R understanding of the mechanism controlling root development. Keywords: Populus trichocarpa, Histone deacetylase, Trichostatin A, Digital gene expressionBackground Histone acetylation, as a major and important posttranslational modification of core histones, was started to be investigated early in 1964 [1]. Histone acetylation modifies chromatin structure, affecting gene transcription and thus regulating multiple cellular processes.* Correspondence: [email protected]; [email protected] State Key Laboratory of Tree Genetics and Breeding (Northeast AnlotinibMedChemExpress Anlotinib Forestry University), Northeast Forestry University, Harbin 150040, ChinaHistone acetylation and deacetylation were regulated by histone acetyltransferases (HATs) and histone deacetylases (HDACs), respectively. HATs add acetyl groups to lysines on core histones, while HDACs remove the acetyls from histones. Histone acetylation catalyzed by HATs leads to the expanded structure PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/26866270 of chromatin, while hypoacetylation of histones mediated by HDACs is generally associated with the condensed structure of chromatin and repression/silencing of genes [2]. HDACs are widely distributed in eukaryotes, including animals,?2016 Ma et al. Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.Ma et al. BMC Genomics (2016) 17:Page 2 ofplants and fungi. To date, HDACs in human and animals have been more widely and deeply investigated than plants. In 1988, HDAC enzyme activity was first detected in pea [3]. However, only in recent years, HDACs in plants have attracted more attention and certain HDAC genes in Arabidopsis and crops have been deeply studied [4]. The available data from these plants showed that HDACs played a key role in plant growth, development and stress responses [4]. Based on sequence homology to yeast HDACs, HDACs in plants were divided into three major groups, namely reduced potassium dependency 3/histone deacetylase 1 (RPD3/ HDA1), histone deacetylase 2 (HD2) and silent information regulator 2 (SIR2). The enzyme activity of RPD3/ HDA1- and HD2-type histone deacetylases could be inhibited by HDAC specific inhibitors trichostatin A (TSA) and butyrate (NaB) [2]. The genome of Black cottonwood (Populus trichocarpa Torr. Gray) was sequenced in 2006 [5] and eleven HDAC genes were identified in the Populus genus. However, functions of these HDACs are remaining to be characterized. In plants, root system development such as root hair development, lateral root formation and primary root growth were epigenetically regulated by HDACs. Early in 2000, Murphy et al. found that TSA and helminthosporium carbonum (HC) toxin were able to halt mitosis in cultured root meristems of Pisum sativum [6]. Recently, HDACs have been reported to be involved in root hair development. For example, in Arabidopsis, TSA treatment altered the cellular pattern of root epidermis and induced hair cell development at non-hair positions [7]. Moreover, HDA18 was further identified to be a key regulator of root d.