Publications

Highlights

(For a full list see below)

ATF3 induction prevents precocious activation of skeletal muscle stem cell by regulating H2B expression

Skeletal muscle stem cells (also called satellite cells, SCs) are important for maintaining muscle tissue homeostasis and damage-induced regeneration. However, it remains poorly understood how SCs enter cell cycle to become activated upon injury. Here we report that AP-1 family member ATF3 (Activating Transcription Factor 3) prevents SC premature activation. Atf3 is rapidly and transiently induced in SCs upon activation. Short-term deletion of Atf3 in SCs accelerates acute injury-induced regeneration, however, its long-term deletion exhausts the SC pool and thus impairs muscle regeneration. The Atf3 loss also provokes SC activation during voluntary exercise and enhances the activation during endurance exercise. Mechanistically, ATF3 directly activates the transcription of Histone 2B genes, whose reduction accelerates nucleosome displacement and gene transcription required for SC activation. Finally, the ATF3-dependent H2B expression also prevents genome instability and replicative senescence in SCs. Therefore, this study has revealed a previously unknown mechanism for preserving the SC population by actively suppressing precocious activation, in which ATF3 is a key regulator.

Suyang Zhang*, Feng Yang, Yile Huang, Liangqiang He, Yuying Li, Yi Ching Esther Wan, Yingzhe Ding, Kui Ming Chan, Ting Xie, Hao Sun & Huating Wang*

Nature Communications 10.1038/s41467-023-40465-w

Multiscale 3D genome reorganization during skeletal muscle stem cell lineage progression and aging

Little is known about three-dimensional (3D) genome organization in skeletal muscle stem cells [also called satellite cells (SCs)]. Here, we comprehensively map the 3D genome topology reorganization during mouse SC lineage progression. Specifically, rewiring at the compartment level is most pronounced when SCs become activated. Marked loss in topologically associating domain (TAD) border insulation and chromatin looping also occurs during early activation process. Meanwhile, TADs can form TAD clusters and super-enhancer–containing TAD clusters orchestrate stage-specific gene expression. Furthermore, we uncover that transcription factor PAX7 is pivotal in enhancer-promoter (E-P) loop formation. We also identify cis-regulatory elements that are crucial for local chromatin organization at Pax7 locus and Pax7 expression. Lastly, we unveil that geriatric SC displays a prominent gain in long-range contacts and loss of TAD border insulation. Together, our results uncover that 3D chromatin extensively reorganizes at multiple architectural levels and underpins the transcriptome remodeling during SC lineage development and SC aging.

YU ZHAO*, YINGZHE DING*, LIANGQIANG HE*, QIN ZHOU, XIAONA CHEN, YUYING LI, MARIA VITTORIA ALFONSI, ZHENGUO WU, HAO SUN, HUATING WANG*

Science Advances 10.1126/sciadv.abo1360

 

Full List

2024

  • Yuwei Zhang, Jieyu Zhao, Xiaona Chen, Yulong Qiao, Jinjin Kang, Xiaofan Guo, Feng Yang, Kaixin Lyu, Yiliang Ding, Yu Zhao, Hao Sun, Huating Wang, Chun Kit Kwok; DHX36 binding induces RNA structurome remodeling and regulates RNA abundance via m6A reader YTHDF1. Nature Communications, 2024.
  • Liqiang He, Hao Sun, Huating Wang; 3D organization of enhancers in MuSCs. Current Topics in Developmental Biology, 2024.
  • Chen, X., Y. Li, J. Xu, Y. Cui, Q. Wu, H. Yin, Y. Li, C. Gao, L. Jiang, H. Wang, Z. Wen, Z. Yao, and Z. Wu. Styxl2 regulates de novo sarcomere assembly by binding to non-muscle myosin IIs and promoting their degradation. eLife, 2024, Doi: 10.7554/eLife.87434.2

    • 2023

  • Zhiming He, Xiaona Chen, Gexin Liu, Yuying Li, Feng Yang, Hao Sun, Huating Wang; Sugt1 loss in skeletal muscle stem cells impairs muscle regeneration and causes premature muscle aging. Life Medicine, 2023, https://academic.oup.com/lifemedi/advance-article/doi/10.1093/lifemedi/lnad039/7336988
  • Stephanie N. Oprescu, Nick Baumann, Xiyue Chen, Qiang Sun, Yu Zhao, Feng Yue, Huating Wang & Shihuan Kuang; Sox11 is enriched in myogenic progenitors but dispensable for development and regeneration of the skeletal muscle. Skeletal Muscle, 2023, https://skeletalmusclejournal.biomedcentral.com/articles/10.1186/s13395-023-00324-0

