Physiology - Division F

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2019

FRQ-CK1 interaction determines the period of circadian rhythms in Neurospora

Liu, X., Chen, A., Caicedo-Casso, A., Cui, G., Du, M., He, Q., Lim, S., Kim, H. J., Hong, C. I. & Liu, Y., Dec 1 2019, In : Nature communications. 10, 1, 4352.

Research output: Contribution to journalArticle

Open Access
1 Scopus citations

Myristoylation-Dependent Palmitoylation of the Receptor Tyrosine Kinase Adaptor FRS2α

Barylko, B., Chen, Y. J., Hennen, J., Angert, I., Chen, Y., Mueller, J. D., Sun, H. Q., Taylor, C. A., Liou, J., Yin, H. & Albanesi, J. P., Jun 25 2019, In : Biochemistry. 58, 25, p. 2809-2813 5 p.

Research output: Contribution to journalArticle

2 Scopus citations
2018

Codon usage biases co-evolve with transcription termination machinery to suppress premature cleavage and polyadenylation

Zhou, Z., Dang, Y., Zhou, M., Yuan, H. & Liu, Y., Mar 16 2018, In : eLife. 7, e33569.

Research output: Contribution to journalArticle

9 Scopus citations

Codon usage regulates human KRAS expression at both transcriptional and translational levels

Fu, J., Dang, Y., Counter, C. & Liu, Y., Nov 16 2018, In : Journal of Biological Chemistry. 293, 46, p. 17929-17940 12 p.

Research output: Contribution to journalArticle

3 Scopus citations

Comobility of GABARAP and Phosphatidylinositol 4-Kinase 2A on Cytoplasmic Vesicles

Chen, Y., Sun, H. Q., Eichorst, J. P., Albanesi, J. P., Yin, H. & Mueller, J. D., Jul 3 2018, In : Biochemistry. 57, 26, p. 3556-3559 4 p.

Research output: Contribution to journalArticle

3 Scopus citations

Transcription factor CBF-1 is critical for circadian gene expression by modulating WHITE COLLAR complex recruitment to the frq locus

Cao, X., Liu, X., Li, H., Fan, Y., Duan, J., Liu, Y. & He, Q., Sep 2018, In : PLoS genetics. 14, 9, e1007570.

Research output: Contribution to journalArticle

4 Scopus citations
2017

Codon usage regulates protein structure and function by affecting translation elongation speed in Drosophila cells

Zhao, F., Yu, C. H. & Liu, Y., Aug 21 2017, In : Nucleic Acids Research. 45, 14, p. 8484-8492 9 p.

Research output: Contribution to journalArticle

21 Scopus citations

DNA Replication Is Required for Circadian Clock Function by Regulating Rhythmic Nucleosome Composition

Liu, X., Dang, Y., Matsu-ura, T., He, Y., He, Q., Hong, C. I. & Liu, Y., Jul 20 2017, In : Molecular Cell. 67, 2, p. 203-213.e4

Research output: Contribution to journalArticle

10 Scopus citations
2016

Antisense transcription licenses nascent transcripts to mediate transcriptional gene silencing

Dang, Y., Cheng, J., Sun, X., Zhou, Z. & Liu, Y., Nov 1 2016, In : Genes and Development. 30, 21, p. 2417-2432 16 p.

Research output: Contribution to journalArticle

8 Scopus citations

Codon usage affects the structure and function of the Drosophila circadian clock protein PERIOD

Fu, J., Murphy, K. A., Zhou, M., Li, Y. H., Lam, V. H., Tabuloc, C. A., Chiu, J. C. & Liu, Y., Aug 1 2016, In : Genes and Development. 30, 15, p. 1761-1775 15 p.

Research output: Contribution to journalArticle

17 Scopus citations

Codon usage is an important determinant of gene expression levels largely through its effects on transcription

Zhoua, Z., Danga, Y., Zhou, M., Li, L., Yu, C. H., Fu, J., Chen, S. & Liu, Y., Oct 11 2016, In : Proceedings of the National Academy of Sciences of the United States of America. 113, 41, p. E6117-E6125

Research output: Contribution to journalArticle

66 Scopus citations

Distinct Roles of HDAC3 in the Core Circadian Negative Feedback Loop Are Critical for Clock Function

Shi, G., Xie, P., Qu, Z., Zhang, Z., Dong, Z., An, Y., Xing, L., Liu, Z., Dong, Y., Xu, G., Yang, L., Liu, Y. & Xu, Y., Feb 2 2016, In : Cell Reports. 14, 4, p. 823-834 12 p.

Research output: Contribution to journalArticle

11 Scopus citations
2015

Codon Usage Influences the Local Rate of Translation Elongation to Regulate Co-translational Protein Folding

Yu, C. H., Dang, Y., Zhou, Z., Wu, C., Zhao, F., Sachs, M. S. & Liu, Y., Sep 3 2015, In : Molecular Cell. 59, 5, p. 744-754 11 p.

