Research Output 1971 2019

2019

Biochemical and Next Generation Sequencing Approaches to Study RNA Regulation

Wagner, E. J. & Goldstrohm, A., Feb 15 2019, In : Methods. 155, p. 1-2 2 p.

Research output: Contribution to journalEditorial

RNA

Both the classical and alternative non-homologous end joining pathways contribute to the fusion of drastically shortened telomeres induced by TRF2 overexpression

Nera, B., Huang, H. S., Hendrickson, E. A. & Xu, L., Apr 18 2019, In : Cell Cycle. 18, 8, p. 880-888 9 p.

Research output: Contribution to journalArticle

Telomere Shortening
Ligases
DNA Ligases
Telomere-Binding Proteins
Chromosomes
3 Citations (Scopus)

Chromothripsis during telomere crisis is independent of NHEJ, and consistent with a replicative origin

Cleal, K., Jones, R. E., Grimstead, J. W., Hendrickson, E. A. & Baird, D. M., May 1 2019, In : Genome research. 29, 5, p. 737-749 13 p.

Research output: Contribution to journalArticle

Open Access
Telomere
Genome
Genomic Instability
Sequence Analysis
Chromothripsis

Conversion tract analysis of homology-directed genome editing using oligonucleotide donors

Kan, Y. & Hendrickson, E. A., Jan 1 2019, Methods in Molecular Biology. Humana Press Inc., p. 131-144 14 p. (Methods in Molecular Biology; vol. 1999).

Research output: Chapter in Book/Report/Conference proceedingChapter

Oligonucleotides
Genetic Loci
Green Fluorescent Proteins
Nucleotides
Gene Editing
1 Citation (Scopus)

CtIP is essential for telomere replication

Stroik, S., Kurtz, K. & Hendrickson, E. A., Sep 26 2019, In : Nucleic acids research. 47, 17, p. 8927-8940 14 p.

Research output: Contribution to journalArticle

Open Access
Telomere
Telomere Shortening
Genomic Instability
Telomere Homeostasis
Double-Stranded DNA Breaks
2 Citations (Scopus)

DNA Ligase 1 is an essential mediator of sister chromatid telomere fusions in G2 cell cycle phase

Liddiard, K., Ruis, B. L., Kan, Y., Cleal, K., Ashelford, K. E., Hendrickson, E. A. & Baird, D. M., Jan 1 2019, In : Nucleic acids research. 47, 5, p. 2402-2424 23 p.

Research output: Contribution to journalArticle

Open Access
DNA Ligases
Chromatids
Telomere
Cell Cycle
Ligases

DNA-PKcs promotes chromatin decondensation to facilitate initiation of the DNA damage response

Lu, H., Saha, J., Beckmann, P. J., Hendrickson, E. A. & Davis, A. J., Oct 10 2019, In : Nucleic acids research. 47, 18, p. 9467-9479 13 p.

Research output: Contribution to journalArticle

Open Access
DNA-Activated Protein Kinase
DNA Damage
Chromatin
Catalytic Domain
Ataxia Telangiectasia

Erratum: Correction: Rapid DNA replication origin licensing protects stem cell pluripotency (eLife (2017) 6 PII: e49040)

Matson, J. P., Dumitru, R., Coryell, P., Baxley, R. M., Chen, W., Twaroski, K., Webber, B. R., Tolar, J., Bielinsky, A. K., Purvis, J. E. & Cook, J. G., Jun 5 2019, In : eLife. 8

Research output: Contribution to journalComment/debate

Open Access
Replication Origin
Licensure
Chromosomes
Stem cells
DNA Replication

Global analysis of RNA metabolism using bio-orthogonal labeling coupled with next-generation RNA sequencing

Wolfe, M. B., Goldstrohm, A. & Freddolino, P. L., Feb 15 2019, In : Methods. 155, p. 88-103 16 p.

