CamoTSS: analysis of alternative transcription start sites for cellular phenotypes and regulatory patterns from 5' scRNA-seq data

Authors: Ruiyan Hou, Chung-Chau Hon, Yuanhua Huang

Source: Nature Communications, Vol 14, Iss 1, Pp 1-16 (2023)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/f573d66c56ca4de6b9b047b8758365c4

Defining super-enhancers by highly ranked histone H4 multi-acetylation levels identifies transcription factors associated with glioblastoma stem-like properties

Authors: Nando D. Das, Jen-Chien Chang, Chung-Chau Hon, S. Thomas Kelly, Shinsuke Ito, Marina Lizio, Bogumil Kaczkowski, Hisami Watanabe, Keisuke Katsushima, Atsushi Natsume, Haruhiko Koseki, Yutaka Kondo, Aki Minoda, Takashi Umehara

Source: BMC Genomics, Vol 24, Iss 1, Pp 1-19 (2023)

Subject Terms: Epigenetics, Histone acetylation, Inhibitor, Nucleosome, Tumorigenesis, Biotechnology, TP248.13-248.65, Genetics, QH426-470

File Description: electronic resource

Relation: https://doaj.org/toc/1471-2164

Access URL: https://doaj.org/article/5b74b7e87b6c485084dc2c0220e913a3

Critical roles of FGF, RA, and WNT signalling in the development of the human otic placode and subsequent lineages in a dish

Authors: Tsubasa Saeki, Sho Yoshimatsu, Mitsuru Ishikawa, Chung-Chau Hon, Ikuko Koya, Shinsuke Shibata, Makoto Hosoya, Chika Saegusa, Kaoru Ogawa, Jay W. Shin, Masato Fujioka, Hideyuki Okano

Source: Regenerative Therapy, Vol 20, Iss , Pp 165-186 (2022)

Subject Terms: Human pluripotent stem cell, Floating culture, Otic placode, Single cell RNA-seq, Hair cell, Medicine (General), R5-920, Cytology, QH573-671

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2352320422000359; https://doaj.org/toc/2352-3204

Access URL: https://doaj.org/article/8f164e0c0729489aa06876e4cf1c3290

Single-cell transcriptomics of human gut T cells identifies cytotoxic CD4+CD8A+ T cells related to mouse CD4 cytotoxic T cells

Authors: Shun Tanemoto, Tomohisa Sujino, Kentaro Miyamoto, Jonathan Moody, Yusuke Yoshimatsu, Yoshinari Ando, Ikuko Koya, Yosuke Harada, Anna Okuzawa Tojo, Keiko Ono, Yukie Hayashi, Kaoru Takabayashi, Koji Okabayashi, Toshiaki Teratani, Yohei Mikami, Nobuhiro Nakamoto, Naoki Hosoe, Haruhiko Ogata, Chung-Chau Hon, Jay W. Shin, Takanori Kanai

Source: Frontiers in Immunology, Vol 13 (2022)

Subject Terms: cytotoxic CD4 T cells, single-cell RNA sequencing, human CD4+CD8A+ T cells, inflammatory bowel disease, intestinal inflammation, Immunologic diseases. Allergy, RC581-607

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fimmu.2022.977117/full; https://doaj.org/toc/1664-3224

Access URL: https://doaj.org/article/64af4c68a566413d876fafee75f8128e

Systematic functional interrogation of human pseudogenes using CRISPRi

Authors: Ming Sun, Yunfei Wang, Caishang Zheng, Yanjun Wei, Jiakai Hou, Peng Zhang, Wei He, Xiangdong Lv, Yao Ding, Han Liang, Chung-Chau Hon, Xi Chen, Han Xu, Yiwen Chen

Source: Genome Biology, Vol 22, Iss 1, Pp 1-29 (2021)

Subject Terms: Pseudogene, Unitary pseudogene, CRISPR interference, Cancer, Luminal A breast cancer, Nucleus, Biology (General), QH301-705.5, Genetics, QH426-470

