Pubfacts - Scientific Publication Data
  • Categories
  • |
  • Journals
  • |
  • Authors
  • Login
  • Categories
  • Journals

Search Our Scientific Publications & Authors

Publications
  • Publications
  • Authors
find publications by category +
Translate page:

DeepMILO: a deep learning approach to predict the impact of non-coding sequence variants on 3D chromatin structure.

Authors:
Tuan Trieu Alexander Martinez-Fundichely Ekta Khurana

Genome Biol 2020 03 26;21(1):79. Epub 2020 Mar 26.

Meyer Cancer Center, Weill Cornell Medicine, New York, NY, 10065, USA.

Non-coding variants have been shown to be related to disease by alteration of 3D genome structures. We propose a deep learning method, DeepMILO, to predict the effects of variants on CTCF/cohesin-mediated insulator loops. Application of DeepMILO on variants from whole-genome sequences of 1834 patients of twelve cancer types revealed 672 insulator loops disrupted in at least 10% of patients. Our results show mutations at loop anchors are associated with upregulation of the cancer driver genes BCL2 and MYC in malignant lymphoma thus pointing to a possible new mechanism for their dysregulation via alteration of insulator loops.

Download full-text PDF

Source
http://dx.doi.org/10.1186/s13059-020-01987-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7098089PMC
March 2020

Publication Analysis

Top Keywords

insulator loops
12
deep learning
8
cancer types
4
twelve cancer
4
patients twelve
4
types revealed
4
revealed 672
4
loops disrupted
4
672 insulator
4
1834 patients
4
whole-genome sequences
4
ctcf/cohesin-mediated insulator
4
variants ctcf/cohesin-mediated
4
effects variants
4
loops application
4
application deepmilo
4
disrupted 10%
4
deepmilo variants
4
sequences 1834
4
patients mutations
4

Altmetric Statistics


Show full details
44 Total Shares
34 Tweets
34 Citations

Similar Publications

The Functions and Mechanisms of Action of Insulators in the Genomes of Higher Eukaryotes.

Authors:
L S Melnikova P G Georgiev A K Golovnin

Acta Naturae 2020 Oct-Dec;12(4):15-33

Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334 Russia.

The mechanisms underlying long-range interactions between chromatin regions and the principles of chromosomal architecture formation are currently under extensive scrutiny. A special class of regulatory elements known as insulators is believed to be involved in the regulation of specific long-range interactions between enhancers and promoters. This review focuses on the insulators of and mammals, and it also briefly characterizes the proteins responsible for their functional activity. Read More

View Article and Full-Text PDF
January 2021
Similar Publications

Magnonic Quadrupole Topological Insulator in Antiskyrmion Crystals.

Authors:
Tomoki Hirosawa Sebastián A Díaz Jelena Klinovaja Daniel Loss

Phys Rev Lett 2020 Nov;125(20):207204

Department of Physics, University of Basel, Klingelbergstrasse 82, CH-4056 Basel, Switzerland.

We uncover that antiskyrmion crystals provide an experimentally accessible platform to realize a magnonic quadrupole topological insulator, whose hallmark signatures are robust magnonic corner states. Furthermore, we show that tuning an applied magnetic field can trigger the self-assembly of antiskyrmions carrying a fractional topological charge along the sample edges. Crucially, these fractional antiskyrmions restore the symmetries needed to enforce the emergence of the magnonic corner states. Read More

View Article and Full-Text PDF
November 2020
Similar Publications

CTCF-Mediated Genome Architecture Regulates the Dosage of Mitotically Stable Mono-allelic Expression of Autosomal Genes.

Authors:
Keerthivasan Raanin Chandradoss Bindia Chawla Shivnarayan Dhuppar Rakhee Nayak Rajesh Ramachandran Sreenivasulu Kurukuti Aprotim Mazumder Kuljeet Singh Sandhu

Cell Rep 2020 Oct;33(4):108302

Department of Biological Sciences, Indian Institute of Science Education and Research (IISER)-Mohali, Knowledge City, Sector 81, SAS Nagar 140306, India. Electronic address:

The mechanisms that guide the clonally stable random mono-allelic expression of autosomal genes remain enigmatic. We show that (1) mono-allelically expressed (MAE) genes are assorted and insulated from bi-allelically expressed (BAE) genes through CTCF-mediated chromatin loops; (2) the cell-type-specific dynamics of mono-allelic expression coincides with the gain and loss of chromatin insulator sites; (3) dosage of MAE genes is more sensitive to the loss of chromatin insulation than that of BAE genes; and (4) inactive alleles of MAE genes are significantly more insulated than active alleles and are de-repressed upon CTCF depletion. This alludes to a topology wherein the inactive alleles of MAE genes are insulated from the spatial interference of transcriptional states from the neighboring bi-allelic domains via CTCF-mediated loops. Read More

View Article and Full-Text PDF
October 2020
Similar Publications

Mechanism and regulation of class switch recombination by IgH transcriptional control elements.

Authors:
Chloé Oudinet Fatima-Zohra Braikia Audrey Dauba Ahmed Amine Khamlichi

Adv Immunol 2020 25;147:89-137. Epub 2020 Jul 25.

Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, Toulouse, France; Institut de Pharmacologie et de Biologie Structurale, CNRS, Université Paul Sabatier, Toulouse, France. Electronic address:

Class switch recombination (CSR) plays an important role in humoral immunity by generating antibodies with different effector functions. CSR to a particular antibody isotype is induced by external stimuli, and occurs between highly repetitive switch (S) sequences. CSR requires transcription across S regions, which generates long non-coding RNAs and secondary structures that promote accessibility of S sequences to activation-induced cytidine deaminase (AID). Read More

View Article and Full-Text PDF
July 2020
Similar Publications

Kerr effect anomaly in magnetic topological insulator superlattices.

Authors:
Jieyi Liu Angadjit Singh Balati Kuerbanjiang Crispin H W Barnes Thorsten Hesjedal

Nanotechnology 2020 Oct 4;31(43):434001. Epub 2020 Aug 4.

Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, OX1 3PU, United Kingdom. Cavendish Laboratory, University of Cambridge, J J Thomson Avenue, Cambridge, CB3 0HE, United Kingdom.

We report the magneto-optical Kerr effect (MOKE) study of magnetic topological insulator superlattice films with alternating transition-metal and rare-earth doping. We observe an unexpected hump in the MOKE hysteresis loops upon magnetization reversal at low temperatures, reminiscent of the topological Hall effect (THE) reported in transport measurements. The THE is commonly associated with the existence of magnetic skyrmions, i. Read More

View Article and Full-Text PDF
October 2020
Similar Publications
© 2021 PubFacts.
  • About PubFacts
  • Privacy Policy
  • Sitemap