Search Results - "Ling, Jonathan P."

TDP-43 repression of nonconserved cryptic exons is compromised in ALS-FTD by Ling, Jonathan P., Pletnikova, Olga, Troncoso, Juan C., Wong, Philip C.

“…Cytoplasmic aggregation of TDP-43, accompanied by its nuclear clearance, is a key common pathological hallmark of amyotrophic lateral sclerosis and…”
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recount3: summaries and queries for large-scale RNA-seq expression and splicing by Wilks, Christopher, Zheng, Shijie C, Chen, Feng Yong, Charles, Rone, Solomon, Brad, Ling, Jonathan P, Imada, Eddie Luidy, Zhang, David, Joseph, Lance, Leek, Jeffrey T, Jaffe, Andrew E, Nellore, Abhinav, Collado-Torres, Leonardo, Hansen, Kasper D, Langmead, Ben

“…We present recount3, a resource consisting of over 750,000 publicly available human and mouse RNA sequencing (RNA-seq) samples uniformly processed by our new…”
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Splicing repression is a major function of TDP-43 in motor neurons by Donde, Aneesh, Sun, Mingkuan, Ling, Jonathan P., Braunstein, Kerstin E., Pang, Bo, Wen, Xinrui, Cheng, Xueying, Chen, Liam, Wong, Philip C.

“…Nuclear depletion of TDP-43, an essential RNA binding protein, may underlie neurodegeneration in amyotrophic lateral sclerosis (ALS). As several functions have…”
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HnRNP L represses cryptic exons by McClory, Sean P, Lynch, Kristen W, Ling, Jonathan P

“…The fidelity of RNA splicing is regulated by a network of splicing enhancers and repressors, although the rules that govern this process are not yet fully…”
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ASCOT identifies key regulators of neuronal subtype-specific splicing by Ling, Jonathan P., Wilks, Christopher, Charles, Rone, Leavey, Patrick J., Ghosh, Devlina, Jiang, Lizhi, Santiago, Clayton P., Pang, Bo, Venkataraman, Anand, Clark, Brian S., Nellore, Abhinav, Langmead, Ben, Blackshaw, Seth

“…Public archives of next-generation sequencing data are growing exponentially, but the difficulty of marshaling this data has led to its underutilization by…”
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Amyloid-beta and tau pathologies act synergistically to induce novel disease stage-specific microglia subtypes by Kim, Dong Won, Tu, Kevin J, Wei, Alice, Lau, Ashley J, Gonzalez-Gil, Anabel, Cao, Tianyu, Braunstein, Kerstin, Ling, Jonathan P, Troncoso, Juan C, Wong, Philip C, Blackshaw, Seth, Schnaar, Ronald L, Li, Tong

“…Amongst risk alleles associated with late-onset Alzheimer's disease (AD), those that converged on the regulation of microglia activity have emerged as central…”
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PTBP1 and PTBP2 Repress Nonconserved Cryptic Exons by Ling, Jonathan P., Chhabra, Resham, Merran, Jonathan D., Schaughency, Paul M., Wheelan, Sarah J., Corden, Jeffry L., Wong, Philip C.

“…The fidelity of RNA splicing is maintained by a network of factors, but the molecular mechanisms that govern this process have yet to be fully elucidated. We…”
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Stage-specific control of oligodendrocyte survival and morphogenesis by TDP-43 by Heo, Dongeun, Ling, Jonathan P, Molina-Castro, Gian C, Langseth, Abraham J, Waisman, Ari, Nave, Klaus-Armin, Möbius, Wiebke, Wong, Phil C, Bergles, Dwight E

“…Generation of oligodendrocytes in the adult brain enables both adaptive changes in neural circuits and regeneration of myelin sheaths destroyed by injury,…”
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Elevated nuclear TDP-43 induces constitutive exon skipping by Carmen-Orozco, Rogger P, Tsao, William, Ye, Yingzhi, Sinha, Irika R, Chang, Koping, Trinh, Vickie T, Chung, William, Bowden, Kyra, Troncoso, Juan C, Blackshaw, Seth, Hayes, Lindsey R, Sun, Shuying, Wong, Philip C, Ling, Jonathan P