File Description: electronic resource

Relation: https://doaj.org/toc/1474-760X

Access URL: https://doaj.org/article/07ce74289b2d45e8b608ea1dcae21694

Analysis of splice variants of the human protein disulfide isomerase (P4HB) gene

Authors: Daniela Kajihara, Chung-Chau Hon, Aimi Naim Abdullah, João Wosniak, Ana Iochabel S. Moretti, Joice F. Poloni, Diego Bonatto, Kosuke Hashimoto, Piero Carninci, Francisco R. M. Laurindo

Source: BMC Genomics, Vol 21, Iss 1, Pp 1-16 (2020)

Subject Terms: Biotechnology, TP248.13-248.65, Genetics, QH426-470

File Description: electronic resource

Relation: http://link.springer.com/article/10.1186/s12864-020-07164-y; https://doaj.org/toc/1471-2164

Access URL: https://doaj.org/article/03a26eaff3a348368fb6dcc6966203e0

C1 CAGE detects transcription start sites and enhancer activity at single-cell resolution

Authors: Tsukasa Kouno, Jonathan Moody, Andrew Tae-Jun Kwon, Youtaro Shibayama, Sachi Kato, Yi Huang, Michael Böttcher, Efthymios Motakis, Mickaël Mendez, Jessica Severin, Joachim Luginbühl, Imad Abugessaisa, Akira Hasegawa, Satoshi Takizawa, Takahiro Arakawa, Masaaki Furuno, Naveen Ramalingam, Jay West, Harukazu Suzuki, Takeya Kasukawa, Timo Lassmann, Chung-Chau Hon, Erik Arner, Piero Carninci, Charles Plessy, Jay W. Shin

Source: Nature Communications, Vol 10, Iss 1, Pp 1-12 (2019)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/2b223db146cd404e9768769b7c47b35c

Long Non-Coding RNAs Associated with Metabolic Traits in Human White Adipose Tissue

Authors: Hui Gao, Alastair Kerr, Hong Jiao, Chung-Chau Hon, Mikael Rydén, Ingrid Dahlman, Peter Arner

Source: EBioMedicine, Vol 30, Iss , Pp 248-260 (2018)

Subject Terms: Medicine, Medicine (General), R5-920

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S235239641830094X; https://doaj.org/toc/2352-3964

Access URL: https://doaj.org/article/04889f6db03c49f99e4ff32066e854ef

JQ1 affects BRD2-dependent and independent transcription regulation without disrupting H4-hyperacetylated chromatin states

Authors: Lusy Handoko, Bogumil Kaczkowski, Chung-Chau Hon, Marina Lizio, Masatoshi Wakamori, Takayoshi Matsuda, Takuhiro Ito, Prashanti Jeyamohan, Yuko Sato, Kensaku Sakamoto, Shigeyuki Yokoyama, Hiroshi Kimura, Aki Minoda, Takashi Umehara

Source: Epigenetics, Vol 13, Iss 4, Pp 410-431 (2018)

Subject Terms: bet, brd2, cage, h4 hyperacetylation, jq1, Genetics, QH426-470

File Description: electronic resource

Relation: https://doaj.org/toc/1559-2294; https://doaj.org/toc/1559-2308

Access URL: https://doaj.org/article/a5a3e24b8e2b44a8ae4456359d3ec093

RNA Sequencing Reveals Widespread Transcription of Natural Antisense RNAs in Entamoeba Species

Authors: Damien Mornico, Chung-Chau Hon, Mikael Koutero, Christian Weber, Jean-Yves Coppée, C Graham Clark, Marie-Agnes Dillies, Nancy Guillen

Source: Microorganisms, Vol 10, Iss 2, p 396 (2022)

Subject Terms: parasite, genomics, transcriptomics, antisense RNA, Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://www.mdpi.com/2076-2607/10/2/396; https://doaj.org/toc/2076-2607

Access URL: https://doaj.org/article/fb44444b376d47d1b3657bbbbdc936f6

Analysis of the genome and transcriptome of Cryptococcus neoformans var. grubii reveals complex RNA expression and microevolution leading to virulence attenuation.

