell line (HSF2), two macaque derived kidney cell lines (LLCMK2 and FrhK-4), and one macaque skin fibroblast cell line (MSF). Briefly, cells were plated in 0.5 ml of growth medium 24h prior to transfection without antibiotics. miR-941 mimics-Lipofectamine 2000 (Invitrogen) complexes were prepared freshly before transfection based on the manufacturer’s protocol. Cells were transfected in six-well plates using miRNA mimics-Lipofectamine 2000 with a final oligonucleotide concentration of 10nmol/L. In parallel, negative control transfections with mock oligonucleotides were conducted according to the manufacturer’s protocol. After 24h, cells were harvested and total RNA were extracted using Trizol reagent (Invitrogen) and further processed and hybridized to Affymetrix Human Genome U133 Plus 2.0 arrays following the manufacturer’s instructions. The R RMA package was used to quantify gene expression levels.

Dataset Information

Evolution of the human-specific microRNA miR-941.

Publications

Evolution of the human-specific microRNA miR-941.

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