Research output: Contribution to journalReview article

Open Access
RNA Sequence Analysis
Metabolism
Labeling
RNA
RNA Stability
1 Citation (Scopus)

Inhibiting transcription in cultured metazoan cells with actinomycin D to monitor mRNA turnover

Lai, W. S., Arvola, R. M., Goldstrohm, A. & Blackshear, P. J., Feb 15 2019, In : Methods. 155, p. 77-87 11 p.

Research output: Contribution to journalReview article

Open Access
RNA Stability
Dactinomycin
Transcription
Cultured Cells
Messenger RNA
7 Citations (Scopus)

Mechanisms of DNA damage tolerance: post-translational regulation of PCNA

Leung, W., Baxley, R. M., Moldovan, G. L. & Bielinsky, A. K., Jan 1 2019, In : Genes. 10, 1, 10.

Research output: Contribution to journalReview article

Proliferating Cell Nuclear Antigen
DNA Damage
Post Translational Protein Processing
Ubiquitin
Genetic Recombination

Preparation of cooperative RNA recognition complexes for crystallographic structural studies

Qiu, C., Goldstrohm, A. & Tanaka Hall, T. M., Jan 1 2019, Methods in Enzymology. Hargrove, A. E. (ed.). Academic Press Inc., p. 1-22 22 p. (Methods in Enzymology; vol. 623).

Research output: Chapter in Book/Report/Conference proceedingChapter

RNA
Messenger RNA
RNA-Binding Proteins
Crystal structure
Crystallization
2 Citations (Scopus)

Ribosome queuing enables non-AUG translation to be resistant to multiple protein synthesis inhibitors

Kearse, M. G., Goldman, D. H., Choi, J., Nwaezeapu, C., Liang, D., Green, K. M., Goldstrohm, A. C., Todd, P. K., Green, R. & Wilusz, J. E., Jul 2019, In : Genes and Development. 33, 13-14, p. 871-885 15 p.

Research output: Contribution to journalArticle

Open Access
Protein Synthesis Inhibitors
Initiator Codon
Ribosomes
Cycloheximide
Messenger RNA

The anti-parasitic agent suramin and several of its analogues are inhibitors of the DNA binding protein Mcm10

Paulson, C. N., John, K., Baxley, R. M., Kurniawan, F., Orellana, K., Francis, R., Sobeck, A., Eichman, B. F., Chazin, W. J., Aihara, H., Georg, G. I., Hawkinson, J. E. & Bielinsky, A. K., Aug 1 2019, In : Open biology. 9, 8, 190117.

Research output: Contribution to journalArticle

Open Access
Minichromosome Maintenance Proteins
Suramin
DNA-Binding Proteins
Fluorescence Polarization
Surface Plasmon Resonance
2018
1 Citation (Scopus)

A role for monomethylation of histone H3-K27 in gene activity in Drosophila

Wang, L., Joshi, P., Miller, E. L., Higgins, L., Slattery, M. G. & Simon, J. A., Mar 1 2018, In : Genetics. 208, 3, p. 1023-1036 14 p.

Research output: Contribution to journalArticle

Open Access
Polycomb Repressive Complex 2
Histones
Drosophila
Genes
Diptera
2 Citations (Scopus)

CTC1-STN1 coordinates G- and C-strand synthesis to regulate telomere length

Gu, P., Jia, S., Takasugi, T., Smith, E., Nandakumar, J., Hendrickson, E. A. & Chang, S., Aug 1 2018, In : Aging cell. 17, 4, e12783.

Research output: Contribution to journalArticle

Telomerase
Telomere
Mutation
DNA
Clustered Regularly Interspaced Short Palindromic Repeats
5 Citations (Scopus)

Flap endonuclease overexpression drives genome instability and DNA damage hypersensitivity in a PCNA-dependent manner

Becker, J. R., Gallo, D., Leung, W., Croissant, T., Thu, Y. M., Nguyen, H. D., Starr, T. K., Brown, G. W. & Bielinsky, A. K., Jan 1 2018, In : Nucleic acids research. 46, 11, p. 5634-5650 17 p.