Research output: Contribution to journalArticle

174 Scopus citations

GABARAP-mediated targeting of PI4K2A/PI4KIIatα autophagosomes regulates PtdIns4P-dependent autophagosome-lysosome fusion

Albanesi, J., Wang, H., Sun, H. Q., Levine, B. & Yin, H., Jan 1 2015, In : Autophagy. 11, 11, p. 2127-2129 3 p.

Research output: Contribution to journalArticle

19 Scopus citations

GABARAPs regulate PI4P-dependent autophagosome: Lysosome fusion

Wang, H., Sun, H. Q., Zhu, X., Zhang, L., Albanesi, J., Levine, B. & Yin, H., Jun 2 2015, In : Proceedings of the National Academy of Sciences of the United States of America. 112, 22, p. 7015-7020 6 p.

Research output: Contribution to journalArticle

73 Scopus citations

Mechanism of siRNA production from repetitive DNA

Yang, Q., Ye, Q. A. & Liu, Y., Jan 1 2015, In : Genes and Development. 29, 5, p. 526-537 12 p.

Research output: Contribution to journalArticle

25 Scopus citations

Mechanism of the Neurospora circadian clock, a FREQUENCY-centric view

Cha, J., Zhou, M. & Liu, Y., Jan 20 2015, In : Biochemistry. 54, 2, p. 150-156 7 p.

Research output: Contribution to journalArticle

19 Scopus citations

Nonoptimal codon usage influences protein structure in intrinsically disordered regions

Zhou, M., Wang, T., Fu, J., Xiao, G. & Liu, Y., Sep 1 2015, In : Molecular Microbiology. 97, 5, p. 974-987 14 p.

Research output: Contribution to journalArticle

35 Scopus citations

Role for protein kinase A in the Neurospora circadian clock by regulating white collar-independent frequency transcription through phosphorylation of RCM-1

Liu, X., Li, H., Liu, Q., Niu, Y., Hu, Q., Deng, H., Cha, J., Wang, Y., Liu, Y. & He, Q., Jan 1 2015, In : Molecular and cellular biology. 35, 12, p. 2088-2102 15 p.

Research output: Contribution to journalArticle

15 Scopus citations
2014

Histone H3K56 acetylation is required for quelling-induced small RNA production through its role in homologous recombination

Zhang, Z., Yang, Q., Sun, G., Chen, S., He, Q., Li, S. & Liu, Y., Mar 30 2014, In : Journal of Biological Chemistry. 289, 13, p. 9365-9371 7 p.

Research output: Contribution to journalArticle

10 Scopus citations

Methods to Study Molecular Mechanisms of the Neurospora Circadian Clock

Cha, J., Zhou, M. & Liu, Y., 2014, (Accepted/In press) In : Methods in Enzymology.

Research output: Contribution to journalArticle

2 Scopus citations

Transcriptional interference by antisense RNA is required for circadian clock function

Xue, Z., Ye, Q., Anson, S. R., Yang, J., Xiao, G., Kowbel, D., Glass, N. L., Crosthwaite, S. K. & Liu, Y., Oct 30 2014, In : Nature. 514, 7524, p. 650-653 4 p.

Research output: Contribution to journalArticle

48 Scopus citations
2013

CATP is a critical component of the Neurospora circadian clock by regulating the nucleosome occupancy rhythm at the frequency locus

Cha, J., Zhou, M. & Liu, Y., Oct 2013, In : EMBO Reports. 14, 10, p. 923-930 8 p.

Research output: Contribution to journalArticle

22 Scopus citations

Convergent Transcription Induces Dynamic DNA Methylation at disiRNA Loci

Dang, Y., Li, L., Guo, W., Xue, Z. & Liu, Y., Sep 1 2013, In : PLoS genetics. 9, 9, e1003761.

Research output: Contribution to journalArticle

28 Scopus citations

Dual roles of FBXL3 in the mammalian circadian feedback loops are important for period determination and robustness of the clock

Shi, G., Xing, L., Liu, Z., Qu, Z., Wu, X., Dong, Z., Wang, X., Gao, X., Huang, M., Yan, J., Yang, L., Liu, Y., Ptáček, L. J. & Xu, Y., Mar 19 2013, In : Proceedings of the National Academy of Sciences of the United States of America. 110, 12, p. 4750-4755 6 p.

Research output: Contribution to journalArticle

26 Scopus citations

Homologous recombination as a mechanism to recognize repetitive DNA sequences in an RNAi pathway

Zhang, Z., Chang, S. S., Zhang, Z., Xue, Z., Zhang, H., Li, S. & Liu, Y., Feb 1 2013, In : Genes and Development. 27, 2, p. 145-150 6 p.