  • Suyang Zhang, Feng Yang, Yile Huang, Liangqiang He, Yuying Li, Yi Ching Esther Wan, Yingzhe Ding, Kui Ming Chan, Ting Xie, Hao Sun & Huating Wang; ATF3 induction prevents precocious activation of skeletal muscle stem cell by regulating H2B expression. Nature Communications, 2023, https://www.nature.com/articles/s41467-023-40465-w

  • YU ZHAO, YINGZHE DING, LIANGQIANG HE, QIN ZHOU, XIAONA CHEN, YUYING LI, MARIA VITTORIA ALFONSI, ZHENGUO WU, HAO SUN, HUATING WANG; Multiscale 3D genome reorganization during skeletal muscle stem cell lineage progression and aging. Science Advances, 2023, https://doi.org/10.1126/sciadv.abo1360

  • Yulong Qiao, Qiang Sun, Xiaona Chen, Liangqiang He, Di Wang, Ruibao Su, Yuanchao Xue, Hao Sun, Huating Wang; Nuclear m6A reader YTHDC1 promotes muscle stem cell activation/proliferation by regulating mRNA splicing and nuclear export. eLife, 2023, https://doi.org/10.7554/eLife.82703

  • Liangqiang He, Zhiming He, Yuying Li, Hao Sun, Huating Wang; In Vivo Investigation of Gene Function in Muscle Stem Cells by CRISPR/Cas9-Mediated Genome Editing. Skeletal Muscle Stem Cells, 2023, https://link.springer.com/protocol/10.1007/978-1-0716-3036-5_21

    • 2022

  • Chien Ting Cheng, Dan Wang, Oscar Kuang-Sheng Lee, HUATING WANG, Dai Fei Elmer Ker; Application of neural networks on in vitro-generated Raman spectra for label-free, ex vivo skeletal muscle detection. Measurement, https://doi.org/10.1016/j.measurement.2022.112172

  • Karl Kam Hei So, Yile Huang, Suyang Zhang, Yulong Qiao, Liangqiang He, Yuying Li, Xiaona Chen, Mai Har Sham, Hao Sun, Huating Wang; seRNA PAM controls skeletal muscle satellite cell proliferation and aging through trans regulation of Timp2 expression synergistically with Ddx5. Aging Cell, https://doi.org/10.1111/acel.13673

  • Di Liu, Kevin Y. Yang, Vicken W. Chan, Wenchu Ye, Charing C.N. Chong, Chi Chiu Wang, Huating Wang, Bin Zhou, Kenneth K.Y. Cheng, Kathy O. Lui; YY1 Regulates Glucose Homeostasis Through Controlling Insulin Transcription in Pancreatic β-Cells. Diabetes, https://doi.org/10.2337/db21-0695

  • Xiaona Chen, Guang Xue, Jieyu Zhao, Yuwei Zhang, Suyang Zhang, Wen Wang, Yang Li, Jie Yuan, Liangqiang He, Chun Yin Chan, Yan Liu, Wei Chen, Yu Zhao, Ping Hu, Hao Sun, Chun Kit Kwok, Huating Wang; Lockd promotes myoblast proliferation and muscle regeneration via binding with DHX36 to facilitate 5′ UTR rG4 unwinding and Anp32e translation. Cell Reports, https://doi.org/10.1016/j.celrep.2022.110927

  • Lifang Han, Gang Wang, Shaopu Zhou, Chenghao Situ, Zhiming He, Yuying Li, Yudan Qiu, Yu Huang, Aimin Xu, Michael Tim Yun Ong, Huating Wang, Jianfa Zhang, Zhenguo Wu; Muscle satellite cells are impaired in type 2 diabetic mice by elevated extracellular adenosine. Cell Reports, https://doi.org/10.1016/j.celrep.2022.110884

