Results 61 to 70 of about 1,628,380 (301)

RNA secondary structure prediction from multi-aligned sequences [PDF]

, 2013
It has been well accepted that the RNA secondary structures of most functional non-coding RNAs (ncRNAs) are closely related to their functions and are conserved during evolution.
A Balik, A Pauli, A Wilm, A Wilm, AC Penn, AR Gruber, AS Richter, B Knudsen, B Knudsen, C Witwer, CB Do, D Jager, D Sankoff, D Wei, DH Mathews, DH Mathews, E Bindewald, E Freyhult, E Rivas, EJ Meer, H Kiryu, H Yonemoto, IA Qureshi, IL Hofacker, IL Hofacker, IV Novikova, J Ruan, J Spirollari, JG Underwood, JM Watts, JR Proctor, JS McCaskill, JT Low, K Katoh, K Sato, K Sato, K Sato, KM Wong, LE Carvalho, M Andronescu, M Andronescu, M Esteller, M Hamada, M Hamada, M Hamada, M Hamada, M Hamada, M Hamada, M Hamada, M Hamada, M Kertesz, ME Nebel, MS Andronescu, P Ge, PP Gardner, PS Pang, R Luck, RD Dowell, RJ Klein, S Washietl, S Washietl, S Washietl, S Washietl, SE Seemann, SE Seemann, SH Bernhart, SM Sahraeian, SW Burge, T Puton, T Xia, Y Kato, Z Sukosd   +71 more
core   +1 more source

RNA-SSPT: RNA Secondary Structure Prediction Tools [PDF]

Bioinformation, 2013
The prediction of RNA structure is useful for understanding evolution for both in silico and in vitro studies. Physical methods like NMR studies to predict RNA secondary structure are expensive and difficult. Computational RNA secondary structure prediction is easier. Comparative sequence analysis provides the best solution.
Ahmad, Freed, Mahboob, Shahid, Gulzar, Tahsin, din, Salah U, Hanif, Tanzeela, Ahmad, Hifza, Afzal, Muhammad   +6 more
openaire   +2 more sources

Protein pyrophosphorylation by inositol pyrophosphates — detection, function, and regulation

FEBS Letters, EarlyView.
Protein pyrophosphorylation is an unusual signaling mechanism that was discovered two decades ago. It can be driven by inositol pyrophosphate messengers and influences various cellular processes. Herein, we summarize the research progress and challenges of this field, covering pathways found to be regulated by this posttranslational modification as ...
Sarah Lampe, Tanmay Kumar Mohanty, Rashna Bhandari, Dorothea Fiedler   +3 more
wiley   +1 more source

Differential analysis of RNA structure probing experiments at nucleotide resolution: uncovering regulatory functions of RNA structure

Nature Communications, 2022
The authors present DiffScan, an advanced tool for normalization and differential analysis of RNA structure probing experiments, combining their power in deciphering the dynamic RNA structurome and facilitating the discovery of RNA regulatory functions.
Bo Yu, Pan Li, Qiangfeng Cliff Zhang, Lin Hou   +3 more
doaj   +1 more source

Molecular principles underlying dual RNA specificity in the Drosophila SNF protein [PDF]

, 2018
The first RNA recognition motif of the Drosophila SNF protein is an example of an RNA binding protein with multi-specificity. It binds different RNA hairpin loops in spliceosomal U1 or U2 small nuclear RNAs, and only in the latter case requires the ...
DeKoster, Gregory T, Hall, Kathleen B, Holton, Nicole, Wahl, Markus C, Weber, Gert   +4 more
core   +3 more sources

The newfound relationship between extrachromosomal DNAs and excised signal circles

FEBS Letters, EarlyView.
Extrachromosomal DNAs (ecDNAs) contribute to the progression of many human cancers. In addition, circular DNA by‐products of V(D)J recombination, excised signal circles (ESCs), have roles in cancer progression but have largely been overlooked. In this Review, we explore the roles of ecDNAs and ESCs in cancer development, and highlight why these ...
Dylan Casey, Zeqian Gao, Joan Boyes
wiley   +1 more source

An upstream open reading frame regulates expression of the mitochondrial protein Slm35 and mitophagy flux

FEBS Letters, EarlyView.
This study reveals how the mitochondrial protein Slm35 is regulated in Saccharomyces cerevisiae. The authors identify stress‐responsive DNA elements and two upstream open reading frames (uORFs) in the 5′ untranslated region of SLM35. One uORF restricts translation, and its mutation increases Slm35 protein levels and mitophagy.
Hernán Romo‐Casanueva, Ariann E. Mendoza‐Martínez, P. Abril Medina‐Flores, Carlos Campero‐Basaldua, Alexander DeLuna, Soledad Funes   +5 more
wiley   +1 more source

Degenerate cysteine patterns mediate two redox sensing mechanisms in the papillomavirus E7 oncoprotein

Redox Biology, 2017
Infection with oncogenic human papillomavirus induces deregulation of cellular redox homeostasis. Virus replication and papillomavirus-induced cell transformation require persistent expression of viral oncoproteins E7 and E6 that must retain their ...
Gabriela Camporeale, Juan R. Lorenzo, Maria G. Thomas, Edgardo Salvatierra, Silvia S. Borkosky, Marikena G. Risso, Ignacio E. Sánchez, Gonzalo de Prat Gay, Leonardo G. Alonso   +8 more
doaj   +1 more source

Sequence determinants of RNA G‐quadruplex unfolding by Arg‐rich regions

FEBS Letters, EarlyView.
We show that Arg‐rich peptides selectively unfold RNA G‐quadruplexes, but not RNA stem‐loops or DNA/RNA duplexes. This length‐dependent activity is inhibited by acidic residues and is conserved among SR and SR‐related proteins (SRSF1, SRSF3, SRSF9, U1‐70K, and U2AF1).
Naiduwadura Ivon Upekala De Silva, Puspa Kunwar, Md Ibnul Rifat Rahman, Joanna Koryo Kwao, Nathan Lehman, Zihan Zhang, Trenton Paul, Claire Cheng, Nicholas Truex, Hui‐Ting Lee, Jun Zhang   +10 more
wiley   +1 more source

The Prediction of Tertiary Structure of RNA Based upon Secondary Structure by Using the Relaxation Method and Texture Mapping Method [PDF]

Journal of Systemics, Cybernetics and Informatics, 2013
In this paper, we propose a method to predict tertiary structure of an RNA sequence. Our prediction method would first find the secondary structure of the given RNA sequence.
C.C. Lin, R.C.T. Lee
doaj