Research output: Contribution to journalArticle

27 Scopus citations

Non-optimal codon usage affects expression, structure and function of clock protein FRQ

Zhou, M., Guo, J., Cha, J., Chae, M., Chen, S., Barral, J. M., Sachs, M. S. & Liu, Y., Mar 7 2013, In : Nature. 494, 7439, p. 111-115 5 p.

Research output: Contribution to journalArticle

190 Scopus citations

Non-optimal codon usage is a mechanism to achieve circadian clock conditionality

Xu, Y., Ma, P., Shah, P., Rokas, A., Liu, Y. & Johnson, C. H., Mar 2013, In : Nature. 495, 7439, p. 116-120 5 p.

Research output: Contribution to journalArticle

96 Scopus citations

Platelets lacking PIP5KIγ have normal integrin activation but impaired cytoskeletal-membrane integrity and adhesion

Wang, Y., Zhao, L., Suzuki, A., Lian, L., Min, S. H., Wang, Z., Litvinov, R. I., Stalker, T. J., Yago, T., Klopocki, A. G., Schmidtke, D. W., Yin, H., Choi, J. K., McEver, R. P., Weisel, J. W., Hartwig, J. H. & Abrams, C. S., Jan 1 2013, In : Blood. 121, 14, p. 2743-2752 10 p.

Research output: Contribution to journalArticle

12 Scopus citations

Suppression of WC-independent frequency transcription by RCO-1 is essential for Neurospora circadian clock

Zhou, Z., Liu, X., Hu, Q., Zhang, N., Sun, G., Cha, J., Wang, Y., Liu, Y. & He, Q., Dec 10 2013, In : Proceedings of the National Academy of Sciences of the United States of America. 110, 50, p. E4867-E4874

Research output: Contribution to journalArticle

25 Scopus citations

The Ccr4-Not protein complex regulates the phase of the neurospora circadian clock by controlling WHITE COLLAR protein stability and activity

Huang, G., He, Q., Guo, J., Cha, J. & Liu, Y., Oct 25 2013, In : Journal of Biological Chemistry. 288, 43, p. 31002-31009 8 p.

Research output: Contribution to journalArticle

3 Scopus citations

The N-terminal region of the NeurosporaNDR kinase COT1 regulates morphology via its interactions with MOB2A/B

Ziv, C., Feldman, D., Aharoni-Kats, L., Chen, S., Liu, Y. & Yarden, O., Oct 1 2013, In : Molecular Microbiology. 90, 2, p. 383-399 17 p.

Research output: Contribution to journalArticle

12 Scopus citations

Transcription of the Major Neurospora crassa microRNA-Like Small RNAs Relies on RNA Polymerase III

Yang, Q., Li, L., Xue, Z., Ye, Q., Zhang, L., Li, S. & Liu, Y., Jan 1 2013, In : PLoS genetics. 9, 1, e1003227.

Research output: Contribution to journalArticle

16 Scopus citations
2012

Phosphatidylinositol 4, 5 bisphosphate and the actin cytoskeleton

Zhang, L., Mao, Y. S., Janmey, P. A. & Yin, H. L., Jan 1 2012, In : Sub-Cellular Biochemistry. 59, p. 177-215 39 p.

Research output: Contribution to journalArticle

43 Scopus citations

Phosphatidylinositol 4-kinase IIα is palmitoylated by golgi-localized palmitoyltransferases in cholesterol-dependent manner

Lu, D., Sun, H. Q., Wang, H., Barylko, B., Fukata, Y., Fukata, M., Albanesi, J. P. & Yin, H. L., Jun 22 2012, In : Journal of Biological Chemistry. 287, 26, p. 21856-21865 10 p.

Research output: Contribution to journalArticle

50 Scopus citations

Reconstitution of an Argonaute-Dependent Small RNA Biogenesis Pathway Reveals a Handover Mechanism Involving the RNA Exosome and the Exonuclease QIP

Xue, Z., Yuan, H., Guo, J. & Liu, Y., May 11 2012, In : Molecular cell. 46, 3, p. 299-310 12 p.

Research output: Contribution to journalArticle

23 Scopus citations

The translin-TRAX complex (C3PO) is a ribonuclease in tRNA processing

Li, L., Gu, W., Liang, C., Liu, Q., Mello, C. C. & Liu, Y., Aug 1 2012, In : Nature Structural and Molecular Biology. 19, 8, p. 824-830 7 p.

Research output: Contribution to journalArticle

17 Scopus citations
2011

Gelsolin and non-muscle myosin IIA interact to mediate calcium-regulated collagen phagocytosis

Arora, P. D., Wang, Y., Janmey, P. A., Bresnick, A., Yin, H. L. & McCulloch, C. A., Oct 30 2011, In : Journal of Biological Chemistry. 286, 39, p. 34184-34198 15 p.

