Histone proteoform analysis reveals epigenetic changes in adult mouse brown adipose tissue in response to cold stress.

Autor: Taylor BC; Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX, USA., Steinthal LH; USDA/ARS Children's Nutrition Research Center, Department of Pediatrics, Division of Nutrition, Baylor College of Medicine, Houston, TX, USA., Dias M; Department of Pediatrics, Division of Neurology, Baylor College of Medicine, Houston, TX, USA., Yalamanchili HK; USDA/ARS Children's Nutrition Research Center, Department of Pediatrics, Division of Nutrition, Baylor College of Medicine, Houston, TX, USA.; Department of Pediatrics, Division of Neurology, Baylor College of Medicine, Houston, TX, USA.; Jan and Dan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA., Ochsner SA; Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA., Zapata GE; USDA/ARS Children's Nutrition Research Center, Department of Pediatrics, Division of Nutrition, Baylor College of Medicine, Houston, TX, USA., Mehta NR; USDA/ARS Children's Nutrition Research Center, Department of Pediatrics, Division of Nutrition, Baylor College of Medicine, Houston, TX, USA., McKenna NJ; Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA., Young NL; Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX, USA. nicolas.young@bcm.edu.; Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA. nicolas.young@bcm.edu.; Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX, USA. nicolas.young@bcm.edu., Nuotio-Antar AM; USDA/ARS Children's Nutrition Research Center, Department of Pediatrics, Division of Nutrition, Baylor College of Medicine, Houston, TX, USA. antar@bcm.edu.

Publikováno v: Epigenetics & chromatin [Epigenetics Chromatin] 2024 Apr 27; Vol. 17 (1), pp. 12. Date of Electronic Publication: 2024 Apr 27.

PolyAMiner-Bulk is a deep learning-based algorithm that decodes alternative polyadenylation dynamics from bulk RNA-seq data.

Autor: Jonnakuti VS; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA; Program in Quantitative and Computational Biology, Baylor College of Medicine, Houston, TX 77030, USA; Medical Scientist Training Program, Baylor College of Medicine, Houston, TX 77030, USA., Wagner EJ; Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA., Maletić-Savatić M; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA., Liu Z; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA; Program in Quantitative and Computational Biology, Baylor College of Medicine, Houston, TX 77030, USA., Yalamanchili HK; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA; USDA/ARS Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA. Electronic address: hari.yalamanchili@bcm.edu.

Publikováno v: Cell reports methods [Cell Rep Methods] 2024 Feb 26; Vol. 4 (2), pp. 100707. Date of Electronic Publication: 2024 Feb 06.

MATR3 pathogenic variants differentially impair its cryptic splicing repression function.

Autor: Khan M; Department of Molecular Genetics, University of Toronto, Canada.; Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, Canada., Chen XXL; Department of Molecular Genetics, University of Toronto, Canada.; Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, Canada., Dias M; Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA.; Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX, USA., Santos JR; Department of Molecular Genetics, University of Toronto, Canada.; Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, Canada., Kour S; Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA, USA., You J; Department of Molecular Genetics, University of Toronto, Canada.; Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, Canada., van Bruggen R; Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, Canada., Youssef MMM; Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, Canada., Wan YW; Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX, USA.; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA., Liu Z; Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA.; Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX, USA., Rosenfeld JA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.; Baylor Genetics Laboratories, Houston, TX, USA., Tan Q; Department of Cell Biology, University of Alberta, Edmonton, Canada., Pandey UB; Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, PA, USA.; Department of Human Genetics, University of Pittsburgh, School of Public Health, Pittsburgh, PA, USA., Yalamanchili HK; Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA.; Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX, USA.; USDA/ARS Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA., Park J; Department of Molecular Genetics, University of Toronto, Canada.; Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, Canada.

Publikováno v: FEBS letters [FEBS Lett] 2024 Feb; Vol. 598 (4), pp. 415-436. Date of Electronic Publication: 2024 Feb 06.

NUDT21 alters glioma migration through differential alternative polyadenylation of LAMC1.

Autor: Jonnakuti VS; Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA.; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, 77030, USA.; Program in Quantitative and Computational Biology, Baylor College of Medicine, Houston, TX, 77030, USA.; Medical Scientist Training Program, Baylor College of Medicine, Houston, TX, 77030, USA., Ji P; Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, 77555, USA., Gao Y; Program in Quantitative and Computational Biology, Baylor College of Medicine, Houston, TX, 77030, USA., Lin A; Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, 77555, USA., Chu Y; Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, 77555, USA., Elrod N; Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, 77555, USA., Huang KL; Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, NY, 14642, USA., Li W; Department of Biological Chemistry, University of California, Irvine, CA, 92697, USA., Yalamanchili HK; Department of Pediatrics, Baylor College of Medicine, Houston, TX, 77030, USA. Hari.Yalamanchili@bcm.edu.; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, 77030, USA. Hari.Yalamanchili@bcm.edu., Wagner EJ; Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, NY, 14642, USA. Eric_Wagner@urmc.rochester.edu.

