Precise temporal regulation of alternative splicing during neural development

Alternative splicing (AS) is one crucial step of gene expression that must be tightly regulated during neurodevelopment. However, the precise timing of developmental splicing switches and the underlying regulatory mechanisms are poorly understood. Here we systematically analyze the temporal regulation of AS in a large number of transcriptome profiles of developing mouse cortices, in vivo purified neuronal subtypes, and neurons differentiated in vitro. Our analysis reveals early-switch and late-switch exons in genes with distinct functions, and these switches accurately define neuronal maturation stages. Integrative modeling suggests that these switches are under direct and combinatorial regulation by distinct sets of neuronal RNA-binding proteins including Nova, Rbfox, Mbnl, and Ptbp. Surprisingly, various neuronal subtypes in the sensory systems lack Nova and/or Rbfox expression. These neurons retain the “immature” splicing program in early-switch exons, affecting numerous synaptic genes. These results provide new insights into the organization and regulation of the neurodevelopmental transcriptome

Transgenic tobacco with resistance to potyvirus generated by artificial miRNAs targeting at highly conserved regions of potyviral genomes

馬鈴薯Y 屬病毒是植物病毒屬中最大也是經濟上最重要的屬，本研究之目的是利用 人工微RNA (artificial miRNA, amiRNA) 的策略產生具有高度抗馬鈴薯Y 屬中不同病毒的轉 基因植物。為了產生具廣泛抗性的轉基因，比對了馬鈴薯Y 屬中16 條不同病毒全基因體 並找出高度保留區。含有273 個鹼基對的阿拉伯芥的微RNA159a (miRNA159a)被選為設計 的骨架，以用於構築人工微RNA，利用寡核苷酸直接突變 (oligonucleotide-directed mutagenesis) 的方式，將產生微RNA 的21 個核苷酸區域取代成可配對至CI、NIb 或CP 基 因高度保留區的21 核苷酸序列。六個帶有單套、一個帶有雙套、及一個帶有參套的人工 微RNA 前趨物被構築。這些突變改造完成的人工微RNA 進一步選殖至貳位元載體 (binary vector) pBA-DC-HA 或pB2T-DC-HA，為了測試這些人工微RNA 能否表現，抽取經過農桿 浸染 (agro-infiltrated) 的全RNA (total RNA)，並用專一性探針以北方墨點法測定相對應的人 工微RNA 的表現，我們的結果指出所有的人工微RNA 構築，皆能有效的表現人工改造的 微RNA 於農桿菌浸染的葉片中。所有的人工微RNA 構築便以農桿菌媒介的方式將這些人 工微RNA 轉殖至菸草中。所產生的大量的植株先以蕪菁嵌紋病毒 (Turnip mosaic virus, TuMV) 在溫室的條件下分析其抗性，有些植株具有延遲發病的效果，其中一個帶有三套 人工微RNA 的轉基因展現了高度的抗病性，這證明了人工微RNA 針對病毒高度保留區是 一個很好的策略以用於生產抗病的轉基因植物，其實際廣泛性的抗病效益尚待進一步測 試。The genus Potyvirus is the largest and economically most important plant virus group. The objective of this study was directed to generate transgenic plants with a high level of resistance against different potyviruses using the artificial micro RNA (amiRNA) approach. In order to create a broad-spectrum resistance to different viruses, highly conserved regions among 16 potyviral genomes were identified by sequence alignment. The 273-nt pre-miR159a from Arabidopsis was chosen as the backbone for the construction and expression of amiRNAs. Using oligonucleotide-directed mutagenesis, a 21 nucleotide region of miR159 was replaced by a synthetic 21-nucleotide sequence targeting at the highly conserved regions of potyviral CI, NIb, or CP genes. Six single, one double and one triple precursor amiRNAs were created. The constructed sequences were then moved to the binary vector pBA-DC-HA or pB2T-DC-HA. To check the expression of designed amiRNAs, the total RNA was isolated from agro-infiltrated leaves and detected by northern blotting with a specific probe against the corresponding amiRNA sequence (21nt). Our results revealed that all constructed amiRNAs in pre-amiRNA constructs were efficiently expressed in agroinfiltrated leaves. Agrobacterium-mediated transformation method was used to transform plants of Nicotiana benthamiana. Transgenic lines were obtained and their resistance against potyvirus was evaluated by mechanical challenge with Turnip mosaic virus under greenhouse conditions. Some transgenic lines showed symptom delay in comparison to non-transgenic plants. One transgenic line expressing the constructed three amiRNAs exhibited a high level of resistance, indicating that the amiRNA approach targeting at highly conserved regions of potyviral genomes is a good strategy for generating transgenic resistance against potyvirus. Whether the transgenic lines provide broad-spectrum resistance against different potyviruses remains to be further tested.Abstract……………..………………………………………….………………… 1 中文摘要…………………………………………………………………….……. 2 Introduction…………………………………………………………………….... 3 Materials and methods……………………………………………………….… 9 Sequence alignment and miRNA design……………………….…………… 9 Construction of single artificial pre-miRNA.………………..………………. 9 Construction of double pre-amiRNA……….……………..……………….. 10 Construction of triple pre-amiRNA……….……………………………..…… 10 Transient expression by agro-infiltration of N. benthamiana………………... 11 Plant Transformation……………………………………………………........ 11 Northern hybridization……………………………………………………… 12 Resistance evaluation………………………………...………………….….. 12 Detection of the TuMV in infected transgenic lines by indirect enzyme-linked immunosorbent assay (ELISA)…………………………………….…........... 13 Results………………………………………………………….………………… 14 Construction of single artificial miRNA…..……………………….………… 14 Construction of double amiRNA…………….…………………….…………. 14 Construction of triple amiRNA…………………………………….……….... 14 Transient expression of amiRNA in leaves of Nicotiana benthamiana ..................................................................................................... 15 Establishment of transgenic lines…………………………….……………… 15 The expression levels of artificial miRNA in transgenic tobacco plants ………………………….…………………………………………..... 16 Resistance evaluation in transgenic tobacco plants…………………….…… 16 III Discussion…………………………………………………..………………... 18 References……………………………………………………………………. 21 Figures and tables..…………………………………………………………… 2

