Epigenomics: beyond CpG islands

MJ Fazzari, JM Greally - Nature Reviews Genetics, 2004 - nature.com
Epigenomic studies aim to define the location and nature of the genomic sequences that are
epigenetically modified. Much progress has been made towards whole-genome epigenetic …

Short retroposons in eukaryotic genomes

DA Kramerov, NS Vassetzky - International review of cytology, 2005 - Elsevier
Short retroposons (SINEs) are repetitive elements amplified in the genome via an RNA
intermediate, using the enzymatic machinery of autonomous retroposons (LINEs). SINEs are …

Homotypic clustering of L1 and B1/Alu repeats compartmentalizes the 3D genome

JY Lu, L Chang, T Li, T Wang, Y Yin, G Zhan, X Han… - Cell research, 2021 - nature.com
Organization of the genome into euchromatin and heterochromatin appears to be
evolutionarily conserved and relatively stable during lineage differentiation. In an effort to …

The landscape of L1 retrotransposons in the human genome is shaped by pre-insertion sequence biases and post-insertion selection

T Sultana, D van Essen, O Siol, M Bailly-Bechet… - Molecular cell, 2019 - cell.com
L1 retrotransposons are transposable elements and major contributors of genetic variation
in humans. Where L1 integrates into the genome can directly impact human evolution and …

Millions of years of evolution preserved: a comprehensive catalog of the processed pseudogenes in the human genome

Z Zhang, PM Harrison, Y Liu, M Gerstein - Genome research, 2003 - genome.cshlp.org
Processed pseudogenes were created by reverse-transcription of mRNAs; they provide
snapshots of ancient genes existing millions of years ago in the genome. To find them in the …

SVA elements: a hominid-specific retroposon family

H Wang, J Xing, D Grover, DJ Hedges, K Han… - Journal of molecular …, 2005 - Elsevier
SVA is a composite repetitive element named after its main components, SINE, VNTR and
Alu. We have identified 2762 SVA elements from the human genome draft sequence …

Retroelement distributions in the human genome: variations associated with age and proximity to genes

P Medstrand, LN Van De Lagemaat… - Genome research, 2002 - genome.cshlp.org
Remnants of more than 3 million transposable elements, primarily retroelements, comprise
nearly half of the human genome and have generated much speculation concerning their …

Genomic repeats categorize genes with distinct functions for orchestrated regulation

JY Lu, W Shao, L Chang, Y Yin, T Li, H Zhang, Y Hong… - Cell reports, 2020 - cell.com
Repetitive elements are abundantly distributed in mammalian genomes. Here, we reveal a
striking association between repeat subtypes and gene function. SINE, L1, and low …

Direct quantification of cell-free, circulating DNA from unpurified plasma

S Breitbach, S Tug, S Helmig, D Zahn, T Kubiak… - PloS one, 2014 - journals.plos.org
Cell-free DNA (cfDNA) in body tissues or fluids is extensively investigated in clinical
medicine and other research fields. In this article we provide a direct quantitative real-time …

Comparative analysis of processed pseudogenes in the mouse and human genomes

Z Zhang, N Carriero, M Gerstein - Trends in Genetics, 2004 - cell.com
Pseudogenes are important resources in evolutionary and comparative genomics because
they provide molecular records of the ancient genes that existed in the genome millions of …