  • Liang C, Ke Q, Liu Z, Ren J, Zhang W, Hu J, Wang Z, Chen H, Xia K, Lai X, Wang Q, Yang K, Li W, Wu Z, Wang C, Yan H, Jiang X, Ji Z, Ma M, Long X, Wang S, Wang H, Sun H, Belmonte JCI, Qu J, Xiang AP, Liu GH; BMAL1 moonlighting as a gatekeeper for LINE1 repression and cellular senescence in primates. Nucleic Acids Res, https://doi.org/10.1093/nar/gkac146

    • 2021

  • Hongye Wang, Yile Huang, Ming Yu, Yang Yu, Sheng Li, Huating Wang, Hao Sun, Bing Li, Guoliang Xu, Ping Hu; Muscle regeneration controlled by a designated DNA dioxygenase. Cell Death Dis, https://doi.org/10.1038/s41419-021-03817-2

  • Liangqiang He, Yingzhe Ding, Yu Zhao, Karl K. So, Xianlu L. Peng, Yuying Li, Jie Yuan, Zhiming He, Xiaona Chen, Hao Sun, Huating Wang; CRISPR/Cas9/AAV9-mediated in vivo editing identifies MYC regulation of 3D genome in skeletal muscle stem cell. Stem Cell Reports, https://doi.org/10.1016/j.stemcr.2021.08.011

  • Xiaona Chen, Jie Yuan, Guang Xue, Silvia Campanario, Di Wang, Wen Wang, Xi Mou, Shiau Wei Liew, Mubarak Ishaq Umar, Joan Isern, Yu Zhao, Liangqiang He, Yuying Li, Christopher J. Mann, Xiaohua Yu, Lei Wang, Eusebio Perdiguero, Wei Chen, Yuanchao Xue, Yoshikuni Nagamine, Chun Kit Kwok, Hao Sun, Pura Muñoz-Cánoves, Huating Wang; Translational control by DHX36 binding to 5′UTR G-quadruplex is essential for muscle stem-cell regenerative functions. Nat Commun, https://doi.org/10.1038/s41467-021-25170-w

  • Yile Huang, Yulong Qiao, Yu Zhao, Yuying Li, Jie Yuan, Jiajian Zhou, Hao Sun, Huating Wang; Large scale RNA-binding proteins/LncRNAs interaction analysis to uncover lncRNA nuclear localization mechanisms. Briefings in Bioinformatics, https://doi.org/10.1093/bib/bbab195

    • 2020

  • Kelahmetoglu Y, Jannig PR, Cervenka I, Koch LG, Britton SL, Zhou J, Wang H, Robinson MM, Nair KS, Ruas JL; Comparative Analysis of Skeletal Muscle Transcriptional Signatures Associated With Aerobic Exercise Capacity or Response to Training in Humans and Rats. Front Endocrinol (Lausanne), 10.3389/fendo.2020.591476

  • Zhang M, Lai Y, Krupalnik V, Guo P, Guo X, Zhou J, Xu Y, Yu Z, Liu L, Jiang A, Li W, Abdul MM, Ma G, Li N, Fu X, Lv Y, Jiang M, Tariq M, Kanwal S, Liu H, Xu X, Zhang H, Huang Y, Wang L, Chen S, Babarinde IA, Luo Z, Wang D, Zhou T, Ward C, He M, Ibañez DP, Li Y, Zhou J, Yuan J, Feng Y, Arumugam K, Di Vicino U, Bao X, Wu G, Schambach A, Wang H,Sun H, Gao F, Qin B, Hutchins AP, Doble BW, Hartmann C, Cosma MP, Qin Y, Xu GL, Chen R, Volpe G, Chen L, Hanna JH, Esteban MA; β-Catenin safeguards the ground state of mousepluripotency by strengthening the robustness of the transcriptional apparatus. Sci Adv, 10.1126/sciadv.aba1593

  • Fan F, Chen D, Zhao Y, Wang H, Sun H, Sun K*; Rapid preliminary purity evaluation of tumor biopsies using deep learning approach. Comput Struct Biotechnol J, 10.1016/j.csbj.2020.06.007

  • Kun Sun, Lishi Li, Li Ma, Yu Zhao, Lin Deng, Wang H, Hao Sun. Msuite: A High-Performance and Versatile DNA Methylation Data-Analysis Toolkit. Patterns,2020 https://doi.org/10.1016/j.patter.2020.100127.