Research output: Contribution to journalArticle

Open Access
Flap Endonucleases
Genomic Instability
Proliferating Cell Nuclear Antigen
DNA Damage
Hypersensitivity
1 Citation (Scopus)

High-throughput identification of noncoding functional SNPs via type IIS enzyme restriction

Li, G., Martínez-Bonet, M., Wu, D., Yang, Y., Cui, J., Nguyen, H. N., Cunin, P., Levescot, A., Bai, M., Westra, H. J., Okada, Y., Brenner, M. B., Raychaudhuri, S., Hendrickson, E. A., Maas, R. L. & Nigrovic, P. A., Aug 1 2018, In : Nature Genetics. 50, 8, p. 1180-1188 9 p.

Research output: Contribution to journalArticle

Open Access
Single Nucleotide Polymorphism
Enzymes
Genome-Wide Association Study
Juvenile Arthritis
Carrier Proteins
11 Citations (Scopus)

Identification of diverse target RNAs that are functionally regulated by human pumilio proteins

Bohn, J. A., Van Etten, J. L., Schagat, T. L., Bowman, B. M., McEachin, R. C., Freddolino, P. L. & Goldstrohm, A., Jan 1 2018, In : Nucleic acids research. 46, 1, p. 362-386 25 p.

Research output: Contribution to journalArticle

Open Access
RNA
Response Elements
Untranslated RNA
Messenger RNA
RNA-Binding Proteins
2 Citations (Scopus)

PARP1 is required for preserving telomeric integrity but is dispensable for A-NHEJ

Harvey, A., Mielke, N., Grimstead, J. W., Jones, R. E., Nguyen, T., Mueller, M., Baird, D. M. & Hendrickson, E. A., Oct 1 2018, In : Oncotarget. 9, 78, p. 34821-34837 17 p.

Research output: Contribution to journalArticle

Telomere
Breast Neoplasms
Genetic Markers
Ovarian Neoplasms
DNA Damage

PARP inhibition prevents escape from a telomere-driven crisis and inhibits cell immortalisation

Ngo, G., Hyatt, S., Grimstead, J., Jones, R., Hendrickson, E. A., Pepper, C. & Baird, D., Dec 1 2018, In : Oncotarget. 9, 101, p. 37549-37563 15 p.

Research output: Contribution to journalArticle

Telomere
Plasma Cell Leukemia
Cell Line
Genomic Instability
Telomerase
1 Citation (Scopus)

Regulatory roles of vertebrate Nocturnin: insights and remaining mysteries

Hughes, K. L., Abshire, E. T. & Goldstrohm, A. C., Oct 3 2018, In : RNA Biology. 15, 10, p. 1255-1267 13 p.

Research output: Contribution to journalReview article

Open Access
Vertebrates
Messenger RNA
RNA Stability
Adipogenesis
Osteogenesis
1 Citation (Scopus)

Telomeres and chromosomal translocations: There’s a ligase at the end of the translocation

Baird, D. M. & Hendrickson, E. A., Jan 1 2018, Advances in Experimental Medicine and Biology. Springer New York LLC, p. 89-112 24 p. (Advances in Experimental Medicine and Biology; vol. 1044).

Research output: Chapter in Book/Report/Conference proceedingChapter

Genetic Translocation
Telomere
Ligases
DNA Repair
Repair
5 Citations (Scopus)

The structure of human Nocturnin reveals a conserved ribonuclease domain that represses target transcript translation and abundance in cells

Abshire, E. T., Chasseur, J., Bohn, J. A., Del Rizzo, P. A., Freddolino, P. L., Goldstrohm, A. C. & Trievel, R. C., Jul 6 2018, In : Nucleic acids research. 46, 12, p. 6257-6270 14 p.

Research output: Contribution to journalArticle

Open Access
Ribonucleases
Exoribonucleases
Catalytic Domain
Messenger RNA
nocturnin
2017
18 Citations (Scopus)

Combinatorial control of messenger RNAs by Pumilio, Nanos and Brain Tumor Proteins

Arvola, R. M., Weidmann, C. A., Tanaka Hall, T. M. & Goldstrohm, A., Nov 2 2017, In : RNA Biology. 14, 11, p. 1445-1456 12 p.

