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Seth Frietze et al.
Genome biology, 13(9), R52-R52 (2012-09-07)
The TCF7L2 transcription factor is linked to a variety of human diseases, including type 2 diabetes and cancer. One mechanism by which TCF7L2 could influence expression of genes involved in diverse diseases is by binding to distinct regulatory regions in
Anne Kristin Aksaas et al.
Journal of molecular signaling, 6, 10-10 (2011-09-02)
Post-transcriptional processing of pre-mRNA takes place in several steps and requires involvement of a number of RNA-binding proteins. How pre-mRNA processing is regulated is in large enigmatic. The catalytic (C) subunit of protein kinase A (PKA) is a serine/threonine kinase
Matthew Bratkowski et al.
Cell reports, 32(5), 107999-107999 (2020-08-07)
The NADase SARM1 is a central switch in injury-activated axon degeneration, an early hallmark of many neurological diseases. Here, we present cryo-electron microscopy (cryo-EM) structures of autoinhibited (3.3 Å) and active SARM1 (6.8 Å) and provide mechanistic insight into the tight regulation
Shi-You Jiang et al.
PLoS genetics, 15(7), e1008289-e1008289 (2019-07-20)
Schnyder corneal dystrophy (SCD) is a rare genetic eye disease characterized by corneal opacification resulted from deposition of excess free cholesterol. UbiA prenyltransferase domain-containing protein-1 (UBIAD1) is an enzyme catalyzing biosynthesis of coenzyme Q10 and vitamin K2. More than 20
Sultan Ciftci-Yilmaz et al.
Genetics, 210(1), 203-218 (2018-07-18)
Centromeric localization of the evolutionarily conserved centromere-specific histone H3 variant CENP-A (Cse4 in yeast) is essential for faithful chromosome segregation. Overexpression and mislocalization of CENP-A lead to chromosome segregation defects in yeast, flies, and human cells. Overexpression of CENP-A has
Artyom A Alekseyenko et al.
Genes & development, 27(8), 853-858 (2013-05-01)
Dosage compensation has arisen in response to the evolution of distinct male (XY) and female (XX) karyotypes. In Drosophila melanogaster, the MSL complex increases male X transcription approximately twofold. X-specific targeting is thought to occur through sequence-dependent binding to chromatin
Kresti Pecani et al.
Genetics, 204(4), 1479-1494 (2016-10-30)
B-type cyclins promote mitotic entry and inhibit mitotic exit. In Saccharomyces cerevisiae, four B-type cyclins, Clb1-4, carry out essential mitotic roles, with substantial but incomplete overlap of function among them. Previous work in many organisms has indicated that B-type cyclin-dependent
D Riley et al.
Oncogene, 20(42), 5941-5950 (2001-10-11)
The tyrosine kinase oncoprotein v-Src can overcome the requirements for serum growth factors and anchorage which restrain normal cell growth. Here we investigated the biochemical mechanisms whereby v-Src induces quiescent cells to enter S phase in the absence of serum
Yuying Huang et al.
The Journal of neuroscience : the official journal of the Society for Neuroscience, 42(3), 513-527 (2021-12-10)
Long-term potentiation (LTP) and long-term depression (LTD) in the spinal dorsal horn reflect activity-dependent synaptic plasticity and central sensitization in chronic pain. Tetanic high-frequency stimulation is commonly used to induce LTP in the spinal cord. However, primary afferent nerves often
David Atencio et al.
G3 (Bethesda, Md.), 4(3), 523-537 (2014-01-29)
The Ess1 prolyl isomerase from Saccharomyces cerevisiae and its human ortholog, Pin1, play critical roles in transcription by regulating RNA polymerase II. In human cells, Pin1 also regulates a variety of signaling proteins, and Pin1 misexpression is linked to several
Antibody structure, instability, and formulation
Wang W, et al.
Journal of Pharmaceutical Sciences (2007)
Zhao Shan et al.
The Journal of biological chemistry, 288(49), 35093-35103 (2013-10-17)
Although lysine methylation is classically known to regulate histone function, its role in modulating antiviral restriction factor activity remains uncharacterized. Interferon-induced transmembrane protein 3 (IFITM3) was found monomethylated on its lysine 88 residue (IFITM3-K88me1) to reduce its antiviral activity, mediated
D L Lafontaine et al.
Genes & development, 12(4), 527-537 (1998-03-21)
Many or all of the sites of pseudouridine (Psi) formation in eukaryotic rRNA are selected by site-specific base-pairing with members of the box H + ACA class of small nucleolar RNAs (snoRNAs). Database searches previously identified strong homology between the
Lionel Tafforeau et al.
The EMBO journal, 25(19), 4547-4556 (2006-10-04)
We describe a new member of the F-box family, Pof14, which forms a canonical, F-box dependent SCF (Skp1, Cullin, F-box protein) ubiquitin ligase complex. The Pof14 protein has intrinsic instability that is abolished by inactivation of its Skp1 interaction motif
Guixin Du et al.
PloS one, 8(12), e81583-e81583 (2013-12-21)
Human cytomegalovirus protein IE2-p86 exerts its functions through interaction with other viral and cellular proteins. To further delineate its protein interaction network, we generated a recombinant virus expressing SG-tagged IE2-p86 and used tandem affinity purification coupled with mass spectrometry. A
Yu Li et al.