  • Gene Chi Wai Man, Jianzhang Wang, Yi Song, Jack Ho Wong, Yu Zhao, Tat San Lau, Kam Tong Leung, Tak Hang Chan, Huating Wang, Joseph Kwong, Tzi Bun Ng & Chi Chiu Wang; Therapeutic potential of a novel prodrug of green tea extract in induction of apoptosis via ERK/JNK and Akt signaling pathway in human endometrial cancer. BMC Cancer, https://doi.org/10.1093/bib/bbab195

  • Sun, K., Wang H & Sun, H; NAMS webserver: coding potential assessment and functional annotation of plant transcripts. Briefings in Bioinformatics, https://doi.org/10.1093/bib/bbaa200

  • Shen’ao Zhou, Wei Zhang, Gaihong Cai, Yingzhe Ding, Caixia Wei, Sheng Li, Yu Yang, Jie Qin, Dan Liu, Hao Zhang, Xiexiang Shao, Jianhua Wang, Hongye Wang, Wenjun Yang, Huating Wang, She Chen, Ping Hu & Liming Sun; Myofiber necroptosis promotes muscle stem cell proliferation via releasing Tenascin-C during regeneration. Cell Research, https://doi.org/10.1038/s41422-020-00393-6

  • Yuying Li, Jie Yuan, Fengyuan Chen, Suyang Zhang, Yu Zhao, Xiaona Chen, Leina Lu, Liang Zhou, Ching Yan Chu, Hao Sun, Huating Wang; Long noncoding RNA SAM promotes myoblast proliferation through stabilizing Sugt1 and facilitating kinetochore assembly. Nat Commun, https://doi.org/10.1038/s41467-020-16553-6

  • Linlin Hou, Yuanjie Wei, Yingying Lin, Xiwei Wang, Yiwei Lai, Menghui Yin, Yanpu Chen, Xiangpeng Guo, Senbin Wu, Yindi Zhu, Jie Yuan, Muqddas Tariq, Na Li, Hao Sun, Huating Wang, Xiaofei Zhang, Jiekai Chen, Xichen Bao, Ralf Jauch; Concurrent binding to DNA and RNA facilitates the pluripotency reprogramming activity of Sox2. Nucleic Acids Research, https://doi.org/10.1093/nar/gkaa067

    • 2019

  • Yu Zhao, Jiajian Zhou, Liangqiang He, Yuying Li, Jie Yuan, Kun Sun, Xiaona Chen, Xichen Bao, Miguel A. Esteban, Hao Sun, Wang H, MyoD induced enhancer RNA interacts with hnRNPL to activate target gene transcription during myogenic differentiation. Nat Commun 10, 5787 (2019). https://doi.org/10.1038/s41467-019-13598-0

  • Malik V, Glaser LV, Zimmer D, Velychko S, Weng M, Holzner M, Arend M, Chen Y, Srivastava Y, Veerapandian V, Shah Z, Esteban MA, Wang H, Chen J, Scholer HR, Hutchins AP, Meijsing SH, Pott S, Jauch R. Pluripotency reprogramming by competent and incompetent POU factors uncovers temporal dependency for Oct4 and Sox2. Nat Commun. 2019 Aug 2;10(1):3477.

  • Zhou J, So KK, Li Y, Li Y, Yuan J, Ding Y, Chen F, Huang Y, Liu J, Lee W, Li G, Ju Z, Sun H, Wang H; Elevated H3K27ac in aged skeletal muscle leads to increase in extracellular matrix and fibrogenic conversion of muscle satellite cells. Aging Cell 2019 Jul 20:e12996.

  • Chen F, Zhou J, Li Y, Zhao Y, Yuan J, Cao Y, Wang L, Zhang Z, Zhang B, Wang CC, Cheung TH, Wu Z, Wong CC, Sun H, Wang H; YY1 regulates skeletal muscle regeneration through controlling metabolic reprogramming of satellite cells. EMBO J. 2019 May 15;38(10).

  • Yuan J, Zhou J, Wang H, Sun H; SKmDB: an integrated database of next generation sequencing information in skeletal muscle. Bioinformatics 2019 Mar 1;35(5):847-855.