Authors: Guilhem Janbon, Kate L Ormerod, Damien Paulet, Edmond J Byrnes, Vikas Yadav, Gautam Chatterjee, Nandita Mullapudi, Chung-Chau Hon, R Blake Billmyre, François Brunel, Yong-Sun Bahn, Weidong Chen, Yuan Chen, Eve W L Chow, Jean-Yves Coppée, Anna Floyd-Averette, Claude Gaillardin, Kimberly J Gerik, Jonathan Goldberg, Sara Gonzalez-Hilarion, Sharvari Gujja, Joyce L Hamlin, Yen-Ping Hsueh, Giuseppe Ianiri, Steven Jones, Chinnappa D Kodira, Lukasz Kozubowski, Woei Lam, Marco Marra, Larry D Mesner, Piotr A Mieczkowski, Frédérique Moyrand, Kirsten Nielsen, Caroline Proux, Tristan Rossignol, Jacqueline E Schein, Sheng Sun, Carolin Wollschlaeger, Ian A Wood, Qiandong Zeng, Cécile Neuvéglise, Carol S Newlon, John R Perfect, Jennifer K Lodge, Alexander Idnurm, Jason E Stajich, James W Kronstad, Kaustuv Sanyal, Joseph Heitman, James A Fraser, Christina A Cuomo, Fred S Dietrich

Source: PLoS Genetics, Vol 10, Iss 4, p e1004261 (2014)

Subject Terms: Genetics, QH426-470

File Description: electronic resource

Relation: http://europepmc.org/articles/PMC3990503?pdf=render; https://doaj.org/toc/1553-7390; https://doaj.org/toc/1553-7404

Access URL: https://doaj.org/article/f123cb606a794c4eb2a9ee8bfde5b129

Gene expression profiling in Entamoeba histolytica identifies key components in iron uptake and metabolism.

Authors: Nora Adriana Hernández-Cuevas, Christian Weber, Chung-Chau Hon, Nancy Guillen

Source: PLoS ONE, Vol 9, Iss 9, p e107102 (2014)

Subject Terms: Medicine, Science

File Description: electronic resource

Relation: http://europepmc.org/articles/PMC4161402?pdf=render; https://doaj.org/toc/1932-6203

Access URL: https://doaj.org/article/140e6fa772f94b528399ebdc1bf53847

Bioassay-guided fractionation of extracts from Codiaeum variegatum against Entamoeba histolytica discovers compounds that modify expression of ceramide biosynthesis related genes.

Authors: Emmanuel Mfotie Njoya, Christian Weber, Nora Adriana Hernandez-Cuevas, Chung-Chau Hon, Yves Janin, Melanie F G Kamini, Paul F Moundipa, Nancy Guillén

Source: PLoS Neglected Tropical Diseases, Vol 8, Iss 1, p e2607 (2014)

Subject Terms: Arctic medicine. Tropical medicine, RC955-962, Public aspects of medicine, RA1-1270

File Description: electronic resource

Relation: http://europepmc.org/articles/PMC3887121?pdf=render; https://doaj.org/toc/1935-2727; https://doaj.org/toc/1935-2735

Access URL: https://doaj.org/article/8143fa364cbb41fcbadc2179fc188fba

Identification of the virulence landscape essential for Entamoeba histolytica invasion of the human colon.

Authors: Roman Thibeaux, Christian Weber, Chung-Chau Hon, Marie-Agnès Dillies, Patrick Avé, Jean-Yves Coppée, Elisabeth Labruyère, Nancy Guillén

Source: PLoS Pathogens, Vol 9, Iss 12, p e1003824 (2013)

Subject Terms: Immunologic diseases. Allergy, RC581-607, Biology (General), QH301-705.5

File Description: electronic resource

Relation: http://europepmc.org/articles/PMC3868522?pdf=render; https://doaj.org/toc/1553-7366; https://doaj.org/toc/1553-7374

Access URL: https://doaj.org/article/e869e4711a4945c3ae56ddff7cfa4923

Endoplasmic reticulum stress-sensing mechanism is activated in Entamoeba histolytica upon treatment with nitric oxide.

