Browsing by Author "Zhu, Jun"

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    A paired-end sequencing strategy to map the complex landscape of transcription initiation.
    (Nature methods, 2010-07) Ni, Ting; Corcoran, David L; Rach, Elizabeth A; Song, Shen; Spana, Eric P; Gao, Yuan; Ohler, Uwe; Zhu, Jun
    Recent studies using high-throughput sequencing protocols have uncovered the complexity of mammalian transcription by RNA polymerase II, helping to define several initiation patterns in which transcription start sites (TSSs) cluster in both narrow and broad genomic windows. Here we describe a paired-end sequencing strategy, which enables more robust mapping and characterization of capped transcripts. We used this strategy to explore the transcription initiation landscape in the Drosophila melanogaster embryo. Extending the previous findings in mammals, we found that fly promoters exhibited distinct initiation patterns, which were linked to specific promoter sequence motifs. Furthermore, we identified many 5' capped transcripts originating from coding exons; our analyses support that they are unlikely the result of alternative TSSs, but rather the product of post-transcriptional modifications. We demonstrated paired-end TSS analysis to be a powerful method to uncover the transcriptional complexity of eukaryotic genomes.
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    Co-limitation towards lower latitudes shapes global forest diversity gradients.
    (Nature ecology & evolution, 2022-08-08) Liang, Jingjing; Gamarra, Javier GP; Picard, Nicolas; Zhou, Mo; Pijanowski, Bryan; Jacobs, Douglass F; Reich, Peter B; Crowther, Thomas W; Nabuurs, Gert-Jan; de-Miguel, Sergio; Fang, Jingyun; Woodall, Christopher W; Svenning, Jens-Christian; Jucker, Tommaso; Bastin, Jean-Francois; Wiser, Susan K; Slik, Ferry; Hérault, Bruno; Alberti, Giorgio; Keppel, Gunnar; Hengeveld, Geerten M; Ibisch, Pierre L; Silva, Carlos A; Ter Steege, Hans; Peri, Pablo L; Coomes, David A; Searle, Eric B; von Gadow, Klaus; Jaroszewicz, Bogdan; Abbasi, Akane O; Abegg, Meinrad; Yao, Yves C Adou; Aguirre-Gutiérrez, Jesús; Zambrano, Angelica M Almeyda; Altman, Jan; Alvarez-Dávila, Esteban; Álvarez-González, Juan Gabriel; Alves, Luciana F; Amani, Bienvenu HK; Amani, Christian A; Ammer, Christian; Ilondea, Bhely Angoboy; Antón-Fernández, Clara; Avitabile, Valerio; Aymard, Gerardo A; Azihou, Akomian F; Baard, Johan A; Baker, Timothy R; Balazy, Radomir; Bastian, Meredith L; Batumike, Rodrigue; Bauters, Marijn; Beeckman, Hans; Benu, Nithanel Mikael Hendrik; Bitariho, Robert; Boeckx, Pascal; Bogaert, Jan; Bongers, Frans; Bouriaud, Olivier; Brancalion, Pedro HS; Brandl, Susanne; Brearley, Francis Q; Briseno-Reyes, Jaime; Broadbent, Eben N; Bruelheide, Helge; Bulte, Erwin; Catlin, Ann Christine; Cazzolla Gatti, Roberto; César, Ricardo G; Chen, Han YH; Chisholm, Chelsea; Cienciala, Emil; Colletta, Gabriel D; Corral-Rivas, José Javier; Cuchietti, Anibal; Cuni-Sanchez, Aida; Dar, Javid A; Dayanandan, Selvadurai; de Haulleville, Thales; Decuyper, Mathieu; Delabye, Sylvain; Derroire, Géraldine; DeVries, Ben; Diisi, John; Do, Tran Van; Dolezal, Jiri; Dourdain, Aurélie; Durrheim, Graham P; Obiang, Nestor Laurier Engone; Ewango, Corneille EN; Eyre, Teresa J; Fayle, Tom M; Feunang, Lethicia Flavine N; Finér, Leena; Fischer, Markus; Fridman, Jonas; Frizzera, Lorenzo; de Gasper, André L; Gianelle, Damiano; Glick, Henry B; Gonzalez-Elizondo, Maria Socorro; Gorenstein, Lev; Habonayo, Richard; Hardy, Olivier J; Harris, David J; Hector, Andrew; Hemp, Andreas; Herold, Martin; Hillers, Annika; Hubau, Wannes; Ibanez, Thomas; Imai, Nobuo; Imani, Gerard; Jagodzinski, Andrzej M; Janecek, Stepan; Johannsen, Vivian Kvist; Joly, Carlos A; Jumbam, Blaise; Kabelong, Banoho LPR; Kahsay, Goytom Abraha; Karminov, Viktor; Kartawinata, Kuswata; Kassi, Justin N; Kearsley, Elizabeth; Kennard, Deborah K; Kepfer-Rojas, Sebastian; Khan, Mohammed Latif; Kigomo, John N; Kim, Hyun Seok; Klauberg, Carine; Klomberg, Yannick; Korjus, Henn; Kothandaraman, Subashree; Kraxner, Florian; Kumar, Amit; Kuswandi, Relawan; Lang, Mait; Lawes, Michael J; Leite, Rodrigo V; Lentner, Geoffrey; Lewis, Simon L; Libalah, Moses B; Lisingo, Janvier; López-Serrano, Pablito Marcelo; Lu, Huicui; Lukina, Natalia