    • 2018

  • Peterson JM, Wang DJ, Shettigar V, Roof SR, Canan BD, Bakkar N, Shintaku J, Gu JM, Little SC, Ratnam NM, Londhe P, Lu L, Gaw CE, Petrosino JM, Liyanarachchi S, Wang H, Janssen PML, Davis JP, Ziolo MT, Sharma SM, Guttridge DC. NF-kappaB inhibition rescues cardiac function by remodeling calcium genes in a Duchenne muscular dystrophy model. Nat Commun. 2018 Aug 24;9(1):3431.

  • Sun K, Wang J, Wang H, Sun H. GeneCT: a generalizable cancerous status and tissue origin classifier for pan-cancer biopsies. Bioinformatics 2018 Dec 1; 34(23):4129-4130.

  • Yao M, Zhou X, Zhou J, Gong S, Hu G, Li J, Huang K, Lai P, Shi G, Hutchins AP, Sun H, Wang H and Yao H. PCGF5 is required for neural differentiation of embryonic stem cells. Nat Commun. 2018 May 15;9(1):1463.

  • Zhou J, Huang Y, Ding Y, Yuan J, Wang H, Sun H. lncFunTK: A toolkit for functional annotation of long noncoding RNAs. Bioinformatics 2018 Oct 1;34(19):3415-3416.

  • Bao X, Guo X, Yin M, Tariq M, Lai Y, Kanwal S, Zhou J, Li N, Lv Y, Pulido-Quetglas C, Wang X, Ji L, Khan MJ, Zhu X, Luo Z, Shao C, Lim DH, Liu X, Li N, Wang W, He M, Liu YL, Ward C, Wang T, Zhang G, Wang D, Yang J, Chen Y, Zhang C, Jauch R, Yang YG, Wang Y, Qin B, Anko ML, Hutchins AP, Sun H, Wang H, Fu XD, Zhang B, and Esteban MA. Capturing the interactome of newly transcribed RNA. Nat Methods. 2018 Mar;15(3):213-220.

  • Li Y, Chen X, Sun H, Wang H. Long non-coding RNAs in the regulation of skeletal myogenesis and diseases. Cancer Lett. 2018 Mar 28;417:58-64.

  • So KK, Peng XL, Sun H, Wang H. Whole Genome Chromatin IP-Sequencing (ChIP-Seq) in Skeletal Muscle Cells. Methods Mol Biol. 2017;1668:15-25.

    • 2017

  • Zhang J, Jiang Y, Zhao Y, Wang W, Xie Y, Wang H, Yang Y. Downregulation of tyrosine threonine kinase inhibits tumor growth via G2/M arrest in human endometrioid endometrial adenocarcinoma. Tumour Biol. 2017 Jul;39(7):1010428317712444.

  • Sun K, Wang H, Sun H. mTFkb: a knowledgebase for fundamental annotation of mouse transcription factors. Sci Rep. 2017 Jun 8; 7(1):3022.

  • An Y, Wang G, Diao Y, Long Y, Fu X, Weng M, Zhou L, Sun K, Cheung TH, Ip NY, Sun H, Wang H, Wu Z. A Molecular Switch Regulating Cell Fate Choice between Muscle Progenitor Cells and Brown Adipocytes. Dev Cell. 2017 May 22;41(4):382-391.e5.

  • Peng X, So KK, He L, Zhao Y, Zhou J, Li Y, Yao M, Xu B, Zhang S, Yao H, Hu P, Sun H, Wang H. MyoD- and FoxO3-mediated hotspot interaction orchestrates super-enhancer activity during myogenic differentiation. Nucleic Acids Res. 2017 Sep 6;45(15):8785-8805.

  • Zhou J, Zhang S, Wang H, Sun H. LncFunNet: an integrated computational framework for identification of functional long noncoding RNAs in mouse skeletal muscle cells. Nucleic Acid Res. 2017 Jul 7;45(12):e108.

  • Chen X, He L, Zhao Y, Li Y, Zhang S, Sun K, So K, Chen F, Zhou L, Lu L, Wang L, Zhu X, Bao X, Esteban MA, Nakagawa S, Prasanth KV, Wu Z, Sun H, Wang H. Malat1 regulates myogenic differentiation and muscle regeneration through modulating MyoD transcriptional activity. Cell Discov. 2017 Mar 14;3:17002.

