Publications
Sort & Filters
Filters
48 results
48 results
2022
Luan J, Vermunt MW, Syrett CM, Cote A, Tome JM, Zhang H, Huang A, Luppino JM, Keller CA, Giardine BM, Zhang S, Dunagin MC, Zhang Z, Joyce EF, Lis JT, Raj A, Hardison RC, Blobel GA. CTCF blocks antisense transcription initiation at divergent promoters.
Nature structural & molecular biology. BERLIN: NATURE PORTFOLIO; 2022;29(11):1136–1144.
Luan J, Vermunt MW, Syrett CM, Cote A, Tome JM, Zhang H, Huang A, Luppino JM, Keller CA, Giardine BM, Zhang S, Dunagin MC, Zhang Z, Joyce EF, Lis JT, Raj A, Hardison RC, Blobel GA. CTCF blocks antisense transcription initiation at divergent promoters.
Nature structural & molecular biology. BERLIN: NATURE PORTFOLIO; 2022;29(11):1136–1144.
Transcription at most promoters is divergent, initiating at closely spaced oppositely oriented core promoters to produce sense transcripts along with often unstable upstream antisense transcripts (uasTrx). How antisense transcription is regulated and to...
Stein C, Field A, Mimoso C, Zhao C, Huang KL, Wagner E, Adelman K. Integrator endonuclease drives promoter-proximal termination at all RNA polymerase II-transcribed loci.
Molecular Cell. Elsevier; 2022;82(22):4232–4245.
Stein C, Field A, Mimoso C, Zhao C, Huang KL, Wagner E, Adelman K. Integrator endonuclease drives promoter-proximal termination at all RNA polymerase II-transcribed loci.
Molecular Cell. Elsevier; 2022;82(22):4232–4245.
Luppino JM, Field A, Nguyen SC, Park DS, Shah PP, Abdill RJ, Lan Y, Yunker R, Jain R, Adelman K, Joyce EF. Co-depletion of NIPBL and WAPL balance cohesin activity to correct gene misexpression.
PLOS Genetics. 2022;18(11):e1010528.
Luppino JM, Field A, Nguyen SC, Park DS, Shah PP, Abdill RJ, Lan Y, Yunker R, Jain R, Adelman K, Joyce EF. Co-depletion of NIPBL and WAPL balance cohesin activity to correct gene misexpression.
PLOS Genetics. 2022;18(11):e1010528.
The relationship between cohesin-mediated chromatin looping and gene expression remains unclear. NIPBL and WAPL are two opposing regulators of cohesin activity; depletion of either is associated with changes in both chromatin folding and transcription...
2021
Liu N, Xu S, Yao Q, Zhu Q, Kai Y, Hsu JY, Sakon P, Pinello L, Yuan GC, Bauer DE, Orkin SH. Transcription factor competition at the γ-globin promoters controls hemoglobin switching.
Nature Genetics. 2021;:1–10.
Liu N, Xu S, Yao Q, Zhu Q, Kai Y, Hsu JY, Sakon P, Pinello L, Yuan GC, Bauer DE, Orkin SH. Transcription factor competition at the γ-globin promoters controls hemoglobin switching.
Nature Genetics. 2021;:1–10.
BCL11A, the major regulator of fetal hemoglobin (HbF, α2γ2) level, represses γ-globin expression through direct promoter binding in adult erythroid cells in a switch to adult hemoglobin (HbA, α2β2). To uncover how BCL11A initiates repression, we used...
Kriz AJ, Colognori D, Sunwoo H, Nabet B, Lee JT. Balancing cohesin eviction and retention prevents aberrant chromosomal interactions, Polycomb-mediated repression, and X-inactivation.
Molecular Cell. 2021;81(9):1970–1987.e9.
Kriz AJ, Colognori D, Sunwoo H, Nabet B, Lee JT. Balancing cohesin eviction and retention prevents aberrant chromosomal interactions, Polycomb-mediated repression, and X-inactivation.
Molecular Cell. 2021;81(9):1970–1987.e9.
Depletion of architectural factors globally alters chromatin structure but only modestly affects gene expression. We revisit the structure-function relationship using the inactive X chromosome (Xi) as a model. We investigate cohesin imbalances by forcing...
Robinson DCL, Ritso M, Nelson GM, Mokhtari Z, Nakka K, Bandukwala H, Goldman SR, Park PJ, Mounier R, Chazaud B, Brand M, Rudnicki MA, Adelman K, Dilworth FJ. Negative elongation factor regulates muscle progenitor expansion for efficient myofiber repair and stem cell pool repopulation.
Developmental Cell. 2021;56(7):1014–1029.e7.
Robinson DCL, Ritso M, Nelson GM, Mokhtari Z, Nakka K, Bandukwala H, Goldman SR, Park PJ, Mounier R, Chazaud B, Brand M, Rudnicki MA, Adelman K, Dilworth FJ. Negative elongation factor regulates muscle progenitor expansion for efficient myofiber repair and stem cell pool repopulation.
Developmental Cell. 2021;56(7):1014–1029.e7.
Negative elongation factor (NELF) is a critical transcriptional regulator that stabilizes paused RNA polymerase to permit rapid gene expression changes in response to environmental cues. Although NELF is essential for embryonic development, its role in...
Cermakova K, Demeulemeester J, Lux V, Nedomova M, Goldman SR, Smith EA, Srb P, Hexnerova R, Fabry M, Madlikova M, Horejsi M, Rijck JD, Debyser Z, Adelman K, Hodges HC, Veverka V. A ubiquitous disordered protein interaction module orchestrates transcription elongation.
Science. 2021;374(6571):1113–1121.
