那些年我们一起读过的paper(2018年7-12月)

phdnote

20181015---CRISPR-Cas9

1.Precise and Predictable CRISPR Chromosomal Rearrangements Reveal Principles of Cas9-Mediated Nucleotide Insertion( By Guang Xue)
https://www.sciencedirect.com/science/article/pii/S1097276518304660
2. Combinatorial CRISPR/Cas9 Approach to Elucidate a Far-Upstream Enhancer Complex for Tissue-Specific Sox9 Expression(By Liangqiang)
https://www.sciencedirect.com/science/article/pii/S153458071830635X

20181009---deep learning

1. Zhou et al., Deep learning sequence-based ab initio prediction of
   variant effects on expression and disease risk. Nature Genetics, 50:1171–1179
   (2018).
   URL: https://www.nature.com/articles/s41588-018-0160-6

20180927---Enhancer

Transcriptional decomposition reveals active chromatin architectures and cell specific regulatory interactions (by Zac)
https://www.nature.com/articles/s41467-017-02798-1

Long-Range Enhancer Interactions Are Prevalent in Mouse Embryonic Stem Cells and Are Reorganized upon Pluripotent State Transition (by Yingzhe)
https://www.sciencedirect.com/science/article/pii/S2211124718302213

20180926--eQTLs

1. Geeleher et al., Cancer expression quantitative trait loci (eQTLs) can
   be determined from heterogeneous tumor gene expression data by modeling
   variation in tumor purity. Genome Biology 19:130 (2018).
   URL:
   https://genomebiology.biomedcentral.com/articles/10.1186/s13059-018-1507-0

20180830--rG4-seq

[1] RNA Helicase DDX1 Converts RNA G-Quadruplex Structures into R-Loops to Promote IgH Class Switch Recombination (by Xiaona)

https://www.cell.com/action/showPdf?pii=S1097-2765%2818%2930269-7

[2] ssHMM: extracting intuitive sequence-structure motifs from high-throughput RNA-binding protein data (by Yile)

https://academic.oup.com/nar/article/45/19/11004/4097614

[3] Pervasive Regulatory Functions of mRNA Structure Revealed by High-Resolution SHAPE Probing (by Jie)

https://www.cell.com/action/showPdf?pii=S0092-8674%2818%2930211-3

[4] In vivo genome-wide profiling of RNA secondary structure reveals novel regulatory features

https://www.nature.com/articles/nature12756.pdf (by Jie)

[5] Global Maps of ProQ Binding In Vivo Reveal Target Recognition via RNA Structure and Stability Control at mRNA 30 Ends (by Guang)

https://www.cell.com/action/showPdf?pii=S1097-2765%2818%2930313-7

Nat Commun. 2018 Jul 20;9(1):2845. doi: 10.1038/s41467-018-05049-z.

Abnormal RNA stability in amyotrophic lateral sclerosis.

20180826---RBP-rG4-seq

RBP-RNA interactions in the 5’ UTR lead to structural changes that alter translation (by Xiaona)

https://www.biorxiv.org/content/biorxiv/early/2018/04/13/174888.full.pdf

RNA Regulations and Functions Decoded by Transcriptome-wide RNA Structure Probing (by Jie)

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5673676/

20180806--SCs

1. Distinct metabolic states govern skeletal muscle stem cell fates during prenatal and postnatal myogenesis.
   https://www.ncbi.nlm.nih.gov/pubmed/30054310 (by Fengyuan)

2. Shisa2 regulates the fusion of muscle progenitors. (by Yuying)
   https://www.ncbi.nlm.nih.gov/pubmed/30007221

3. SOXF factors regulate murine satellite cell self-renewal and function through inhibition of β-catenin activity.(by Xiaoqiang)
   https://www.ncbi.nlm.nih.gov/pubmed/29882512

4. Niche Cadherins Control the Quiescence-to-Activation Transition in Muscle Stem Cells. (by Suyang)
   https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5702939/

20180801--lncRNAs

Mol Cell. 2018 Jul 19;71(2):256-270.e10. doi: 10.1016/j.molcel.2018.06.032.

HuD Is a Neural Translation Enhancer Acting on mTORC1-Responsive Genes and Counteracted by the Y3 Small Non-coding RNA. (by Xiaona)

Genes Dev. 2018 Jul 24. doi: 10.1101/gad.316034.118. [Epub ahead of print]

Coordinate regulation of alternative pre-mRNA splicing events by the human RNA chaperone proteins hnRNPA1 and DDX5. (by Zac)

IEEE/ACM Trans Comput Biol Bioinform. 2018 May 14. doi: 10.1109/TCBB.2018.2834387. [Epub ahead of print] (by Jie)

Identification and analysis of key residues in protein-RNA complexes.

20180722---RBP-chromatin

1.
Precise and Predictable CRISPR Chromosomal Rearrangements Reveal Principles of Cas9-Mediated Nucleotide Insertion
https://www.cell.com/molecular-cell/fulltext/S1097-2765(18)30466-0
2.
The Nucleosome Remodeling and Deacetylation Complex Modulates Chromatin Structure at Sites of Active Transcription to Fine-Tune Gene Expression
https://www.sciencedirect.com/science/article/pii/S1097276518304453?via%3Dihub
3.
microRNA-122 amplifies hepatitis C virus translation by shaping the structure of the internal ribosomal entry site
https://www.nature.com/articles/s41467-018-05053-3
4.
Dedicated surveillance mechanism controls G-quadruplex forming non-coding RNAs in human mitochondria
https://www.nature.com/articles/s41467-018-05007-9

20180709---phrase seperation

1. A Muscle-Specific Enhancer RNA Mediates Cohesin Recruitment and Regulates Transcription In trans (By Xiaoqiang)
   https://www.cell.com/molecular-cell/fulltext/S1097-2765(18)30450-7

2. Functional Domains of NEAT1 Architectural lncRNA Induce Paraspeckle Assembly through Phase Separation (by Zac)
   https://www.cell.com/molecular-cell/fulltext/S1097-2765(18)30393-9

3. Long-read sequencing of nascent RNA reveals coupling among RNA processing events (by Yile)
   https://genome.cshlp.org/content/28/7/1008.full

20180613--- CRISPRa

1. Higher-order inter-chromosomal hubs shape 3-dimensional genome (by Karl)
   organization in the nucleus
   https://www.biorxiv.org/content/early/2017/11/18/219683

2.An Integrated Genome-wide CRISPRa Approach to Functionalize lncRNAs in Drug Resistance (by Yuying)
https://www.cell.com/cell/fulltext/S0092-8674(18)30384-2

20180612--RBPs

1. Sequence, Structure, and Context Preferences of Human RNA Binding Proteins (by Yile)
   https://www.cell.com/molecular-cell/fulltext/S1097-2765(18)30351-4

2. HuR regulates telomerase activity through TERC methylation (by Xiaona)
   https://www.nature.com/articles/s41467-018-04617-7

3. rbFOX1/MBNL1 competition for CCUG RNA repeats binding contributes to myotonic dystrophy type 1/type 2 differences (by Guang)
   https://www.nature.com/articles/s41467-018-04370-x