“…Cytoplasmic inclusions and loss of nuclear TDP-43 are key pathological features found in several neurodegenerative disorders, suggesting both gain- and…”
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Multivalent GU-rich oligonucleotides sequester TDP-43 in the nucleus by inducing high molecular weight RNP complexes by Zhang, Xi, Das, Tanuza, Chao, Tiffany F., Trinh, Vickie, Carmen-Orozco, Rogger P., Ling, Jonathan P., Kalab, Petr, Hayes, Lindsey R.

“…TDP-43 nuclear clearance and cytoplasmic aggregation are hallmarks of TDP-43 proteinopathies. We recently demonstrated that binding to endogenous nuclear…”
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A fluid biomarker reveals loss of TDP-43 splicing repression in presymptomatic ALS–FTD by Irwin, Katherine E., Jasin, Pei, Braunstein, Kerstin E., Sinha, Irika R., Garret, Mark A., Bowden, Kyra D., Chang, Koping, Troncoso, Juan C., Moghekar, Abhay, Oh, Esther S., Raitcheva, Denitza, Bartlett, Dan, Miller, Timothy, Berry, James D., Traynor, Bryan J., Ling, Jonathan P., Wong, Philip C.

“…Although loss of TAR DNA-binding protein 43 kDa (TDP-43) splicing repression is well documented in postmortem tissues of amyotrophic lateral sclerosis (ALS)…”
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Loss of TDP-43 splicing repression occurs early in the aging population and is associated with Alzheimer’s disease neuropathologic changes and cognitive decline by Chang, Koping, Ling, Jonathan P., Redding-Ochoa, Javier, An, Yang, Li, Ling, Dean, Stephanie A., Blanchard, Thomas G., Pylyukh, Tatiana, Barrett, Alexander, Irwin, Katherine E., Moghekar, Abhay, Resnick, Susan M., Wong, Philip C., Troncoso, Juan C.

“…LATE-NC, the neuropathologic changes of limbic-predominant age-related TAR DNA-binding protein 43 kDa (TDP-43) encephalopathy are frequently associated with…”
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Cryptic exon incorporation occurs in Alzheimer’s brain lacking TDP-43 inclusion but exhibiting nuclear clearance of TDP-43 by Sun, Mingkuan, Bell, William, LaClair, Katherine D., Ling, Jonathan P., Han, Heather, Kageyama, Yusuke, Pletnikova, Olga, Troncoso, Juan C., Wong, Philip C., Chen, Liam L.

“…Abnormal accumulation of TDP-43 into cytoplasmic or nuclear inclusions with accompanying nuclear clearance, a common pathology initially identified in…”
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Loss of TDP-43 function and rimmed vacuoles persist after T cell depletion in a xenograft model of sporadic inclusion body myositis by Britson, Kyla A, Ling, Jonathan P, Braunstein, Kerstin E, Montagne, Janelle M, Kastenschmidt, Jenna M, Wilson, Andrew, Ikenaga, Chiseko, Tsao, William, Pinal-Fernandez, Iago, Russell, Katelyn A, Reed, Nicole, Mozaffar, Tahseen, Wagner, Kathryn R, Ostrow, Lyle W, Corse, Andrea M, Mammen, Andrew L, Villalta, S Armando, Larman, H Benjamin, Wong, Philip C, Lloyd, Thomas E

“…Sporadic inclusion body myositis (IBM) is the most common acquired muscle disease in adults over age 50, yet it remains unclear whether the disease is…”
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Author Correction: A fluid biomarker reveals loss of TDP-43 splicing repression in presymptomatic ALS–FTD by Irwin, Katherine E., Jasin, Pei, Braunstein, Kerstin E., Sinha, Irika R., Garret, Mark A., Bowden, Kyra D., Chang, Koping, Troncoso, Juan C., Moghekar, Abhay, Oh, Esther S., Raitcheva, Denitza, Bartlett, Dan, Miller, Timothy, Berry, James D., Traynor, Bryan J., Ling, Jonathan P., Wong, Philip C.