  • Peng X, Sun K, Zhou J, Sun H, Wang H. Bioinformatics for Novel Long Intergenic Noncoding RNA (lincRNA) Identification in Skeletal Muscle Cells. Peng X, Sun K, Zhou J, Sun H, Wang H. Methods Mol Biol. 2017;1556:355-362.

    • 2016

  • Stunnenberg HG, International Human Epigenome Consortium., Hirst M. The International Human Epigenome Consortium: A Blueprint for Scientific Collaboration and Discovery. Cell 2016 Nov 17;167(5):1145-1149.

  • Tsang DP, Wu WK, Kang W, Lee YY, Wu F, Yu Z, Xiong L, Chan AW, Tong JH, Yang W, Li MS, Lau SS, Li X, Lee SD, Yang Y, Lai PB, Yu DY, Xu G, Lo KW, Chan MT, Wang H, Lee TL, Yu J, Wong N, Yip KY, To KF, Cheng AS. Yin Yang 1-mediated epigenetic silencing of tumour-suppressive microRNAs activates nuclear factor-?B in hepatocellular carcinoma. J Pathol. 2016 Apr;238(5):651-64.

  • Zhu H, Xiao F, Wang G, Wei X, Jiang L, Chen Y, Zhu L, Wang H, Diao Y, Wang H, Ip NY, Cheung TH, Wu Z. STAT3 Regulates Self-Renewal of Adult Muscle Satellite Cells during Injury-Induced Muscle Regeneration. Cell Rep. 2016 Aug 23;16(8):2102-15.

  • Zhao Y, Sun H, Wang H. Long noncoding RNAs in DNA methylation: new players stepping into the old game. Cell Biosci. 2016 Jul 11;6:45.

  • Sun K, Zhou L, Zhao Y, Wang H, Sun H. Genome-wide RNA-seq and ChIP-seq reveal Linc-YY1 function in regulating YY1/PRC2 activity during skeletal myogenesis. Genomics Data 2016, Mar;7:247-249.

    • 2015

  • Zhou L, Sun K, Zhao Y, Zhang S, Wang X, Li Y, Lu L, Chen X, Chen F, Bao X, Zhu X, Wang L, Tang LY, Esteban MA, Wang R, Jauch R, Sun H, Wang H. Linc-YY1, a novel functional long non-coding RNA in myogenic differentiation and muscle regeneration. Nat Commun. 2015, Dec 11;6:10026. DOI: 10.1038/ncomms10026.

  • Fu X, Xiao J, Wei Y, Li S, Liu Y, Yin J, Sun K, Sun H, Wang H, Zhang Z, Zhang BT, Sheng C, Wang H, Hu P. Combination of Inflammation-related Cytokines Promotes Long-term Muscle Stem Cell Expansion. Cell Res. 2015 Jun; 25(6):655-673. DOI:10.1038/cr.2015.58.

  • Wang L, Zhao Y, Bao X, Zhu X, Kwok YK, Sun K, Chen X, Huang Y, Jauch R, Esteban MA, Sun H, Wang H. LncRNA Dum Interacts with Dnmts to Regulate Dppa2 Expression during Myogenic Differentiation and Muscle Regeneration. Cell Res. 2015 Mar; 25(3):335?350. DOI:10.1038/cr.2015.21.

  • Fu X, Wang H, Hu P. Stem Cell Activation in Skeletal Muscle Regeneration. Cellular and Molecular Life Sciences 2015 May; 72(9):1663-1677. DOI:10.1007/s00018-014-1819-5.

  • Bao X, Wu H, Zhu X, Guo X, Hutchins AP, Luo Z, Song H, Chen Y, Lai K, Yin M, Xu L, Zhou L, Chen J, Wang D, Qin B, Frampton J, Tse HF, Pei D, Wang H, Zhang B, Esteban MA. The p53-induced LincRNA-p21 Derails Somatic cell Reprogramming by Sustaining H3K9me3 and CpG Methylation at Pluripotency Gene Promoters. Cell Res. 2015 Jan; 25(1):80?92. DOI:10.1038/cr.2014.165.

