Moso bamboo (Phyllostachys edulis) represents one of the fastest-spreading plants in the world, due in part to its well-developed rhizome system. However, the post-transcriptional mechanism for the development of the rhizome system in bamboo has not been comprehensively studied. We therefore used a combination of single-molecule long-read sequencing technology and polyadenylation site sequencing (PAS-seq) to re-annotate the bamboo genome, and identify genome-wide alternative splicing (AS) and alternative polyadenylation (APA) in the rhizome system. In total, 145 522 mapped full-length non-chimeric (FLNC) reads were analyzed, resulting in the correction of 2241 mis-annotated genes and the identification of 8091 previously unannotated loci. Notably, more than 42 280 distinct splicing isoforms were derived from 128 667 intron-containing full-length FLNC reads, including a large number of AS events associated with rhizome systems. In addition, we characterized 25 069 polyadenylation sites from 11 450 genes, 6311 of which have APA sites. Further analysis of intronic polyadenylation revealed that LTR/Gypsy and LTR/Copia were two major transposable elements within the intronic polyadenylation region. Furthermore, this study provided a quantitative atlas of poly(A) usage. Several hundred differential poly(A) sites in the rhizome-root system were identified. Taken together, these results suggest that post-transcriptional regulation may potentially have a vital role in the underground rhizome-root system.

Plant cryptochromes undergo blue light-dependent phosphorylation to regulate their activity and abundance, but the protein kinases that phosphorylate plant cryptochromes have remained unclear. Here we show that photoexcited Arabidopsis cryptochrome 2 (CRY2) is phosphorylated in vivo on as many as 24 different residues, including 7 major phosphoserines. We demonstrate that four closely related Photoregulatory Protein Kinases (previously referred to as MUT9-like kinases) interact with and phosphorylate photoexcited CRY2. Analyses of the ppk123 and ppk124 triple mutants and amiR4k artificial microRNA-expressing lines demonstrate that PPKs catalyse blue light-dependent CRY2 phosphorylation to both activate and destabilize the photoreceptor. Phenotypic analyses of these mutant lines indicate that PPKs may have additional substrates, including those involved in the phytochrome signal transduction pathway. These results reveal a mechanism underlying the co-action of cryptochromes and phytochromes to coordinate plant growth and development in response to different wavelengths of solar radiation in nature.

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IntroductionOsteoarthritis (OA) is a common joint disease that can cause gradual disability among the aging population. Nuclear factor (erythroid-derived 2)-like 2 (Nrf2) is a key transcription factor that regulates the expression of phase II antioxidant enzymes that provide protection against oxidative stress and tissue damage. The use of histone deacetylase inhibitors (HDACi) has emerged as a potential therapeutic strategy for various diseases. They have displayed chondroprotective effects in various animal models of arthritis. Previous studies have established that Nrf2 acetylation enhances Nrf2 functions. Here we explore the role of Nrf2 in the development of OA and the involvement of Nrf2 acetylation in HDACi protection of OA.MethodsTwo OA models—monosodium iodoacetate (MIA) articular injection and destabilization of the medial meniscus (DMM)—were used with wild-type (WT) and Nrf2-knockout (Nrf2-KO) mice to demonstrate the role of Nrf2 in OA progression. A pan-HDACi, trichostatin A (TSA), was administered to examine the effectiveness of HDACi on protection from cartilage damage. The histological sections were scored. The expression of OA-associated matrix metalloproteinases (MMPs) 1, 3, and 13 and proinflammatory cytokines tumor necrosis factor (TNF)-α, interleukin (IL)-1β, and IL-6 were assayed. The effectiveness of HDACi on OA protection was compared between WT and Nrf2-KO mice.ResultsNrf2-KO mice displayed more severe cartilage damage in both the MIA and DMM models. TSA promoted the induction of Nrf2 downstream proteins in SW1353 chondrosarcoma cells and in mouse joint tissues. TSA also reduced the expression of OA-associated proteins MMP1, MMP3, and MMP13 and proinflammatory cytokines TNF-α, IL-1β, and IL-6. TSA markedly reduced the cartilage damage in both OA models but offered no significant protection in Nrf2-KO mice.ConclusionsNrf2 has a major chondroprotective role in progression of OA and is a critical molecule in HDACi-mediated OA protection.

IntroductionImatinib mesylate, or IM (Gleevec; Novartis Pharma, Basel, Switzerland), has demonstrated a remarkable efficacy in the treatment of BCR/ABL ϩ leukemias, with most patients in early chronic phase achieving complete cytogenetic remissions (CCRs). 1 Despite this, BCR/ABL ϩ disease remains detectable in essentially all patients with chronic-phase chronic myelogenous leukemia (CML), and CML always recurs after cessation of IM treatment. 2 This reflects disease persistence under IM therapy. Mechanisms of stem and progenitor cell persistence are presumably progenitor cell quiescence, 3,4 BCR/ABL overexpression, 5 BCR/ABL kinase mutations, 6 and influx and efflux pump expression 7,8 regulating intracellular concentrations of IM. However, additional aberrations may be required to cause a fully drug-resistant phenotype. 9 Clinically manifest IM resistance primarily occurs in advanced stages of CML and in BCR/ABL ϩ acute lymphoblastic leukemia (ALL), and is frequently associated with mutations 10-17 in the causative oncogene of CML, BCR/ABL. 18,19 BCR/ABL kinase mutations are today the best-characterized IM resistance mechanism.To overcome mutation-dependent IM resistance, more selective second-generation ABL kinase inhibitors such as nilotinib (NI; AMN107) 20 and dasatinib (DA), 21 a dual-kinase inhibitor of Abl and Src kinases, were developed and recently also introduced into clinical practice. 22,23 However, DA and NI failed to achieve sustained responses in IM-resistant CML blast crisis and ALL. [22][23][24] Interestingly, neither the response nor the depth of response to NI (hematologic or cytogenetic) depended on the presence or absence of kinase mutations in IM-resistant CML and BCR/ABL ϩ ALL 22 . This implies that BCR/ABL-independent resistance mechanisms 25,26 contribute to IM and NI resistance in a major cohort of patients.Using clonal populations of LAMA cells, we have previously shown that a BCR/ABL-independent activation of the PI3K/Akt signaling cascade precedes kinase mutation-dependent IM resistance development in vitro, 27 and that this autonomous pathway activation mediates early BCR/ABL-independent IM resistance. Others have shown a growth factor-dependent, BCR/ABLindependent activation of the Ras-signaling pathway in CD34 ϩ CML progenitors under IM exposure. 28 Here we were seeking to identify putative factors present in the culture supernatant of IM-exposed BCR/ABL ϩ cells that confer IM resistance. Materials and methods Drugs and reagentsIM and NI was kindly supplied by Drs E. Buchdunger and P. Manley (both of Novartis Pharma). NI was dissolved in dimethyl sulfoxide (DMSO) as a For personal use only. on May 11, 2018. by guest www.bloodjournal.org From 10-mM stock solution and stored in aliquots at Ϫ20°C; IM was stored at Ϫ20°C at 10 mM in distilled water. AG490 29 was obtained from CalbiochemNovabiochem (Bad Soden, Germany). Stock solutions (50 mM) were prepared in DMSO and stored in aliquots at Ϫ20°C. Fresh working solutions were prepared in RPMI-1640 for each experiment. The recombinant ...