Research output: Contribution to journalReview article

Open Access
RNA-Binding Proteins
Brain Neoplasms
Messenger RNA
Proteins
RNA
Open Access
Sex Chromatin
Comb and Wattles
Homeobox Genes
Drosophila
Cell Biology
2 Citations (Scopus)

Degradation of Mrc1 promotes recombination-mediated restart of stalled replication forks

Chaudhury, I. & Koepp, D., Mar 17 2017, In : Nucleic acids research. 45, 5, p. 2558-2570 13 p.

Research output: Contribution to journalArticle

Open Access
S Phase Cell Cycle Checkpoints
Genetic Recombination
DNA Damage
DNA
Ligases
7 Citations (Scopus)

FANCI and FANCD2 have common as well as independent functions during the cellular replication stress response

Thompson, E. L., Yeo, J. E., Lee, E. A., Kan, Y., Raghunandan, M., Wiek, C., Hanenberg, H., Schärer, O. D., Hendrickson, E. A. & Sobeck, A., Jan 1 2017, In : Nucleic acids research. 45, 20, p. 11837-11857 21 p.

Research output: Contribution to journalArticle

Open Access
Fanconi Anemia
Fanconi Anemia Complementation Group D2 Protein
Chromatin
Fanconi Anemia Complementation Group Proteins
Null Lymphocytes
4 Citations (Scopus)

Human somatic cells deficient for RAD52 are impaired for viral integration and compromised for most aspects of homology-directed repair

Kan, Y., Batada, N. N. & Hendrickson, E. A., Jul 1 2017, In : DNA Repair. 55, p. 64-75 12 p.

Research output: Contribution to journalArticle

Open Access
Virus Integration
Repair
Radiation
Genes
Annealing
12 Citations (Scopus)

Mcm10: A dynamic scaffold at eukaryotic replication forks

Baxley, R. M. & Bielinsky, A. K., Feb 17 2017, In : Genes. 8, 2, 73.

Research output: Contribution to journalReview article

Open Access
Minichromosome Maintenance Proteins
DNA Replication
DNA
Single-Stranded DNA
Proliferating Cell Nuclear Antigen
20 Citations (Scopus)

Mechanisms of precise genome editing using oligonucleotide donors

Kan, Y., Ruis, B. L., Takasugi, T. & Hendrickson, E. A., Jul 1 2017, In : Genome research. 27, 7, p. 1099-1111 13 p.

Research output: Contribution to journalArticle

Open Access
Oligonucleotides
Oligodeoxyribonucleotides
Clustered Regularly Interspaced Short Palindromic Repeats
Gene Conversion
Deoxyribonuclease I
15 Citations (Scopus)

Rapid DNA replication origin licensing protects stem cell pluripotency

Matson, J. P., Dumitru, R., Coryell, P., Baxley, R. M., Chen, W., Twaroski, K., Webber, B. R., Tolar, J., Bielinsky, A. K., Purvis, J. E. & Cook, J. G., Nov 17 2017, In : eLife. 6, e30473.

Research output: Contribution to journalArticle

Open Access
Replication Origin
Licensure
Stem cells
DNA Replication
Stem Cells
2016
52 Citations (Scopus)

CGG Repeat-Associated Non-AUG Translation Utilizes a Cap-Dependent Scanning Mechanism of Initiation to Produce Toxic Proteins

Kearse, M. G., Green, K. M., Krans, A., Rodriguez, C. M., Linsalata, A. E., Goldstrohm, A. & Todd, P. K., Apr 21 2016, In : Molecular Cell. 62, 2, p. 314-322 9 p.

Research output: Contribution to journalArticle

Initiator Codon
Poisons
Reading Frames
Proteins
Nucleotides
1 Citation (Scopus)

Mapping ubiquitination sites of S. cerevisiae Mcm10

Zhang, T., Fultz, B. L., Das-Bradoo, S. & Bielinsky, A. K., Dec 1 2016, In : Biochemistry and Biophysics Reports. 8, p. 212-218 7 p.