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Depletion of TDP-43 decreases fibril and plaque β-amyloid and exacerbates neurodegeneration in an Alzheimer’s mouse model by LaClair, Katherine D., Donde, Aneesh, Ling, Jonathan P., Jeong, Yun Ha, Chhabra, Resham, Martin, Lee J., Wong, Philip C.

“…TDP-43 proteinopathy, initially associated with ALS and FTD, is also found in 30–60% of Alzheimer’s disease (AD) cases and correlates with worsened cognition…”
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Cell-specific regulation of gene expression using splicing-dependent frameshifting by Ling, Jonathan P., Bygrave, Alexei M., Santiago, Clayton P., Carmen-Orozco, Rogger P., Trinh, Vickie T., Yu, Minzhong, Li, Yini, Liu, Ying, Bowden, Kyra D., Duncan, Leighton H., Han, Jeong, Taneja, Kamil, Dongmo, Rochinelle, Babola, Travis A., Parker, Patrick, Jiang, Lizhi, Leavey, Patrick J., Smith, Jennifer J., Vistein, Rachel, Gimmen, Megan Y., Dubner, Benjamin, Helmenstine, Eric, Teodorescu, Patric, Karantanos, Theodoros, Ghiaur, Gabriel, Kanold, Patrick O., Bergles, Dwight, Langmead, Ben, Sun, Shuying, Nielsen, Kristina J., Peachey, Neal, Singh, Mandeep S., Dalton, W. Brian, Rajaii, Fatemeh, Huganir, Richard L., Blackshaw, Seth

“…Precise and reliable cell-specific gene delivery remains technically challenging. Here we report a splicing-based approach for controlling gene expression…”
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Tdp-43 cryptic exons are highly variable between cell types by Jeong, Yun Ha, Ling, Jonathan P, Lin, Sophie Z, Donde, Aneesh N, Braunstein, Kerstin E, Majounie, Elisa, Traynor, Bryan J, LaClair, Katherine D, Lloyd, Thomas E, Wong, Philip C

“…TDP-43 proteinopathy is a prominent pathological feature that occurs in a number of human diseases including amyotrophic lateral sclerosis (ALS),…”
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An LHX1-Regulated Transcriptional Network Controls Sleep/Wake Coupling and Thermal Resistance of the Central Circadian Clockworks by Bedont, Joseph L., LeGates, Tara A., Buhr, Ethan, Bathini, Abhijith, Ling, Jonathan P., Bell, Benjamin, Wu, Mark N., Wong, Philip C., Van Gelder, Russell N., Mongrain, Valerie, Hattar, Samer, Blackshaw, Seth

“…The suprachiasmatic nucleus (SCN) is the central circadian clock in mammals. It is entrained by light but resistant to temperature shifts that entrain…”
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The E592K variant of SF3B1 creates unique RNA missplicing and associates with high-risk MDS without ring sideroblasts by Choi, In Young, Ling, Jonathan P., Zhang, Jian, Helmenstine, Eric, Walter, Wencke, Tsakiroglou, Panagiotis, Bergman, Riley E., Philippe, Céline, Manley, James L., Rouault-Pierre, Kevin, Li, Bing, Wiseman, Daniel H., Batta, Kiran, Ouseph, Madhu, Bernard, Elsa, Dubner, Benjamin, Li, Xiao, Haferlach, Torsten, Koget, Anna, Fazal, Salman, Jain, Tania, Gocke, Christopher D., DeZern, Amy E., Dalton, William Brian

“…•The E592K variant of SF3B1 induces unique RNA missplicing that is nonoverlapping with other MDS-associated variants.•E592K is associated with elevated blasts,…”
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