Transgenic tobacco with resistance to potyvirus generated by artificial miRNAs targeting at highly conserved regions of potyviral genomes

馬鈴薯Y 屬病毒是植物病毒屬中最大也是經濟上最重要的屬，本研究之目的是利用 人工微RNA (artificial miRNA, amiRNA) 的策略產生具有高度抗馬鈴薯Y 屬中不同病毒的轉 基因植物。為了產生具廣泛抗性的轉基因，比對了馬鈴薯Y 屬中16 條不同病毒全基因體 並找出高度保留區。含有273 個鹼基對的阿拉伯芥的微RNA159a (miRNA159a)被選為設計 的骨架，以用於構築人工微RNA，利用寡核苷酸直接突變 (oligonucleotide-directed mutagenesis) 的方式，將產生微RNA 的21 個核苷酸區域取代成可配對至CI、NIb 或CP 基 因高度保留區的21 核苷酸序列。六個帶有單套、一個帶有雙套、及一個帶有參套的人工 微RNA 前趨物被構築。這些突變改造完成的人工微RNA 進一步選殖至貳位元載體 (binary vector) pBA-DC-HA 或pB2T-DC-HA，為了測試這些人工微RNA 能否表現，抽取經過農桿 浸染 (agro-infiltrated) 的全RNA (total RNA)，並用專一性探針以北方墨點法測定相對應的人 工微RNA 的表現，我們的結果指出所有的人工微RNA 構築，皆能有效的表現人工改造的 微RNA 於農桿菌浸染的葉片中。所有的人工微RNA 構築便以農桿菌媒介的方式將這些人 工微RNA 轉殖至菸草中。所產生的大量的植株先以蕪菁嵌紋病毒 (Turnip mosaic virus, TuMV) 在溫室的條件下分析其抗性，有些植株具有延遲發病的效果，其中一個帶有三套 人工微RNA 的轉基因展現了高度的抗病性，這證明了人工微RNA 針對病毒高度保留區是 一個很好的策略以用於生產抗病的轉基因植物，其實際廣泛性的抗病效益尚待進一步測 試。The genus Potyvirus is the largest and economically most important plant virus group. The objective of this study was directed to generate transgenic plants with a high level of resistance against different potyviruses using the artificial micro RNA (amiRNA) approach. In order to create a broad-spectrum resistance to different viruses, highly conserved regions among 16 potyviral genomes were identified by sequence alignment. The 273-nt pre-miR159a from Arabidopsis was chosen as the backbone for the construction and expression of amiRNAs. Using oligonucleotide-directed mutagenesis, a 21 nucleotide region of miR159 was replaced by a synthetic 21-nucleotide sequence targeting at the highly conserved regions of potyviral CI, NIb, or CP genes. Six single, one double and one triple precursor amiRNAs were created. The constructed sequences were then moved to the binary vector pBA-DC-HA or pB2T-DC-HA. To check the expression of designed amiRNAs, the total RNA was isolated from agro-infiltrated leaves and detected by northern blotting with a specific probe against the corresponding amiRNA sequence (21nt). Our results revealed that all constructed amiRNAs in pre-amiRNA constructs were efficiently expressed in agroinfiltrated leaves. Agrobacterium-mediated transformation method was used to transform plants of Nicotiana benthamiana. Transgenic lines were obtained and their resistance against potyvirus was evaluated by mechanical challenge with Turnip mosaic virus under greenhouse conditions. Some transgenic lines showed symptom delay in comparison to non-transgenic plants. One transgenic line expressing the constructed three amiRNAs exhibited a high level of resistance, indicating that the amiRNA approach targeting at highly conserved regions of potyviral genomes is a good strategy for generating transgenic resistance against potyvirus. Whether the transgenic lines provide broad-spectrum resistance against different potyviruses remains to be further tested.Abstract……………..………………………………………….………………… 1 中文摘要…………………………………………………………………….……. 2 Introduction…………………………………………………………………….... 3 Materials and methods……………………………………………………….… 9 Sequence alignment and miRNA design……………………….…………… 9 Construction of single artificial pre-miRNA.………………..………………. 9 Construction of double pre-amiRNA……….……………..……………….. 10 Construction of triple pre-amiRNA……….……………………………..…… 10 Transient expression by agro-infiltration of N. benthamiana………………... 11 Plant Transformation……………………………………………………........ 11 Northern hybridization……………………………………………………… 12 Resistance evaluation………………………………...………………….….. 12 Detection of the TuMV in infected transgenic lines by indirect enzyme-linked immunosorbent assay (ELISA)…………………………………….…........... 13 Results………………………………………………………….………………… 14 Construction of single artificial miRNA…..……………………….………… 14 Construction of double amiRNA…………….…………………….…………. 14 Construction of triple amiRNA…………………………………….……….... 14 Transient expression of amiRNA in leaves of Nicotiana benthamiana ..................................................................................................... 15 Establishment of transgenic lines…………………………….……………… 15 The expression levels of artificial miRNA in transgenic tobacco plants ………………………….…………………………………………..... 16 Resistance evaluation in transgenic tobacco plants…………………….…… 16 III Discussion…………………………………………………..………………... 18 References……………………………………………………………………. 21 Figures and tables..…………………………………………………………… 2