Research output: Contribution to journalArticle

Ubiquitination
Lysine
Saccharomyces cerevisiae
Proliferating Cell Nuclear Antigen
Machinery
8 Citations (Scopus)

Mcm10: The glue at replication forks

Bielinsky, A. K., Nov 16 2016, In : Cell Cycle. 15, 22, p. 3024-3025 2 p.

Research output: Contribution to journalComment/debate

DNA Replication
Adhesives
Phosphorylation

Not just for coding: a new role for histone tails in replication enzyme activation

Bielinsky, A. K. & Leung, W., Dec 1 2016, In : FEBS Journal. 283, 23, p. 4244-4246 3 p.

Research output: Contribution to journalComment/debate

Flap Endonucleases
Saccharomyces cerevisiae Proteins
Enzyme Activation
Nucleosomes
DNA Replication
21 Citations (Scopus)

Radiosensitization by PARP Inhibition in DNA Repair Proficient and Deficient Tumor Cells: Proliferative Recovery in Senescent Cells

Alotaibi, M., Sharma, K., Saleh, T., Povirk, L. F., Hendrickson, E. A. & Gewirtz, D. A., Mar 1 2016, In : Radiation research. 185, 3, p. 229-245 17 p.

Research output: Contribution to journalArticle

DNA Repair-Deficiency Disorders
Autophagy
tumors
deoxyribonucleic acid
recovery
5 Citations (Scopus)

Recovery from the DNA replication checkpoint

Chaudhury, I. & Koepp, D., Nov 1 2016, In : Genes. 7, 11, 94.

Research output: Contribution to journalReview article

S Phase Cell Cycle Checkpoints
DNA Replication
Cell Cycle
Genomic Instability
DNA
7 Citations (Scopus)

Restoration of ATM expression in DNA-PKcs-deficient cells inhibits signal end joining

Neal, J. A., Xu, Y., Abe, M., Hendrickson, E. A. & Meek, K., Apr 1 2016, In : Journal of Immunology. 196, 7, p. 3032-3042 11 p.

Research output: Contribution to journalArticle

DNA-Activated Protein Kinase
Catalytic Domain
V(D)J Recombination
Cell Line
Cultured Cells
9 Citations (Scopus)

Slx5/Slx8 Promotes Replication Stress Tolerance by Facilitating Mitotic Progression

Thu, Y. M., Van Riper, S. K., Higgins, L. A., Zhang, T., Becker, J. R., Markowski, T. W., Nguyen, H. D., Griffin, T. J. & Bielinsky, A. K., May 10 2016, In : Cell reports. 15, 6, p. 1254-1265 12 p.

Research output: Contribution to journalArticle

Minichromosome Maintenance Proteins
M Phase Cell Cycle Checkpoints
Ligases
Methyl Methanesulfonate
Protein Deficiency
1 Citation (Scopus)

The role of Mcm10 in replication initiation

Baxley, R. M., Thu, Y-M. & Bielinsky, A. K., Jan 1 2016, The Initiation of DNA Replication in Eukaryotes. Springer International Publishing, p. 319-341 23 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Minichromosome Maintenance Proteins
proteins
DNA
DNA-Directed DNA Polymerase
DNA-directed DNA polymerase
2015
1 Citation (Scopus)

Alternative end joining, clonal evolution, and escape from a telomere-driven crisis

Hendrickson, E. A. & Baird, D. M., Jan 2 2015, In : Molecular and Cellular Oncology. 2, 1, e975623.

Research output: Contribution to journalArticle

Clonal Evolution
Telomere
Genomic Instability
Neoplasms
54 Citations (Scopus)

ATRX represses alternative lengthening of telomeres

Napier, C. E., Huschtscha, L. I., Harvey, A., Bower, K., Noble, J. R., Hendrickson, E. A. & Reddel, R. R., Jan 1 2015, In : Oncotarget. 6, 18, p. 16543-16558 16 p.