V; Lykke, Anne Mette; Maicher, Vincent; Maitner, Brian S; Marcon, Eric; Marshall, Andrew R; Martin, Emanuel H; Martynenko, Olga; Mbayu, Faustin M; Mbuvi, Musingo TE; Meave, Jorge A; Merow, Cory; Miscicki, Stanislaw; Moreno, Vanessa S; Morera, Albert; Mukul, Sharif A; Müller, Jörg C; Murdjoko, Agustinus; Nava-Miranda, Maria Guadalupe; Ndive, Litonga Elias; Neldner, Victor J; Nevenic, Radovan V; Nforbelie, Louis N; Ngoh, Michael L; N'Guessan, Anny E; Ngugi, Michael R; Ngute, Alain SK; Njila, Emile Narcisse N; Nyako, Melanie C; Ochuodho, Thomas O; Oleksyn, Jacek; Paquette, Alain; Parfenova, Elena I; Park, Minjee; Parren, Marc; Parthasarathy, Narayanaswamy; Pfautsch, Sebastian; Phillips, Oliver L; Piedade, Maria TF; Piotto, Daniel; Pollastrini, Martina; Poorter, Lourens; Poulsen, John R; Poulsen, Axel Dalberg; Pretzsch, Hans; Rodeghiero, Mirco; Rolim, Samir G; Rovero, Francesco; Rutishauser, Ervan; Sagheb-Talebi, Khosro; Saikia, Purabi; Sainge, Moses Nsanyi; Salas-Eljatib, Christian; Salis, Antonello; Schall, Peter; Schepaschenko, Dmitry; Scherer-Lorenzen, Michael; Schmid, Bernhard; Schöngart, Jochen; Šebeň, Vladimír; Sellan, Giacomo; Selvi, Federico; Serra-Diaz, Josep M; Sheil, Douglas; Shvidenko, Anatoly Z; Sist, Plinio; Souza, Alexandre F; Stereńczak, Krzysztof J; Sullivan, Martin JP; Sundarapandian, Somaiah; Svoboda, Miroslav; Swaine, Mike D; Targhetta, Natalia; Tchebakova, Nadja; Trethowan, Liam A; Tropek, Robert; Mukendi, John Tshibamba; Umunay, Peter Mbanda; Usoltsev, Vladimir A; Vaglio Laurin, Gaia; Valentini, Riccardo; Valladares, Fernando; van der Plas, Fons; Vega-Nieva, Daniel José; Verbeeck, Hans; Viana, Helder; Vibrans, Alexander C; Vieira, Simone A; Vleminckx, Jason; Waite, Catherine E; Wang, Hua-Feng; Wasingya, Eric Katembo; Wekesa, Chemuku; Westerlund, Bertil; Wittmann, Florian; Wortel, Verginia; Zawiła-Niedźwiecki, Tomasz; Zhang, Chunyu; Zhao, Xiuhai; Zhu, Jun; Zhu, Xiao; Zhu, Zhi-Xin; Zo-Bi, Irie C; Hui, Cang
    The latitudinal diversity gradient (LDG) is one of the most recognized global patterns of species richness exhibited across a wide range of taxa. Numerous hypotheses have been proposed in the past two centuries to explain LDG, but rigorous tests of the drivers of LDGs have been limited by a lack of high-quality global species richness data. Here we produce a high-resolution (0.025° × 0.025°) map of local tree species richness using a global forest inventory database with individual tree information and local biophysical characteristics from ~1.3 million sample plots. We then quantify drivers of local tree species richness patterns across latitudes. Generally, annual mean temperature was a dominant predictor of tree species richness, which is most consistent with the metabolic theory of biodiversity (MTB). However, MTB underestimated LDG in the tropics, where high species richness was also moderated by topographic, soil and anthropogenic factors operating at local scales. Given that local landscape variables operate synergistically with bioclimatic factors in shaping the global LDG pattern, we suggest that MTB be extended to account for co-limitation by subordinate drivers.
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    ItemOpen Access
    The prevalence and regulation of antisense transcripts in Schizosaccharomyces pombe.
    (PLoS One, 2010-12-20) Ni, Ting; Tu, Kang; Wang, Zhong; Song, Shen; Wu, Han; Xie, Bin; Scott, Kristin C; Grewal, Shiv I; Gao, Yuan; Zhu, Jun
    A strand-specific transcriptome sequencing strategy, directional ligation sequencing or DeLi-seq, was employed to profile antisense transcriptome of Schizosaccharomyces pombe. Under both normal and heat shock conditions, we found that polyadenylated antisense transcripts are broadly expressed while distinct expression patterns were observed for protein-coding and non-coding loci. Dominant antisense expression is enriched in protein-coding genes involved in meiosis or stress response pathways. Detailed analyses further suggest that antisense transcripts are independently regulated with respect to their sense transcripts, and diverse mechanisms might be potentially involved in the biogenesis and degradation of antisense RNAs. Taken together, antisense transcription may have profound impacts on global gene regulation in S. pombe.