    • 2014

  • Liu L, Xu Y, He M, Zhang M, Cui F, Lu L, Yao M, Tian W, Benda C, Zhuang Q, Huang Z, Li W, Li X, Zhao P, Fan W, Luo Z, Li Y, Wu Y, Hutchins AP, Wang D, Tse HF, Schambach A, Frampton J, Qin B, Bao X, Yao H, Zhang B, Sun H, Pei D, Wang H, Wang J, Esteban MA. Transcriptional Pause Release is a Rate-limiting Step for Somatic Cell Reprogramming. Cell Stem Cell. 2014 Nov 6; 15(5):574-88. DOI: 10.1016/j.stem.2014.09.018.

  • Zhao Y, Yang Y, Trovik J, Sun K, Zhou L, Jiang P, Lau TS, Hoivik EA, Salvesen HB, Sun H, Wang H. A Novel Wnt Regulatory Axis in Endometrioid Endometrial Cancer. Cancer Res. 2014 Sep 15; 74(18):5103-17. DOI: 10.1158/0008-5472.CAN-14-0427.

  • Sun K, Yuen Y, Wang H, Sun H. Online Diagnosis System: A Webserver for Analysis of Sanger Sequencing-based Genetic Testing Data. Methods 2014 Oct 1; 69(3):230-6. DOI: 10.1016/j.ymeth.2014.07.002.

  • Jiang P, Sun K, Lun F, Guo AM, Wang H, Chan KC, Chiu RW, Lo YM, Sun H. Methy-Pipe: An Integrated Bioinformatics Pipeline for Whole Genome Bisulfite Sequencing Data Analysis. PLoS One 2014 Jun 19; 9(6):e100360. DOI:10.1371/journal.pone.0100360.

  • Sun K, Zhao Y, Wang H, Sun H. Sebnif: An Integrated Bioinformatics Pipeline for the Identification of Novel Large Intergenic Noncoding RNAs (lincRNAs) - Application in Human Skeletal Muscle Cells. PLoS One 2014 Jan 6; 9(1):e84500. DOI:10.1371/journal.pone.0084500.

  • Sun K, Lu L, Wang H, Sun H. Genome-wide profiling of YY1 binding sites during skeletal myogenesis. Genomics Data 2014, 2:89-91.

    • 2013

  • Lu L, Sun K, Chen X, Zhao Y, Wang L, Zhou L, Sun H, Wang H. Genome-wide Survey Reveals YY1 Regulation of LincRNA in Skeletal Myogenesis. EMBO J. 2013 Oct 2; 32(19): 2575?2588. DOI: 10.1038/emboj.2013.182.

  • Song X, Wang M, Chen YP, Wang H, Han P, Sun H. Prediction of Pre-miRNA with Multiple Stem-loops Using Pruning Algorithm. Comput Biol Med. 2013 Jun; 43(5): 409?416. DOI: 10.1016/j.compbiomed.2013.02.003.

  • Sun K, Chen X, Jiang P, Song X, Wang H, Sun H. iSeeRNA: Identification of Long Intergenic Non-coding RNA Transcripts from Transcriptome Sequencing Data. BMC Genomics. 2013, 14 Suppl 2:S7 DOI:10.1186/1471-2164-14-S2-S7.

  • Guo AM, Sun K, Su X, Wang H, Sun H. YY1 TargetDB: An Integral Information Resource for Yin Yang 1 Target Loci. Database (Oxford) 2013 Feb 14; 2013:bat007. DOI: 10.1093/database/bat007.

    • 2012

  • Diao Y, Guo X, Li Y, Sun K, Lu L, Jiang L, Fu X, Zhu H, Sun H, Wang H, Wu Z. Pax3/7BP is a Pax7- and Pax3-binding Protein that Regulates the Proliferation of Muscle Precursor Cells by an Epigenetic Mechanism. Cell Stem Cell 2012 Aug 3;11(2):231-241. DOI: 10.1016/j.stem.2012.05.022.

  • Zhou L, Wang L, Lu L, Jiang P, Sun H, Wang H. A Novel Target of microRNA-29, Ring1 and YY1 Binding Protein (Rybp), Negatively Regulates Skeletal Myogenesis. J Biol Chem. 2012 Jul 20; 287(30):25255-65. DOI: 10.1074/jbc.M112.357053.