Publikováno v: Journal of neuro-oncology [J Neurooncol] 2023 Jul; Vol. 163 (3), pp. 623-634. Date of Electronic Publication: 2023 Jun 30.

Alternative polyadenylation alters protein dosage by switching between intronic and 3'UTR sites.

Autor: de Prisco N; Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, USA.; Columbia Stem Cell Initiative, Columbia University Irving Medical Center, New York, NY, USA., Ford C; Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, USA.; Department of Pediatrics, College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA., Elrod ND; Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, Galveston, TX, USA., Lee W; Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, USA.; Department Ophthalmology, Columbia University Irving Medical Center, New York, NY, USA., Tang LC; Department of Biological Sciences, Columbia University, New York, NY, USA., Huang KL; Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, Galveston, TX, USA.; Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA., Lin A; Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, WC67+HC Dongcheng, Beijing, China., Ji P; Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, Galveston, TX, USA., Jonnakuti VS; Department of Pediatrics, Baylor College of Medicine and Texas Children's Hospital, Houston, TX, USA.; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA.; Program in Quantitative and Computational Biology, Baylor College of Medicine, Houston, TX, USA.; Medical Scientist Training Program, Baylor College of Medicine, Houston, TX, USA., Boyle L; Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, USA.; Department of Pediatrics, College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA., Cabaj M; Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, USA., Botta S; Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, USA.; Department of Translational Medical Science, University of Campania Luigi Vanvitelli, Caserta, Italy., Õunap K; Department of Clinical Genetics, Genetics and Personalized Medicine Clinic, Tartu University Hospital, Tartu, Estonia.; Institute of Clinical Medicine, University of Tartu, Tartu, Estonia., Reinson K; Department of Clinical Genetics, Genetics and Personalized Medicine Clinic, Tartu University Hospital, Tartu, Estonia.; Institute of Clinical Medicine, University of Tartu, Tartu, Estonia., Wojcik MH; Broad Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA., Rosenfeld JA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.; Baylor Genetics Laboratories, Houston, TX, USA., Bi W; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.; Baylor Genetics Laboratories, Houston, TX, USA., Tveten K; Department of Medical Genetics, Telemark Hospital Trust, 3710 Skien, Norway., Prescott T; Department of Medical Genetics, Telemark Hospital Trust, 3710 Skien, Norway., Gerstner T; Department of Child Neurology and Rehabilitation and Department of Pediatrics, Hospital of Southern Norway, Arendal, Norway., Schroeder A; Division of Medical Genetics, University of Rochester Medical Center, Rochester, NY, USA., Fong CT; Department of Pediatrics and of Medicine, University of Rochester Medical Center, Rochester, NY, USA., George-Abraham JK; Dell Children's Medical Group, Austin, TX, USA.; Department of Pediatrics, The University of Texas at Austin Dell Medical School, Austin, TX, USA., Buchanan CA; Dell Children's Medical Group, Austin, TX, USA., Hanson-Khan A; Department of Pediatrics, Division of Medical Genetics, Stanford School of Medicine, Palo Alto, CA, USA.; Department of Genetics, Stanford School of Medicine, Palo Alto, CA, USA., Bernstein JA; Department of Pediatrics, Division of Medical Genetics, Stanford School of Medicine, Palo Alto, CA, USA., Nella AA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA., Chung WK; Department of Pediatrics, College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA.; Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA., Brandt V; Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, USA., Jovanovic M; Department of Biological Sciences, Columbia University, New York, NY, USA., Targoff KL; Columbia Stem Cell Initiative, Columbia University Irving Medical Center, New York, NY, USA.; Department of Pediatrics, College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA., Yalamanchili HK; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA.; USDA/ARS Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA., Wagner EJ; Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, Galveston, TX, USA.; Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA., Gennarino VA; Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, USA.; Columbia Stem Cell Initiative, Columbia University Irving Medical Center, New York, NY, USA.; Department of Pediatrics, College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA.; Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA.; Initiative for Columbia Ataxia and Tremor, Columbia University Irving Medical Center, New York, NY, USA.

Publikováno v: Science advances [Sci Adv] 2023 Feb 17; Vol. 9 (7), pp. eade4814. Date of Electronic Publication: 2023 Feb 17.