Methods in molecular biology (Clifton, N.J.), 1077, 81-104 (2013-09-10)
Improved sample preparation techniques and increasingly sensitive mass spectrometry (MS) analysis have revolutionized the study of protein post-translational modifications (PTMs) (Rush et al., Nat Biotechnol 23:94-101, 2005). Here, we describe a general approach for immunopurification and MS-based identification of acetylated
Taras Y Nazarko et al.
The Journal of cell biology, 204(4), 541-557 (2014-02-19)
Autophagy is a membrane trafficking pathway that sequesters proteins and organelles into autophagosomes. The selectivity of this pathway is determined by autophagy receptors, such as the Pichia pastoris autophagy-related protein 30 (Atg30), which controls the selective autophagy of peroxisomes (pexophagy)
Ka-Yiu Edwin Kong et al.
Nucleic acids research, 42(1), 643-660 (2013-10-08)
Most unwanted RNA transcripts in the nucleus of eukaryotic cells, such as splicing-defective pre-mRNAs and spliced-out introns, are rapidly degraded by the nuclear exosome. In budding yeast, a number of these unwanted RNA transcripts, including spliced-out introns, are first recognized
Xiaowen Wang et al.
Nature, 524(7566), 481-484 (2015-07-21)
Mitochondria are multifunctional organelles whose dysfunction leads to neuromuscular degeneration and ageing. The multi-functionality poses a great challenge for understanding the mechanisms by which mitochondrial dysfunction causes specific pathologies. Among the leading mitochondrial mediators of cell death are energy depletion
Soumya Mukherjee et al.
Developmental cell, 49(1), 63-76 (2019-02-26)
During mitosis, motor proteins associate with microtubules to exert pushing forces that establish a mitotic spindle. These pushing forces generate opposing tension in the chromatin that connects oppositely attached sister chromatids, which may then act as a mechanical signal to
Lingjuan Shan et al.
Journal of genetics and genomics = Yi chuan xue bao, 44(2), 95-106 (2017-02-14)
In the sexually reproductive organisms, gametes are produced by meiosis following a limited mitotic amplification. However, the intrinsic program switching cells from mitotic to meiotic cycle is unclear. Alternative polyadenylation (APA) is a highly conserved means of gene regulation and
Claus-Peter Witte et al.
Plant molecular biology, 55(1), 135-147 (2004-12-18)
Beyond the rewards of plant genome analysis and gene identification, characterisation of protein activities, post-translational modifications and protein complex composition remains a challenge for plant biologists. Ideally, methods should allow rapid isolation of proteins from plant material achieving a high
Artyom A Alekseyenko et al.
Current protocols in molecular biology, 109, 21-21 (2015-01-07)
In order to understand how chromatin complexes function in the nucleus, it is important to obtain a comprehensive picture of their protein, DNA, and RNA components, as well as their mutual interactions. This unit presents a chromatin cross-linking approach (BioTAP-XL)
D L Lafontaine et al.
RNA (New York, N.Y.), 5(3), 455-467 (1999-03-27)
Eukaryotic nucleoli contain a large family of box C+D small nucleolar RNA (snoRNA) species, all of which are associated with a common protein Nop1p/fibrillarin. Nop58p was identified in a screen for synthetic lethality with Nop1p and shown to be an
Jing-Jing Zhou et al.
Journal of neurochemistry, 161(1), 40-52 (2022-01-18)
Glutamate AMPA receptors (AMPARs) lacking GluA2 subunit are calcium permeable (CP-AMPARs), which are increased in the hypothalamic paraventricular nucleus (PVN) and maintain sympathetic outflow in hypertension. Here, we determined the role of α2δ-1, an NMDA receptor-interacting protein, in regulating synaptic
Qi Zhou et al.
PLoS genetics, 11(6), e1005331-e1005331 (2015-06-27)
Sex chromosomes evolve distinctive types of chromatin from a pair of ancestral autosomes that are usually euchromatic. In Drosophila, the dosage-compensated X becomes enriched for hyperactive chromatin in males (mediated by H4K16ac), while the Y chromosome acquires silencing heterochromatin (enriched
Artyom A Alekseyenko et al.
Proceedings of the National Academy of Sciences of the United States of America, 111(7), 2488-2493 (2014-02-20)
Understanding the composition of epigenetic regulators remains an important challenge in chromatin biology. Traditional biochemical analysis of chromatin-associated complexes requires their release from DNA under conditions that can also disrupt key interactions. Here we develop a complementary approach (BioTAP-XL), in
Sebastien Leon et al.
Methods in molecular biology (Clifton, N.J.), 389, 219-238 (2007-10-24)
With the approaching completion of the Pichia pastoris genome, a greater emphasis will have to be placed on the proteome and the protein-protein interactions between its constituents. This chapter discusses methods that have been used for the study of such
Shiyu Xu et al.
PLoS genetics, 18(7), e1010302-e1010302 (2022-07-20)
Perturbation of huntingtin (HTT)'s physiological function is one postulated pathogenic factor in Huntington's disease (HD). However, little is known how HTT is regulated in vivo. In a proteomic study, we isolated a novel ~40kDa protein as a strong binding partner
Daniel J Hogan et al.
PLoS biology, 6(10), e255-e255 (2008-10-31)
RNA-binding proteins (RBPs) have roles in the regulation of many post-transcriptional steps in gene expression, but relatively few RBPs have been systematically studied. We searched for the RNA targets of 40 proteins in the yeast Saccharomyces cerevisiae: a selective sample
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