  • Wang S, Cheng Y, Du W, Lu L, Zhou L, Wang H, Kang W, Li X, Tao Q, Sung JJ, Yu J. Zinc-finger Protein 545 is a Novel Tumour Suppressor that Acts by Inhibiting Ribosomal RNA Transcription in Gastric Cancer. Gut 2013 Jun; 62(6):833-41. DOI: 10.1136/gutjnl-2011-301776.

  • Yang Y, Zhou L, Lu L, Wang L, Li X, Jiang P, Chan LK, Zhang T, Yu J, Kwong J, Cheung TH, Chung T, Mak K, Sun H, Wang H. A Novel miR-193a-5p-YY1-APC Regulatory Axis in Human Endometrioid Endometrial Adenocarcinoma. Oncogene 2013 Jul 18;32(29):3432-42. DOI: 10.1038/onc.2012.360.

  • Zhou L, Wang L, Lu L, Jiang P, Sun H, Wang H. Inhibition of miR-29 by TGF-beta-Smad3 Signaling through Dual Mechanisms Promotes Transdifferentiation of Mouse Myoblasts into Myofibroblasts. PLoS One 2012; 7(3):e33766. DOI: 10.1371/journal.pone.0033766.

  • Wang L, Zhou L, Jiang P, Lu L, Chen X, Lan H, Guttridge DC, Sun H, Wang H. Loss of miR-29 in Myoblasts Contributes to Dystrophic Muscle Pathogenesis. Mol Ther. 2012 Jun; 20(6):1222-1233. DOI: 10.1038/mt.2012.35.

  • Lu L, Zhou L, Chen EZ, Sun K, Jiang P, Wang L, Su X, Sun H, Wang H. A Novel YY1-miR-1 Regulatory Circuit in Skeletal Myogenesis Revealed by Genome-wide Prediction of YY1-miRNA Network. PLoS One 2012; 7(2):e27596. DOI: 10.1371/journal.pone.0027596.

    • Before 2010

  • Acharyya S, Sharma SM, Cheng AS, Ladner KJ, He W, Kline W, Wang H, Ostrowski MC, Huang TH, Guttridge DC. TNF Inhibits Notch-1 in Skeletal Muscle Cells by Ezh2 and DNA Methylation Mediated Repression: Implications in Duchenne Muscular Dystrophy. PLoS One 2010 Aug 30;5(8):e12479. DOI: 10.1371/journal.pone.0012479.

  • Raices RM; Kannan Y, Bellamkonda-Athmaram V, Seshadri S, Wang H, Guttridge DC, Wewers MD. A Novel Role for IkappaBzeta in the Regulation of IFNgamma Production. PLoS One 2009 Aug 26;4(8):e6776. DOI: 10.1371/journal.pone.0006776.

  • Wang H, Sun H and Guttridge DC. MicroRNAs: Novel Components in a Muscle Gene Regulatory Network. Cell Cycle 2009 Jun 15;8(12):1833-7. DOI:10.4161/cc.8.12.8851.

  • Wang H, Garzon R, Sun H, Ladner KJ, Singh R, Dahlman J, Cheng A, Hall BM, Qualman SJ, Chandler DS, Croce CM, Guttridge DC. NF-kappaB-YY1-miR-29 Regulatory Circuitry in Skeletal Myogenesis and Rhabdomyosarcoma. Cancer Cell 2008 Nov 4; 14(5):369-381. DOI: 10.1016/j.ccr.2008.10.006.

  • Bakkar N, Wang J, Ladner KJ, Wang H, Dahlman JM, Carathers M, Acharyya S, Rudnicki MA, Hollenbach AD, Guttridge DC. IKK/NF-kappaB Regulates Skeletal Myogenesis Via a Signaling Switch to Inhibit Differentiation and Promote Mitochondrial Biogenesis. J Cell Biol. 2008 Feb; 25;180(4):787-802. DOI: 10.1083/jcb.200707179.

  • Wang H, Hertlein E, Bakkar N, Sun H, Acharyya S, Wang J, Carathers M, Davuluri R, Guttridge DC. NF-kappaB Regulation of YY1 Inhibits Skeletal Myogenesis through Transcriptional Silencing of Myofibrillar Genes. Mol. Cell. Biol. 2007 Jun; 27(12):4374-4387. DOI: 10.1128/MCB.02020-06

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