TUT-DIS3L2 is a mammalian surveillance pathway for aberrant structured non-coding RNAs

Uridylation of various cellular RNA species at the 3' end has been generally linked to RNA degradation. In mammals, uridylated pre-let-7 miRNAs and mRNAs are targeted by the 3' to 5' exoribonuclease DIS3L2. Mutations in DIS3L2 have been associated with Perlman syndrome and with Wilms tumor susceptibility. Using in vivo cross-linking and immunoprecipitation (CLIP) method, we discovered the DIS3L2-dependent cytoplasmic uridylome of human cells. We found a broad spectrum of uridylated RNAs including rRNAs, snRNAs, snoRNAs, tRNAs, vault, 7SL, Y RNAs, mRNAs, lncRNAs, and transcripts from pseudogenes. The unifying features of most of these identified RNAs are aberrant processing and the presence of stable secondary structures. Most importantly, we demonstrate that uridylation mediates DIS3L2 degradation of short RNA polymerase II-derived RNAs. Our findings establish the role of DIS3L2 and oligouridylation as the cytoplasmic quality control for highly structured ncRNAs

LIN28 Selectively Modulates a Subclass of Let-7 MicroRNAs

LIN28 is a bipartite RNA-binding protein that posttranscriptionallyinhibits the biogenesis of let-7 microRNAs to regulate development and influence disease states. However, the mechanisms of let-7 suppression remain poorly understood because LIN28 recognition depends on coordinated targeting by both the zinc knuckle domain (ZKD), which binds a GGAG-like element in the precursor, and the cold shock domain (CSD), whose binding sites have not been systematically characterized. By leveraging single-nucleotide-resolution mapping of LIN28 binding sites in vivo, we determined that the CSD recognizes a (U) GAU motif. This motif partitions the let-7 microRNAs into two subclasses, precursors with both CSD and ZKD binding sites (CSD+) and precursors with ZKD but no CSD binding sites (CSD-). LIN28 in vivo recognition-and subsequent 3' uridylation and degradation-of CSD+ precursors is more efficient, leading to their stronger suppression in LIN28-activated cells and cancers. Thus, CSD binding sites amplify the regulatory effects of LIN28