Research output: Contribution to journalArticle

9 Scopus citations

Phosphatidylinositol (4,5) bisphosphate controls T cell activation by regulating T cell rigidity and organization

Sun, Y., Dandekar, R. D., Mao, Y. S., Yin, H. L. & Wülfing, C., Nov 11 2011, In : PloS one. 6, 11, e27227.

Research output: Contribution to journalArticle

25 Scopus citations

Regulation of the activity and cellular localization of the circadian clock protein FRQ

Cha, J., Yuan, H. & Liu, Y., Apr 1 2011, In : Journal of Biological Chemistry. 286, 13, p. 11469-11478 10 p.

Research output: Contribution to journalArticle

24 Scopus citations

Stabilization of phosphatidylinositol 4-kinase type IIβ by interaction with Hsp90

Jung, G., Barylko, B., Lu, D., Shu, H., Yin, H. & Albanesi, J. P., Apr 8 2011, In : Journal of Biological Chemistry. 286, 14, p. 12775-12784 10 p.

Research output: Contribution to journalArticle

18 Scopus citations
2010

Biochemical methods used to study the gene expression and protein complexes in the filamentous fungus Neurospora crassa.

Guo, J., Huang, G., Cha, J. & Liu, Y., 2010, In : Methods in molecular biology (Clifton, N.J.). 638, p. 189-200 12 p.

Research output: Contribution to journalArticle

4 Scopus citations

Diverse Pathways Generate MicroRNA-like RNAs and Dicer-Independent Small Interfering RNAs in Fungi

Lee, H. C., Li, L., Gu, W., Xue, Z., Crosthwaite, S. K., Pertsemlidis, A., Lewis, Z. A., Freitag, M., Selker, E. U., Mello, C. C. & Liu, Y., Jun 1 2010, In : Molecular cell. 38, 6, p. 803-814 12 p.

Research output: Contribution to journalArticle

199 Scopus citations

Diverse pathways generate microRNA-like RNAs and Dicer-independent small interfering RNAs in fungi.

Lee, H. C., Li, L., Gu, W., Xue, Z., Crosthwaite, S. K., Pertsemlidis, A., Lewis, Z. A., Freitag, M., Selker, E. U., Mello, C. C. & Liu, Y., Jun 25 2010, In : Molecular Cell. 38, 6, p. 803-814 12 p.

Research output: Contribution to journalArticle

Functional significance of FRH in regulating the phosphorylation and stability of Neurospora circadian clock protein FRQ

Guo, J., Cheng, P. & Liu, Y., Apr 9 2010, In : Journal of Biological Chemistry. 285, 15, p. 11508-11515 8 p.

Research output: Contribution to journalArticle

36 Scopus citations

The DNA/RNA-dependent RNA polymerase QDE-1 generates aberrant RNA and dsRNA for RNAi in a process requiring replication protein a and a DNA helicase

Liu, Y., Lee, H. C., Aalto, A. P., Yang, Q., Chang, S. S., Huang, G., Fisher, D., Cha, J., Poranen, M. M. & Bamford, D. H., Oct 1 2010, In : PLoS biology. 8, 10, e1000496.

Research output: Contribution to journalArticle

51 Scopus citations
2009
25 Scopus citations

Essential and unique roles of PIP5K-γ and - α in Fcγ receptor-mediated phagocytosis

Mao, Y. S., Yamaga, M., Zhu, X., Wei, Y., Sun, H. Q., Wang, J., Yun, M., Wang, Y., Di Paolo, G., Bennett, M., Mellman, I., Abrams, C. S., De Camilli, P., Lu, C. Y. & Yin, H. L., Jan 26 2009, In : Journal of Cell Biology. 184, 2, p. 281-296 16 p.

Research output: Contribution to journalArticle

74 Scopus citations

Oxidative stress decreases phosphatidylinositol 4,5-bisphosphate levels by deactivating phosphatidylinositol-4-phosphate 5-kinase β in a Syk-dependent manner

Chen, M. Z., Zhu, X., Sun, H. Q., Mao, Y. S., Wei, Y., Yamamoto, M. & Yin, H. L., Aug 28 2009, In : Journal of Biological Chemistry. 284, 35, p. 23743-23753 11 p.

Research output: Contribution to journalArticle

15 Scopus citations

Palmitoylation controls the catalytic activity and subcellular distribution of phosphatidylinositol 4-kinase IIα

Barylko, B., Mao, Y. S., Wlodarski, P., Jung, G., Binns, D. D., Sun, H. Q., Yin, H. L. & Albanesi, J. P., Apr 10 2009, In : Journal of Biological Chemistry. 284, 15, p. 9994-10003 10 p.

Research output: Contribution to journalArticle

50 Scopus citations