Research output: Contribution to journalArticle

Telomere Homeostasis
Telomerase
Telomere Shortening
Chromatin Assembly and Disassembly
Homologous Recombination
27 Citations (Scopus)

A versatile reporter system for CRISPR-mediated chromosomal rearrangements

Li, Y., Park, A. I., Mou, H., Colpan, C., Bizhanova, A., Akama-Garren, E., Joshi, N., Hendrickson, E. A., Feldser, D., Yin, H., Anderson, D. G., Jacks, T., Weng, Z. & Xue, W., May 28 2015, In : Genome biology. 16, 1, 111.

Research output: Contribution to journalArticle

Clustered Regularly Interspaced Short Palindromic Repeats
DNA Breaks
Gene Rearrangement
Nucleotides
Liver
22 Citations (Scopus)

Cockayne syndrome group B protein regulates DNA double-strand break repair and checkpoint activation

Batenburg, N. L., Thompson, E. L., Hendrickson, E. A. & Zhu, X. D., May 12 2015, In : EMBO Journal. 34, 10, p. 1399-1416 18 p.

Research output: Contribution to journalArticle

Cockayne Syndrome
Double-Stranded DNA Breaks
Chromatin
Repair
Chemical activation
125 Citations (Scopus)

DNA2 drives processing and restart of reversed replication forks in human cells

Thangavel, S., Berti, M., Levikova, M., Pinto, C., Gomathinayagam, S., Vujanovic, M., Zellweger, R., Moore, H., Lee, E. H., Hendrickson, E. A., Cejka, P., Stewart, S., Lopes, M. & Vindigni, A., Jan 1 2015, In : Journal of Cell Biology. 208, 5, p. 545-562 18 p.

Research output: Contribution to journalArticle

DNA Replication
Homologous Recombination
DNA Damage
Adenosine Triphosphatases
Genome
9 Citations (Scopus)

EIF4E threshold levels differ in governing normal and neoplastic expansion of mammary stem and luminal progenitor cells

Avdulov, S. V., Herrera, J., Smith, K., Peterson, M., Gomez-Garcia, J., Beadnell, T. C., Schwertfeger, K., Benyumov, A., Manivel, J. C., Li, S., Bielinsky, A. K., Yee, D., Bitterman, P. B. & Polunovsky, V. A., Feb 15 2015, In : Cancer Research. 75, 4, p. 687-697 11 p.

Research output: Contribution to journalArticle

Eukaryotic Initiation Factor-4E
Breast
Stem Cells
DNA Replication
Lactation
34 Citations (Scopus)

FANCI Regulates Recruitment of the FA Core Complex at Sites of DNA Damage Independently of FANCD2

Castella, M., Jacquemont, C., Thompson, E. L., Yeo, J. E., Cheung, R. S., Huang, J. W., Sobeck, A., Hendrickson, E. A. & Taniguchi, T., Jan 1 2015, In : PLoS Genetics. 11, 10, e1005563.

Research output: Contribution to journalArticle

Fanconi Anemia
anemia
DNA damage
DNA Damage
DNA

Penetrating enemy territory: Soluble PCNA-peptides stress out MYCN-overexpressing neuroblastomas

Bielinsky, A. K., Dec 1 2015, In : EBioMedicine. 2, 12, p. 1844-1845 2 p.

Research output: Contribution to journalComment/debate

Oncogene Proteins
Proliferating Cell Nuclear Antigen
Peptides
27 Citations (Scopus)

XRCC4/XLF Interaction is variably required for DNA repair and is not required for ligase IV stimulation

Roy, S., de Melo, A. J., Xu, Y., Tadi, S. K., Négrel, A., Hendrickson, E., Modesti, M. & Meek, K., Jan 1 2015, In : Molecular and cellular biology. 35, 17, p. 3017-3028 12 p.

Research output: Contribution to journalArticle

Ligases
DNA Repair
Ligation
DNA
In Vitro Techniques