Cermakova K, Demeulemeester J, Lux V, Nedomova M, Goldman SR, Smith EA, Srb P, Hexnerova R, Fabry M, Madlikova M, Horejsi M, Rijck JD, Debyser Z, Adelman K, Hodges HC, Veverka V. A ubiquitous disordered protein interaction module orchestrates transcription elongation.
Science. 2021;374(6571):1113–1121.
Organized by unstructured motifs The high degree of conservation in protein sequences thought to be unstructured has hinted that these regions may have important biological functions. Although unstructured regions are widely viewed to be crucial for...
Rosenberg M, Blum R, Kesner B, Aeby E, Garant JM, Szanto A, Lee JT. Motif-driven interactions between RNA and PRC2 are rheostats that regulate transcription elongation.
Nature Structural & Molecular Biology. 2021;28(1):103–117.
Rosenberg M, Blum R, Kesner B, Aeby E, Garant JM, Szanto A, Lee JT. Motif-driven interactions between RNA and PRC2 are rheostats that regulate transcription elongation.
Nature Structural & Molecular Biology. 2021;28(1):103–117.
Although polycomb repressive complex 2 (PRC2) is now recognized as an RNA-binding complex, the full range of binding motifs and why PRC2–RNA complexes often associate with active genes have not been elucidated. Here, we identify high-affinity RNA motifs...
2020
Santoriello C, Sporrij A, Yang S, Flynn RA, Henriques T, Dorjsuren B, Custo Greig E, McCall W, Stanhope ME, Fazio M, Superdock M, Lichtig A, Adatto I, Abraham BJ, Kalocsay M, Jurynec M, Zhou Y, Adelman K, Calo E, Zon LI. RNA helicase DDX21 mediates nucleotide stress responses in neural crest and melanoma cells.
Nature Cell Biology. 2020;22(4):372–379.
Santoriello C, Sporrij A, Yang S, Flynn RA, Henriques T, Dorjsuren B, Custo Greig E, McCall W, Stanhope ME, Fazio M, Superdock M, Lichtig A, Adatto I, Abraham BJ, Kalocsay M, Jurynec M, Zhou Y, Adelman K, Calo E, Zon LI. RNA helicase DDX21 mediates nucleotide stress responses in neural crest and melanoma cells.
Nature Cell Biology. 2020;22(4):372–379.
The availability of nucleotides has a direct impact on transcription. The inhibition of dihydroorotate dehydrogenase (DHODH) with leflunomide impacts nucleotide pools by reducing pyrimidine levels. Leflunomide abrogates the effective transcription...
Pan L, Lemieux M, Thomas T, Rogers J, Lipper C, Lee W, Johnson C, Sholl L, South A, Marto J, Adelmant G, Blacklow S, Aster J. IER5, a DNA damage response gene, is required for Notch-mediated induction of squamous cell differentiation.
Sarin A, Akhmanova A, Schramek D, Radtke F, editors. eLife. 2020;9:e58081.
Pan L, Lemieux M, Thomas T, Rogers J, Lipper C, Lee W, Johnson C, Sholl L, South A, Marto J, Adelmant G, Blacklow S, Aster J. IER5, a DNA damage response gene, is required for Notch-mediated induction of squamous cell differentiation.
Sarin A, Akhmanova A, Schramek D, Radtke F, editors. eLife. 2020;9:e58081.
Notch signaling regulates squamous cell proliferation and differentiation and is frequently disrupted in squamous cell carcinomas, in which Notch is tumor suppressive. Here, we show that conditional activation of Notch in squamous cells activates a...
2019
Etchegaray JP, Zhong L, Li C, Henriques T, Ablondi E, Nakadai T, Van Rechem C, Ferrer C, Ross K, Choi JE, Samarakkody A, Ji F, Chang A, Sadreyev R, Ramaswamy S, Nechaev S, Whetstine J, Roeder R, Adelman K, Goren A, Mostoslavsky R. The Histone Deacetylase SIRT6 Restrains Transcription Elongation via Promoter-Proximal Pausing.
Mol Cell. 2019;75(4):683–699.e7. PMID: 31399344
Etchegaray JP, Zhong L, Li C, Henriques T, Ablondi E, Nakadai T, Van Rechem C, Ferrer C, Ross K, Choi JE, Samarakkody A, Ji F, Chang A, Sadreyev R, Ramaswamy S, Nechaev S, Whetstine J, Roeder R, Adelman K, Goren A, Mostoslavsky R. The Histone Deacetylase SIRT6 Restrains Transcription Elongation via Promoter-Proximal Pausing.
Mol Cell. 2019;75(4):683–699.e7. PMID: 31399344
Transcriptional regulation in eukaryotes occurs at promoter-proximal regions wherein transcriptionally engaged RNA polymerase II (Pol II) pauses before proceeding toward productive elongation. The role of chromatin in pausing remains poorly understood...
Sendinc E, Valle-Garcia D, Dhall A, Chen H, Henriques T, Navarrete-Perea J, Sheng W, Gygi SP, Adelman K, Shi Y. PCIF1 Catalyzes m6Am mRNA Methylation to Regulate Gene Expression.
Molecular Cell. 2019;
Sendinc E, Valle-Garcia D, Dhall A, Chen H, Henriques T, Navarrete-Perea J, Sheng W, Gygi SP, Adelman K, Shi Y. PCIF1 Catalyzes m6Am mRNA Methylation to Regulate Gene Expression.
Molecular Cell. 2019;
Summary mRNA modifications play important roles in regulating gene expression. One of the most abundant mRNA modifications is N6,2-O-dimethyladenosine (m6Am). Here, we demonstrate that m6Am is an evolutionarily conserved mRNA modification mediated by the...