Authors: Julien Santi-Rocca, Sherri Smith, Christian Weber, Erika Pineda, Chung-Chau Hon, Emma Saavedra, Alfonso Olivos-García, Sandrine Rousseau, Marie-Agnès Dillies, Jean-Yves Coppée, Nancy Guillén

Source: PLoS ONE, Vol 7, Iss 2, p e31777 (2012)

Subject Terms: Medicine, Science

File Description: electronic resource

Relation: http://europepmc.org/articles/PMC3286455?pdf=render; https://doaj.org/toc/1932-6203

Access URL: https://doaj.org/article/5b5bb923a29b459dac3bf84e2b9afa11

A proteomic and cellular analysis of uropods in the pathogen Entamoeba histolytica.

Authors: Jacques Marquay Markiewicz, Sylvie Syan, Chung-Chau Hon, Christian Weber, Daniela Faust, Nancy Guillen

Source: PLoS Neglected Tropical Diseases, Vol 5, Iss 4, p e1002 (2011)

Subject Terms: Arctic medicine. Tropical medicine, RC955-962, Public aspects of medicine, RA1-1270

File Description: electronic resource

Relation: http://europepmc.org/articles/PMC3071361?pdf=render; https://doaj.org/toc/1935-2735

Access URL: https://doaj.org/article/0c7814a8a2de47e2b719b6d19c7d9f26

Evolutionary and transmission dynamics of reassortant H5N1 influenza virus in Indonesia.

Authors: Tommy Tsan-Yuk Lam, Chung-Chau Hon, Oliver G Pybus, Sergei L Kosakovsky Pond, Raymond Tze-Yeung Wong, Chi-Wai Yip, Fanya Zeng, Frederick Chi-Ching Leung

Source: PLoS Pathogens, Vol 4, Iss 8, p e1000130 (2008)

Subject Terms: Immunologic diseases. Allergy, RC581-607, Biology (General), QH301-705.5

File Description: electronic resource

Relation: http://europepmc.org/articles/PMC2515348?pdf=render; https://doaj.org/toc/1553-7366; https://doaj.org/toc/1553-7374

Access URL: https://doaj.org/article/7bd83e45235e402ba6441e0d915394b1

Enhancer target prediction: state-of-the-art approaches and future prospects.

Authors: Umarov, Ramzan¹, Chung-Chau Hon¹ chungchau.hon@riken.jp

Source: Biochemical Society Transactions. Oct2023, Vol. 51 Issue 5, p1975-1988. 14p.

Subject Terms: *SUPERVISED learning, *GENE enhancers, *GENE expression, *DISEASE susceptibility, *FORECASTING, *CHROMATIN

Heterogeneity among enhancer RNAs: origins, consequences and perspectives.

Authors: Syed, Khaja Mohieddin, Chung-Chau Hon

Source: Essays in Biochemistry; Oct2021, Vol. 65 Issue 4, p709-721, 13p

Strand-specific RNA-Seq reveals widespread and developmentally regulated transcription of natural antisense transcripts in Plasmodium falciparum.

Authors: Siegel, T. Nicolai^1,2,3 nicolai.siegel@uni-wuerzburg.de, Chung-Chau Hon^4,5 chung-chau.hon@pasteur.fr, Qinfeng Zhang^1,2,6 qinf_zhang@yahoo.com.cn, Lopez-Rubio, Jose-Juan^1,2 jose-juan.lopez-rubio@pasteur.fr, Scheidig-Benatar, Christine^1,2 christine.scheidig-benatar@pasteur.fr, Martins, Rafael M.^1,2 rmartins@pasteur.fr, Sismeiro, Odile⁷ osisme@pasteur.fr, Coppée, Jean-Yves⁷ jycoppee@pasteur.fr, Scherf, Artur^1,2 artur.scherf@pasteur.fr

Source: BMC Genomics. 2014, Vol. 15 Issue 1, p1-30. 30p.

Subject Terms: *PLASMODIUM falciparum genetics, *GENE expression, *PROTOZOA genetics, *GENETIC transcription, *MESSENGER RNA, *NON-coding RNA, *MICROORGANISMS